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Sample records for agent-based simulation framework

  1. A Conceptual Framework for Representing Human Behavior Characteristics in a System of Systems Agent-Based Survivability Simulation

    DTIC Science & Technology

    2010-11-22

    distribution is unlimited. A CONCEPTUAL FRAMEWORK FOR REPRESENTING HUMAN BEHAVIOR CHARACTERISTICS IN A SYSTEM OF SYSTEMS AGENT-BASED SURVIVABILITY...27411 -0001 ABSTRACT A CONCEPTUAL FRAMEWORK FOR REPRESENTING HUMAN BEHAVIOR CHARACTERISTICS IN A SYSTEM OF SYSTEMS AGENT-BASED SURVIVABILITY SIMULATION...TITLE AND SUBTITLE A CONCEPTUAL FRAMEWORK FOR REPRESENTING HUMAN BEHAVIOR CHARACTERISTICS IN A SYSTEM OF SYSTEMS AGENT-BASED SURVIVABILITY

  2. A Multi Agent-Based Framework for Simulating Household PHEV Distribution and Electric Distribution Network Impact

    SciTech Connect

    Cui, Xiaohui; Liu, Cheng; Kim, Hoe Kyoung; Kao, Shih-Chieh; Tuttle, Mark A; Bhaduri, Budhendra L

    2011-01-01

    The variation of household attributes such as income, travel distance, age, household member, and education for different residential areas may generate different market penetration rates for plug-in hybrid electric vehicle (PHEV). Residential areas with higher PHEV ownership could increase peak electric demand locally and require utilities to upgrade the electric distribution infrastructure even though the capacity of the regional power grid is under-utilized. Estimating the future PHEV ownership distribution at the residential household level can help us understand the impact of PHEV fleet on power line congestion, transformer overload and other unforeseen problems at the local residential distribution network level. It can also help utilities manage the timing of recharging demand to maximize load factors and utilization of existing distribution resources. This paper presents a multi agent-based simulation framework for 1) modeling spatial distribution of PHEV ownership at local residential household level, 2) discovering PHEV hot zones where PHEV ownership may quickly increase in the near future, and 3) estimating the impacts of the increasing PHEV ownership on the local electric distribution network with different charging strategies. In this paper, we use Knox County, TN as a case study to show the simulation results of the agent-based model (ABM) framework. However, the framework can be easily applied to other local areas in the US.

  3. A Scaffolding Framework to Support Learning of Emergent Phenomena Using Multi-Agent-Based Simulation Environments

    NASA Astrophysics Data System (ADS)

    Basu, Satabdi; Sengupta, Pratim; Biswas, Gautam

    2015-04-01

    Students from middle school to college have difficulties in interpreting and understanding complex systems such as ecological phenomena. Researchers have suggested that students experience difficulties in reconciling the relationships between individuals, populations, and species, as well as the interactions between organisms and their environment in the ecosystem. Multi-agent-based computational models (MABMs) can explicitly capture agents and their interactions by representing individual actors as computational objects with assigned rules. As a result, the collective aggregate-level behavior of the population dynamically emerges from simulations that generate the aggregation of these interactions. Past studies have used a variety of scaffolds to help students learn ecological phenomena. Yet, there is no theoretical framework that supports the systematic design of scaffolds to aid students' learning in MABMs. Our paper addresses this issue by proposing a comprehensive framework for the design, analysis, and evaluation of scaffolding to support students' learning of ecology in a MABM. We present a study in which middle school students used a MABM to investigate and learn about a desert ecosystem. We identify the different types of scaffolds needed to support inquiry learning activities in this simulation environment and use our theoretical framework to demonstrate the effectiveness of our scaffolds in helping students develop a deep understanding of the complex ecological behaviors represented in the simulation..

  4. Agent-Based Spatiotemporal Simulation of Biomolecular Systems within the Open Source MASON Framework

    PubMed Central

    Pérez-Rodríguez, Gael; Pérez-Pérez, Martín; Glez-Peña, Daniel; Azevedo, Nuno F.; Lourenço, Anália

    2015-01-01

    Agent-based modelling is being used to represent biological systems with increasing frequency and success. This paper presents the implementation of a new tool for biomolecular reaction modelling in the open source Multiagent Simulator of Neighborhoods framework. The rationale behind this new tool is the necessity to describe interactions at the molecular level to be able to grasp emergent and meaningful biological behaviour. We are particularly interested in characterising and quantifying the various effects that facilitate biocatalysis. Enzymes may display high specificity for their substrates and this information is crucial to the engineering and optimisation of bioprocesses. Simulation results demonstrate that molecule distributions, reaction rate parameters, and structural parameters can be adjusted separately in the simulation allowing a comprehensive study of individual effects in the context of realistic cell environments. While higher percentage of collisions with occurrence of reaction increases the affinity of the enzyme to the substrate, a faster reaction (i.e., turnover number) leads to a smaller number of time steps. Slower diffusion rates and molecular crowding (physical hurdles) decrease the collision rate of reactants, hence reducing the reaction rate, as expected. Also, the random distribution of molecules affects the results significantly. PMID:25874228

  5. GridLAB-D: An Agent-Based Simulation Framework for Smart Grids

    DOE PAGES

    Chassin, David P.; Fuller, Jason C.; Djilali, Ned

    2014-01-01

    Simulation of smart grid technologies requires a fundamentally new approach to integrated modeling of power systems, energy markets, building technologies, and the plethora of other resources and assets that are becoming part of modern electricity production, delivery, and consumption systems. As a result, the US Department of Energy’s Office of Electricity commissioned the development of a new type of power system simulation tool called GridLAB-D that uses an agent-based approach to simulating smart grids. This paper presents the numerical methods and approach to time-series simulation used by GridLAB-D and reviews applications in power system studies, market design, building control systemmore » design, and integration of wind power in a smart grid.« less

  6. GridLAB-D: An Agent-Based Simulation Framework for Smart Grids

    SciTech Connect

    Chassin, David P.; Fuller, Jason C.; Djilali, Ned

    2014-06-23

    Simulation of smart grid technologies requires a fundamentally new approach to integrated modeling of power systems, energy markets, building technologies, and the plethora of other resources and assets that are becoming part of modern electricity production, delivery, and consumption systems. As a result, the US Department of Energy’s Office of Electricity commissioned the development of a new type of power system simulation tool called GridLAB-D that uses an agent-based approach to simulating smart grids. This paper presents the numerical methods and approach to time-series simulation used by GridLAB-D and reviews applications in power system studies, market design, building control system design, and integration of wind power in a smart grid.

  7. A framework for the use of agent based modeling to simulate ...

    EPA Pesticide Factsheets

    Simulation of human behavior in exposure modeling is a complex task. Traditionally, inter-individual variation in human activity has been modeled by drawing from a pool of single day time-activity diaries such as the US EPA Consolidated Human Activity Database (CHAD). Here, an agent-based model (ABM) is used to simulate population distributions of longitudinal patterns of four macro activities (sleeping, eating, working, and commuting) in populations of adults over a period of one year. In this ABM, an individual is modeled as an agent whose movement through time and space is determined by a set of decision rules. The rules are based on the agent having time-varying “needs” that are satisfied by performing actions. Needs are modeled as increasing over time, and taking an action reduces the need. Need-satisfying actions include sleeping (meeting the need for rest), eating (meeting the need for food), and commuting/working (meeting the need for income). Every time an action is completed, the model determines the next action the agent will take based on the magnitude of each of the agent’s needs at that point in time. Different activities advertise their ability to satisfy various needs of the agent (such as food to eat or sleeping in a bed or on a couch). The model then chooses the activity that satisfies the greatest of the agent’s needs. When multiple actions could address a need, the model will choose the most effective of the actions (bed over the couc

  8. On-lattice agent-based simulation of populations of cells within the open-source Chaste framework.

    PubMed

    Figueredo, Grazziela P; Joshi, Tanvi V; Osborne, James M; Byrne, Helen M; Owen, Markus R

    2013-04-06

    Over the years, agent-based models have been developed that combine cell division and reinforced random walks of cells on a regular lattice, reaction-diffusion equations for nutrients and growth factors; and ordinary differential equations for the subcellular networks regulating the cell cycle. When linked to a vascular layer, this multiple scale model framework has been applied to tumour growth and therapy. Here, we report on the creation of an agent-based multi-scale environment amalgamating the characteristics of these models within a Virtual Physiological Human (VPH) Exemplar Project. This project enables reuse, integration, expansion and sharing of the model and relevant data. The agent-based and reaction-diffusion parts of the multi-scale model have been implemented and are available for download as part of the latest public release of Chaste (Cancer, Heart and Soft Tissue Environment; http://www.cs.ox.ac.uk/chaste/), part of the VPH Toolkit (http://toolkit.vph-noe.eu/). The environment functionalities are verified against the original models, in addition to extra validation of all aspects of the code. In this work, we present the details of the implementation of the agent-based environment, including the system description, the conceptual model, the development of the simulation model and the processes of verification and validation of the simulation results. We explore the potential use of the environment by presenting exemplar applications of the 'what if' scenarios that can easily be studied in the environment. These examples relate to tumour growth, cellular competition for resources and tumour responses to hypoxia (low oxygen levels). We conclude our work by summarizing the future steps for the expansion of the current system.

  9. Diffusion dynamics and concentration of toxic materials from quantum dots-based nanotechnologies: an agent-based modeling simulation framework

    NASA Astrophysics Data System (ADS)

    Agusdinata, Datu Buyung; Amouie, Mahbod; Xu, Tao

    2015-01-01

    Due to their favorable electrical and optical properties, quantum dots (QDs) nanostructures have found numerous applications including nanomedicine and photovoltaic cells. However, increased future production, use, and disposal of engineered QD products also raise concerns about their potential environmental impacts. The objective of this work is to establish a modeling framework for predicting the diffusion dynamics and concentration of toxic materials released from Trioctylphosphine oxide-capped CdSe. To this end, an agent-based model simulation with reaction kinetics and Brownian motion dynamics was developed. Reaction kinetics is used to model the stability of surface capping agent particularly due to oxidation process. The diffusion of toxic Cd2+ ions in aquatic environment was simulated using an adapted Brownian motion algorithm. A calibrated parameter to reflect sensitivity to reaction rate is proposed. The model output demonstrates the stochastic spatial distribution of toxic Cd2+ ions under different values of proxy environmental factor parameters. With the only chemistry considered was oxidation, the simulation was able to replicate Cd2+ ion release from Thiol-capped QDs in aerated water. The agent-based method is the first to be developed in the QDs application domain. It adds both simplicity of the solubility and rate of release of Cd2+ ions and complexity of tracking of individual atoms of Cd at the same time.

  10. An Empirical Agent-Based Model to Simulate the Adoption of Water Reuse Using the Social Amplification of Risk Framework.

    PubMed

    Kandiah, Venu; Binder, Andrew R; Berglund, Emily Z

    2017-01-11

    Water reuse can serve as a sustainable alternative water source for urban areas. However, the successful implementation of large-scale water reuse projects depends on community acceptance. Because of the negative perceptions that are traditionally associated with reclaimed water, water reuse is often not considered in the development of urban water management plans. This study develops a simulation model for understanding community opinion dynamics surrounding the issue of water reuse, and how individual perceptions evolve within that context, which can help in the planning and decision-making process. Based on the social amplification of risk framework, our agent-based model simulates consumer perceptions, discussion patterns, and their adoption or rejection of water reuse. The model is based on the "risk publics" model, an empirical approach that uses the concept of belief clusters to explain the adoption of new technology. Each household is represented as an agent, and parameters that define their behavior and attributes are defined from survey data. Community-level parameters-including social groups, relationships, and communication variables, also from survey data-are encoded to simulate the social processes that influence community opinion. The model demonstrates its capabilities to simulate opinion dynamics and consumer adoption of water reuse. In addition, based on empirical data, the model is applied to investigate water reuse behavior in different regions of the United States. Importantly, our results reveal that public opinion dynamics emerge differently based on membership in opinion clusters, frequency of discussion, and the structure of social networks.

  11. Towards a conceptual multi-agent-based framework to simulate the spatial group decision-making process

    NASA Astrophysics Data System (ADS)

    Ghavami, Seyed Morsal; Taleai, Mohammad

    2017-04-01

    Most spatial problems are multi-actor, multi-issue and multi-phase in nature. In addition to their intrinsic complexity, spatial problems usually involve groups of actors from different organizational and cognitive backgrounds, all of whom participate in a social structure to resolve or reduce the complexity of a given problem. Hence, it is important to study and evaluate what different aspects influence the spatial problem resolution process. Recently, multi-agent systems consisting of groups of separate agent entities all interacting with each other have been put forward as appropriate tools to use to study and resolve such problems. In this study, then in order to generate a better level of understanding regarding the spatial problem group decision-making process, a conceptual multi-agent-based framework is used that represents and specifies all the necessary concepts and entities needed to aid group decision making, based on a simulation of the group decision-making process as well as the relationships that exist among the different concepts involved. The study uses five main influencing entities as concepts in the simulation process: spatial influence, individual-level influence, group-level influence, negotiation influence and group performance measures. Further, it explains the relationship among different concepts in a descriptive rather than explanatory manner. To illustrate the proposed framework, the approval process for an urban land use master plan in Zanjan—a provincial capital in Iran—is simulated using MAS, the results highlighting the effectiveness of applying an MAS-based framework when wishing to study the group decision-making process used to resolve spatial problems.

  12. Towards a conceptual multi-agent-based framework to simulate the spatial group decision-making process

    NASA Astrophysics Data System (ADS)

    Ghavami, Seyed Morsal; Taleai, Mohammad

    2016-11-01

    Most spatial problems are multi-actor, multi-issue and multi-phase in nature. In addition to their intrinsic complexity, spatial problems usually involve groups of actors from different organizational and cognitive backgrounds, all of whom participate in a social structure to resolve or reduce the complexity of a given problem. Hence, it is important to study and evaluate what different aspects influence the spatial problem resolution process. Recently, multi-agent systems consisting of groups of separate agent entities all interacting with each other have been put forward as appropriate tools to use to study and resolve such problems. In this study, then in order to generate a better level of understanding regarding the spatial problem group decision-making process, a conceptual multi-agent-based framework is used that represents and specifies all the necessary concepts and entities needed to aid group decision making, based on a simulation of the group decision-making process as well as the relationships that exist among the different concepts involved. The study uses five main influencing entities as concepts in the simulation process: spatial influence, individual-level influence, group-level influence, negotiation influence and group performance measures. Further, it explains the relationship among different concepts in a descriptive rather than explanatory manner. To illustrate the proposed framework, the approval process for an urban land use master plan in Zanjan—a provincial capital in Iran—is simulated using MAS, the results highlighting the effectiveness of applying an MAS-based framework when wishing to study the group decision-making process used to resolve spatial problems.

  13. Agent Based Modeling and Simulation Framework for Supply Chain Risk Management

    DTIC Science & Technology

    2012-03-01

    timed Petri net based simulation (Tuncel and Alpan 2010), and Monte Carlo (White 1995, Wu and Olson 2008, and Schmitt and Singh 2009). More detail...benefit costs. (Li and Li 2008) 26 Chen, Zhou, and Hu propose an agent-oriented Petri net model for an inventory- scheduling model, with focus on the...problems of analysis and modeling of multi-agent systems. Petri net aims at researching the organization structure and dynamic behavior of a system

  14. Agent Based Simulation Output Analysis

    DTIC Science & Technology

    2011-12-01

    over long periods of time) not to have a steady state, but apparently does. These simulation models are available free from sigmawiki.com 2.1...are used in computer animations and movies (for example, in the movie Jurassic Park) as well as to look for emergent social behavior in groups

  15. A framework for the use of agent based modeling to simulate inter- and intraindividual variation in human behaviors

    EPA Science Inventory

    Simulation of human behavior in exposure modeling is a complex task. Traditionally, inter-individual variation in human activity has been modeled by drawing from a pool of single day time-activity diaries such as the US EPA Consolidated Human Activity Database (CHAD). Here, an ag...

  16. An Agent-based Framework for Web Query Answering.

    ERIC Educational Resources Information Center

    Wang, Huaiqing; Liao, Stephen; Liao, Lejian

    2000-01-01

    Discusses discrepancies between user queries on the Web and the answers provided by information sources; proposes an agent-based framework for Web mining tasks; introduces an object-oriented deductive data model and a flexible query language; and presents a cooperative mechanism for query answering. (Author/LRW)

  17. SPARK: A Framework for Multi-Scale Agent-Based Biomedical Modeling.

    PubMed

    Solovyev, Alexey; Mikheev, Maxim; Zhou, Leming; Dutta-Moscato, Joyeeta; Ziraldo, Cordelia; An, Gary; Vodovotz, Yoram; Mi, Qi

    2010-01-01

    Multi-scale modeling of complex biological systems remains a central challenge in the systems biology community. A method of dynamic knowledge representation known as agent-based modeling enables the study of higher level behavior emerging from discrete events performed by individual components. With the advancement of computer technology, agent-based modeling has emerged as an innovative technique to model the complexities of systems biology. In this work, the authors describe SPARK (Simple Platform for Agent-based Representation of Knowledge), a framework for agent-based modeling specifically designed for systems-level biomedical model development. SPARK is a stand-alone application written in Java. It provides a user-friendly interface, and a simple programming language for developing Agent-Based Models (ABMs). SPARK has the following features specialized for modeling biomedical systems: 1) continuous space that can simulate real physical space; 2) flexible agent size and shape that can represent the relative proportions of various cell types; 3) multiple spaces that can concurrently simulate and visualize multiple scales in biomedical models; 4) a convenient graphical user interface. Existing ABMs of diabetic foot ulcers and acute inflammation were implemented in SPARK. Models of identical complexity were run in both NetLogo and SPARK; the SPARK-based models ran two to three times faster.

  18. Agent-Based Simulations for Project Management

    NASA Technical Reports Server (NTRS)

    White, J. Chris; Sholtes, Robert M.

    2011-01-01

    Currently, the most common approach used in project planning tools is the Critical Path Method (CPM). While this method was a great improvement over the basic Gantt chart technique being used at the time, it now suffers from three primary flaws: (1) task duration is an input, (2) productivity impacts are not considered , and (3) management corrective actions are not included. Today, computers have exceptional computational power to handle complex simulations of task e)(eculion and project management activities (e.g ., dynamically changing the number of resources assigned to a task when it is behind schedule). Through research under a Department of Defense contract, the author and the ViaSim team have developed a project simulation tool that enables more realistic cost and schedule estimates by using a resource-based model that literally turns the current duration-based CPM approach "on its head." The approach represents a fundamental paradigm shift in estimating projects, managing schedules, and reducing risk through innovative predictive techniques.

  19. Cognitive Modeling for Agent-Based Simulation of Child Maltreatment

    NASA Astrophysics Data System (ADS)

    Hu, Xiaolin; Puddy, Richard

    This paper extends previous work to develop cognitive modeling for agent-based simulation of child maltreatment (CM). The developed model is inspired from parental efficacy, parenting stress, and the theory of planned behavior. It provides an explanatory, process-oriented model of CM and incorporates causality relationship and feedback loops from different factors in the social ecology in order for simulating the dynamics of CM. We describe the model and present simulation results to demonstrate the features of this model.

  20. Validation techniques of agent based modelling for geospatial simulations

    NASA Astrophysics Data System (ADS)

    Darvishi, M.; Ahmadi, G.

    2014-10-01

    One of the most interesting aspects of modelling and simulation study is to describe the real world phenomena that have specific properties; especially those that are in large scales and have dynamic and complex behaviours. Studying these phenomena in the laboratory is costly and in most cases it is impossible. Therefore, Miniaturization of world phenomena in the framework of a model in order to simulate the real phenomena is a reasonable and scientific approach to understand the world. Agent-based modelling and simulation (ABMS) is a new modelling method comprising of multiple interacting agent. They have been used in the different areas; for instance, geographic information system (GIS), biology, economics, social science and computer science. The emergence of ABM toolkits in GIS software libraries (e.g. ESRI's ArcGIS, OpenMap, GeoTools, etc) for geospatial modelling is an indication of the growing interest of users to use of special capabilities of ABMS. Since ABMS is inherently similar to human cognition, therefore it could be built easily and applicable to wide range applications than a traditional simulation. But a key challenge about ABMS is difficulty in their validation and verification. Because of frequent emergence patterns, strong dynamics in the system and the complex nature of ABMS, it is hard to validate and verify ABMS by conventional validation methods. Therefore, attempt to find appropriate validation techniques for ABM seems to be necessary. In this paper, after reviewing on Principles and Concepts of ABM for and its applications, the validation techniques and challenges of ABM validation are discussed.

  1. Solution of partial differential equations by agent-based simulation

    NASA Astrophysics Data System (ADS)

    Szilagyi, Miklos N.

    2014-01-01

    The purpose of this short note is to demonstrate that partial differential equations can be quickly solved by agent-based simulation with high accuracy. There is no need for the solution of large systems of algebraic equations. This method is especially useful for quick determination of potential distributions and demonstration purposes in teaching electromagnetism.

  2. Simulating cancer growth with multiscale agent-based modeling.

    PubMed

    Wang, Zhihui; Butner, Joseph D; Kerketta, Romica; Cristini, Vittorio; Deisboeck, Thomas S

    2015-02-01

    There have been many techniques developed in recent years to in silico model a variety of cancer behaviors. Agent-based modeling is a specific discrete-based hybrid modeling approach that allows simulating the role of diversity in cell populations as well as within each individual cell; it has therefore become a powerful modeling method widely used by computational cancer researchers. Many aspects of tumor morphology including phenotype-changing mutations, the adaptation to microenvironment, the process of angiogenesis, the influence of extracellular matrix, reactions to chemotherapy or surgical intervention, the effects of oxygen and nutrient availability, and metastasis and invasion of healthy tissues have been incorporated and investigated in agent-based models. In this review, we introduce some of the most recent agent-based models that have provided insight into the understanding of cancer growth and invasion, spanning multiple biological scales in time and space, and we further describe several experimentally testable hypotheses generated by those models. We also discuss some of the current challenges of multiscale agent-based cancer models.

  3. A mathematical framework for agent based models of complex biological networks.

    PubMed

    Hinkelmann, Franziska; Murrugarra, David; Jarrah, Abdul Salam; Laubenbacher, Reinhard

    2011-07-01

    Agent-based modeling and simulation is a useful method to study biological phenomena in a wide range of fields, from molecular biology to ecology. Since there is currently no agreed-upon standard way to specify such models, it is not always easy to use published models. Also, since model descriptions are not usually given in mathematical terms, it is difficult to bring mathematical analysis tools to bear, so that models are typically studied through simulation. In order to address this issue, Grimm et al. proposed a protocol for model specification, the so-called ODD protocol, which provides a standard way to describe models. This paper proposes an addition to the ODD protocol which allows the description of an agent-based model as a dynamical system, which provides access to computational and theoretical tools for its analysis. The mathematical framework is that of algebraic models, that is, time-discrete dynamical systems with algebraic structure. It is shown by way of several examples how this mathematical specification can help with model analysis. This mathematical framework can also accommodate other model types such as Boolean networks and the more general logical models, as well as Petri nets.

  4. Agent-based simulation of a financial market

    NASA Astrophysics Data System (ADS)

    Raberto, Marco; Cincotti, Silvano; Focardi, Sergio M.; Marchesi, Michele

    2001-10-01

    This paper introduces an agent-based artificial financial market in which heterogeneous agents trade one single asset through a realistic trading mechanism for price formation. Agents are initially endowed with a finite amount of cash and a given finite portfolio of assets. There is no money-creation process; the total available cash is conserved in time. In each period, agents make random buy and sell decisions that are constrained by available resources, subject to clustering, and dependent on the volatility of previous periods. The model proposed herein is able to reproduce the leptokurtic shape of the probability density of log price returns and the clustering of volatility. Implemented using extreme programming and object-oriented technology, the simulator is a flexible computational experimental facility that can find applications in both academic and industrial research projects.

  5. Using Agent Based Modeling (ABM) to Develop Cultural Interaction Simulations

    NASA Technical Reports Server (NTRS)

    Drucker, Nick; Jones, Phillip N.

    2012-01-01

    Today, most cultural training is based on or built around "cultural engagements" or discrete interactions between the individual learner and one or more cultural "others". Often, success in the engagement is the end or the objective. In reality, these interactions usually involve secondary and tertiary effects with potentially wide ranging consequences. The concern is that learning culture within a strict engagement context might lead to "checklist" cultural thinking that will not empower learners to understand the full consequence of their actions. We propose the use of agent based modeling (ABM) to collect, store, and, simulating the effects of social networks, promulgate engagement effects over time, distance, and consequence. The ABM development allows for rapid modification to re-create any number of population types, extending the applicability of the model to any requirement for social modeling.

  6. Agent-based modeling of the immune system: NetLogo, a promising framework.

    PubMed

    Chiacchio, Ferdinando; Pennisi, Marzio; Russo, Giulia; Motta, Santo; Pappalardo, Francesco

    2014-01-01

    Several components that interact with each other to evolve a complex, and, in some cases, unexpected behavior, represents one of the main and fascinating features of the mammalian immune system. Agent-based modeling and cellular automata belong to a class of discrete mathematical approaches in which entities (agents) sense local information and undertake actions over time according to predefined rules. The strength of this approach is characterized by the appearance of a global behavior that emerges from interactions among agents. This behavior is unpredictable, as it does not follow linear rules. There are a lot of works that investigates the immune system with agent-based modeling and cellular automata. They have shown the ability to see clearly and intuitively into the nature of immunological processes. NetLogo is a multiagent programming language and modeling environment for simulating complex phenomena. It is designed for both research and education and is used across a wide range of disciplines and education levels. In this paper, we summarize NetLogo applications to immunology and, particularly, how this framework can help in the development and formulation of hypotheses that might drive further experimental investigations of disease mechanisms.

  7. Agent-Based Modeling of the Immune System: NetLogo, a Promising Framework

    PubMed Central

    Chiacchio, Ferdinando; Russo, Giulia; Pappalardo, Francesco

    2014-01-01

    Several components that interact with each other to evolve a complex, and, in some cases, unexpected behavior, represents one of the main and fascinating features of the mammalian immune system. Agent-based modeling and cellular automata belong to a class of discrete mathematical approaches in which entities (agents) sense local information and undertake actions over time according to predefined rules. The strength of this approach is characterized by the appearance of a global behavior that emerges from interactions among agents. This behavior is unpredictable, as it does not follow linear rules. There are a lot of works that investigates the immune system with agent-based modeling and cellular automata. They have shown the ability to see clearly and intuitively into the nature of immunological processes. NetLogo is a multiagent programming language and modeling environment for simulating complex phenomena. It is designed for both research and education and is used across a wide range of disciplines and education levels. In this paper, we summarize NetLogo applications to immunology and, particularly, how this framework can help in the development and formulation of hypotheses that might drive further experimental investigations of disease mechanisms. PMID:24864263

  8. Agent-based modeling to simulate the dengue spread

    NASA Astrophysics Data System (ADS)

    Deng, Chengbin; Tao, Haiyan; Ye, Zhiwei

    2008-10-01

    In this paper, we introduce a novel method ABM in simulating the unique process for the dengue spread. Dengue is an acute infectious disease with a long history of over 200 years. Unlike the diseases that can be transmitted directly from person to person, dengue spreads through a must vector of mosquitoes. There is still no any special effective medicine and vaccine for dengue up till now. The best way to prevent dengue spread is to take precautions beforehand. Thus, it is crucial to detect and study the dynamic process of dengue spread that closely relates to human-environment interactions where Agent-Based Modeling (ABM) effectively works. The model attempts to simulate the dengue spread in a more realistic way in the bottom-up way, and to overcome the limitation of ABM, namely overlooking the influence of geographic and environmental factors. Considering the influence of environment, Aedes aegypti ecology and other epidemiological characteristics of dengue spread, ABM can be regarded as a useful way to simulate the whole process so as to disclose the essence of the evolution of dengue spread.

  9. Serious games experiment toward agent-based simulation

    USGS Publications Warehouse

    Wein, Anne; Labiosa, William

    2013-01-01

    We evaluate the potential for serious games to be used as a scientifically based decision-support product that supports the United States Geological Survey’s (USGS) mission--to provide integrated, unbiased scientific information that can make a substantial contribution to societal well-being for a wide variety of complex environmental challenges. Serious or pedagogical games are an engaging way to educate decisionmakers and stakeholders about environmental challenges that are usefully informed by natural and social scientific information and knowledge and can be designed to promote interactive learning and exploration in the face of large uncertainties, divergent values, and complex situations. We developed two serious games that use challenging environmental-planning issues to demonstrate and investigate the potential contributions of serious games to inform regional-planning decisions. Delta Skelta is a game emulating long-term integrated environmental planning in the Sacramento-San Joaquin Delta, California, that incorporates natural hazards (flooding and earthquakes) and consequences for California water supplies amidst conflicting water interests. Age of Ecology is a game that simulates interactions between economic and ecologic processes, as well as natural hazards while implementing agent-based modeling. The content of these games spans the USGS science mission areas related to water, ecosystems, natural hazards, land use, and climate change. We describe the games, reflect on design and informational aspects, and comment on their potential usefulness. During the process of developing these games, we identified various design trade-offs involving factual information, strategic thinking, game-winning criteria, elements of fun, number and type of players, time horizon, and uncertainty. We evaluate the two games in terms of accomplishments and limitations. Overall, we demonstrated the potential for these games to usefully represent scientific information

  10. Identifying Evacuees' Demand of Tsunami Shelters using Agent Based Simulation

    NASA Astrophysics Data System (ADS)

    Mas, E.; Adriano, B.; Koshimura, S.; Imamura, F.; Kuroiwa, J.; Yamazaki, F.; Zavala, C.; Estrada, M.

    2012-12-01

    Amongst the lessons learned in tsunami events such as the 2004 Indian Ocean and 2011 Great Tohoku Japan earthquake is that sometimes nature exceeds structural countermeasures like seawalls, breakwaters or tsunami gates. In such situations it is a challenging task for people in plain areas to find sheltering places. The vertical evacuation to multistory buildings is one alternative to provide areas for sheltering in a complex environment of evacuation. However, if the spatial distribution and the available capacity of these structures are not well displayed, conditions of evacuee over-demand or under-demand might be observed in several structures. In this study, we present the integration of the tsunami numerical modeling and the agent based simulation of evacuation as the method to estimate the sheltering demand of evacuees in an emergent behavior approach. The case study is set in La Punta district in Peru. Here, we used in the tsunami simulation a seismic source of slip distribution model (Pulido et.al. ,2011; Chlieh et.al, 2011) for a possible future tsunami scenario in the central Andes. We modeled three alternatives of evacuation. First, the horizontal evacuation scenario was analyzed to support the necessity of the sheltering-in-place option for the district. Second, the vertical evacuation scenario and third, the combination of vertical and horizontal evacuation scenarios of pedestrians and vehicles were conducted. In the last two alternatives, the demand of evacuees were measured at each official tsunami evacuation building and compared to the sheltering capacity of the structure. Results showed that out of twenty tsunami evacuation buildings, thirteen resulted with over-demands and seven were still with available space. Also it is confirmed that in this case the horizontal evacuation might lead to a high number of casualties due to the traffic congestion at the neck of the district. Finally the vertical evacuation would be a suitable solution for this area

  11. Agent-based Approaches to Dynamic Team Simulation

    DTIC Science & Technology

    2008-09-01

    behavior. The second section reviews agent-based models of teamwork describing work involving both teamwork approaches to design of multiagent systems...there is less direct evidence for teams. Hough (1992), for example, found that ratings on conscientiousness, emotional stability, and agreeableness...Peeters, Rutte, Tuijl, and Reymen (2006) who found agreeableness and emotional stability positively related to satisfaction with the team make

  12. Agent-based modeling: Methods and techniques for simulating human systems

    PubMed Central

    Bonabeau, Eric

    2002-01-01

    Agent-based modeling is a powerful simulation modeling technique that has seen a number of applications in the last few years, including applications to real-world business problems. After the basic principles of agent-based simulation are briefly introduced, its four areas of application are discussed by using real-world applications: flow simulation, organizational simulation, market simulation, and diffusion simulation. For each category, one or several business applications are described and analyzed. PMID:12011407

  13. Agent-Based Knowledge Discovery for Modeling and Simulation

    SciTech Connect

    Haack, Jereme N.; Cowell, Andrew J.; Marshall, Eric J.; Fligg, Alan K.; Gregory, Michelle L.; McGrath, Liam R.

    2009-09-15

    This paper describes an approach to using agent technology to extend the automated discovery mechanism of the Knowledge Encapsulation Framework (KEF). KEF is a suite of tools to enable the linking of knowledge inputs (relevant, domain-specific evidence) to modeling and simulation projects, as well as other domains that require an effective collaborative workspace for knowledge-based tasks. This framework can be used to capture evidence (e.g., trusted material such as journal articles and government reports), discover new evidence (covering both trusted and social media), enable discussions surrounding domain-specific topics and provide automatically generated semantic annotations for improved corpus investigation. The current KEF implementation is presented within a semantic wiki environment, providing a simple but powerful collaborative space for team members to review, annotate, discuss and align evidence with their modeling frameworks. The novelty in this approach lies in the combination of automatically tagged and user-vetted resources, which increases user trust in the environment, leading to ease of adoption for the collaborative environment.

  14. A Systematic Review of Agent-Based Modelling and Simulation Applications in the Higher Education Domain

    ERIC Educational Resources Information Center

    Gu, X.; Blackmore, K. L.

    2015-01-01

    This paper presents the results of a systematic review of agent-based modelling and simulation (ABMS) applications in the higher education (HE) domain. Agent-based modelling is a "bottom-up" modelling paradigm in which system-level behaviour (macro) is modelled through the behaviour of individual local-level agent interactions (micro).…

  15. Agent-based modeling of the spread of influenza-like illness in an emergency department: a simulation study.

    PubMed

    Laskowski, Marek; Demianyk, Bryan C P; Witt, Julia; Mukhi, Shamir N; Friesen, Marcia R; McLeod, Robert D

    2011-11-01

    The objective of this paper was to develop an agent-based modeling framework in order to simulate the spread of influenza virus infection on a layout based on a representative hospital emergency department in Winnipeg, Canada. In doing so, the study complements mathematical modeling techniques for disease spread, as well as modeling applications focused on the spread of antibiotic-resistant nosocomial infections in hospitals. Twenty different emergency department scenarios were simulated, with further simulation of four infection control strategies. The agent-based modeling approach represents systems modeling, in which the emergency department was modeled as a collection of agents (patients and healthcare workers) and their individual characteristics, behaviors, and interactions. The framework was coded in C++ using Qt4 libraries running under the Linux operating system. A simple ordinary least squares (OLS) regression was used to analyze the data, in which the percentage of patients that became infected in one day within the simulation was the dependent variable. The results suggest that within the given instance context, patient-oriented infection control policies (alternate treatment streams, masking symptomatic patients) tend to have a larger effect than policies that target healthcare workers. The agent-based modeling framework is a flexible tool that can be made to reflect any given environment; it is also a decision support tool for practitioners and policymakers to assess the relative impact of infection control strategies. The framework illuminates scenarios worthy of further investigation, as well as counterintuitive findings.

  16. Integrated Agent-Based and Production Cost Modeling Framework for Renewable Energy Studies: Preprint

    SciTech Connect

    Gallo, Giulia

    2015-10-07

    The agent-based framework for renewable energy studies (ARES) is an integrated approach that adds an agent-based model of industry actors to PLEXOS and combines the strengths of the two to overcome their individual shortcomings. It can examine existing and novel wholesale electricity markets under high penetrations of renewables. ARES is demonstrated by studying how increasing levels of wind will impact the operations and the exercise of market power of generation companies that exploit an economic withholding strategy. The analysis is carried out on a test system that represents the Electric Reliability Council of Texas energy-only market in the year 2020. The results more realistically reproduce the operations of an energy market under different and increasing penetrations of wind, and ARES can be extended to address pressing issues in current and future wholesale electricity markets.

  17. Integrated Agent-Based and Production Cost Modeling Framework for Renewable Energy Studies

    SciTech Connect

    Gallo, Giulia

    2016-01-08

    The agent-based framework for renewable energy studies (ARES) is an integrated approach that adds an agent-based model of industry actors to PLEXOS and combines the strengths of the two to overcome their individual shortcomings. It can examine existing and novel wholesale electricity markets under high penetrations of renewables. ARES is demonstrated by studying how increasing levels of wind will impact the operations and the exercise of market power of generation companies that exploit an economic withholding strategy. The analysis is carried out on a test system that represents the Electric Reliability Council of Texas energy-only market in the year 2020. The results more realistically reproduce the operations of an energy market under different and increasing penetrations of wind, and ARES can be extended to address pressing issues in current and future wholesale electricity markets.

  18. Agent-Based Framework for Personalized Service Provisioning in Converged IP Networks

    NASA Astrophysics Data System (ADS)

    Podobnik, Vedran; Matijasevic, Maja; Lovrek, Ignac; Skorin-Kapov, Lea; Desic, Sasa

    In a global multi-service and multi-provider market, the Internet Service Providers will increasingly need to differentiate in the service quality they offer and base their operation on new, consumer-centric business models. In this paper, we propose an agent-based framework for the Business-to-Consumer (B2C) electronic market, comprising the Consumer Agents, Broker Agents and Content Agents, which enable Internet consumers to select a content provider in an automated manner. We also discuss how to dynamically allocate network resources to provide end-to-end Quality of Service (QoS) for a given consumer and content provider.

  19. Agent Based Simulation Design for Aggregation and Disaggregation

    DTIC Science & Technology

    2011-12-01

    Development of a Generic Data-Driven Simulation.‖ In Proceed- ings of the 2010 Winter Simulation Conference, edited by B. Johansson, S. Jain, J. Montoya ...DARPA, Santa Monica, CA. Davis, P. and R. Hillestad. 1993. ―Families of Models that Cross Levels of Resolution: Issues for Design, Calibration and...Issues, and Prin- ciples.‖ RAND N-3400-DARPA, Santa Monica, CA. Department of Defense. 1995. ―Department of Defense Modeling and Simulation Master

  20. Agent-Based Crowd Simulation Considering Emotion Contagion for Emergency Evacuation Problem

    NASA Astrophysics Data System (ADS)

    Faroqi, H.; Mesgari, M.-S.

    2015-12-01

    During emergencies, emotions greatly affect human behaviour. For more realistic multi-agent systems in simulations of emergency evacuations, it is important to incorporate emotions and their effects on the agents. In few words, emotional contagion is a process in which a person or group influences the emotions or behavior of another person or group through the conscious or unconscious induction of emotion states and behavioral attitudes. In this study, we simulate an emergency situation in an open square area with three exits considering Adults and Children agents with different behavior. Also, Security agents are considered in order to guide Adults and Children for finding the exits and be calm. Six levels of emotion levels are considered for each agent in different scenarios and situations. The agent-based simulated model initialize with the random scattering of agent populations and then when an alarm occurs, each agent react to the situation based on its and neighbors current circumstances. The main goal of each agent is firstly to find the exit, and then help other agents to find their ways. Numbers of exited agents along with their emotion levels and damaged agents are compared in different scenarios with different initialization in order to evaluate the achieved results of the simulated model. NetLogo 5.2 is used as the multi-agent simulation framework with R language as the developing language.

  1. Towards a framework for agent-based image analysis of remote-sensing data.

    PubMed

    Hofmann, Peter; Lettmayer, Paul; Blaschke, Thomas; Belgiu, Mariana; Wegenkittl, Stefan; Graf, Roland; Lampoltshammer, Thomas Josef; Andrejchenko, Vera

    2015-04-03

    Object-based image analysis (OBIA) as a paradigm for analysing remotely sensed image data has in many cases led to spatially and thematically improved classification results in comparison to pixel-based approaches. Nevertheless, robust and transferable object-based solutions for automated image analysis capable of analysing sets of images or even large image archives without any human interaction are still rare. A major reason for this lack of robustness and transferability is the high complexity of image contents: Especially in very high resolution (VHR) remote-sensing data with varying imaging conditions or sensor characteristics, the variability of the objects' properties in these varying images is hardly predictable. The work described in this article builds on so-called rule sets. While earlier work has demonstrated that OBIA rule sets bear a high potential of transferability, they need to be adapted manually, or classification results need to be adjusted manually in a post-processing step. In order to automate these adaptation and adjustment procedures, we investigate the coupling, extension and integration of OBIA with the agent-based paradigm, which is exhaustively investigated in software engineering. The aims of such integration are (a) autonomously adapting rule sets and (b) image objects that can adopt and adjust themselves according to different imaging conditions and sensor characteristics. This article focuses on self-adapting image objects and therefore introduces a framework for agent-based image analysis (ABIA).

  2. Towards a framework for agent-based image analysis of remote-sensing data

    PubMed Central

    Hofmann, Peter; Lettmayer, Paul; Blaschke, Thomas; Belgiu, Mariana; Wegenkittl, Stefan; Graf, Roland; Lampoltshammer, Thomas Josef; Andrejchenko, Vera

    2015-01-01

    Object-based image analysis (OBIA) as a paradigm for analysing remotely sensed image data has in many cases led to spatially and thematically improved classification results in comparison to pixel-based approaches. Nevertheless, robust and transferable object-based solutions for automated image analysis capable of analysing sets of images or even large image archives without any human interaction are still rare. A major reason for this lack of robustness and transferability is the high complexity of image contents: Especially in very high resolution (VHR) remote-sensing data with varying imaging conditions or sensor characteristics, the variability of the objects’ properties in these varying images is hardly predictable. The work described in this article builds on so-called rule sets. While earlier work has demonstrated that OBIA rule sets bear a high potential of transferability, they need to be adapted manually, or classification results need to be adjusted manually in a post-processing step. In order to automate these adaptation and adjustment procedures, we investigate the coupling, extension and integration of OBIA with the agent-based paradigm, which is exhaustively investigated in software engineering. The aims of such integration are (a) autonomously adapting rule sets and (b) image objects that can adopt and adjust themselves according to different imaging conditions and sensor characteristics. This article focuses on self-adapting image objects and therefore introduces a framework for agent-based image analysis (ABIA). PMID:27721916

  3. An Observation-Driven Agent-Based Modeling and Analysis Framework for C. elegans Embryogenesis.

    PubMed

    Wang, Zi; Ramsey, Benjamin J; Wang, Dali; Wong, Kwai; Li, Husheng; Wang, Eric; Bao, Zhirong

    2016-01-01

    With cutting-edge live microscopy and image analysis, biologists can now systematically track individual cells in complex tissues and quantify cellular behavior over extended time windows. Computational approaches that utilize the systematic and quantitative data are needed to understand how cells interact in vivo to give rise to the different cell types and 3D morphology of tissues. An agent-based, minimum descriptive modeling and analysis framework is presented in this paper to study C. elegans embryogenesis. The framework is designed to incorporate the large amounts of experimental observations on cellular behavior and reserve data structures/interfaces that allow regulatory mechanisms to be added as more insights are gained. Observed cellular behaviors are organized into lineage identity, timing and direction of cell division, and path of cell movement. The framework also includes global parameters such as the eggshell and a clock. Division and movement behaviors are driven by statistical models of the observations. Data structures/interfaces are reserved for gene list, cell-cell interaction, cell fate and landscape, and other global parameters until the descriptive model is replaced by a regulatory mechanism. This approach provides a framework to handle the ongoing experiments of single-cell analysis of complex tissues where mechanistic insights lag data collection and need to be validated on complex observations.

  4. An Observation-Driven Agent-Based Modeling and Analysis Framework for C. elegans Embryogenesis

    PubMed Central

    Wang, Zi; Ramsey, Benjamin J.; Wang, Dali; Wong, Kwai; Li, Husheng; Wang, Eric; Bao, Zhirong

    2016-01-01

    With cutting-edge live microscopy and image analysis, biologists can now systematically track individual cells in complex tissues and quantify cellular behavior over extended time windows. Computational approaches that utilize the systematic and quantitative data are needed to understand how cells interact in vivo to give rise to the different cell types and 3D morphology of tissues. An agent-based, minimum descriptive modeling and analysis framework is presented in this paper to study C. elegans embryogenesis. The framework is designed to incorporate the large amounts of experimental observations on cellular behavior and reserve data structures/interfaces that allow regulatory mechanisms to be added as more insights are gained. Observed cellular behaviors are organized into lineage identity, timing and direction of cell division, and path of cell movement. The framework also includes global parameters such as the eggshell and a clock. Division and movement behaviors are driven by statistical models of the observations. Data structures/interfaces are reserved for gene list, cell-cell interaction, cell fate and landscape, and other global parameters until the descriptive model is replaced by a regulatory mechanism. This approach provides a framework to handle the ongoing experiments of single-cell analysis of complex tissues where mechanistic insights lag data collection and need to be validated on complex observations. PMID:27851808

  5. An Agent-Based Optimization Framework for Engineered Complex Adaptive Systems with Application to Demand Response in Electricity Markets

    NASA Astrophysics Data System (ADS)

    Haghnevis, Moeed

    The main objective of this research is to develop an integrated method to study emergent behavior and consequences of evolution and adaptation in engineered complex adaptive systems (ECASs). A multi-layer conceptual framework and modeling approach including behavioral and structural aspects is provided to describe the structure of a class of engineered complex systems and predict their future adaptive patterns. The approach allows the examination of complexity in the structure and the behavior of components as a result of their connections and in relation to their environment. This research describes and uses the major differences of natural complex adaptive systems (CASs) with artificial/engineered CASs to build a framework and platform for ECAS. While this framework focuses on the critical factors of an engineered system, it also enables one to synthetically employ engineering and mathematical models to analyze and measure complexity in such systems. In this way concepts of complex systems science are adapted to management science and system of systems engineering. In particular an integrated consumer-based optimization and agent-based modeling (ABM) platform is presented that enables managers to predict and partially control patterns of behaviors in ECASs. Demonstrated on the U.S. electricity markets, ABM is integrated with normative and subjective decision behavior recommended by the U.S. Department of Energy (DOE) and Federal Energy Regulatory Commission (FERC). The approach integrates social networks, social science, complexity theory, and diffusion theory. Furthermore, it has unique and significant contribution in exploring and representing concrete managerial insights for ECASs and offering new optimized actions and modeling paradigms in agent-based simulation.

  6. An extensible simulation environment and movement metrics for testing walking behavior in agent-based models

    SciTech Connect

    Paul M. Torrens; Atsushi Nara; Xun Li; Haojie Zhu; William A. Griffin; Scott B. Brown

    2012-01-01

    Human movement is a significant ingredient of many social, environmental, and technical systems, yet the importance of movement is often discounted in considering systems complexity. Movement is commonly abstracted in agent-based modeling (which is perhaps the methodological vehicle for modeling complex systems), despite the influence of movement upon information exchange and adaptation in a system. In particular, agent-based models of urban pedestrians often treat movement in proxy form at the expense of faithfully treating movement behavior with realistic agency. There exists little consensus about which method is appropriate for representing movement in agent-based schemes. In this paper, we examine popularly-used methods to drive movement in agent-based models, first by introducing a methodology that can flexibly handle many representations of movement at many different scales and second, introducing a suite of tools to benchmark agent movement between models and against real-world trajectory data. We find that most popular movement schemes do a relatively poor job of representing movement, but that some schemes may well be 'good enough' for some applications. We also discuss potential avenues for improving the representation of movement in agent-based frameworks.

  7. Efficient Allocation of Resources for Defense of Spatially Distributed Networks Using Agent-Based Simulation.

    PubMed

    Kroshl, William M; Sarkani, Shahram; Mazzuchi, Thomas A

    2015-09-01

    This article presents ongoing research that focuses on efficient allocation of defense resources to minimize the damage inflicted on a spatially distributed physical network such as a pipeline, water system, or power distribution system from an attack by an active adversary, recognizing the fundamental difference between preparing for natural disasters such as hurricanes, earthquakes, or even accidental systems failures and the problem of allocating resources to defend against an opponent who is aware of, and anticipating, the defender's efforts to mitigate the threat. Our approach is to utilize a combination of integer programming and agent-based modeling to allocate the defensive resources. We conceptualize the problem as a Stackelberg "leader follower" game where the defender first places his assets to defend key areas of the network, and the attacker then seeks to inflict the maximum damage possible within the constraints of resources and network structure. The criticality of arcs in the network is estimated by a deterministic network interdiction formulation, which then informs an evolutionary agent-based simulation. The evolutionary agent-based simulation is used to determine the allocation of resources for attackers and defenders that results in evolutionary stable strategies, where actions by either side alone cannot increase its share of victories. We demonstrate these techniques on an example network, comparing the evolutionary agent-based results to a more traditional, probabilistic risk analysis (PRA) approach. Our results show that the agent-based approach results in a greater percentage of defender victories than does the PRA-based approach.

  8. Research on monocentric model of urbanization by agent-based simulation

    NASA Astrophysics Data System (ADS)

    Xue, Ling; Yang, Kaizhong

    2008-10-01

    Over the past years, GIS have been widely used for modeling urbanization from a variety of perspectives such as digital terrain representation and overlay analysis using cell-based data platform. Similarly, simulation of urban dynamics has been achieved with the use of Cellular Automata. In contrast to these approaches, agent-based simulation provides a much more powerful set of tools. This allows researchers to set up a counterpart for real environmental and urban systems in computer for experimentation and scenario analysis. This Paper basically reviews the research on the economic mechanism of urbanization and an agent-based monocentric model is setup for further understanding the urbanization process and mechanism in China. We build an endogenous growth model with dynamic interactions between spatial agglomeration and urban development by using agent-based simulation. It simulates the migration decisions of two main types of agents, namely rural and urban households between rural and urban area. The model contains multiple economic interactions that are crucial in understanding urbanization and industrial process in China. These adaptive agents can adjust their supply and demand according to the market situation by a learning algorithm. The simulation result shows this agent-based urban model is able to perform the regeneration and to produce likely-to-occur projections of reality.

  9. Evaluation of wholesale electric power market rules and financial risk management by agent-based simulations

    NASA Astrophysics Data System (ADS)

    Yu, Nanpeng

    dissertation, basic financial risk management concepts relevant for wholesale electric power markets are carefully explained and illustrated. In addition, the financial risk management problem in wholesale electric power markets is generalized as a four-stage process. Within the proposed financial risk management framework, the critical problem of financial bilateral contract negotiation is addressed. This dissertation analyzes a financial bilateral contract negotiation process between a generating company and a load-serving entity in a wholesale electric power market with congestion managed by locational marginal pricing. Nash bargaining theory is used to model a Pareto-efficient settlement point. The model predicts negotiation results under varied conditions and identifies circumstances in which the two parties might fail to reach an agreement. Both analysis and agent-based simulation are used to gain insight regarding how relative risk aversion and biased price estimates influence negotiated outcomes. These results should provide useful guidance to market participants in their bilateral contract negotiation processes.

  10. An agent-based simulation of extirpation of Ceratitis capitata applied to invasions in California

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We describe and validate an Agent-Based Simulation(ABS) of invasive insects and use it to investigate the time to extirpation of Ceratitis capitata using data from seven outbreaks that occurred in California from 2008-2010. Results are compared with the length of intervention and quarantine imposed ...

  11. UAV Swarm Tactics: An Agent-Based Simulation and Markov Process Analysis

    DTIC Science & Technology

    2013-06-01

    NPS NAVAL POSTGRADUATE SCHOOL MONTEREY, CALIFORNIA THESIS UAV SWARM TACTICS: AN AGENT-BASED SIM ULATION AND MARKOV PROCESS ANALYSIS Thesis...inina; tho d ... _ . aod oompiotinl and ~_i .. tho roIloction of .. form. tion. Sond oommonu fQPrdina; thi!; burdon Mlim. m 0< a ny <>tho< ...,oct...TACTICS : AN AGENT-BASED SIMULATION AND MARKOV PROCESS ANALYSIS 1 So. " NUMBER ’. AU 1 Sd. PROJECT Uwe Gaertner 1 s.. TASK NUMBER 1 sr. WORK UNIT

  12. Collaborative Multi-Agent Based Simulations: Stakeholder-Focused Innovation in Water Resources Management and Decision-Support Modeling

    NASA Astrophysics Data System (ADS)

    Kock, B. E.

    2006-12-01

    The combined use of multi-agent based simulations and collaborative modeling approaches is emerging as a highly effective tool for representing complex coupled social-biophysical water resource systems. A collaboratively-designed, multi-agent based simulation can be used both as a decision-support tool and as a didactic method for improving stakeholder understanding and engagement with water resources policymaking and management. Major technical and non-technical obstacles remain to the efficient and effective development of multi-agent models of human society, to integrating these models with GIS and other numerical models, and to building a process for engaging stakeholders with model design, implementation and use. It is proposed here to tackle some of these obstacles through a collaborative multi-agent based simulation process framework, intended for practical use in resolving disputes and environmental challenges over sustainable irrigated agriculture in the Western United States. A practical implementation of this framework will be conducted in collaboration with a diverse stakeholder group representing farmers and local, state and federal water managers. Through the use of simulation gaming, interviewing and computer-based knowledge elicitation, a multi-agent model representing local and regional social dynamics will be developed to support the acceptable and sustainable implementation of management alternatives for reducing regional problems of salinization and high selenium concentrations in soils and irrigation water. The development of a socially and scientifically credible simulation platform in this setting can make a significant contribution to ensuring the non-adversarial use of high quality science, enhance the engagement of stakeholders with policymaking, and help meet the challenges of integrating dynamic models of human society with more traditional biophysical systems models.

  13. A CSP-Based Agent Modeling Framework for the Cougaar Agent-Based Architecture

    NASA Technical Reports Server (NTRS)

    Gracanin, Denis; Singh, H. Lally; Eltoweissy, Mohamed; Hinchey, Michael G.; Bohner, Shawn A.

    2005-01-01

    Cognitive Agent Architecture (Cougaar) is a Java-based architecture for large-scale distributed agent-based applications. A Cougaar agent is an autonomous software entity with behaviors that represent a real-world entity (e.g., a business process). A Cougaar-based Model Driven Architecture approach, currently under development, uses a description of system's functionality (requirements) to automatically implement the system in Cougaar. The Communicating Sequential Processes (CSP) formalism is used for the formal validation of the generated system. Two main agent components, a blackboard and a plugin, are modeled as CSP processes. A set of channels represents communications between the blackboard and individual plugins. The blackboard is represented as a CSP process that communicates with every agent in the collection. The developed CSP-based Cougaar modeling framework provides a starting point for a more complete formal verification of the automatically generated Cougaar code. Currently it is used to verify the behavior of an individual agent in terms of CSP properties and to analyze the corresponding Cougaar society.

  14. A Participatory Agent-Based Simulation for Indoor Evacuation Supported by Google Glass

    PubMed Central

    Sánchez, Jesús M.; Carrera, Álvaro; Iglesias, Carlos Á.; Serrano, Emilio

    2016-01-01

    Indoor evacuation systems are needed for rescue and safety management. One of the challenges is to provide users with personalized evacuation routes in real time. To this end, this project aims at exploring the possibilities of Google Glass technology for participatory multiagent indoor evacuation simulations. Participatory multiagent simulation combines scenario-guided agents and humans equipped with Google Glass that coexist in a shared virtual space and jointly perform simulations. The paper proposes an architecture for participatory multiagent simulation in order to combine devices (Google Glass and/or smartphones) with an agent-based social simulator and indoor tracking services. PMID:27563911

  15. A Participatory Agent-Based Simulation for Indoor Evacuation Supported by Google Glass.

    PubMed

    Sánchez, Jesús M; Carrera, Álvaro; Iglesias, Carlos Á; Serrano, Emilio

    2016-08-24

    Indoor evacuation systems are needed for rescue and safety management. One of the challenges is to provide users with personalized evacuation routes in real time. To this end, this project aims at exploring the possibilities of Google Glass technology for participatory multiagent indoor evacuation simulations. Participatory multiagent simulation combines scenario-guided agents and humans equipped with Google Glass that coexist in a shared virtual space and jointly perform simulations. The paper proposes an architecture for participatory multiagent simulation in order to combine devices (Google Glass and/or smartphones) with an agent-based social simulator and indoor tracking services.

  16. Comparing stochastic differential equations and agent-based modelling and simulation for early-stage cancer.

    PubMed

    Figueredo, Grazziela P; Siebers, Peer-Olaf; Owen, Markus R; Reps, Jenna; Aickelin, Uwe

    2014-01-01

    There is great potential to be explored regarding the use of agent-based modelling and simulation as an alternative paradigm to investigate early-stage cancer interactions with the immune system. It does not suffer from some limitations of ordinary differential equation models, such as the lack of stochasticity, representation of individual behaviours rather than aggregates and individual memory. In this paper we investigate the potential contribution of agent-based modelling and simulation when contrasted with stochastic versions of ODE models using early-stage cancer examples. We seek answers to the following questions: (1) Does this new stochastic formulation produce similar results to the agent-based version? (2) Can these methods be used interchangeably? (3) Do agent-based models outcomes reveal any benefit when compared to the Gillespie results? To answer these research questions we investigate three well-established mathematical models describing interactions between tumour cells and immune elements. These case studies were re-conceptualised under an agent-based perspective and also converted to the Gillespie algorithm formulation. Our interest in this work, therefore, is to establish a methodological discussion regarding the usability of different simulation approaches, rather than provide further biological insights into the investigated case studies. Our results show that it is possible to obtain equivalent models that implement the same mechanisms; however, the incapacity of the Gillespie algorithm to retain individual memory of past events affects the similarity of some results. Furthermore, the emergent behaviour of ABMS produces extra patters of behaviour in the system, which was not obtained by the Gillespie algorithm.

  17. Emulating a System Dynamics Model with Agent-Based Models: A Methodological Case Study in Simulation of Diabetes Progression

    DOE PAGES

    Schryver, Jack; Nutaro, James; Shankar, Mallikarjun

    2015-10-30

    An agent-based simulation model hierarchy emulating disease states and behaviors critical to progression of diabetes type 2 was designed and implemented in the DEVS framework. The models are translations of basic elements of an established system dynamics model of diabetes. In this model hierarchy, which mimics diabetes progression over an aggregated U.S. population, was dis-aggregated and reconstructed bottom-up at the individual (agent) level. Four levels of model complexity were defined in order to systematically evaluate which parameters are needed to mimic outputs of the system dynamics model. Moreover, the four estimated models attempted to replicate stock counts representing disease statesmore » in the system dynamics model, while estimating impacts of an elderliness factor, obesity factor and health-related behavioral parameters. Health-related behavior was modeled as a simple realization of the Theory of Planned Behavior, a joint function of individual attitude and diffusion of social norms that spread over each agent s social network. Although the most complex agent-based simulation model contained 31 adjustable parameters, all models were considerably less complex than the system dynamics model which required numerous time series inputs to make its predictions. In all three elaborations of the baseline model provided significantly improved fits to the output of the system dynamics model. The performances of the baseline agent-based model and its extensions illustrate a promising approach to translate complex system dynamics models into agent-based model alternatives that are both conceptually simpler and capable of capturing main effects of complex local agent-agent interactions.« less

  18. Emulating a System Dynamics Model with Agent-Based Models: A Methodological Case Study in Simulation of Diabetes Progression

    SciTech Connect

    Schryver, Jack; Nutaro, James; Shankar, Mallikarjun

    2015-10-30

    An agent-based simulation model hierarchy emulating disease states and behaviors critical to progression of diabetes type 2 was designed and implemented in the DEVS framework. The models are translations of basic elements of an established system dynamics model of diabetes. In this model hierarchy, which mimics diabetes progression over an aggregated U.S. population, was dis-aggregated and reconstructed bottom-up at the individual (agent) level. Four levels of model complexity were defined in order to systematically evaluate which parameters are needed to mimic outputs of the system dynamics model. Moreover, the four estimated models attempted to replicate stock counts representing disease states in the system dynamics model, while estimating impacts of an elderliness factor, obesity factor and health-related behavioral parameters. Health-related behavior was modeled as a simple realization of the Theory of Planned Behavior, a joint function of individual attitude and diffusion of social norms that spread over each agent s social network. Although the most complex agent-based simulation model contained 31 adjustable parameters, all models were considerably less complex than the system dynamics model which required numerous time series inputs to make its predictions. In all three elaborations of the baseline model provided significantly improved fits to the output of the system dynamics model. The performances of the baseline agent-based model and its extensions illustrate a promising approach to translate complex system dynamics models into agent-based model alternatives that are both conceptually simpler and capable of capturing main effects of complex local agent-agent interactions.

  19. iCrowd: agent-based behavior modeling and crowd simulator

    NASA Astrophysics Data System (ADS)

    Kountouriotis, Vassilios I.; Paterakis, Manolis; Thomopoulos, Stelios C. A.

    2016-05-01

    Initially designed in the context of the TASS (Total Airport Security System) FP-7 project, the Crowd Simulation platform developed by the Integrated Systems Lab of the Institute of Informatics and Telecommunications at N.C.S.R. Demokritos, has evolved into a complete domain-independent agent-based behavior simulator with an emphasis on crowd behavior and building evacuation simulation. Under continuous development, it reflects an effort to implement a modern, multithreaded, data-oriented simulation engine employing latest state-of-the-art programming technologies and paradigms. It is based on an extensible architecture that separates core services from the individual layers of agent behavior, offering a concrete simulation kernel designed for high-performance and stability. Its primary goal is to deliver an abstract platform to facilitate implementation of several Agent-Based Simulation solutions with applicability in several domains of knowledge, such as: (i) Crowd behavior simulation during [in/out] door evacuation. (ii) Non-Player Character AI for Game-oriented applications and Gamification activities. (iii) Vessel traffic modeling and simulation for Maritime Security and Surveillance applications. (iv) Urban and Highway Traffic and Transportation Simulations. (v) Social Behavior Simulation and Modeling.

  20. Applications of agent-based simulation for human socio-cultural behavior modeling.

    PubMed

    Jiang, Hong; Karwowski, Waldemar; Ahram, Tareq Z

    2012-01-01

    Agent-based modeling and simulation (ABMS) has gained wide attention over the past few years. ABMS is a powerful simulation modeling technique that has a number of applications, including applications to real-world business problems [1]. This modeling technique has been used by scientists to analyze complex system-level behavior by simulating the system from the bottom up. The major application of ABMS includes social, political, biology, and economic sciences. This paper provides an overview of ABMS applications with the emphasis on modeling human socio-cultural behavior (HSCB).

  1. An Agent-Based Model of New Venture Creation: Conceptual Design for Simulating Entrepreneurship

    NASA Technical Reports Server (NTRS)

    Provance, Mike; Collins, Andrew; Carayannis, Elias

    2012-01-01

    There is a growing debate over the means by which regions can foster the growth of entrepreneurial activity in order to stimulate recovery and growth of their economies. On one side, agglomeration theory suggests the regions grow because of strong clusters that foster knowledge spillover locally; on the other side, the entrepreneurial action camp argues that innovative business models are generated by entrepreneurs with unique market perspectives who draw on knowledge from more distant domains. We will show you the design for a novel agent-based model of new venture creation that will demonstrate the relationship between agglomeration and action. The primary focus of this model is information exchange as the medium for these agent interactions. Our modeling and simulation study proposes to reveal interesting relationships in these perspectives, offer a foundation on which these disparate theories from economics and sociology can find common ground, and expand the use of agent-based modeling into entrepreneurship research.

  2. Graceful Failure and Societal Resilience Analysis Via Agent-Based Modeling and Simulation

    NASA Astrophysics Data System (ADS)

    Schopf, P. S.; Cioffi-Revilla, C.; Rogers, J. D.; Bassett, J.; Hailegiorgis, A. B.

    2014-12-01

    Agent-based social modeling is opening up new methodologies for the study of societal response to weather and climate hazards, and providing measures of resiliency that can be studied in many contexts, particularly in coupled human and natural-technological systems (CHANTS). Since CHANTS are complex adaptive systems, societal resiliency may or may not occur, depending on dynamics that lack closed form solutions. Agent-based modeling has been shown to provide a viable theoretical and methodological approach for analyzing and understanding disasters and societal resiliency in CHANTS. Our approach advances the science of societal resilience through computational modeling and simulation methods that complement earlier statistical and mathematical approaches. We present three case studies of social dynamics modeling that demonstrate the use of these agent based models. In Central Asia, we exmaine mutltiple ensemble simulations with varying climate statistics to see how droughts and zuds affect populations, transmission of wealth across generations, and the overall structure of the social system. In Eastern Africa, we explore how successive episodes of drought events affect the adaptive capacity of rural households. Human displacement, mainly, rural to urban migration, and livelihood transition particularly from pastoral to farming are observed as rural households interacting dynamically with the biophysical environment and continually adjust their behavior to accommodate changes in climate. In the far north case we demonstrate one of the first successful attempts to model the complete climate-permafrost-infrastructure-societal interaction network as a complex adaptive system/CHANTS implemented as a ``federated'' agent-based model using evolutionary computation. Analysis of population changes resulting from extreme weather across these and other cases provides evidence for the emergence of new steady states and shifting patterns of resilience.

  3. An Agent-Based Framework for Building Decision Support System in Supply Chain Management

    NASA Astrophysics Data System (ADS)

    Kazemi, A.; Fazel Zarandi, M. H.

    In this study, two scenarios are presented for solving Production-Distribution Panning Problem (PDPP) in a Decision Support System (DSS) framework. In the first scenario, a Traditional Decision Support System (TDSS) is presented for PDPP and a Genetic Algorithm (GA) is used for solving it. In the second scenario, a Multi-agent Decision Support System (MADSS) is considered for PDPP and three algorithms are used for solving it: Genetic Algorithm (GA), Tabu Search (TS) and Simulated Annealing (SA). Then an algorithm is suggested by using multi-agent system and A Teams concept. The obtained results reveal that the use of MADSS delivers better solutions to us.

  4. Model reduction for agent-based social simulation: coarse-graining a civil violence model.

    PubMed

    Zou, Yu; Fonoberov, Vladimir A; Fonoberova, Maria; Mezic, Igor; Kevrekidis, Ioannis G

    2012-06-01

    Agent-based modeling (ABM) constitutes a powerful computational tool for the exploration of phenomena involving emergent dynamic behavior in the social sciences. This paper demonstrates a computer-assisted approach that bridges the significant gap between the single-agent microscopic level and the macroscopic (coarse-grained population) level, where fundamental questions must be rationally answered and policies guiding the emergent dynamics devised. Our approach will be illustrated through an agent-based model of civil violence. This spatiotemporally varying ABM incorporates interactions between a heterogeneous population of citizens [active (insurgent), inactive, or jailed] and a population of police officers. Detailed simulations exhibit an equilibrium punctuated by periods of social upheavals. We show how to effectively reduce the agent-based dynamics to a stochastic model with only two coarse-grained degrees of freedom: the number of jailed citizens and the number of active ones. The coarse-grained model captures the ABM dynamics while drastically reducing the computation time (by a factor of approximately 20).

  5. Using an agent-based model to simulate children’s active travel to school

    PubMed Central

    2013-01-01

    Background Despite the multiple advantages of active travel to school, only a small percentage of US children and adolescents walk or bicycle to school. Intervention studies are in a relatively early stage and evidence of their effectiveness over long periods is limited. The purpose of this study was to illustrate the utility of agent-based models in exploring how various policies may influence children’s active travel to school. Methods An agent-based model was developed to simulate children’s school travel behavior within a hypothetical city. The model was used to explore the plausible implications of policies targeting two established barriers to active school travel: long distance to school and traffic safety. The percent of children who walk to school was compared for various scenarios. Results To maximize the percent of children who walk to school the school locations should be evenly distributed over space and children should be assigned to the closest school. In the case of interventions to improve traffic safety, targeting a smaller area around the school with greater intensity may be more effective than targeting a larger area with less intensity. Conclusions Despite the challenges they present, agent based models are a useful complement to other analytical strategies in studying the plausible impact of various policies on active travel to school. PMID:23705953

  6. Model reduction for agent-based social simulation: Coarse-graining a civil violence model

    NASA Astrophysics Data System (ADS)

    Zou, Yu; Fonoberov, Vladimir A.; Fonoberova, Maria; Mezic, Igor; Kevrekidis, Ioannis G.

    2012-06-01

    Agent-based modeling (ABM) constitutes a powerful computational tool for the exploration of phenomena involving emergent dynamic behavior in the social sciences. This paper demonstrates a computer-assisted approach that bridges the significant gap between the single-agent microscopic level and the macroscopic (coarse-grained population) level, where fundamental questions must be rationally answered and policies guiding the emergent dynamics devised. Our approach will be illustrated through an agent-based model of civil violence. This spatiotemporally varying ABM incorporates interactions between a heterogeneous population of citizens [active (insurgent), inactive, or jailed] and a population of police officers. Detailed simulations exhibit an equilibrium punctuated by periods of social upheavals. We show how to effectively reduce the agent-based dynamics to a stochastic model with only two coarse-grained degrees of freedom: the number of jailed citizens and the number of active ones. The coarse-grained model captures the ABM dynamics while drastically reducing the computation time (by a factor of approximately 20).

  7. An agent based model for simulating the spread of sexually transmitted infections.

    PubMed

    Rutherford, Grant; Friesen, Marcia R; McLeod, Robert D

    2012-01-01

    This work uses agent-based modelling (ABM) to simulate sexually transmitted infection (STIs) spread within a population of 1000 agents over a 10-year period, as a preliminary investigation of the suitability of ABM methodology to simulate STI spread. The work contrasts compartmentalized mathematical models that fail to account for individual agents, and ABMs commonly applied to simulate the spread of respiratory infections. The model was developed in C++ using the Boost 1.47.0 libraries for the normal distribution and OpenGL for visualization. Sixteen agent parameters interact individually and in combination to govern agent profiles and behaviours relative to infection probabilities. The simulation results provide qualitative comparisons of STI mitigation strategies, including the impact of condom use, promiscuity, the form of the friend network, and mandatory STI testing. Individual and population-wide impacts were explored, with individual risk being impacted much more dramatically by population-level behaviour changes as compared to individual behaviour changes.

  8. ModelforAnalyzing Human Communication Network Based onAgent-Based Simulation

    NASA Astrophysics Data System (ADS)

    Matsuyama, Shinako; Terano, Takao

    This paper discusses dynamic properties of human communications networks, which appears as a result of informationexchanges among people. We propose agent-based simulation (ABS) to examine implicit mechanisms behind the dynamics. The ABS enables us to reveal the characteristics and the differences of the networks regarding the specific communicationgroups. We perform experiments on the ABS with activity data from questionnaires survey and with virtual data which isdifferent from the activity data. We compare the difference between them and show the effectiveness of the ABS through theexperiments.

  9. Agent-based model of angiogenesis simulates capillary sprout initiation in multicellular networks.

    PubMed

    Walpole, J; Chappell, J C; Cluceru, J G; Mac Gabhann, F; Bautch, V L; Peirce, S M

    2015-09-01

    Many biological processes are controlled by both deterministic and stochastic influences. However, efforts to model these systems often rely on either purely stochastic or purely rule-based methods. To better understand the balance between stochasticity and determinism in biological processes a computational approach that incorporates both influences may afford additional insight into underlying biological mechanisms that give rise to emergent system properties. We apply a combined approach to the simulation and study of angiogenesis, the growth of new blood vessels from existing networks. This complex multicellular process begins with selection of an initiating endothelial cell, or tip cell, which sprouts from the parent vessels in response to stimulation by exogenous cues. We have constructed an agent-based model of sprouting angiogenesis to evaluate endothelial cell sprout initiation frequency and location, and we have experimentally validated it using high-resolution time-lapse confocal microscopy. ABM simulations were then compared to a Monte Carlo model, revealing that purely stochastic simulations could not generate sprout locations as accurately as the rule-informed agent-based model. These findings support the use of rule-based approaches for modeling the complex mechanisms underlying sprouting angiogenesis over purely stochastic methods.

  10. An Agent-Based Epidemic Simulation of Social Behaviors Affecting HIV Transmission among Taiwanese Homosexuals

    PubMed Central

    2015-01-01

    Computational simulations are currently used to identify epidemic dynamics, to test potential prevention and intervention strategies, and to study the effects of social behaviors on HIV transmission. The author describes an agent-based epidemic simulation model of a network of individuals who participate in high-risk sexual practices, using number of partners, condom usage, and relationship length to distinguish between high- and low-risk populations. Two new concepts—free links and fixed links—are used to indicate tendencies among individuals who either have large numbers of short-term partners or stay in long-term monogamous relationships. An attempt was made to reproduce epidemic curves of reported HIV cases among male homosexuals in Taiwan prior to using the agent-based model to determine the effects of various policies on epidemic dynamics. Results suggest that when suitable adjustments are made based on available social survey statistics, the model accurately simulates real-world behaviors on a large scale. PMID:25815047

  11. An Agent-Based Labor Market Simulation with Endogenous Skill-Demand

    NASA Astrophysics Data System (ADS)

    Gemkow, S.

    This paper considers an agent-based labor market simulation to examine the influence of skills on wages and unemployment rates. Therefore less and highly skilled workers as well as less and highly productive vacancies are implemented. The skill distribution is exogenous whereas the distribution of the less and highly productive vacancies is endogenous. The different opportunities of the skill groups on the labor market are established by skill requirements. This means that a highly productive vacancy can only be filled by a highly skilled unemployed. Different skill distributions, which can also be interpreted as skill-biased technological change, are simulated by incrementing the skill level of highly skilled persons exogenously. This simulation also provides a microeconomic foundation of the matching function often used in theoretical approaches.

  12. Security Analysis of Selected AMI Failure Scenarios Using Agent Based Game Theoretic Simulation

    SciTech Connect

    Abercrombie, Robert K; Schlicher, Bob G; Sheldon, Frederick T

    2014-01-01

    Information security analysis can be performed using game theory implemented in dynamic Agent Based Game Theoretic (ABGT) simulations. Such simulations can be verified with the results from game theory analysis and further used to explore larger scale, real world scenarios involving multiple attackers, defenders, and information assets. We concentrated our analysis on the Advanced Metering Infrastructure (AMI) functional domain which the National Electric Sector Cyber security Organization Resource (NESCOR) working group has currently documented 29 failure scenarios. The strategy for the game was developed by analyzing five electric sector representative failure scenarios contained in the AMI functional domain. From these five selected scenarios, we characterize them into three specific threat categories affecting confidentiality, integrity and availability (CIA). The analysis using our ABGT simulation demonstrates how to model the AMI functional domain using a set of rationalized game theoretic rules decomposed from the failure scenarios in terms of how those scenarios might impact the AMI network with respect to CIA.

  13. Agent-based modeling to simulate contamination events and evaluate threat management strategies in water distribution systems.

    PubMed

    Zechman, Emily M

    2011-05-01

    In the event of contamination of a water distribution system, decisions must be made to mitigate the impact of the contamination and to protect public health. Making threat management decisions while a contaminant spreads through the network is a dynamic and interactive process. Response actions taken by the utility managers and water consumption choices made by the consumers will affect the hydraulics, and thus the spread of the contaminant plume, in the network. A modeling framework that allows the simulation of a contamination event under the effects of actions taken by utility managers and consumers will be a useful tool for the analysis of alternative threat mitigation and management strategies. This article presents a multiagent modeling framework that combines agent-based, mechanistic, and dynamic methods. Agents select actions based on a set of rules that represent an individual's autonomy, goal-based desires, and reaction to the environment and the actions of other agents. Consumer behaviors including ingestion, mobility, reduction of water demands, and word-of-mouth communication are simulated. Management strategies are evaluated, including opening hydrants to flush the contaminant and broadcasts. As actions taken by consumer agents and utility operators affect demands and flows in the system, the mechanistic model is updated. Management strategies are evaluated based on the exposure of the population to the contaminant. The framework is designed to consider the typical issues involved in water distribution threat management and provides valuable analysis of threat containment strategies for water distribution system contamination events.

  14. Modeling the Information Age Combat Model: An Agent-Based Simulation of Network Centric Operations

    NASA Technical Reports Server (NTRS)

    Deller, Sean; Rabadi, Ghaith A.; Bell, Michael I.; Bowling, Shannon R.; Tolk, Andreas

    2010-01-01

    The Information Age Combat Model (IACM) was introduced by Cares in 2005 to contribute to the development of an understanding of the influence of connectivity on force effectiveness that can eventually lead to quantitative prediction and guidelines for design and employment. The structure of the IACM makes it clear that the Perron-Frobenius Eigenvalue is a quantifiable metric with which to measure the organization of a networked force. The results of recent experiments presented in Deller, et aI., (2009) indicate that the value of the Perron-Frobenius Eigenvalue is a significant measurement of the performance of an Information Age combat force. This was accomplished through the innovative use of an agent-based simulation to model the IACM and represents an initial contribution towards a new generation of combat models that are net-centric instead of using the current platform-centric approach. This paper describes the intent, challenges, design, and initial results of this agent-based simulation model.

  15. Simulating the elimination of sleeping sickness with an agent-based model

    PubMed Central

    Grébaut, Pascal; Girardin, Killian; Fédérico, Valentine; Bousquet, François

    2016-01-01

    Although Human African Trypanosomiasis is largely considered to be in the process of extinction today, the persistence of human and animal reservoirs, as well as the vector, necessitates a laborious elimination process. In this context, modeling could be an effective tool to evaluate the ability of different public health interventions to control the disease. Using the Cormas® system, we developed HATSim, an agent-based model capable of simulating the possible endemic evolutions of sleeping sickness and the ability of National Control Programs to eliminate the disease. This model takes into account the analysis of epidemiological, entomological, and ecological data from field studies conducted during the last decade, making it possible to predict the evolution of the disease within this area over a 5-year span. In this article, we first present HATSim according to the Overview, Design concepts, and Details (ODD) protocol that is classically used to describe agent-based models, then, in a second part, we present predictive results concerning the evolution of Human African Trypanosomiasis in the village of Lambi (Cameroon), in order to illustrate the interest of such a tool. Our results are consistent with what was observed in the field by the Cameroonian National Control Program (CNCP). Our simulations also revealed that regular screening can be sufficient, although vector control applied to all areas with human activities could be significantly more efficient. Our results indicate that the current model can already help decision-makers in planning the elimination of the disease in foci. PMID:28008825

  16. AN AGENT-BASED SIMULATION STUDY OF A COMPLEX ADAPTIVE COLLABORATION NETWORK

    SciTech Connect

    Ozmen, Ozgur; Smith, Jeffrey; Yilmaz, Levent

    2013-01-01

    One of the most significant problems in organizational scholarship is to discern how social collectives govern, organize, and coordinate the actions of individuals to achieve collective outcomes. The collectives are usually interpreted as complex adaptive systems (CAS). The understanding of CAS is more likely to arise with the help of computer-based simulations. In this tutorial, using agent-based modeling approach, a complex adaptive social communication network model is introduced. The objective is to present the underlying dynamics of the system in a form of computer simulation that enables analyzing the impacts of various mechanisms on network topologies and emergent behaviors. The ultimate goal is to further our understanding of the dynamics in the system and facilitate developing informed policies for decision-makers.

  17. Promoting Conceptual Change for Complex Systems Understanding: Outcomes of an Agent-Based Participatory Simulation

    NASA Astrophysics Data System (ADS)

    Rates, Christopher A.; Mulvey, Bridget K.; Feldon, David F.

    2016-08-01

    Components of complex systems apply across multiple subject areas, and teaching these components may help students build unifying conceptual links. Students, however, often have difficulty learning these components, and limited research exists to understand what types of interventions may best help improve understanding. We investigated 32 high school students' understandings of complex systems components and whether an agent-based simulation could improve their understandings. Pretest and posttest essays were coded for changes in six components to determine whether students showed more expert thinking about the complex system of the Chesapeake Bay watershed. Results showed significant improvement for the components Emergence ( r = .26, p = .03), Order ( r = .37, p = .002), and Tradeoffs ( r = .44, p = .001). Implications include that the experiential nature of the simulation has the potential to support conceptual change for some complex systems components, presenting a promising option for complex systems instruction.

  18. Multi-Agent-Based Simulation of a Complex Ecosystem of Mental Health Care.

    PubMed

    Kalton, Alan; Falconer, Erin; Docherty, John; Alevras, Dimitris; Brann, David; Johnson, Kyle

    2016-02-01

    This paper discusses the creation of an Agent-Based Simulation that modeled the introduction of care coordination capabilities into a complex system of care for patients with Serious and Persistent Mental Illness. The model describes the engagement between patients and the medical, social and criminal justice services they interact with in a complex ecosystem of care. We outline the challenges involved in developing the model, including process mapping and the collection and synthesis of data to support parametric estimates, and describe the controls built into the model to support analysis of potential changes to the system. We also describe the approach taken to calibrate the model to an observable level of system performance. Preliminary results from application of the simulation are provided to demonstrate how it can provide insights into potential improvements deriving from introduction of care coordination technology.

  19. Automated multi-objective calibration of biological agent-based simulations.

    PubMed

    Read, Mark N; Alden, Kieran; Rose, Louis M; Timmis, Jon

    2016-09-01

    Computational agent-based simulation (ABS) is increasingly used to complement laboratory techniques in advancing our understanding of biological systems. Calibration, the identification of parameter values that align simulation with biological behaviours, becomes challenging as increasingly complex biological domains are simulated. Complex domains cannot be characterized by single metrics alone, rendering simulation calibration a fundamentally multi-metric optimization problem that typical calibration techniques cannot handle. Yet calibration is an essential activity in simulation-based science; the baseline calibration forms a control for subsequent experimentation and hence is fundamental in the interpretation of results. Here, we develop and showcase a method, built around multi-objective optimization, for calibrating ABSs against complex target behaviours requiring several metrics (termed objectives) to characterize. Multi-objective calibration (MOC) delivers those sets of parameter values representing optimal trade-offs in simulation performance against each metric, in the form of a Pareto front. We use MOC to calibrate a well-understood immunological simulation against both established a priori and previously unestablished target behaviours. Furthermore, we show that simulation-borne conclusions are broadly, but not entirely, robust to adopting baseline parameter values from different extremes of the Pareto front, highlighting the importance of MOC's identification of numerous calibration solutions. We devise a method for detecting overfitting in a multi-objective context, not previously possible, used to save computational effort by terminating MOC when no improved solutions will be found. MOC can significantly impact biological simulation, adding rigour to and speeding up an otherwise time-consuming calibration process and highlighting inappropriate biological capture by simulations that cannot be well calibrated. As such, it produces more accurate

  20. Understanding the Dynamics of Violent Political Revolutions in an Agent-Based Framework

    PubMed Central

    Moro, Alessandro

    2016-01-01

    This paper develops an agent-based computational model of violent political revolutions in which a subjugated population of citizens and an armed revolutionary organisation attempt to overthrow a central authority and its loyal forces. The model replicates several patterns of rebellion consistent with major historical revolutions, and provides an explanation for the multiplicity of outcomes that can arise from an uprising. The relevance of the heterogeneity of scenarios predicted by the model can be understood by considering the recent experience of the Arab Spring involving several rebellions that arose in an apparently similar way, but resulted in completely different political outcomes: the successful revolution in Tunisia, the failed protests in Saudi Arabia and Bahrain, and civil war in Syria and Libya. PMID:27104855

  1. Changing crops in response to climate: virtual Nang Rong, Thailand in an agent based simulation.

    PubMed

    Malanson, George P; Verdery, Ashton M; Walsh, Stephen J; Sawangdee, Yothin; Heumann, Benjamin W; McDaniel, Philip M; Frizzelle, Brian G; Williams, Nathalie E; Yao, Xiaozheng; Entwisle, Barbara; Rindfuss, Ronald R

    2014-09-01

    The effects of extended climatic variability on agricultural land use were explored for the type of system found in villages of northeastern Thailand. An agent based model developed for the Nang Rong district was used to simulate land allotted to jasmine rice, heavy rice, cassava, and sugar cane. The land use choices in the model depended on likely economic outcomes, but included elements of bounded rationality in dependence on household demography. The socioeconomic dynamics are endogenous in the system, and climate changes were added as exogenous drivers. Villages changed their agricultural effort in many different ways. Most villages reduced the amount of land under cultivation, primarily with reduction in jasmine rice, but others did not. The variation in responses to climate change indicates potential sensitivity to initial conditions and path dependence for this type of system. The differences between our virtual villages and the real villages of the region indicate effects of bounded rationality and limits on model applications.

  2. Agent-based simulation as a tool for the built environment.

    PubMed

    Gaudiano, Paolo

    2013-08-01

    There is a growing need to increase the performance of the built environment through a combination of improved design, retrofitting of existing structures, and behavioral and policy change. Increased performance includes decreasing construction and operational costs, improving efficiency, reducing energy consumption and overall carbon footprint, and increasing the health, safety, and comfort of building occupants. Data collection and analysis are central to ongoing efforts in performance improvement. The growth of sensor and monitoring technologies, coupled with the proliferation of building automation systems, is quickly leading to an explosion in the amount, quality, and format of building performance data. What is needed are methodologies for extracting viable information from these data and using the results to effect meaningful change. Furthermore, occupant behavior and attitudes must be taken into account. This paper summarizes agent-based simulation and describes its potential as an approach to support analysis, design, and performance improvements in the built environment.

  3. Changing crops in response to climate: virtual Nang Rong, Thailand in an agent based simulation

    PubMed Central

    Malanson, George P.; Verdery, Ashton M.; Walsh, Stephen J.; Sawangdee, Yothin; Heumann, Benjamin W.; McDaniel, Philip M.; Frizzelle, Brian G.; Williams, Nathalie E.; Yao, Xiaozheng; Entwisle, Barbara; Rindfuss, Ronald R.

    2014-01-01

    The effects of extended climatic variability on agricultural land use were explored for the type of system found in villages of northeastern Thailand. An agent based model developed for the Nang Rong district was used to simulate land allotted to jasmine rice, heavy rice, cassava, and sugar cane. The land use choices in the model depended on likely economic outcomes, but included elements of bounded rationality in dependence on household demography. The socioeconomic dynamics are endogenous in the system, and climate changes were added as exogenous drivers. Villages changed their agricultural effort in many different ways. Most villages reduced the amount of land under cultivation, primarily with reduction in jasmine rice, but others did not. The variation in responses to climate change indicates potential sensitivity to initial conditions and path dependence for this type of system. The differences between our virtual villages and the real villages of the region indicate effects of bounded rationality and limits on model applications. PMID:25061240

  4. Method for distributed agent-based non-expert simulation of manufacturing process behavior

    DOEpatents

    Ivezic, Nenad; Potok, Thomas E.

    2004-11-30

    A method for distributed agent based non-expert simulation of manufacturing process behavior on a single-processor computer comprises the steps of: object modeling a manufacturing technique having a plurality of processes; associating a distributed agent with each the process; and, programming each the agent to respond to discrete events corresponding to the manufacturing technique, wherein each discrete event triggers a programmed response. The method can further comprise the step of transmitting the discrete events to each agent in a message loop. In addition, the programming step comprises the step of conditioning each agent to respond to a discrete event selected from the group consisting of a clock tick message, a resources received message, and a request for output production message.

  5. An agent-based simulation model to study accountable care organizations.

    PubMed

    Liu, Pai; Wu, Shinyi

    2016-03-01

    Creating accountable care organizations (ACOs) has been widely discussed as a strategy to control rapidly rising healthcare costs and improve quality of care; however, building an effective ACO is a complex process involving multiple stakeholders (payers, providers, patients) with their own interests. Also, implementation of an ACO is costly in terms of time and money. Immature design could cause safety hazards. Therefore, there is a need for analytical model-based decision-support tools that can predict the outcomes of different strategies to facilitate ACO design and implementation. In this study, an agent-based simulation model was developed to study ACOs that considers payers, healthcare providers, and patients as agents under the shared saving payment model of care for congestive heart failure (CHF), one of the most expensive causes of sometimes preventable hospitalizations. The agent-based simulation model has identified the critical determinants for the payment model design that can motivate provider behavior changes to achieve maximum financial and quality outcomes of an ACO. The results show nonlinear provider behavior change patterns corresponding to changes in payment model designs. The outcomes vary by providers with different quality or financial priorities, and are most sensitive to the cost-effectiveness of CHF interventions that an ACO implements. This study demonstrates an increasingly important method to construct a healthcare system analytics model that can help inform health policy and healthcare management decisions. The study also points out that the likely success of an ACO is interdependent with payment model design, provider characteristics, and cost and effectiveness of healthcare interventions.

  6. Prediction Markets and Beliefs about Climate: Results from Agent-Based Simulations

    NASA Astrophysics Data System (ADS)

    Gilligan, J. M.; John, N. J.; van der Linden, M.

    2015-12-01

    Climate scientists have long been frustrated by persistent doubts a large portion of the public expresses toward the scientific consensus about anthropogenic global warming. The political and ideological polarization of this doubt led Vandenbergh, Raimi, and Gilligan [1] to propose that prediction markets for climate change might influence the opinions of those who mistrust the scientific community but do trust the power of markets.We have developed an agent-based simulation of a climate prediction market in which traders buy and sell future contracts that will pay off at some future year with a value that depends on the global average temperature at that time. The traders form a heterogeneous population with different ideological positions, different beliefs about anthropogenic global warming, and different degrees of risk aversion. We also vary characteristics of the market, including the topology of social networks among the traders, the number of traders, and the completeness of the market. Traders adjust their beliefs about climate according to the gains and losses they and other traders in their social network experience. This model predicts that if global temperature is predominantly driven by greenhouse gas concentrations, prediction markets will cause traders' beliefs to converge toward correctly accepting anthropogenic warming as real. This convergence is largely independent of the structure of the market and the characteristics of the population of traders. However, it may take considerable time for beliefs to converge. Conversely, if temperature does not depend on greenhouse gases, the model predicts that traders' beliefs will not converge. We will discuss the policy-relevance of these results and more generally, the use of agent-based market simulations for policy analysis regarding climate change, seasonal agricultural weather forecasts, and other applications.[1] MP Vandenbergh, KT Raimi, & JM Gilligan. UCLA Law Rev. 61, 1962 (2014).

  7. Agent-based computer simulation and sirs: building a bridge between basic science and clinical trials.

    PubMed

    An, G

    2001-10-01

    The management of Systemic Inflammatory Response Syndrome (SIRS)/Multiple Organ Failure (MOF) remains the greatest challenge in the field of critical care. There has been uniform difficulty in translating the results of basic science research into effective therapeutic regimes. We propose that this is due in part to a failure to account for the complex, nonlinear nature of the inflammatory process of which SIRS/MOF represents a disordered state. Attempts to manipulate this process without an understanding of the dynamics of the system may potentially produce unintended consequences. Agent-Based Computer Simulation (ABCS) provides a means to synthesize the information acquired from the linear analysis of basic science into a model that preserves the complexity of the inflammatory system. We have constructed an abstracted version of the inflammatory process using an ABCS that is based at the cellular level. Despite its abstraction, the simulation produces non-linear behavior and reproduces the dynamic structure of the inflammatory response. Furthermore, adjustment of the simulation to model one of the unsuccessful initial anti-inflammatory trials of the 1990's demonstrates the adverse outcome that was observed in those clinical trials. It must be emphasized that the current model is extremely abstract and simplified. However, it is hoped that future ABCSs of sufficient sophistication eventually may provide an important bridging tool to translate basic science discoveries into clinical applications. Creating these simulations will require a large collaborative effort, and it is hoped that this paper will stimulate interest in this form of analysis.

  8. Design of a Mobile Agent-Based Adaptive Communication Middleware for Federations of Critical Infrastructure Simulations

    NASA Astrophysics Data System (ADS)

    Görbil, Gökçe; Gelenbe, Erol

    The simulation of critical infrastructures (CI) can involve the use of diverse domain specific simulators that run on geographically distant sites. These diverse simulators must then be coordinated to run concurrently in order to evaluate the performance of critical infrastructures which influence each other, especially in emergency or resource-critical situations. We therefore describe the design of an adaptive communication middleware that provides reliable and real-time one-to-one and group communications for federations of CI simulators over a wide-area network (WAN). The proposed middleware is composed of mobile agent-based peer-to-peer (P2P) overlays, called virtual networks (VNets), to enable resilient, adaptive and real-time communications over unreliable and dynamic physical networks (PNets). The autonomous software agents comprising the communication middleware monitor their performance and the underlying PNet, and dynamically adapt the P2P overlay and migrate over the PNet in order to optimize communications according to the requirements of the federation and the current conditions of the PNet. Reliable communications is provided via redundancy within the communication middleware and intelligent migration of agents over the PNet. The proposed middleware integrates security methods in order to protect the communication infrastructure against attacks and provide privacy and anonymity to the participants of the federation. Experiments with an initial version of the communication middleware over a real-life networking testbed show that promising improvements can be obtained for unicast and group communications via the agent migration capability of our middleware.

  9. Investigating the role of water in the Diffusion of Cholera using Agent-Based simulation

    NASA Astrophysics Data System (ADS)

    Augustijn, Ellen-Wien; Doldersum, Tom; Augustijn, Denie

    2014-05-01

    Traditionally, cholera was considered to be a waterborne disease. Currently we know that many other factors can contribute to the spread of this disease including human mobility and human behavior. However, the hydrological component in cholera diffusion is significant. The interplay between cholera and water includes bacteria (V. cholera) that survive in the aquatic environment, the possibility that run-off water from dumpsites carries the bacteria to surface water (rivers and lakes), and when the bacteria reach streams they can be carried downstream to infect new locations. Modelling is a very important tool to build theory on the interplay between different types of transmission mechanisms that together are responsible for the spread of Cholera. Agent-based simulation models are very suitable to incorporate behavior at individual level and to reproduce emergence. However, it is more difficult to incorporate the hydrological components in this type of model. In this research we present the hydrological component of an Agent-Based Cholera model developed to study a Cholera epidemic in Kumasi (Ghana) in 2005. The model was calibrated on the relative contribution of each community to the distributed pattern of cholera rather than the absolute number of incidences. Analysis of the results shows that water plays an important role in the diffusion of cholera: 75% of the cholera cases were infected via river water that was contaminated by runoff from the dumpsites. To initiate infections upstream, the probability of environment-to-human transmission seemed to be overestimated compared to what may be expected from literature. Scenario analyses show that there is a strong relation between the epidemic curve and the rainfall. Removing dumpsites that are situated close to the river resulted in a strong decrease in the number of cholera cases. Results are sensitive to the scheduling of the daily activities and the survival time of the cholera bacteria.

  10. Impact of urban planning on household's residential decisions: An agent-based simulation model for Vienna☆

    PubMed Central

    Gaube, Veronika; Remesch, Alexander

    2013-01-01

    Interest in assessing the sustainability of socio-ecological systems of urban areas has increased notably, with additional attention generated due to the fact that half the world's population now lives in cities. Urban areas face both a changing urban population size and increasing sustainability issues in terms of providing good socioeconomic and environmental living conditions. Urban planning has to deal with both challenges. Households play a major role by being affected by urban planning decisions on the one hand and by being responsible – among many other factors – for the environmental performance of a city (e.g. energy use). We here present an agent-based decision model referring to the city of Vienna, the capital of Austria, with a population of about 1.7 million (2.3 million within the metropolitan area, the latter being more than 25% of Austria's total population). Since the early 1990s, after decades of negative population growth, Vienna has been experiencing a steady increase in population, mainly driven by immigration. The aim of the agent-based decision model is to simulate new residential patterns of different household types based on demographic development and migration scenarios. Model results were used to assess spatial patterns of energy use caused by different household types in the four scenarios (1) conventional urban planning, (2) sustainable urban planning, (3) expensive centre and (4) no green area preference. Outcomes show that changes in preferences of households relating to the presence of nearby green areas have the most important impact on the distribution of households across the small-scaled city area. Additionally, the results demonstrate the importance of the distribution of different household types regarding spatial patterns of energy use. PMID:27667962

  11. Impact of urban planning on household's residential decisions: An agent-based simulation model for Vienna.

    PubMed

    Gaube, Veronika; Remesch, Alexander

    2013-07-01

    Interest in assessing the sustainability of socio-ecological systems of urban areas has increased notably, with additional attention generated due to the fact that half the world's population now lives in cities. Urban areas face both a changing urban population size and increasing sustainability issues in terms of providing good socioeconomic and environmental living conditions. Urban planning has to deal with both challenges. Households play a major role by being affected by urban planning decisions on the one hand and by being responsible - among many other factors - for the environmental performance of a city (e.g. energy use). We here present an agent-based decision model referring to the city of Vienna, the capital of Austria, with a population of about 1.7 million (2.3 million within the metropolitan area, the latter being more than 25% of Austria's total population). Since the early 1990s, after decades of negative population growth, Vienna has been experiencing a steady increase in population, mainly driven by immigration. The aim of the agent-based decision model is to simulate new residential patterns of different household types based on demographic development and migration scenarios. Model results were used to assess spatial patterns of energy use caused by different household types in the four scenarios (1) conventional urban planning, (2) sustainable urban planning, (3) expensive centre and (4) no green area preference. Outcomes show that changes in preferences of households relating to the presence of nearby green areas have the most important impact on the distribution of households across the small-scaled city area. Additionally, the results demonstrate the importance of the distribution of different household types regarding spatial patterns of energy use.

  12. Agent-based Modeling to Simulate the Diffusion of Water-Efficient Innovations and the Emergence of Urban Water Sustainability

    NASA Astrophysics Data System (ADS)

    Kanta, L.; Giacomoni, M.; Shafiee, M. E.; Berglund, E.

    2014-12-01

    The sustainability of water resources is threatened by urbanization, as increasing demands deplete water availability, and changes to the landscape alter runoff and the flow regime of receiving water bodies. Utility managers typically manage urban water resources through the use of centralized solutions, such as large reservoirs, which may be limited in their ability balance the needs of urbanization and ecological systems. Decentralized technologies, on the other hand, may improve the health of the water resources system and deliver urban water services. For example, low impact development technologies, such as rainwater harvesting, and water-efficient technologies, such as low-flow faucets and toilets, may be adopted by households to retain rainwater and reduce demands, offsetting the need for new centralized infrastructure. Decentralized technologies may create new complexities in infrastructure and water management, as decentralization depends on community behavior and participation beyond traditional water resources planning. Messages about water shortages and water quality from peers and the water utility managers can influence the adoption of new technologies. As a result, feedbacks between consumers and water resources emerge, creating a complex system. This research develops a framework to simulate the diffusion of water-efficient innovations and the sustainability of urban water resources, by coupling models of households in a community, hydrologic models of a water resources system, and a cellular automata model of land use change. Agent-based models are developed to simulate the land use and water demand decisions of individual households, and behavioral rules are encoded to simulate communication with other agents and adoption of decentralized technologies, using a model of the diffusion of innovation. The framework is applied for an illustrative case study to simulate water resources sustainability over a long-term planning horizon.

  13. [Research on multi-agent based modeling and simulation of hospital system].

    PubMed

    Zhao, Junping; Yang, Hongqiao; Guo, Huayuan; Li, Yi; Zhang, Zhenjiang; Li, Shuzhang

    2010-12-01

    In this paper, the theory of complex adaptive system (CAS) and its modeling method are introduced. The complex characters of the hospital system is analyzed. The agile manufacturing and cell reconstruction technologies are used to reconstruct the hospital system. Then we set forth a research for simulation of hospital system based on the methodology of Multi-Agent technology and high level architecture (HLA). Finally, a simulation framework based on HLA for hospital system is presented.

  14. A Generic, Agent-Based Framework for Design and Development of UAV/UCAV Control Systems

    DTIC Science & Technology

    2004-02-27

    37 EID Principles .................................................................................................. 38 Experimental Support for EID...Year 2 Interface design and implementation; creation of the simulation environment; Year 3 Demonstration of the concept and experimental evaluation...UAV/UCAV control in which operators can experience high cognitive workloads. There are several ways in which systems can construct user models by

  15. An agent-based simulation of extirpation of Ceratitis capitata applied to invasions in California.

    PubMed

    Manoukis, Nicholas C; Hoffman, Kevin

    2014-01-01

    We present an agent-based simulation (ABS) of Ceratitis capitata ("Medfly") developed for estimating the time to extirpation of this pest in areas where quarantines and eradication treatments were immediately imposed. We use the ABS, implemented in the program MED-FOES, to study seven different outbreaks that occurred in Southern California from 2008 to 2010. Results are compared with the length of intervention and quarantine imposed by the State, based on a linear developmental model (thermal unit accumulation, or "degree-day"). MED-FOES is a useful tool for invasive species managers as it incorporates more information from the known biology of the Medfly, and includes the important feature of being demographically explicit, providing significant improvements over simple degree-day calculations. While there was general agreement between the length of quarantine by degree-day and the time to extirpation indicated by MED-FOES, the ABS suggests that the margin of safety varies among cases and that in two cases the quarantine may have been excessively long. We also examined changes in the number of individuals over time in MED-FOES and conducted a sensitivity analysis for one of the outbreaks to explore the role of various input parameters on simulation outcomes. While our implementation of the ABS in this work is motivated by C. capitata and takes extirpation as a postulate, the simulation is very flexible and can be used to study a variety of questions on the invasion biology of pest insects and methods proposed to manage or eradicate such species.

  16. Semantic Agent-Based Service Middleware and Simulation for Smart Cities.

    PubMed

    Liu, Ming; Xu, Yang; Hu, Haixiao; Mohammed, Abdul-Wahid

    2016-12-21

    With the development of Machine-to-Machine (M2M) technology, a variety of embedded and mobile devices is integrated to interact via the platform of the Internet of Things, especially in the domain of smart cities. One of the primary challenges is that selecting the appropriate services or service combination for upper layer applications is hard, which is due to the absence of a unified semantical service description pattern, as well as the service selection mechanism. In this paper, we define a semantic service representation model from four key properties: Capability (C), Deployment (D), Resource (R) and IOData (IO). Based on this model, an agent-based middleware is built to support semantic service enablement. In this middleware, we present an efficient semantic service discovery and matching approach for a service combination process, which calculates the semantic similarity between services, and a heuristic algorithm to search the service candidates for a specific service request. Based on this design, we propose a simulation of virtual urban fire fighting, and the experimental results manifest the feasibility and efficiency of our design.

  17. Semantic Agent-Based Service Middleware and Simulation for Smart Cities

    PubMed Central

    Liu, Ming; Xu, Yang; Hu, Haixiao; Mohammed, Abdul-Wahid

    2016-01-01

    With the development of Machine-to-Machine (M2M) technology, a variety of embedded and mobile devices is integrated to interact via the platform of the Internet of Things, especially in the domain of smart cities. One of the primary challenges is that selecting the appropriate services or service combination for upper layer applications is hard, which is due to the absence of a unified semantical service description pattern, as well as the service selection mechanism. In this paper, we define a semantic service representation model from four key properties: Capability (C), Deployment (D), Resource (R) and IOData (IO). Based on this model, an agent-based middleware is built to support semantic service enablement. In this middleware, we present an efficient semantic service discovery and matching approach for a service combination process, which calculates the semantic similarity between services, and a heuristic algorithm to search the service candidates for a specific service request. Based on this design, we propose a simulation of virtual urban fire fighting, and the experimental results manifest the feasibility and efficiency of our design. PMID:28009818

  18. Deriving effective vaccine allocation strategies for pandemic influenza: Comparison of an agent-based simulation and a compartmental model

    PubMed Central

    Dalgıç, Özden O.; Özaltın, Osman Y.; Ciccotelli, William A.; Erenay, Fatih S.

    2017-01-01

    Individuals are prioritized based on their risk profiles when allocating limited vaccine stocks during an influenza pandemic. Computationally expensive but realistic agent-based simulations and fast but stylized compartmental models are typically used to derive effective vaccine allocation strategies. A detailed comparison of these two approaches, however, is often omitted. We derive age-specific vaccine allocation strategies to mitigate a pandemic influenza outbreak in Seattle by applying derivative-free optimization to an agent-based simulation and also to a compartmental model. We compare the strategies derived by these two approaches under various infection aggressiveness and vaccine coverage scenarios. We observe that both approaches primarily vaccinate school children, however they may allocate the remaining vaccines in different ways. The vaccine allocation strategies derived by using the agent-based simulation are associated with up to 70% decrease in total cost and 34% reduction in the number of infections compared to the strategies derived by using the compartmental model. Nevertheless, the latter approach may still be competitive for very low and/or very high infection aggressiveness. Our results provide insights about potential differences between the vaccine allocation strategies derived by using agent-based simulations and those derived by using compartmental models. PMID:28222123

  19. An agent-based modeling framework for evaluating hypotheses on risks for developing autism: effects of the gut microbial environment.

    PubMed

    Weston, Bronson; Fogal, Benjamin; Cook, Daniel; Dhurjati, Prasad

    2015-04-01

    The number of cases diagnosed with Autism Spectrum Disorders is rising at an alarming rate with the Centers for Disease Control estimating the 2014 incidence rate as 1 in 68. Recently, it has been hypothesized that gut bacteria may contribute to the development of autism. Specifically, the relative balances between the inflammatory microbes clostridia and desulfovibrio and the anti-inflammatory microbe bifidobacteria may become destabilized prior to autism development. The imbalance leads to a leaky gut, characterized by a more porous epithelial membrane resulting in microbial toxin release into the blood, which may contribute to brain inflammation and autism development. To test how changes in population dynamics of the gut microbiome may lead to the imbalanced microbial populations associated with autism patients, we constructed a novel agent-based model of clostridia, desulfovibrio, and bifidobacteria population interactions in the gut. The model demonstrates how changing physiological conditions in the gut can affect the population dynamics of the microbiome. Simulations using our agent-based model indicate that despite large perturbations to initial levels of bacteria, the populations robustly achieve a single steady-state given similar gut conditions. These simulation results suggests that disturbance such as a prebiotic or antibiotic treatment may only transiently affect the gut microbiome. However, sustained prebiotic treatments may correct low population counts of bifidobacteria. Furthermore, our simulations suggest that clostridia growth rate is a key determinant of risk of autism development. Treatment of high-risk infants with supra-physiological levels of lysozymes may suppress clostridia growth rate, resulting in a steep decrease in the clostridia population and therefore reduced risk of autism development.

  20. Biophysically realistic filament bending dynamics in agent-based biological simulation.

    PubMed

    Alberts, Jonathan B

    2009-01-01

    An appealing tool for study of the complex biological behaviors that can emerge from networks of simple molecular interactions is an agent-based, computational simulation that explicitly tracks small-scale local interactions--following thousands to millions of states through time. For many critical cell processes (e.g. cytokinetic furrow specification, nuclear centration, cytokinesis), the flexible nature of cytoskeletal filaments is likely to be critical. Any computer model that hopes to explain the complex emergent behaviors in these processes therefore needs to encode filament flexibility in a realistic manner. Here I present a numerically convenient and biophysically realistic method for modeling cytoskeletal filament flexibility in silico. Each cytoskeletal filament is represented by a series of rigid segments linked end-to-end in series with a variable attachment point for the translational elastic element. This connection scheme allows an empirically tuning, for a wide range of segment sizes, viscosities, and time-steps, that endows any filament species with the experimentally observed (or theoretically expected) static force deflection, relaxation time-constant, and thermal writhing motions. I additionally employ a unique pair of elastic elements--one representing the axial and the other the bending rigidity- that formulate the restoring force in terms of single time-step constraint resolution. This method is highly local -adjacent rigid segments of a filament only interact with one another through constraint forces-and is thus well-suited to simulations in which arbitrary additional forces (e.g. those representing interactions of a filament with other bodies or cross-links / entanglements between filaments) may be present. Implementation in code is straightforward; Java source code is available at www.celldynamics.org.

  1. Agent-based evacuation simulation for spatial allocation assessment of urban shelters

    NASA Astrophysics Data System (ADS)

    Yu, Jia; Wen, Jiahong; Jiang, Yong

    2015-12-01

    The construction of urban shelters is one of the most important work in urban planning and disaster prevention. The spatial allocation assessment is a fundamental pre-step for spatial location-allocation of urban shelters. This paper introduces a new method which makes use of agent-based technology to implement evacuation simulation so as to conduct dynamic spatial allocation assessment of urban shelters. The method can not only accomplish traditional geospatial evaluation for urban shelters, but also simulate the evacuation process of the residents to shelters. The advantage of utilizing this method lies into three aspects: (1) the evacuation time of each citizen from a residential building to the shelter can be estimated more reasonably; (2) the total evacuation time of all the residents in a region is able to be obtained; (3) the road congestions in evacuation in sheltering can be detected so as to take precautionary measures to prevent potential risks. In this study, three types of agents are designed: shelter agents, government agents and resident agents. Shelter agents select specified land uses as shelter candidates for different disasters. Government agents delimitate the service area of each shelter, in other words, regulate which shelter a person should take, in accordance with the administrative boundaries and road distance between the person's position and the location of the shelter. Resident agents have a series of attributes, such as ages, positions, walking speeds, and so on. They also have several behaviors, such as reducing speed when walking in the crowd, helping old people and children, and so on. Integrating these three types of agents which are correlated with each other, evacuation procedures can be simulated and dynamic allocation assessment of shelters will be achieved. A case study in Jing'an District, Shanghai, China, was conducted to demonstrate the feasibility of the method. A scenario of earthquake disaster which occurs in nighttime

  2. Autonomous Agent-Based Simulation of a Model Simulating the Human Air-Threat Assessment Process

    DTIC Science & Technology

    2004-03-01

    multi - agent system (MAS) technology and is implemented in Java programming language. This research is a portion of Red Intent Project whose goal is to ultimately implement a model to predict the intent of any given track in the environment. For any air track in the simulation, two sets of agents are created, one for controlling track actions and one for predicting its identity and intent based on information received from track, the geopolitical situation and intelligence. The simulation is also capable of identifying coordinated actions between air tracks. We

  3. Understanding coupled natural and human systems on fire prone landscapes: integrating wildfire simulation into an agent based planning system.

    NASA Astrophysics Data System (ADS)

    Barros, Ana; Ager, Alan; Preisler, Haiganoush; Day, Michelle; Spies, Tom; Bolte, John

    2015-04-01

    Agent-based models (ABM) allow users to examine the long-term effects of agent decisions in complex systems where multiple agents and processes interact. This framework has potential application to study the dynamics of coupled natural and human systems where multiple stimuli determine trajectories over both space and time. We used Envision, a landscape based ABM, to analyze long-term wildfire dynamics in a heterogeneous, multi-owner landscape in Oregon, USA. Landscape dynamics are affected by land management policies, actors decisions, and autonomous processes such as vegetation succession, wildfire, or at a broader scale, climate change. Key questions include: 1) How are landscape dynamics influenced by policies and institutions, and 2) How do land management policies and actor decisions interact to produce intended and unintended consequences with respect to wildfire on fire-prone landscapes. Applying Envision to address these questions required the development of a wildfire module that could accurately simulate wildfires on the heterogeneous landscapes within the study area in terms of replicating historical fire size distribution, spatial distribution and fire intensity. In this paper we describe the development and testing of a mechanistic fire simulation system within Envision and application of the model on a 3.2 million fire prone landscape in central Oregon USA. The core fire spread equations use the Minimum Travel Time algorithm developed by M Finney. The model operates on a daily time step and uses a fire prediction system based on the relationship between energy release component and historical fires. Specifically, daily wildfire probabilities and sizes are generated from statistical analyses of historical fires in relation to daily ERC values. The MTT was coupled with the vegetation dynamics module in Envision to allow communication between the respective subsystem and effectively model fire effects and vegetation dynamics after a wildfire. Canopy and

  4. The Umbra Simulation Framework

    SciTech Connect

    GOTTLIEB,ERIC; HARRIGAN,RAYMOND W.; MCDONALD,MICHAEL J.; OPPEL III,FRED J.; XAVIER,PATRICK G.

    2001-06-01

    Umbra is a new Sandia-developed modeling and simulation framework. The Umbra framework allows users to quickly build models and simulations for intelligent system development, analysis, experimentation, and control and supports tradeoff analyses of complex robotic systems, device, and component concepts. Umbra links together heterogeneous collections of modeling tools. The models in Umbra include 3D geometry and physics models of robots, devices and their environments. Model components can be built with varying levels of fidelity and readily switched to allow models built with low fidelity for conceptual analysis to be gradually converted to high fidelity models for later phase detailed analysis. Within control environments, the models can be readily replaced with actual control elements. This paper describes Umbra at a functional level and describes issues that Sandia uses Umbra to address.

  5. Modelling Temporal Schedule of Urban Trains Using Agent-Based Simulation and NSGA2-BASED Multiobjective Optimization Approaches

    NASA Astrophysics Data System (ADS)

    Sahelgozin, M.; Alimohammadi, A.

    2015-12-01

    Increasing distances between locations of residence and services leads to a large number of daily commutes in urban areas. Developing subway systems has been taken into consideration of transportation managers as a response to this huge amount of travel demands. In developments of subway infrastructures, representing a temporal schedule for trains is an important task; because an appropriately designed timetable decreases Total passenger travel times, Total Operation Costs and Energy Consumption of trains. Since these variables are not positively correlated, subway scheduling is considered as a multi-criteria optimization problem. Therefore, proposing a proper solution for subway scheduling has been always a controversial issue. On the other hand, research on a phenomenon requires a summarized representation of the real world that is known as Model. In this study, it is attempted to model temporal schedule of urban trains that can be applied in Multi-Criteria Subway Schedule Optimization (MCSSO) problems. At first, a conceptual framework is represented for MCSSO. Then, an agent-based simulation environment is implemented to perform Sensitivity Analysis (SA) that is used to extract the interrelations between the framework components. These interrelations is then taken into account in order to construct the proposed model. In order to evaluate performance of the model in MCSSO problems, Tehran subway line no. 1 is considered as the case study. Results of the study show that the model was able to generate an acceptable distribution of Pareto-optimal solutions which are applicable in the real situations while solving a MCSSO is the goal. Also, the accuracy of the model in representing the operation of subway systems was significant.

  6. Comparing administered and market-based water allocation systems through a consistent agent-based modeling framework.

    PubMed

    Zhao, Jianshi; Cai, Ximing; Wang, Zhongjing

    2013-07-15

    Water allocation can be undertaken through administered systems (AS), market-based systems (MS), or a combination of the two. The debate on the performance of the two systems has lasted for decades but still calls for attention in both research and practice. This paper compares water users' behavior under AS and MS through a consistent agent-based modeling framework for water allocation analysis that incorporates variables particular to both MS (e.g., water trade and trading prices) and AS (water use violations and penalties/subsidies). Analogous to the economic theory of water markets under MS, the theory of rational violation justifies the exchange of entitled water under AS through the use of cross-subsidies. Under water stress conditions, a unique water allocation equilibrium can be achieved by following a simple bargaining rule that does not depend upon initial market prices under MS, or initial economic incentives under AS. The modeling analysis shows that the behavior of water users (agents) depends on transaction, or administrative, costs, as well as their autonomy. Reducing transaction costs under MS or administrative costs under AS will mitigate the effect that equity constraints (originating with primary water allocation) have on the system's total net economic benefits. Moreover, hydrologic uncertainty is shown to increase market prices under MS and penalties/subsidies under AS and, in most cases, also increases transaction, or administrative, costs.

  7. An integrated modeling framework of socio-economic, biophysical, and hydrological processes in Midwest landscapes: Remote sensing data, agro-hydrological model, and agent-based model

    NASA Astrophysics Data System (ADS)

    Ding, Deng

    Intensive human-environment interactions are taking place in Midwestern agricultural systems. An integrated modeling framework is suitable for predicting dynamics of key variables of the socio-economic, biophysical, hydrological processes as well as exploring the potential transitions of system states in response to changes of the driving factors. The purpose of this dissertation is to address issues concerning the interacting processes and consequent changes in land use, water balance, and water quality using an integrated modeling framework. This dissertation is composed of three studies in the same agricultural watershed, the Clear Creek watershed in East-Central Iowa. In the first study, a parsimonious hydrologic model, the Threshold-Exceedance-Lagrangian Model (TELM), is further developed into RS-TELM (Remote Sensing TELM) to integrate remote sensing vegetation data for estimating evapotranspiration. The goodness of fit of RS-TELM is comparable to a well-calibrated SWAT (Soil and Water Assessment Tool) and even slightly superior in capturing intra-seasonal variability of stream flow. The integration of RS LAI (Leaf Area Index) data improves the model's performance especially over the agriculture dominated landscapes. The input of rainfall datasets with spatially explicit information plays a critical role in increasing the model's goodness of fit. In the second study, an agent-based model is developed to simulate farmers' decisions on crop type and fertilizer application in response to commodity and biofuel crop prices. The comparison between simulated crop land percentage and crop rotations with satellite-based land cover data suggest that farmers may be underestimating the effects that continuous corn production has on yields (yield drag). The simulation results given alternative market scenarios based on a survey of agricultural land owners and operators in the Clear Creek Watershed show that, farmers see cellulosic biofuel feedstock production in the form

  8. Proposal of Classification Method of Time Series Data in International Emissions Trading Market Using Agent-based Simulation

    NASA Astrophysics Data System (ADS)

    Nakada, Tomohiro; Takadama, Keiki; Watanabe, Shigeyoshi

    This paper proposes the classification method using Bayesian analytical method to classify the time series data in the international emissions trading market depend on the agent-based simulation and compares the case with Discrete Fourier transform analytical method. The purpose demonstrates the analytical methods mapping time series data such as market price. These analytical methods have revealed the following results: (1) the classification methods indicate the distance of mapping from the time series data, it is easier the understanding and inference than time series data; (2) these methods can analyze the uncertain time series data using the distance via agent-based simulation including stationary process and non-stationary process; and (3) Bayesian analytical method can show the 1% difference description of the emission reduction targets of agent.

  9. Bee++: An Object-Oriented, Agent-Based Simulator for Honey Bee Colonies.

    PubMed

    Betti, Matthew; LeClair, Josh; Wahl, Lindi M; Zamir, Mair

    2017-03-10

    We present a model and associated simulation package (www.beeplusplus.ca) to capture the natural dynamics of a honey bee colony in a spatially-explicit landscape, with temporally-variable, weather-dependent parameters. The simulation tracks bees of different ages and castes, food stores within the colony, pollen and nectar sources and the spatial position of individual foragers outside the hive. We track explicitly the intake of pesticides in individual bees and their ability to metabolize these toxins, such that the impact of sub-lethal doses of pesticides can be explored. Moreover, pathogen populations (in particular, Nosema apis, Nosema cerenae and Varroa mites) have been included in the model and may be introduced at any time or location. The ability to study interactions among pesticides, climate, biodiversity and pathogens in this predictive framework should prove useful to a wide range of researchers studying honey bee populations. To this end, the simulation package is written in open source, object-oriented code (C++) and can be easily modified by the user. Here, we demonstrate the use of the model by exploring the effects of sub-lethal pesticide exposure on the flight behaviour of foragers.

  10. Bee++: An Object-Oriented, Agent-Based Simulator for Honey Bee Colonies

    PubMed Central

    Betti, Matthew; LeClair, Josh; Wahl, Lindi M.; Zamir, Mair

    2017-01-01

    We present a model and associated simulation package (www.beeplusplus.ca) to capture the natural dynamics of a honey bee colony in a spatially-explicit landscape, with temporally-variable, weather-dependent parameters. The simulation tracks bees of different ages and castes, food stores within the colony, pollen and nectar sources and the spatial position of individual foragers outside the hive. We track explicitly the intake of pesticides in individual bees and their ability to metabolize these toxins, such that the impact of sub-lethal doses of pesticides can be explored. Moreover, pathogen populations (in particular, Nosema apis, Nosema cerenae and Varroa mites) have been included in the model and may be introduced at any time or location. The ability to study interactions among pesticides, climate, biodiversity and pathogens in this predictive framework should prove useful to a wide range of researchers studying honey bee populations. To this end, the simulation package is written in open source, object-oriented code (C++) and can be easily modified by the user. Here, we demonstrate the use of the model by exploring the effects of sub-lethal pesticide exposure on the flight behaviour of foragers. PMID:28287445

  11. Simulating Land-Use Change using an Agent-Based Land Transaction Model

    NASA Astrophysics Data System (ADS)

    Bakker, M. M.; van Dijk, J.; Alam, S. J.

    2013-12-01

    In the densely populated cultural landscapes of Europe, the vast majority of all land is owned by private parties, be it farmers (the majority), nature organizations, property developers, or citizens. Therewith, the vast majority of all land-use change arises from land transactions between different owner types: successful farms expand at the expense of less successful farms, and meanwhile property developers, individual citizens, and nature organizations also actively purchase land. These land transactions are driven by specific properties of the land, by governmental policies, and by the (economic) motives of both buyers and sellers. Climate/global change can affect these drivers at various scales: at the local scale changes in hydrology can make certain land less or more desirable; at the global scale the agricultural markets will affect motives of farmers to buy or sell land; while at intermediate (e.g. provincial) scales property developers and nature conservationists may be encouraged or discouraged to purchase land. The cumulative result of all these transactions becomes manifest in changing land-use patterns, and consequent environmental responses. Within the project Climate Adaptation for Rural Areas an agent-based land-use model was developed that explores the future response of individual land users to climate change, within the context of wider global change (i.e. policy and market change). It simulates the exchange of land among farmers and between farmers and nature organizations and property developers, for a specific case study area in the east of the Netherlands. Results show that local impacts of climate change can result in a relative stagnation in the land market in waterlogged areas. Furthermore, the increase in dairying at the expense of arable cultivation - as has been observed in the area in the past - is slowing down as arable produce shows a favourable trend in the agricultural world market. Furthermore, budgets for nature managers are

  12. Impact of Different Policies on Unhealthy Dietary Behaviors in an Urban Adult Population: An Agent-Based Simulation Model

    PubMed Central

    Giabbanelli, Philippe J.; Arah, Onyebuchi A.; Zimmerman, Frederick J.

    2014-01-01

    Objectives. Unhealthy eating is a complex-system problem. We used agent-based modeling to examine the effects of different policies on unhealthy eating behaviors. Methods. We developed an agent-based simulation model to represent a synthetic population of adults in Pasadena, CA, and how they make dietary decisions. Data from the 2007 Food Attitudes and Behaviors Survey and other empirical studies were used to calibrate the parameters of the model. Simulations were performed to contrast the potential effects of various policies on the evolution of dietary decisions. Results. Our model showed that a 20% increase in taxes on fast foods would lower the probability of fast-food consumption by 3 percentage points, whereas improving the visibility of positive social norms by 10%, either through community-based or mass-media campaigns, could improve the consumption of fruits and vegetables by 7 percentage points and lower fast-food consumption by 6 percentage points. Zoning policies had no significant impact. Conclusions. Interventions emphasizing healthy eating norms may be more effective than directly targeting food prices or regulating local food outlets. Agent-based modeling may be a useful tool for testing the population-level effects of various policies within complex systems. PMID:24832414

  13. The effects of social interactions on fertility decline in nineteenth-century France: an agent-based simulation experiment.

    PubMed

    González-Bailón, Sandra; Murphy, Tommy E

    2013-07-01

    We built an agent-based simulation, incorporating geographic and demographic data from nineteenth-century France, to study the role of social interactions in fertility decisions. The simulation made experimentation possible in a context where other empirical strategies were precluded by a lack of data. We evaluated how different decision rules, with and without interdependent decision-making, caused variations in population growth and fertility levels. The analyses show that incorporating social influence into the model allows empirically observed behaviour to be mimicked, especially at a national level. These findings shed light on individual-level mechanisms through which the French demographic transition may have developed.

  14. Multi-Agent Based Simulation of Optimal Urban Land Use Allocation in the Middle Reaches of the Yangtze River, China

    NASA Astrophysics Data System (ADS)

    Zeng, Y.; Huang, W.; Jin, W.; Li, S.

    2016-06-01

    The optimization of land-use allocation is one of important approaches to achieve regional sustainable development. This study selects Chang-Zhu-Tan agglomeration as study area and proposed a new land use optimization allocation model. Using multi-agent based simulation model, the future urban land use optimization allocation was simulated in 2020 and 2030 under three different scenarios. This kind of quantitative information about urban land use optimization allocation and urban expansions in future would be of great interest to urban planning, water and land resource management, and climate change research.

  15. A Novel Framework for Characterizing Exposure-Related Behaviors Using Agent-Based Models Embedded with Needs-Based Artificial Intelligence (CSSSA2016)

    EPA Science Inventory

    Descriptions of where and how individuals spend their time are important for characterizing exposures to chemicals in consumer products and in indoor environments. Herein we create an agent-based model (ABM) that is able to simulate longitudinal patterns in behaviors. By basing o...

  16. Applying GIS and high performance agent-based simulation for managing an Old World Screwworm fly invasion of Australia.

    PubMed

    Welch, M C; Kwan, P W; Sajeev, A S M

    2014-10-01

    Agent-based modelling has proven to be a promising approach for developing rich simulations for complex phenomena that provide decision support functions across a broad range of areas including biological, social and agricultural sciences. This paper demonstrates how high performance computing technologies, namely General-Purpose Computing on Graphics Processing Units (GPGPU), and commercial Geographic Information Systems (GIS) can be applied to develop a national scale, agent-based simulation of an incursion of Old World Screwworm fly (OWS fly) into the Australian mainland. The development of this simulation model leverages the combination of massively data-parallel processing capabilities supported by NVidia's Compute Unified Device Architecture (CUDA) and the advanced spatial visualisation capabilities of GIS. These technologies have enabled the implementation of an individual-based, stochastic lifecycle and dispersal algorithm for the OWS fly invasion. The simulation model draws upon a wide range of biological data as input to stochastically determine the reproduction and survival of the OWS fly through the different stages of its lifecycle and dispersal of gravid females. Through this model, a highly efficient computational platform has been developed for studying the effectiveness of control and mitigation strategies and their associated economic impact on livestock industries can be materialised.

  17. Using the Integration of Discrete Event and Agent-Based Simulation to Enhance Outpatient Service Quality in an Orthopedic Department

    PubMed Central

    Kittipittayakorn, Cholada

    2016-01-01

    Many hospitals are currently paying more attention to patient satisfaction since it is an important service quality index. Many Asian countries' healthcare systems have a mixed-type registration, accepting both walk-in patients and scheduled patients. This complex registration system causes a long patient waiting time in outpatient clinics. Different approaches have been proposed to reduce the waiting time. This study uses the integration of discrete event simulation (DES) and agent-based simulation (ABS) to improve patient waiting time and is the first attempt to apply this approach to solve this key problem faced by orthopedic departments. From the data collected, patient behaviors are modeled and incorporated into a massive agent-based simulation. The proposed approach is an aid for analyzing and modifying orthopedic department processes, allows us to consider far more details, and provides more reliable results. After applying the proposed approach, the total waiting time of the orthopedic department fell from 1246.39 minutes to 847.21 minutes. Thus, using the correct simulation model significantly reduces patient waiting time in an orthopedic department. PMID:27195606

  18. Linking Bayesian and Agent-Based Models to Simulate Complex Social-Ecological Systems in the Sonoran Desert

    NASA Astrophysics Data System (ADS)

    Pope, A.; Gimblett, R.

    2013-12-01

    Interdependencies of ecologic, hydrologic, and social systems challenge traditional approaches to natural resource management in semi-arid regions. As a complex social-ecological system, water demands in the Sonoran Desert from agricultural and urban users often conflicts with water needs for its ecologically-significant riparian corridors. To explore this system, we developed an agent-based model to simulate complex feedbacks between human decisions and environmental conditions. Cognitive mapping in conjunction with stakeholder participation produced a Bayesian model of conditional probabilities of local human decision-making processes resulting to changes in water demand. Probabilities created in the Bayesian model were incorporated into the agent-based model, so that each agent had a unique probability to make a positive decision based on its perceived environment at each point in time and space. By using a Bayesian approach, uncertainty in the human decision-making process could be incorporated. The spatially-explicit agent-based model simulated changes in depth-to-groundwater by well pumping based on an agent's water demand. Depth-to-groundwater was then used as an indicator of unique vegetation guilds within the riparian corridor. Each vegetation guild provides varying levels of ecosystem services, the changes of which, along with changes in depth-to-groundwater, feedback to influence agent behavior. Using this modeling approach allowed us to examine resilience of semi-arid riparian corridors and agent behavior under various scenarios. The insight provided by the model contributes to understanding how specific interventions may alter the complex social-ecological system in the future.

  19. Can human-like Bots control collective mood: agent-based simulations of online chats

    NASA Astrophysics Data System (ADS)

    Tadić, Bosiljka; Šuvakov, Milovan

    2013-10-01

    Using an agent-based modeling approach, in this paper, we study self-organized dynamics of interacting agents in the presence of chat Bots. Different Bots with tunable ‘human-like’ attributes, which exchange emotional messages with agents, are considered, and the collective emotional behavior of agents is quantitatively analyzed. In particular, using detrended fractal analysis we determine persistent fluctuations and temporal correlations in time series of agent activity and statistics of avalanches carrying emotional messages of agents when Bots favoring positive/negative affects are active. We determine the impact of Bots and identify parameters that can modulate that impact. Our analysis suggests that, by these measures, the emotional Bots induce collective emotion among interacting agents by suitably altering the fractal characteristics of the underlying stochastic process. Positive emotion Bots are slightly more effective than negative emotion Bots. Moreover, Bots which periodically alternate between positive and negative emotion can enhance fluctuations in the system, leading to avalanches of agent messages that are reminiscent of self-organized critical states.

  20. Evaluating the effect of human activity patterns on air pollution exposure using an integrated field-based and agent-based modelling framework

    NASA Astrophysics Data System (ADS)

    Schmitz, Oliver; Beelen, Rob M. J.; de Bakker, Merijn P.; Karssenberg, Derek

    2015-04-01

    Constructing spatio-temporal numerical models to support risk assessment, such as assessing the exposure of humans to air pollution, often requires the integration of field-based and agent-based modelling approaches. Continuous environmental variables such as air pollution are best represented using the field-based approach which considers phenomena as continuous fields having attribute values at all locations. When calculating human exposure to such pollutants it is, however, preferable to consider the population as a set of individuals each with a particular activity pattern. This would allow to account for the spatio-temporal variation in a pollutant along the space-time paths travelled by individuals, determined, for example, by home and work locations, road network, and travel times. Modelling this activity pattern requires an agent-based or individual based modelling approach. In general, field- and agent-based models are constructed with the help of separate software tools, while both approaches should play together in an interacting way and preferably should be combined into one modelling framework, which would allow for efficient and effective implementation of models by domain specialists. To overcome this lack in integrated modelling frameworks, we aim at the development of concepts and software for an integrated field-based and agent-based modelling framework. Concepts merging field- and agent-based modelling were implemented by extending PCRaster (http://www.pcraster.eu), a field-based modelling library implemented in C++, with components for 1) representation of discrete, mobile, agents, 2) spatial networks and algorithms by integrating the NetworkX library (http://networkx.github.io), allowing therefore to calculate e.g. shortest routes or total transport costs between locations, and 3) functions for field-network interactions, allowing to assign field-based attribute values to networks (i.e. as edge weights), such as aggregated or averaged

  1. Real-Time Agent-Based Modeling Simulation with in-situ Visualization of Complex Biological Systems

    PubMed Central

    Seekhao, Nuttiiya; Shung, Caroline; JaJa, Joseph; Mongeau, Luc; Li-Jessen, Nicole Y. K.

    2016-01-01

    We present an efficient and scalable scheme for implementing agent-based modeling (ABM) simulation with In Situ visualization of large complex systems on heterogeneous computing platforms. The scheme is designed to make optimal use of the resources available on a heterogeneous platform consisting of a multicore CPU and a GPU, resulting in minimal to no resource idle time. Furthermore, the scheme was implemented under a client-server paradigm that enables remote users to visualize and analyze simulation data as it is being generated at each time step of the model. Performance of a simulation case study of vocal fold inflammation and wound healing with 3.8 million agents shows 35× and 7× speedup in execution time over single-core and multi-core CPU respectively. Each iteration of the model took less than 200 ms to simulate, visualize and send the results to the client. This enables users to monitor the simulation in real-time and modify its course as needed. PMID:27547508

  2. Agent-Based Simulations of Malaria Transmissions with Applications to a Study Site in Thailand

    NASA Technical Reports Server (NTRS)

    Kiang, Richard K.; Adimi, Farida; Zollner, Gabriela E.; Coleman, Russell E.

    2006-01-01

    The dynamics of malaria transmission are driven by environmental, biotic and socioeconomic factors. Because of the geographic dependency of these factors and the complex interactions among them, it is difficult to generalize the key factors that perpetuate or intensify malaria transmission. Methods: Discrete event simulations were used for modeling the detailed interactions among the vector life cycle, sporogonic cycle and human infection cycle, under the explicit influences of selected extrinsic and intrinsic factors. Meteorological and environmental parameters may be derived from satellite data. The output of the model includes the individual infection status and the quantities normally observed in field studies, such as mosquito biting rates, sporozoite infection rates, gametocyte prevalence and incidence. Results were compared with mosquito vector and human malaria data acquired over 4.5 years (June 1999 - January 2004) in Kong Mong Tha, a remote village in Kanchanaburi Province, western Thailand. Results: Three years of transmissions of vivax and falciparum malaria were simulated for a hypothetical hamlet with approximately 1/7 of the study site population. The model generated results for a number of scenarios, including applications of larvicide and insecticide, asymptomatic cases receiving or not receiving treatment, blocking malaria transmission in mosquito vectors, and increasing the density of farm (host) animals in the hamlet. Transmission characteristics and trends in the simulated results are comparable to actual data collected at the study site.

  3. The contribution of agent-based simulations to conservation management on a Natura 2000 site.

    PubMed

    Dupont, Hélène; Gourmelon, Françoise; Rouan, Mathias; Le Viol, Isabelle; Kerbiriou, Christian

    2016-03-01

    The conservation of biodiversity today must include the participation and support of local stakeholders. Natura 2000 can be considered as a conservation system that, in its application in most EU countries, relies on the participation of local stakeholders. Our study proposes a scientific method for participatory modelling, with the aim of contributing to the conservation management of habitats and species at a Natura 2000 site (Crozon Peninsula, Bretagne, France) that is representative of in landuse changes in coastal areas. We make use of companion modelling and its associated tools (scenario-planning, GIS, multi-agent modelling and simulations) to consider possible futures through the co-construction of management scenarios and the understanding of their consequences on different indicators of biodiversity status (habitats, avifauna, flora). The maintenance of human activities as they have been carried out since the creation of the Natura 2000s zone allows the biodiversity values to remain stable. Extensive agricultural activities have been shown to be essential to this maintenance, whereas management sustained by the multiplication of conservation actions brings about variable results according to the indicators. None of the scenarios has a positive incidence on the set of indicators. However, an understanding of the modelling system and the results of the simulations allow for the refining of the selection of conservation actions in relation to the species to be preserved.

  4. Evolutionary Agent-Based Simulation of the Introduction of New Technologies in Air Traffic Management

    NASA Technical Reports Server (NTRS)

    Yliniemi, Logan; Agogino, Adrian K.; Tumer, Kagan

    2014-01-01

    Accurate simulation of the effects of integrating new technologies into a complex system is critical to the modernization of our antiquated air traffic system, where there exist many layers of interacting procedures, controls, and automation all designed to cooperate with human operators. Additions of even simple new technologies may result in unexpected emergent behavior due to complex human/ machine interactions. One approach is to create high-fidelity human models coming from the field of human factors that can simulate a rich set of behaviors. However, such models are difficult to produce, especially to show unexpected emergent behavior coming from many human operators interacting simultaneously within a complex system. Instead of engineering complex human models, we directly model the emergent behavior by evolving goal directed agents, representing human users. Using evolution we can predict how the agent representing the human user reacts given his/her goals. In this paradigm, each autonomous agent in a system pursues individual goals, and the behavior of the system emerges from the interactions, foreseen or unforeseen, between the agents/actors. We show that this method reflects the integration of new technologies in a historical case, and apply the same methodology for a possible future technology.

  5. ActivitySim: large-scale agent based activity generation for infrastructure simulation

    SciTech Connect

    Gali, Emmanuel; Eidenbenz, Stephan; Mniszewski, Sue; Cuellar, Leticia; Teuscher, Christof

    2008-01-01

    The United States' Department of Homeland Security aims to model, simulate, and analyze critical infrastructure and their interdependencies across multiple sectors such as electric power, telecommunications, water distribution, transportation, etc. We introduce ActivitySim, an activity simulator for a population of millions of individual agents each characterized by a set of demographic attributes that is based on US census data. ActivitySim generates daily schedules for each agent that consists of a sequence of activities, such as sleeping, shopping, working etc., each being scheduled at a geographic location, such as businesses or private residences that is appropriate for the activity type and for the personal situation of the agent. ActivitySim has been developed as part of a larger effort to understand the interdependencies among national infrastructure networks and their demand profiles that emerge from the different activities of individuals in baseline scenarios as well as emergency scenarios, such as hurricane evacuations. We present the scalable software engineering principles underlying ActivitySim, the socia-technical modeling paradigms that drive the activity generation, and proof-of-principle results for a scenario in the Twin Cities, MN area of 2.6 M agents.

  6. An Agent-Based Simulation for Investigating the Impact of Stereotypes on Task-Oriented Group Formation

    NASA Astrophysics Data System (ADS)

    Maghami, Mahsa; Sukthankar, Gita

    In this paper, we introduce an agent-based simulation for investigating the impact of social factors on the formation and evolution of task-oriented groups. Task-oriented groups are created explicitly to perform a task, and all members derive benefits from task completion. However, even in cases when all group members act in a way that is locally optimal for task completion, social forces that have mild effects on choice of associates can have a measurable impact on task completion performance. In this paper, we show how our simulation can be used to model the impact of stereotypes on group formation. In our simulation, stereotypes are based on observable features, learned from prior experience, and only affect an agent's link formation preferences. Even without assuming stereotypes affect the agents' willingness or ability to complete tasks, the long-term modifications that stereotypes have on the agents' social network impair the agents' ability to form groups with sufficient diversity of skills, as compared to agents who form links randomly. An interesting finding is that this effect holds even in cases where stereotype preference and skill existence are completely uncorrelated.

  7. Simulating Brain Tumor Heterogeneity with a Multiscale Agent-Based Model: Linking Molecular Signatures, Phenotypes and Expansion Rate

    PubMed Central

    Zhang, Le; Strouthos, Costas G.; Wang, Zhihui; Deisboeck, Thomas S.

    2008-01-01

    We have extended our previously developed 3D multi-scale agent-based brain tumor model to simulate cancer heterogeneity and to analyze its impact across the scales of interest. While our algorithm continues to employ an epidermal growth factor receptor (EGFR) gene-protein interaction network to determine the cells’ phenotype, it now adds an implicit treatment of tumor cell adhesion related to the model’s biochemical microenvironment. We simulate a simplified tumor progression pathway that leads to the emergence of five distinct glioma cell clones with different EGFR density and cell ‘search precisions’. The in silico results show that microscopic tumor heterogeneity can impact the tumor system’s multicellular growth patterns. Our findings further confirm that EGFR density results in the more aggressive clonal populations switching earlier from proliferation-dominated to a more migratory phenotype. Moreover, analyzing the dynamic molecular profile that triggers the phenotypic switch between proliferation and migration, our in silico oncogenomics data display spatial and temporal diversity in documenting the regional impact of tumorigenesis, and thus support the added value of multi-site and repeated assessments in vitro and in vivo. Potential implications from this in silico work for experimental and computational studies are discussed. PMID:20047002

  8. An agent-based simulation model of patient choice of health care providers in accountable care organizations.

    PubMed

    Alibrahim, Abdullah; Wu, Shinyi

    2016-10-04

    Accountable care organizations (ACO) in the United States show promise in controlling health care costs while preserving patients' choice of providers. Understanding the effects of patient choice is critical in novel payment and delivery models like ACO that depend on continuity of care and accountability. The financial, utilization, and behavioral implications associated with a patient's decision to forego local health care providers for more distant ones to access higher quality care remain unknown. To study this question, we used an agent-based simulation model of a health care market composed of providers able to form ACO serving patients and embedded it in a conditional logit decision model to examine patients capable of choosing their care providers. This simulation focuses on Medicare beneficiaries and their congestive heart failure (CHF) outcomes. We place the patient agents in an ACO delivery system model in which provider agents decide if they remain in an ACO and perform a quality improving CHF disease management intervention. Illustrative results show that allowing patients to choose their providers reduces the yearly payment per CHF patient by $320, reduces mortality rates by 0.12 percentage points and hospitalization rates by 0.44 percentage points, and marginally increases provider participation in ACO. This study demonstrates a model capable of quantifying the effects of patient choice in a theoretical ACO system and provides a potential tool for policymakers to understand implications of patient choice and assess potential policy controls.

  9. An agent-based model to simulate tsetse fly distribution and control techniques: a case study in Nguruman, Kenya

    PubMed Central

    Lin, Shengpan; DeVisser, Mark H.; Messina, Joseph P.

    2015-01-01

    Background African trypanosomiasis, also known as “sleeping sickness” in humans and “nagana” in livestock is an important vector-borne disease in Sub-Saharan Africa. Control of trypanosomiasis has focused on eliminating the vector, the tsetse fly (Glossina, spp.). Effective tsetse fly control planning requires models to predict tsetse population and distribution changes over time and space. Traditional planning models have used statistical tools to predict tsetse distributions and have been hindered by limited field survey data. Methodology/Results We developed an Agent-Based Model (ABM) to provide timing and location information for tsetse fly control without presence/absence training data. The model is driven by daily remotely-sensed environment data. The model provides a flexible tool linking environmental changes with individual biology to analyze tsetse control methods such as aerial insecticide spraying, wild animal control, releasing irradiated sterile tsetse males, and land use and cover modification. Significance This is a bottom-up process-based model with freely available data as inputs that can be easily transferred to a new area. The tsetse population simulation more closely approximates real conditions than those using traditional statistical models making it a useful tool in tsetse fly control planning. PMID:26309347

  10. Multiobjective Decision Making Policies and Coordination Mechanisms in Hierarchical Organizations: Results of an Agent-Based Simulation

    PubMed Central

    2014-01-01

    This paper analyses how different coordination modes and different multiobjective decision making approaches interfere with each other in hierarchical organizations. The investigation is based on an agent-based simulation. We apply a modified NK-model in which we map multiobjective decision making as adaptive walk on multiple performance landscapes, whereby each landscape represents one objective. We find that the impact of the coordination mode on the performance and the speed of performance improvement is critically affected by the selected multiobjective decision making approach. In certain setups, the performances achieved with the more complex multiobjective decision making approaches turn out to be less sensitive to the coordination mode than the performances achieved with the less complex multiobjective decision making approaches. Furthermore, we present results on the impact of the nature of interactions among decisions on the achieved performance in multiobjective setups. Our results give guidance on how to control the performance contribution of objectives to overall performance and answer the question how effective certain multiobjective decision making approaches perform under certain circumstances (coordination mode and interdependencies among decisions). PMID:25152926

  11. Agent based simulation on the process of human flesh search-From perspective of knowledge and emotion

    NASA Astrophysics Data System (ADS)

    Zhu, Hou; Hu, Bin

    2017-03-01

    Human flesh search as a new net crowed behavior, on the one hand can help us to find some special information, on the other hand may lead to privacy leaking and offending human right. In order to study the mechanism of human flesh search, this paper proposes a simulation model based on agent-based model and complex networks. The computational experiments show some useful results. Discovered information quantity and involved personal ratio are highly correlated, and most of net citizens will take part in the human flesh search or will not take part in the human flesh search. Knowledge quantity does not influence involved personal ratio, but influences whether HFS can find out the target human. When the knowledge concentrates on hub nodes, the discovered information quantity is either perfect or almost zero. Emotion of net citizens influences both discovered information quantity and involved personal ratio. Concretely, when net citizens are calm to face the search topic, it will be hardly to find out the target; But when net citizens are agitated, the target will be found out easily.

  12. Modeling the 2014 Ebola Virus Epidemic - Agent-Based Simulations, Temporal Analysis and Future Predictions for Liberia and Sierra Leone.

    PubMed

    Siettos, Constantinos; Anastassopoulou, Cleo; Russo, Lucia; Grigoras, Christos; Mylonakis, Eleftherios

    2015-03-09

    We developed an agent-based model to investigate the epidemic dynamics of Ebola virus disease (EVD) in Liberia and Sierra Leone from May 27 to December 21, 2014. The dynamics of the agent-based simulator evolve on small-world transmission networks of sizes equal to the population of each country, with adjustable densities to account for the effects of public health intervention policies and individual behavioral responses to the evolving epidemic. Based on time series of the official case counts from the World Health Organization (WHO), we provide estimates for key epidemiological variables by employing the so-called Equation-Free approach. The underlying transmission networks were characterized by rather random structures in the two countries with densities decreasing by ~19% from the early (May 27-early August) to the last period (mid October-December 21). Our estimates for the values of key epidemiological variables, such as the mean time to death, recovery and the case fatality rate, are very close to the ones reported by the WHO Ebola response team during the early period of the epidemic (until September 14) that were calculated based on clinical data. Specifically, regarding the effective reproductive number Re, our analysis suggests that until mid October, Re was above 2.3 in both countries; from mid October to December 21, Re dropped well below unity in Liberia, indicating a saturation of the epidemic, while in Sierra Leone it was around 1.9, indicating an ongoing epidemic. Accordingly, a ten-week projection from December 21 estimated that the epidemic will fade out in Liberia in early March; in contrast, our results flashed a note of caution for Sierra Leone since the cumulative number of cases could reach as high as 18,000, and the number of deaths might exceed 5,000, by early March 2015. However, by processing the reported data of the very last period (December 21, 2014-January 18, 2015), we obtained more optimistic estimates indicative of a remission of

  13. Product Design Network Self-contextualization: Enterprise Knowledge-Based Approach and Agent-Based Technological Framework

    NASA Astrophysics Data System (ADS)

    Levashova, Tatiana; Sandkuhl, Kurt; Shilov, Nikolay; Smirnov, Alexander; Tarasov, Vladimir

    The paper introduces self-contextualization in a service infrastructure for product design networks as novel application field for multi-agent technology. The main contributions of this paper are (1) identification of requirements from product design networks to the supporting service infrastructure, (2) the use of enterprise knowledge modelling techniques for the representation of computable context models, (3) a technological framework based on agent technology for self-contextualization based on enterprise knowledge models.

  14. Simulating the time series of a selected gene expression profile in an agent-based tumor model

    NASA Astrophysics Data System (ADS)

    Mansury, Yuri; Deisboeck, Thomas S.

    2004-09-01

    To elucidate the role of environmental conditions in molecular-level dynamics and to study their impact on macroscopic brain tumor growth patterns, the expression of the genes Tenascin C and PCNA in a 2D agent-based model for the migratory trait is calibrated using experimental data from the literature, while the expression of these genes for the proliferative trait is obtained as the model output. Numerical results confirm that the gene expression of Tenascin C is indeed consistently higher in the migratory glioma cell phenotype and show that the expression of PCNA is consistently higher among proliferating tumor cells. Intriguingly, the time series of the tumor cells’ gene expression exhibit a sudden change in behavior during the invasion of the tumor into a nutrient-abundant region, showing a robust positive correlation between the expression of Tenascin C and the tumor’s diameter, yet a strong negative correlation between the expression of PCNA and the diameter. These molecular-level dynamics correspond to the emergence of a structural asymmetry in the form of a bulging tumor rim in the nutrient-abundant region. The simulated time series thus supports the critical role of the migratory cell phenotype during both the tumor system’s overall macroscopic expansion and the evolvement of regional growth patterns, particularly in the later stages. Furthermore, detrended fluctuation analysis (DFA) suggests that for prediction purposes, the simulated gene expression profiles of Tenascin C and PCNA that were determined separately for the migrating and proliferating phenotypes exhibit lesser predictability than those of the phenotypic mixture combining all viable tumor cells typically found in clinical biopsies. Finally, partitioning the tumor into distinct geographic regions of interest (ROI) reveals that the gene expression profile of tumor cells in the quadrant close to the nutrient-abundant region is representative for the entire tumor whereas the expression

  15. A Scaffolding Framework to Support Learning of Emergent Phenomena Using Multi-Agent-Based Simulation Environments

    ERIC Educational Resources Information Center

    Basu, Satabdi; Sengupta, Pratim; Biswas, Gautam

    2015-01-01

    Students from middle school to college have difficulties in interpreting and understanding complex systems such as ecological phenomena. Researchers have suggested that students experience difficulties in reconciling the relationships between individuals, populations, and species, as well as the interactions between organisms and their environment…

  16. Agent Based Modeling Applications for Geosciences

    NASA Astrophysics Data System (ADS)

    Stein, J. S.

    2004-12-01

    Agent-based modeling techniques have successfully been applied to systems in which complex behaviors or outcomes arise from varied interactions between individuals in the system. Each individual interacts with its environment, as well as with other individuals, by following a set of relatively simple rules. Traditionally this "bottom-up" modeling approach has been applied to problems in the fields of economics and sociology, but more recently has been introduced to various disciplines in the geosciences. This technique can help explain the origin of complex processes from a relatively simple set of rules, incorporate large and detailed datasets when they exist, and simulate the effects of extreme events on system-wide behavior. Some of the challenges associated with this modeling method include: significant computational requirements in order to keep track of thousands to millions of agents, methods and strategies of model validation are lacking, as is a formal methodology for evaluating model uncertainty. Challenges specific to the geosciences, include how to define agents that control water, contaminant fluxes, climate forcing and other physical processes and how to link these "geo-agents" into larger agent-based simulations that include social systems such as demographics economics and regulations. Effective management of limited natural resources (such as water, hydrocarbons, or land) requires an understanding of what factors influence the demand for these resources on a regional and temporal scale. Agent-based models can be used to simulate this demand across a variety of sectors under a range of conditions and determine effective and robust management policies and monitoring strategies. The recent focus on the role of biological processes in the geosciences is another example of an area that could benefit from agent-based applications. A typical approach to modeling the effect of biological processes in geologic media has been to represent these processes in

  17. Agent-based modelling in synthetic biology

    PubMed Central

    2016-01-01

    Biological systems exhibit complex behaviours that emerge at many different levels of organization. These span the regulation of gene expression within single cells to the use of quorum sensing to co-ordinate the action of entire bacterial colonies. Synthetic biology aims to make the engineering of biology easier, offering an opportunity to control natural systems and develop new synthetic systems with useful prescribed behaviours. However, in many cases, it is not understood how individual cells should be programmed to ensure the emergence of a required collective behaviour. Agent-based modelling aims to tackle this problem, offering a framework in which to simulate such systems and explore cellular design rules. In this article, I review the use of agent-based models in synthetic biology, outline the available computational tools, and provide details on recently engineered biological systems that are amenable to this approach. I further highlight the challenges facing this methodology and some of the potential future directions. PMID:27903820

  18. An Economic Analysis of Strategies to Control Clostridium Difficile Transmission and Infection Using an Agent-Based Simulation Model

    PubMed Central

    Nelson, Richard E.; Jones, Makoto; Leecaster, Molly; Samore, Matthew H.; Ray, William; Huttner, Angela; Huttner, Benedikt; Khader, Karim; Stevens, Vanessa W.; Gerding, Dale; Schweizer, Marin L.; Rubin, Michael A.

    2016-01-01

    Background A number of strategies exist to reduce Clostridium difficile (C. difficile) transmission. We conducted an economic evaluation of “bundling” these strategies together. Methods We constructed an agent-based computer simulation of nosocomial C. difficile transmission and infection in a hospital setting. This model included the following components: interactions between patients and health care workers; room contamination via C. difficile shedding; C. difficile hand carriage and removal via hand hygiene; patient acquisition of C. difficile via contact with contaminated rooms or health care workers; and patient antimicrobial use. Six interventions were introduced alone and "bundled" together: (a) aggressive C. difficile testing; (b) empiric isolation and treatment of symptomatic patients; (c) improved adherence to hand hygiene and (d) contact precautions; (e) improved use of soap and water for hand hygiene; and (f) improved environmental cleaning. Our analysis compared these interventions using values representing 3 different scenarios: (1) base-case (BASE) values that reflect typical hospital practice, (2) intervention (INT) values that represent implementation of hospital-wide efforts to reduce C. diff transmission, and (3) optimal (OPT) values representing the highest expected results from strong adherence to the interventions. Cost parameters for each intervention were obtained from published literature. We performed our analyses assuming low, normal, and high C. difficile importation prevalence and transmissibility of C. difficile. Results INT levels of the “bundled” intervention were cost-effective at a willingness-to-pay threshold of $100,000/quality-adjusted life-year in all importation prevalence and transmissibility scenarios. OPT levels of intervention were cost-effective for normal and high importation prevalence and transmissibility scenarios. When analyzed separately, hand hygiene compliance, environmental decontamination, and empiric

  19. Estimation of the age-specific per-contact probability of Ebola virus transmission in Liberia using agent-based simulations

    NASA Astrophysics Data System (ADS)

    Siettos, Constantinos I.; Anastassopoulou, Cleo; Russo, Lucia; Grigoras, Christos; Mylonakis, Eleftherios

    2016-06-01

    Based on multiscale agent-based computations we estimated the per-contact probability of transmission by age of the Ebola virus disease (EVD) that swept through Liberia from May 2014 to March 2015. For the approximation of the epidemic dynamics we have developed a detailed agent-based model with small-world interactions between individuals categorized by age. For the estimation of the structure of the evolving contact network as well as the per-contact transmission probabilities by age group we exploited the so called Equation-Free framework. Model parameters were fitted to official case counts reported by the World Health Organization (WHO) as well as to recently published data of key epidemiological variables, such as the mean time to death, recovery and the case fatality rate.

  20. Unified Simulation and Analysis Framework for Deep Space Navigation Design

    NASA Technical Reports Server (NTRS)

    Anzalone, Evan; Chuang, Jason; Olsen, Carrie

    2013-01-01

    As the technology that enables advanced deep space autonomous navigation continues to develop and the requirements for such capability continues to grow, there is a clear need for a modular expandable simulation framework. This tool's purpose is to address multiple measurement and information sources in order to capture system capability. This is needed to analyze the capability of competing navigation systems as well as to develop system requirements, in order to determine its effect on the sizing of the integrated vehicle. The development for such a framework is built upon Model-Based Systems Engineering techniques to capture the architecture of the navigation system and possible state measurements and observations to feed into the simulation implementation structure. These models also allow a common environment for the capture of an increasingly complex operational architecture, involving multiple spacecraft, ground stations, and communication networks. In order to address these architectural developments, a framework of agent-based modules is implemented to capture the independent operations of individual spacecraft as well as the network interactions amongst spacecraft. This paper describes the development of this framework, and the modeling processes used to capture a deep space navigation system. Additionally, a sample implementation describing a concept of network-based navigation utilizing digitally transmitted data packets is described in detail. This developed package shows the capability of the modeling framework, including its modularity, analysis capabilities, and its unification back to the overall system requirements and definition.

  1. A Parallel Sliding Region Algorithm to Make Agent-Based Modeling Possible for a Large-Scale Simulation: Modeling Hepatitis C Epidemics in Canada.

    PubMed

    Wong, William W L; Feng, Zeny Z; Thein, Hla-Hla

    2016-11-01

    Agent-based models (ABMs) are computer simulation models that define interactions among agents and simulate emergent behaviors that arise from the ensemble of local decisions. ABMs have been increasingly used to examine trends in infectious disease epidemiology. However, the main limitation of ABMs is the high computational cost for a large-scale simulation. To improve the computational efficiency for large-scale ABM simulations, we built a parallelizable sliding region algorithm (SRA) for ABM and compared it to a nonparallelizable ABM. We developed a complex agent network and performed two simulations to model hepatitis C epidemics based on the real demographic data from Saskatchewan, Canada. The first simulation used the SRA that processed on each postal code subregion subsequently. The second simulation processed the entire population simultaneously. It was concluded that the parallelizable SRA showed computational time saving with comparable results in a province-wide simulation. Using the same method, SRA can be generalized for performing a country-wide simulation. Thus, this parallel algorithm enables the possibility of using ABM for large-scale simulation with limited computational resources.

  2. Thread Group Multithreading: Accelerating the Computation of an Agent-Based Power System Modeling and Simulation Tool -- C GridLAB-D

    SciTech Connect

    Jin, Shuangshuang; Chassin, David P.

    2014-01-06

    GridLAB-DTM is an open source next generation agent-based smart-grid simulator that provides unprecedented capability to model the performance of smart grid technologies. Over the past few years, GridLAB-D has been used to conduct important analyses of smart grid concepts, but it is still quite limited by its computational performance. In order to break through the performance bottleneck to meet the need for large scale power grid simulations, we develop a thread group mechanism to implement highly granular multithreaded computation in GridLAB-D. We achieve close to linear speedups on multithreading version compared against the single-thread version of the same code running on general purpose multi-core commodity for a benchmark simple house model. The performance of the multithreading code shows favorable scalability properties and resource utilization, and much shorter execution time for large-scale power grid simulations.

  3. Rural-urban migration including formal and informal workers in the urban sector: an agent-based numerical simulation study

    NASA Astrophysics Data System (ADS)

    Branco, Nilton; Oliveira, Tharnier; Silveira, Jaylson

    2012-02-01

    The goal of this work is to study rural-urban migration in the early stages of industrialization. We use an agent-based model and take into account the existence of informal and formal workers on the urban sector and possible migration movements, dependent on the agents' social and private utilities. Our agents are place on vertices of a square lattice, such that each vertex has only one agent. Rural, urban informal and urban formal workers are represented by different states of a three-state Ising model. At every step, a fraction a of the agents may change sectors or migrate. The total utility of a given agent is then calculated and compared to a random utility, in order to check if this agent turns into an actual migrant or changes sector. The dynamics is carried out until an equilibrium state is reached and equilibrium variables are then calculated and compared to available data. We find that a generalized Harris-Todaro condition is satisfied [1] on these equilibrium regimes, i.e, the ratio between expected wages between any pair of sectors reach a constant value. [4pt] [1] J. J. Silveira, A. L. Esp'indola and T. J. Penna, Physica A, 364, 445 (2006).

  4. Autonomous Agent-Based Simulation of an AEGIS Cruiser Combat Information Center Performing Battle Group Air Defense Commander Operations

    DTIC Science & Technology

    2003-03-01

    objects from O. • Operations with the task of representing the application of these operations and the reaction of the world to this attempt at... clickable ) (4) Simulation Interface: Tactical Display Contact Icons. • Contact Attributes (specific to the contact) 52 (5...Icon (6) Simulation Interface: CIC Agent Display • CIC Agent Icons ( clickable ) • CIC Equipment Icons ( clickable ) (7) Simulation Interface

  5. Ideal free distribution or dynamic game? An agent-based simulation study of trawling strategies with varying information

    NASA Astrophysics Data System (ADS)

    Beecham, J. A.; Engelhard, G. H.

    2007-10-01

    An ecological economic model of trawling is presented to demonstrate the effect of trawling location choice strategy on net input (rate of economic gain of fish caught per time spent less costs). Fishing location choice is considered to be a dynamic process whereby trawlers chose from among a repertoire of plastic strategies that they modify if their gains fall below a fixed proportion of the mean gains of the fleet as a whole. The distribution of fishing across different areas of a fishery follows an approximate ideal free distribution (IFD) with varying noise due to uncertainty. The least-productive areas are not utilised because initial net input never reaches the mean yield of better areas subject to competitive exploitation. In cases, where there is a weak temporal autocorrelation between fish stocks in a specific location, a plastic strategy of local translocation between trawls mixed with longer-range translocation increases realised input. The trawler can change its translocation strategy in the light of information about recent trawling success compared to its long-term average but, in contrast to predictions of the Marginal Value Theorem (MVT) model, does not know for certain what it will find by moving, so may need to sample new patches. The combination of the two types of translocation mirrored beam-trawling strategies used by the Dutch fleet and the resultant distribution of trawling effort is confirmed by analysis of historical effort distribution of British otter trawling fleets in the North Sea. Fisheries exploitation represents an area where dynamic agent-based adaptive models may be a better representation of the economic dynamics of a fleet than classically inspired optimisation models.

  6. Flexible Residential Smart Grid Simulation Framework

    NASA Astrophysics Data System (ADS)

    Xiang, Wang

    Different scheduling and coordination algorithms controlling household appliances' operations can potentially lead to energy consumption reduction and/or load balancing in conjunction with different electricity pricing methods used in smart grid programs. In order to easily implement different algorithms and evaluate their efficiency against other ideas, a flexible simulation framework is desirable in both research and business fields. However, such a platform is currently lacking or underdeveloped. In this thesis, we provide a simulation framework to focus on demand side residential energy consumption coordination in response to different pricing methods. This simulation framework, equipped with an appliance consumption library using realistic values, aims to closely represent the average usage of different types of appliances. The simulation results of traditional usage yield close matching values compared to surveyed real life consumption records. Several sample coordination algorithms, pricing schemes, and communication scenarios are also implemented to illustrate the use of the simulation framework.

  7. Experimental Evaluation of Suitability of Selected Multi-Criteria Decision-Making Methods for Large-Scale Agent-Based Simulations

    PubMed Central

    2016-01-01

    Multi-criteria decision-making (MCDM) can be formally implemented by various methods. This study compares suitability of four selected MCDM methods, namely WPM, TOPSIS, VIKOR, and PROMETHEE, for future applications in agent-based computational economic (ACE) models of larger scale (i.e., over 10 000 agents in one geographical region). These four MCDM methods were selected according to their appropriateness for computational processing in ACE applications. Tests of the selected methods were conducted on four hardware configurations. For each method, 100 tests were performed, which represented one testing iteration. With four testing iterations conducted on each hardware setting and separated testing of all configurations with the–server parameter de/activated, altogether, 12800 data points were collected and consequently analyzed. An illustrational decision-making scenario was used which allows the mutual comparison of all of the selected decision making methods. Our test results suggest that although all methods are convenient and can be used in practice, the VIKOR method accomplished the tests with the best results and thus can be recommended as the most suitable for simulations of large-scale agent-based models. PMID:27806061

  8. Framework for Network Co-Simulation

    SciTech Connect

    Daily, Jeff; Ciraci, PNNL Selim; Fuller, PNNL Jason; Marinovici, PNNL Laurentiu; Fisher, PNNL Andrew; Lo, PNNL Chaomei; Hauer, PNNL Matthew

    2014-01-09

    The Framework for Network Co-Simulation (FNCS) uses a federated approach to integrate simulations which may have differing time scales. Special consideration is given to integration with a communication network simulation such that inter-simulation messages may be optionally routed through and delayed by such a simulation. In addition, FNCS uses novel time synchronization algorithms to accelerate co-simulation including the application of speculative multithreading. FNCS accomplishes all of these improvements with minimal end user intervention. Simulations can be integrated using FNCS while maintaining their original model input files simply by linking with the FNCS library and making appropriate calls into the FNCS API.

  9. A Software Framework for Aircraft Simulation

    NASA Technical Reports Server (NTRS)

    Curlett, Brian P.

    2008-01-01

    The National Aeronautics and Space Administration Dryden Flight Research Center has a long history in developing simulations of experimental fixed-wing aircraft from gliders to suborbital vehicles on platforms ranging from desktop simulators to pilot-in-the-loop/aircraft-in-the-loop simulators. Regardless of the aircraft or simulator hardware, much of the software framework is common to all NASA Dryden simulators. Some of this software has withstood the test of time, but in recent years the push toward high-fidelity user-friendly simulations has resulted in some significant changes. This report presents an overview of the current NASA Dryden simulation software framework and capabilities with an emphasis on the new features that have permitted NASA to develop more capable simulations while maintaining the same staffing levels.

  10. Autonomous-Agent Based Simulation of Anti- Submarine Warfare Operations with the Goal of Protecting a High Value Unit

    DTIC Science & Technology

    2004-03-01

    Multi Agent System (MAS) technique. The simulation interface is a Horizontal Display Center (HDC) which is very similar to a MEKQ2OO class Frigate Combat Information Center’s (CIC) HDC. The program uses Extensible Markup Language (XML) files for reading data for program scenarios; parameters are initialized before each run time begins. The simulation also provides all the output data at the end of run time for analysis purposes. The program user’s goal, and the purpose of the program, is to decrease the number of successful attacks against surface

  11. Real-Time Agent-Based Modeling Simulation with in-situ Visualization of Complex Biological Systems: A Case Study on Vocal Fold Inflammation and Healing.

    PubMed

    Seekhao, Nuttiiya; Shung, Caroline; JaJa, Joseph; Mongeau, Luc; Li-Jessen, Nicole Y K

    2016-05-01

    We present an efficient and scalable scheme for implementing agent-based modeling (ABM) simulation with In Situ visualization of large complex systems on heterogeneous computing platforms. The scheme is designed to make optimal use of the resources available on a heterogeneous platform consisting of a multicore CPU and a GPU, resulting in minimal to no resource idle time. Furthermore, the scheme was implemented under a client-server paradigm that enables remote users to visualize and analyze simulation data as it is being generated at each time step of the model. Performance of a simulation case study of vocal fold inflammation and wound healing with 3.8 million agents shows 35× and 7× speedup in execution time over single-core and multi-core CPU respectively. Each iteration of the model took less than 200 ms to simulate, visualize and send the results to the client. This enables users to monitor the simulation in real-time and modify its course as needed.

  12. EPOCHS: A Platform for Agent-Based Electric Power and Communication Simulation Built from Commercial Off-The-Shelf Components

    DTIC Science & Technology

    2005-04-01

    to simplify the development of EMTDC scenarios. PSCAD is produced by the Manitoba HVDC Research Centre [25]. EMTDC simulates power scenarios in...Manitoba HVDC Research Centre, PSCAD/EMTDC Manual Getting Started. Winnipeg, Manitoba, Canada, 1998. [26] General Electric, "PSLF Manual," vol. 2003

  13. Development Approaches Coupled with Verification and Validation Methodologies for Agent-Based Mission-Level Analytical Combat Simulations

    DTIC Science & Technology

    2004-03-01

    Where Computers Meet Biology, Vintage Books, a division of Random House, Inc.: New York NY. 117. Liu, Bing, Siew-Hwee Choo , Shee-Ling Lok, Sing-Meng...Simpkins, Scott D., Eugene P. Paulo, , and Lyn R. Whitaker (2001) “Case Study in Modeling and Simulation Validation Methodology”. Proceedings of

  14. Integrating the simulation of domestic water demand behaviour to an urban water model using agent based modelling

    NASA Astrophysics Data System (ADS)

    Koutiva, Ifigeneia; Makropoulos, Christos

    2015-04-01

    The urban water system's sustainable evolution requires tools that can analyse and simulate the complete cycle including both physical and cultural environments. One of the main challenges, in this regard, is the design and development of tools that are able to simulate the society's water demand behaviour and the way policy measures affect it. The effects of these policy measures are a function of personal opinions that subsequently lead to the formation of people's attitudes. These attitudes will eventually form behaviours. This work presents the design of an ABM tool for addressing the social dimension of the urban water system. The created tool, called Urban Water Agents' Behaviour (UWAB) model, was implemented, using the NetLogo agent programming language. The main aim of the UWAB model is to capture the effects of policies and environmental pressures to water conservation behaviour of urban households. The model consists of agents representing urban households that are linked to each other creating a social network that influences the water conservation behaviour of its members. Household agents are influenced as well by policies and environmental pressures, such as drought. The UWAB model simulates behaviour resulting in the evolution of water conservation within an urban population. The final outcome of the model is the evolution of the distribution of different conservation levels (no, low, high) to the selected urban population. In addition, UWAB is implemented in combination with an existing urban water management simulation tool, the Urban Water Optioneering Tool (UWOT) in order to create a modelling platform aiming to facilitate an adaptive approach of water resources management. For the purposes of this proposed modelling platform, UWOT is used in a twofold manner: (1) to simulate domestic water demand evolution and (2) to simulate the response of the water system to the domestic water demand evolution. The main advantage of the UWAB - UWOT model

  15. Agent-based models in translational systems biology

    PubMed Central

    An, Gary; Mi, Qi; Dutta-Moscato, Joyeeta; Vodovotz, Yoram

    2013-01-01

    Effective translational methodologies for knowledge representation are needed in order to make strides against the constellation of diseases that affect the world today. These diseases are defined by their mechanistic complexity, redundancy, and nonlinearity. Translational systems biology aims to harness the power of computational simulation to streamline drug/device design, simulate clinical trials, and eventually to predict the effects of drugs on individuals. The ability of agent-based modeling to encompass multiple scales of biological process as well as spatial considerations, coupled with an intuitive modeling paradigm, suggests that this modeling framework is well suited for translational systems biology. This review describes agent-based modeling and gives examples of its translational applications in the context of acute inflammation and wound healing. PMID:20835989

  16. Incorporating fault tolerance in distributed agent based systems by simulating bio-computing model of stress pathways

    NASA Astrophysics Data System (ADS)

    Bansal, Arvind K.

    2006-05-01

    Bio-computing model of 'Distributed Multiple Intelligent Agents Systems' (BDMIAS) models agents as genes, a cooperating group of agents as operons - commonly regulated groups of genes, and the complex task as a set of interacting pathways such that the pathways involve multiple cooperating operons. The agents (or groups of agents) interact with each other using message passing and pattern based bindings that may reconfigure agent's function temporarily. In this paper, a technique has been described for incorporating fault tolerance in BDMIAS. The scheme is based upon simulating BDMIAS, exploiting the modeling of biological stress pathways, integration of fault avoidance, and distributed fault recovery of the crashed agents. Stress pathways are latent pathways in biological system that gets triggered very quickly, regulate the complex biological system by temporarily regulating or inactivating the undesirable pathways, and are essential to avoid catastrophic failures. Pattern based interaction between messages and agents allow multiple agents to react concurrently in response to single condition change represented by a message broadcast. The fault avoidance exploits the integration of the intelligent processing rate control using message based loop feedback and temporary reconfiguration that alters the data flow between functional modules within an agent, and may alter. The fault recovery exploits the concept of semi passive shadow agents - one on the local machine and other on the remote machine, dynamic polling of machines, logically time stamped messages to avoid message losses, and distributed archiving of volatile part of agent state on distributed machines. Various algorithms have been described.

  17. Object-oriented framework for distributed simulation

    NASA Astrophysics Data System (ADS)

    Hunter, Julia; Carson, John A.; Colley, Martin; Standeven, John; Callaghan, Victor

    1999-06-01

    The benefits of object-oriented technology are widely recognized in software engineering. This paper describes the use of the object-oriented paradigm to create distributed simulations. The University of Essex Robotics and Intelligent Machines group has been carrying out research into distributed vehicle simulation since 1992. Part of this research has focused on the development of simulation systems to assist in the design of robotic vehicles. This paper describes the evolution of these systems, from an early toolkit used for teaching robotics to recent work on using simulation as a design tool in the creation of a new generation of unmanned underwater vehicles. It outlines experiences gained in using PVM, and ongoing research into the use of the emerging High Level Architecture as the basis for these frameworks. The paper concludes with the perceived benefits of adopting object-oriented methodologies as the basis for simulation frameworks.

  18. Agent Based Computing Machine

    DTIC Science & Technology

    2005-12-09

    coordinates as in cellular automata systems. But using biology as a model suggests that the most general systems must provide for partial, but constrained...17. SECURITY CLASSIFICATION OF 118. SECURITY CLASSIFICATION OF 19. SECURITY CLASSIFICATION OF 20. LIMITATION OF ABSTRA REPORT THIS PAGE ABSTRACT...system called an "agent based computing" machine (ABC Machine). The ABC Machine is motivated by cellular biochemistry and it is based upon a concept

  19. Use of an agent-based simulation model to evaluate a mobile-based system for supporting emergency evacuation decision making.

    PubMed

    Tian, Yu; Zhou, Tian-Shu; Yao, Qin; Zhang, Mao; Li, Jing-Song

    2014-12-01

    Recently, mass casualty incidents (MCIs) have been occurring frequently and have gained international attention. There is an urgent need for scientifically proven and effective emergency responses to MCIs, particularly as the severity of incidents is continuously increasing. The emergency response to MCIs is a multi-dimensional and multi-participant dynamic process that changes in real-time. The evacuation decisions that assign casualties to different hospitals in a region are very important and impact both the results of emergency treatment and the efficiency of medical resource utilization. Previously, decisions related to casualty evacuation were made by an incident commander with emergency experience and in accordance with macro emergency guidelines. There are few decision-supporting tools available to reduce the difficulty and psychological pressure associated with the evacuation decisions an incident commander must make. In this study, we have designed a mobile-based system to collect medical and temporal data produced during an emergency response to an MCI. Using this information, our system's decision-making model can provide personal evacuation suggestions that improve the overall outcome of an emergency response. The effectiveness of our system in reducing overall mortality has been validated by an agent-based simulation model established to simulate an emergency response to an MCI.

  20. Development of a three-dimensional multiscale agent-based tumor model: simulating gene-protein interaction profiles, cell phenotypes and multicellular patterns in brain cancer.

    PubMed

    Zhang, Le; Athale, Chaitanya A; Deisboeck, Thomas S

    2007-01-07

    Experimental evidence suggests that epidermal growth factor receptor (EGFR)-mediated activation of the signaling protein phospholipase Cgamma plays a critical role in a cancer cell's phenotypic decision to either proliferate or to migrate at a given point in time. Here, we present a novel three-dimensional multiscale agent-based model to simulate this cellular decision process in the context of a virtual brain tumor. Each tumor cell is equipped with an EGFR gene-protein interaction network module that also connects to a simplified cell cycle description. The simulation results show that over time proliferative and migratory cell populations not only oscillate but also directly impact the spatio-temporal expansion patterns of the entire cancer system. The percentage change in the concentration of the sub-cellular interaction network's molecular components fluctuates, and, for the 'proliferation-to-migration' switch we find that the phenotype triggering molecular profile to some degree varies as the tumor system grows and the microenvironment changes. We discuss potential implications of these findings for experimental and clinical cancer research.

  1. Agent Frameworks for Discrete Event Social Simulations

    DTIC Science & Technology

    2010-03-01

    of a general modeling approach to social simulation that embeds a multi - agent system within a DES framework, and propose several reusable agent... agent system to simulate changes in the beliefs, values, and interests (BVIs) of large social groups (Alt, Jackson, Hudak, & Steven Lieberman, 2010...to events from A. 2.3 Cultural Geography Model The Cultural Geography (CG) Model is an implementation of a DESS that uses an embedded multi

  2. Onyx-Advanced Aeropropulsion Simulation Framework Created

    NASA Technical Reports Server (NTRS)

    Reed, John A.

    2001-01-01

    The Numerical Propulsion System Simulation (NPSS) project at the NASA Glenn Research Center is developing a new software environment for analyzing and designing aircraft engines and, eventually, space transportation systems. Its purpose is to dramatically reduce the time, effort, and expense necessary to design and test jet engines by creating sophisticated computer simulations of an aerospace object or system (refs. 1 and 2). Through a university grant as part of that effort, researchers at the University of Toledo have developed Onyx, an extensible Java-based (Sun Micro-systems, Inc.), objectoriented simulation framework, to investigate how advanced software design techniques can be successfully applied to aeropropulsion system simulation (refs. 3 and 4). The design of Onyx's architecture enables users to customize and extend the framework to add new functionality or adapt simulation behavior as required. It exploits object-oriented technologies, such as design patterns, domain frameworks, and software components, to develop a modular system in which users can dynamically replace components with others having different functionality.

  3. Agent-based Modeling with MATSim for Hazards Evacuation Planning

    NASA Astrophysics Data System (ADS)

    Jones, J. M.; Ng, P.; Henry, K.; Peters, J.; Wood, N. J.

    2015-12-01

    Hazard evacuation planning requires robust modeling tools and techniques, such as least cost distance or agent-based modeling, to gain an understanding of a community's potential to reach safety before event (e.g. tsunami) arrival. Least cost distance modeling provides a static view of the evacuation landscape with an estimate of travel times to safety from each location in the hazard space. With this information, practitioners can assess a community's overall ability for timely evacuation. More information may be needed if evacuee congestion creates bottlenecks in the flow patterns. Dynamic movement patterns are best explored with agent-based models that simulate movement of and interaction between individual agents as evacuees through the hazard space, reacting to potential congestion areas along the evacuation route. The multi-agent transport simulation model MATSim is an agent-based modeling framework that can be applied to hazard evacuation planning. Developed jointly by universities in Switzerland and Germany, MATSim is open-source software written in Java and freely available for modification or enhancement. We successfully used MATSim to illustrate tsunami evacuation challenges in two island communities in California, USA, that are impacted by limited escape routes. However, working with MATSim's data preparation, simulation, and visualization modules in an integrated development environment requires a significant investment of time to develop the software expertise to link the modules and run a simulation. To facilitate our evacuation research, we packaged the MATSim modules into a single application tailored to the needs of the hazards community. By exposing the modeling parameters of interest to researchers in an intuitive user interface and hiding the software complexities, we bring agent-based modeling closer to practitioners and provide access to the powerful visual and analytic information that this modeling can provide.

  4. The Umbra Simulation and Integration Framework Applied to Emergency Response Training

    NASA Technical Reports Server (NTRS)

    Hamilton, Paul Lawrence; Britain, Robert

    2010-01-01

    The Mine Emergency Response Interactive Training Simulation (MERITS) is intended to prepare personnel to manage an emergency in an underground coal mine. The creation of an effective training environment required realistic emergent behavior in response to simulation events and trainee interventions, exploratory modification of miner behavior rules, realistic physics, and incorporation of legacy code. It also required the ability to add rich media to the simulation without conflicting with normal desktop security settings. Our Umbra Simulation and Integration Framework facilitated agent-based modeling of miners and rescuers and made it possible to work with subject matter experts to quickly adjust behavior through script editing, rather than through lengthy programming and recompilation. Integration of Umbra code with the WebKit browser engine allowed the use of JavaScript-enabled local web pages for media support. This project greatly extended the capabilities of Umbra in support of training simulations and has implications for simulations that combine human behavior, physics, and rich media.

  5. Evolutionary game theory using agent-based methods.

    PubMed

    Adami, Christoph; Schossau, Jory; Hintze, Arend

    2016-12-01

    Evolutionary game theory is a successful mathematical framework geared towards understanding the selective pressures that affect the evolution of the strategies of agents engaged in interactions with potential conflicts. While a mathematical treatment of the costs and benefits of decisions can predict the optimal strategy in simple settings, more realistic settings such as finite populations, non-vanishing mutations rates, stochastic decisions, communication between agents, and spatial interactions, require agent-based methods where each agent is modeled as an individual, carries its own genes that determine its decisions, and where the evolutionary outcome can only be ascertained by evolving the population of agents forward in time. While highlighting standard mathematical results, we compare those to agent-based methods that can go beyond the limitations of equations and simulate the complexity of heterogeneous populations and an ever-changing set of interactors. We conclude that agent-based methods can predict evolutionary outcomes where purely mathematical treatments cannot tread (for example in the weak selection-strong mutation limit), but that mathematics is crucial to validate the computational simulations.

  6. Pattern-oriented modeling of agent-based complex systems: Lessons from ecology

    USGS Publications Warehouse

    Grimm, Volker; Revilla, Eloy; Berger, Uta; Jeltsch, Florian; Mooij, Wolf M.; Railsback, Steven F.; Thulke, Hans-Hermann; Weiner, Jacob; Wiegand, Thorsten; DeAngelis, Donald L.

    2005-01-01

    Agent-based complex systems are dynamic networks of many interacting agents; examples include ecosystems, financial markets, and cities. The search for general principles underlying the internal organization of such systems often uses bottom-up simulation models such as cellular automata and agent-based models. No general framework for designing, testing, and analyzing bottom-up models has yet been established, but recent advances in ecological modeling have come together in a general strategy we call pattern-oriented modeling. This strategy provides a unifying framework for decoding the internal organization of agent-based complex systems and may lead toward unifying algorithmic theories of the relation between adaptive behavior and system complexity.

  7. Pattern-oriented modeling of agent-based complex systems: lessons from ecology.

    PubMed

    Grimm, Volker; Revilla, Eloy; Berger, Uta; Jeltsch, Florian; Mooij, Wolf M; Railsback, Steven F; Thulke, Hans-Hermann; Weiner, Jacob; Wiegand, Thorsten; DeAngelis, Donald L

    2005-11-11

    Agent-based complex systems are dynamic networks of many interacting agents; examples include ecosystems, financial markets, and cities. The search for general principles underlying the internal organization of such systems often uses bottom-up simulation models such as cellular automata and agent-based models. No general framework for designing, testing, and analyzing bottom-up models has yet been established, but recent advances in ecological modeling have come together in a general strategy we call pattern-oriented modeling. This strategy provides a unifying framework for decoding the internal organization of agent-based complex systems and may lead toward unifying algorithmic theories of the relation between adaptive behavior and system complexity.

  8. Little by Little Does the Trick: Design and Construction of a Discrete Event Agent-Based Simulation Framework

    DTIC Science & Technology

    2007-12-01

    been shown to be “Turing complete.” More simple and extensible than other constructs used in DES, such as Petri Nets , it makes an ideal tool for...the effects of homogeneity (or non-homogeneity) in a group of agents, be it a group of villagers or a special-forces platoon . When an agent is

  9. A Computational Framework for Bioimaging Simulation

    PubMed Central

    Watabe, Masaki; Arjunan, Satya N. V.; Fukushima, Seiya; Iwamoto, Kazunari; Kozuka, Jun; Matsuoka, Satomi; Shindo, Yuki; Ueda, Masahiro; Takahashi, Koichi

    2015-01-01

    Using bioimaging technology, biologists have attempted to identify and document analytical interpretations that underlie biological phenomena in biological cells. Theoretical biology aims at distilling those interpretations into knowledge in the mathematical form of biochemical reaction networks and understanding how higher level functions emerge from the combined action of biomolecules. However, there still remain formidable challenges in bridging the gap between bioimaging and mathematical modeling. Generally, measurements using fluorescence microscopy systems are influenced by systematic effects that arise from stochastic nature of biological cells, the imaging apparatus, and optical physics. Such systematic effects are always present in all bioimaging systems and hinder quantitative comparison between the cell model and bioimages. Computational tools for such a comparison are still unavailable. Thus, in this work, we present a computational framework for handling the parameters of the cell models and the optical physics governing bioimaging systems. Simulation using this framework can generate digital images of cell simulation results after accounting for the systematic effects. We then demonstrate that such a framework enables comparison at the level of photon-counting units. PMID:26147508

  10. Simulation framework for intelligent transportation systems

    SciTech Connect

    Ewing, T.; Doss, E.; Hanebutte, U.; Tentner, A.

    1996-10-01

    A simulation framework has been developed for a large-scale, comprehensive, scaleable simulation of an Intelligent Transportation System (ITS). The simulator is designed for running on parallel computers and distributed (networked) computer systems, but can run on standalone workstations for smaller simulations. The simulator currently models instrumented smart vehicles with in-vehicle navigation units capable of optimal route planning and Traffic Management Centers (TMC). The TMC has probe vehicle tracking capabilities (display position and attributes of instrumented vehicles), and can provide two-way interaction with traffic to provide advisories and link times. Both the in-vehicle navigation module and the TMC feature detailed graphical user interfaces to support human-factors studies. Realistic modeling of variations of the posted driving speed are based on human factors studies that take into consideration weather, road conditions, driver personality and behavior, and vehicle type. The prototype has been developed on a distributed system of networked UNIX computers but is designed to run on parallel computers, such as ANL`s IBM SP-2, for large-scale problems. A novel feature of the approach is that vehicles are represented by autonomous computer processes which exchange messages with other processes. The vehicles have a behavior model which governs route selection and driving behavior, and can react to external traffic events much like real vehicles. With this approach, the simulation is scaleable to take advantage of emerging massively parallel processor (MPP) systems.

  11. Investigating biocomplexity through the agent-based paradigm

    PubMed Central

    Kaul, Himanshu

    2015-01-01

    Capturing the dynamism that pervades biological systems requires a computational approach that can accommodate both the continuous features of the system environment as well as the flexible and heterogeneous nature of component interactions. This presents a serious challenge for the more traditional mathematical approaches that assume component homogeneity to relate system observables using mathematical equations. While the homogeneity condition does not lead to loss of accuracy while simulating various continua, it fails to offer detailed solutions when applied to systems with dynamically interacting heterogeneous components. As the functionality and architecture of most biological systems is a product of multi-faceted individual interactions at the sub-system level, continuum models rarely offer much beyond qualitative similarity. Agent-based modelling is a class of algorithmic computational approaches that rely on interactions between Turing-complete finite-state machines—or agents—to simulate, from the bottom-up, macroscopic properties of a system. In recognizing the heterogeneity condition, they offer suitable ontologies to the system components being modelled, thereby succeeding where their continuum counterparts tend to struggle. Furthermore, being inherently hierarchical, they are quite amenable to coupling with other computational paradigms. The integration of any agent-based framework with continuum models is arguably the most elegant and precise way of representing biological systems. Although in its nascence, agent-based modelling has been utilized to model biological complexity across a broad range of biological scales (from cells to societies). In this article, we explore the reasons that make agent-based modelling the most precise approach to model biological systems that tend to be non-linear and complex. PMID:24227161

  12. An Active Learning Exercise for Introducing Agent-Based Modeling

    ERIC Educational Resources Information Center

    Pinder, Jonathan P.

    2013-01-01

    Recent developments in agent-based modeling as a method of systems analysis and optimization indicate that students in business analytics need an introduction to the terminology, concepts, and framework of agent-based modeling. This article presents an active learning exercise for MBA students in business analytics that demonstrates agent-based…

  13. Architecting a Simulation Framework for Model Rehosting

    NASA Technical Reports Server (NTRS)

    Madden, Michael M.

    2004-01-01

    The utility of vehicle math models extends beyond human-in-the-loop simulation. It is desirable to deploy a given model across a multitude of applications that target design, analysis, and research. However, the vehicle model alone represents an incomplete simulation. One must also replicate the environment models (e.g., atmosphere, gravity, terrain) to achieve identical vehicle behavior across all applications. Environment models are increasing in complexity and represent a substantial investment to re-engineer for a new application. A software component that can be rehosted in each application is one solution to the deployment problem. The component must encapsulate both the vehicle and environment models. The component must have a well-defined interface that abstracts the bulk of the logic to operate the models. This paper examines the characteristics of a rehostable modeling component from the perspective of a human-in-the-loop simulation framework. The Langley Standard Real-Time Simulation in C++ (LaSRS++) is used as an example. LaSRS++ was recently redesigned to transform its modeling package into a rehostable component.

  14. Argonne simulation framework for intelligent transportation systems

    SciTech Connect

    Ewing, T.; Doss, E.; Hanebutte, U.; Canfield, T.; Brown-VanHoozer, A.; Tentner, A.

    1996-04-01

    A simulation framework has been developed which defines a high-level architecture for a large-scale, comprehensive, scalable simulation of an Intelligent Transportation System (ITS). The simulator is designed to run on parallel computers and distributed (networked) computer systems; however, a version for a stand alone workstation is also available. The ITS simulator includes an Expert Driver Model (EDM) of instrumented ``smart`` vehicles with in-vehicle navigation units. The EDM is capable of performing optimal route planning and communicating with Traffic Management Centers (TMC). A dynamic road map data base is sued for optimum route planning, where the data is updated periodically to reflect any changes in road or weather conditions. The TMC has probe vehicle tracking capabilities (display position and attributes of instrumented vehicles), and can provide 2-way interaction with traffic to provide advisories and link times. Both the in-vehicle navigation module and the TMC feature detailed graphical user interfaces that includes human-factors studies to support safety and operational research. Realistic modeling of variations of the posted driving speed are based on human factor studies that take into consideration weather, road conditions, driver`s personality and behavior and vehicle type. The simulator has been developed on a distributed system of networked UNIX computers, but is designed to run on ANL`s IBM SP-X parallel computer system for large scale problems. A novel feature of the developed simulator is that vehicles will be represented by autonomous computer processes, each with a behavior model which performs independent route selection and reacts to external traffic events much like real vehicles. Vehicle processes interact with each other and with ITS components by exchanging messages. With this approach, one will be able to take advantage of emerging massively parallel processor (MPP) systems.

  15. An agent-based modeling framework linking inflammation and cancer using evolutionary principles: description of a generative hierarchy for the hallmarks of cancer and developing a bridge between mechanism and epidemiological data.

    PubMed

    An, Gary; Kulkarni, Swati

    2015-02-01

    Inflammation plays a critical role in the development and progression of cancer, evident in multiple patient populations manifesting increased, non-resolving inflammation, such as inflammatory bowel disease, viral hepatitis and obesity. Given the complexity of both the inflammatory response and the process of oncogenesis, we utilize principles from the field of Translational Systems Biology to bridge the gap between basic mechanistic knowledge and clinical/epidemiologic data by integrating inflammation and oncogenesis within an agent-based model, the Inflammation and Cancer Agent-based Model (ICABM). The ICABM utilizes two previously published and clinically/epidemiologically validated mechanistic models to demonstrate the role of an increased inflammatory milieu on oncogenesis. Development of the ICABM required the creation of a generative hierarchy of the basic hallmarks of cancer to provide a foundation to ground the plethora of molecular and pathway components currently being studied. The ordering schema emphasizes the essential role of a fitness/selection frame shift to sub-organismal evolution as a basic property of cancer, where the generation of genetic instability as a negative effect for multicellular eukaryotic organisms represents the restoration of genetic plasticity used as an adaptive strategy by colonies of prokaryotic unicellular organisms. Simulations with the ICABM demonstrate that inflammation provides a functional environmental context that drives the shift to sub-organismal evolution, where increasingly inflammatory environments led to increasingly damaged genomes in microtumors (tumors below clinical detection size) and cancers. The flexibility of this platform readily facilitates tailoring the ICABM to specific cancers, their associated mechanisms and available epidemiological data. One clinical example of an epidemiological finding that could be investigated with this platform is the increased incidence of triple negative breast cancers in

  16. An Agent-Based Cockpit Task Management System

    NASA Technical Reports Server (NTRS)

    Funk, Ken

    1997-01-01

    An agent-based program to facilitate Cockpit Task Management (CTM) in commercial transport aircraft is developed and evaluated. The agent-based program called the AgendaManager (AMgr) is described and evaluated in a part-task simulator study using airline pilots.

  17. MCdevelop - a universal framework for Stochastic Simulations

    NASA Astrophysics Data System (ADS)

    Slawinska, M.; Jadach, S.

    2011-03-01

    We present MCdevelop, a universal computer framework for developing and exploiting the wide class of Stochastic Simulations (SS) software. This powerful universal SS software development tool has been derived from a series of scientific projects for precision calculations in high energy physics (HEP), which feature a wide range of functionality in the SS software needed for advanced precision Quantum Field Theory calculations for the past LEP experiments and for the ongoing LHC experiments at CERN, Geneva. MCdevelop is a "spin-off" product of HEP to be exploited in other areas, while it will still serve to develop new SS software for HEP experiments. Typically SS involve independent generation of large sets of random "events", often requiring considerable CPU power. Since SS jobs usually do not share memory it makes them easy to parallelize. The efficient development, testing and running in parallel SS software requires a convenient framework to develop software source code, deploy and monitor batch jobs, merge and analyse results from multiple parallel jobs, even before the production runs are terminated. Throughout the years of development of stochastic simulations for HEP, a sophisticated framework featuring all the above mentioned functionality has been implemented. MCdevelop represents its latest version, written mostly in C++ (GNU compiler gcc). It uses Autotools to build binaries (optionally managed within the KDevelop 3.5.3 Integrated Development Environment (IDE)). It uses the open-source ROOT package for histogramming, graphics and the mechanism of persistency for the C++ objects. MCdevelop helps to run multiple parallel jobs on any computer cluster with NQS-type batch system. Program summaryProgram title:MCdevelop Catalogue identifier: AEHW_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHW_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http

  18. Agent-Based Modeling in Systems Pharmacology.

    PubMed

    Cosgrove, J; Butler, J; Alden, K; Read, M; Kumar, V; Cucurull-Sanchez, L; Timmis, J; Coles, M

    2015-11-01

    Modeling and simulation (M&S) techniques provide a platform for knowledge integration and hypothesis testing to gain insights into biological systems that would not be possible a priori. Agent-based modeling (ABM) is an M&S technique that focuses on describing individual components rather than homogenous populations. This tutorial introduces ABM to systems pharmacologists, using relevant case studies to highlight how ABM-specific strengths have yielded success in the area of preclinical mechanistic modeling.

  19. An agent-based model of collective emotions in online communities

    NASA Astrophysics Data System (ADS)

    Schweitzer, F.; Garcia, D.

    2010-10-01

    We develop an agent-based framework to model the emergence of collective emotions, which is applied to online communities. Agent’s individual emotions are described by their valence and arousal. Using the concept of Brownian agents, these variables change according to a stochastic dynamics, which also considers the feedback from online communication. Agents generate emotional information, which is stored and distributed in a field modeling the online medium. This field affects the emotional states of agents in a non-linear manner. We derive conditions for the emergence of collective emotions, observable in a bimodal valence distribution. Dependent on a saturated or a superlinear feedback between the information field and the agent’s arousal, we further identify scenarios where collective emotions only appear once or in a repeated manner. The analytical results are illustrated by agent-based computer simulations. Our framework provides testable hypotheses about the emergence of collective emotions, which can be verified by data from online communities.

  20. A Large Scale, High Resolution Agent-Based Insurgency Model

    DTIC Science & Technology

    2013-09-30

    for understanding and analyzing human behavior in a civil violence paradigm. This model employed two types of agents: an agent that can become...cognitions and behaviors. Unlike previous agent-based models of civil violence , this work includes the use of a hidden Markov process for simulating...these models can portray real insurgent environments. Keywords simulation · agent based model · insurgency · civil violence · graphics processing

  1. An equation-free approach to agent-based computation: Bifurcation analysis and control of stationary states

    NASA Astrophysics Data System (ADS)

    Siettos, C. I.; Gear, C. W.; Kevrekidis, I. G.

    2012-08-01

    We show how the equation-free approach can be exploited to enable agent-based simulators to perform system-level computations such as bifurcation, stability analysis and controller design. We illustrate these tasks through an event-driven agent-based model describing the dynamic behaviour of many interacting investors in the presence of mimesis. Using short bursts of appropriately initialized runs of the detailed, agent-based simulator, we construct the coarse-grained bifurcation diagram of the (expected) density of agents and investigate the stability of its multiple solution branches. When the mimetic coupling between agents becomes strong enough, the stable stationary state loses its stability at a coarse turning point bifurcation. We also demonstrate how the framework can be used to design a wash-out dynamic controller that stabilizes open-loop unstable stationary states even under model uncertainty.

  2. Dshell++: A Component Based, Reusable Space System Simulation Framework

    NASA Technical Reports Server (NTRS)

    Lim, Christopher S.; Jain, Abhinandan

    2009-01-01

    This paper describes the multi-mission Dshell++ simulation framework for high fidelity, physics-based simulation of spacecraft, robotic manipulation and mobility systems. Dshell++ is a C++/Python library which uses modern script driven object-oriented techniques to allow component reuse and a dynamic run-time interface for complex, high-fidelity simulation of spacecraft and robotic systems. The goal of the Dshell++ architecture is to manage the inherent complexity of physicsbased simulations while supporting component model reuse across missions. The framework provides several features that support a large degree of simulation configurability and usability.

  3. Study of photo-oxidative reactivity of sunscreening agents based on photo-oxidation of uric acid by kinetic Monte Carlo simulation.

    PubMed

    Moradmand Jalali, Hamed; Bashiri, Hadis; Rasa, Hossein

    2015-05-01

    In the present study, the mechanism of free radical production by light-reflective agents in sunscreens (TiO2, ZnO and ZrO2) was obtained by applying kinetic Monte Carlo simulation. The values of the rate constants for each step of the suggested mechanism have been obtained by simulation. The effect of the initial concentration of mineral oxides and uric acid on the rate of uric acid photo-oxidation by irradiation of some sun care agents has been studied. The kinetic Monte Carlo simulation results agree qualitatively with the existing experimental data for the production of free radicals by sun care agents.

  4. Agent-based forward analysis

    SciTech Connect

    Kerekes, Ryan A.; Jiao, Yu; Shankar, Mallikarjun; Potok, Thomas E.; Lusk, Rick M.

    2008-01-01

    We propose software agent-based "forward analysis" for efficient information retrieval in a network of sensing devices. In our approach, processing is pushed to the data at the edge of the network via intelligent software agents rather than pulling data to a central facility for processing. The agents are deployed with a specific query and perform varying levels of analysis of the data, communicating with each other and sending only relevant information back across the network. We demonstrate our concept in the context of face recognition using a wireless test bed comprised of PDA cell phones and laptops. We show that agent-based forward analysis can provide a significant increase in retrieval speed while decreasing bandwidth usage and information overload at the central facility. n

  5. A Multiscale/Multifidelity CFD Framework for Robust Simulations

    NASA Astrophysics Data System (ADS)

    Lee, Seungjoon; Kevrekidis, Yannis; Karniadakis, George

    2015-11-01

    We develop a general CFD framework based on multifidelity simulations to target multiscale problems but also resilience in exascale simulations, where faulty processors may lead to gappy simulated fields. We combine approximation theory and domain decomposition together with machine learning techniques, e.g. co-Kriging, to estimate boundary conditions and minimize communications by performing independent parallel runs. To demonstrate this new simulation approach, we consider two benchmark problems. First, we solve the heat equation with different patches of the domain simulated by finite differences at fine resolution or very low resolution but also with Monte Carlo, hence fusing multifidelity and heterogeneous models to obtain the final answer. Second, we simulate the flow in a driven cavity by fusing finite difference solutions with solutions obtained by dissipative particle dynamics - a coarse-grained molecular dynamics method. In addition to its robustness and resilience, the new framework generalizes previous multiscale approaches (e.g. continuum-atomistic) in a unified parallel computational framework.

  6. A Simulation and Modeling Framework for Space Situational Awareness

    SciTech Connect

    Olivier, S S

    2008-09-15

    This paper describes the development and initial demonstration of a new, integrated modeling and simulation framework, encompassing the space situational awareness enterprise, for quantitatively assessing the benefit of specific sensor systems, technologies and data analysis techniques. The framework is based on a flexible, scalable architecture to enable efficient, physics-based simulation of the current SSA enterprise, and to accommodate future advancements in SSA systems. In particular, the code is designed to take advantage of massively parallel computer systems available, for example, at Lawrence Livermore National Laboratory. The details of the modeling and simulation framework are described, including hydrodynamic models of satellite intercept and debris generation, orbital propagation algorithms, radar cross section calculations, optical brightness calculations, generic radar system models, generic optical system models, specific Space Surveillance Network models, object detection algorithms, orbit determination algorithms, and visualization tools. The use of this integrated simulation and modeling framework on a specific scenario involving space debris is demonstrated.

  7. The Astrophysics Simulation Collaboratory portal: A framework foreffective distributed research

    SciTech Connect

    Bondarescu, Ruxandra; Allen, Gabrielle; Daues, Gregory; Kelly,Ian; Russell, Michael; Seidel, Edward; Shalf, John; Tobias, Malcolm

    2003-03-03

    We describe the motivation, architecture, and implementation of the Astrophysics Simulation Collaboratory (ASC) portal. The ASC project provides a web-based problem solving framework for the astrophysics community that harnesses the capabilities of emerging computational grids.

  8. Data-driven agent-based modeling, with application to rooftop solar adoption

    DOE PAGES

    Zhang, Haifeng; Vorobeychik, Yevgeniy; Letchford, Joshua; ...

    2016-01-25

    Agent-based modeling is commonly used for studying complex system properties emergent from interactions among many agents. We present a novel data-driven agent-based modeling framework applied to forecasting individual and aggregate residential rooftop solar adoption in San Diego county. Our first step is to learn a model of individual agent behavior from combined data of individual adoption characteristics and property assessment. We then construct an agent-based simulation with the learned model embedded in artificial agents, and proceed to validate it using a holdout sequence of collective adoption decisions. We demonstrate that the resulting agent-based model successfully forecasts solar adoption trends andmore » provides a meaningful quantification of uncertainty about its predictions. We utilize our model to optimize two classes of policies aimed at spurring solar adoption: one that subsidizes the cost of adoption, and another that gives away free systems to low-income house- holds. We find that the optimal policies derived for the latter class are significantly more efficacious, whereas the policies similar to the current California Solar Initiative incentive scheme appear to have a limited impact on overall adoption trends.« less

  9. Data-driven agent-based modeling, with application to rooftop solar adoption

    SciTech Connect

    Zhang, Haifeng; Vorobeychik, Yevgeniy; Letchford, Joshua; Lakkaraju, Kiran

    2016-01-25

    Agent-based modeling is commonly used for studying complex system properties emergent from interactions among many agents. We present a novel data-driven agent-based modeling framework applied to forecasting individual and aggregate residential rooftop solar adoption in San Diego county. Our first step is to learn a model of individual agent behavior from combined data of individual adoption characteristics and property assessment. We then construct an agent-based simulation with the learned model embedded in artificial agents, and proceed to validate it using a holdout sequence of collective adoption decisions. We demonstrate that the resulting agent-based model successfully forecasts solar adoption trends and provides a meaningful quantification of uncertainty about its predictions. We utilize our model to optimize two classes of policies aimed at spurring solar adoption: one that subsidizes the cost of adoption, and another that gives away free systems to low-income house- holds. We find that the optimal policies derived for the latter class are significantly more efficacious, whereas the policies similar to the current California Solar Initiative incentive scheme appear to have a limited impact on overall adoption trends.

  10. FACET: A simulation software framework for modeling complex societal processes and interactions

    SciTech Connect

    Christiansen, J. H.

    2000-06-02

    FACET, the Framework for Addressing Cooperative Extended Transactions, was developed at Argonne National Laboratory to address the need for a simulation software architecture in the style of an agent-based approach, but with sufficient robustness, expressiveness, and flexibility to be able to deal with the levels of complexity seen in real-world social situations. FACET is an object-oriented software framework for building models of complex, cooperative behaviors of agents. It can be used to implement simulation models of societal processes such as the complex interplay of participating individuals and organizations engaged in multiple concurrent transactions in pursuit of their various goals. These transactions can be patterned on, for example, clinical guidelines and procedures, business practices, government and corporate policies, etc. FACET can also address other complex behaviors such as biological life cycles or manufacturing processes. To date, for example, FACET has been applied to such areas as land management, health care delivery, avian social behavior, and interactions between natural and social processes in ancient Mesopotamia.

  11. Games and Simulations in Online Learning: Research and Development Frameworks

    ERIC Educational Resources Information Center

    Gibson, David; Aldrich, Clark; Prensky, Marc

    2007-01-01

    Games and Simulations in Online Learning: Research and Development Frameworks examines the potential of games and simulations in online learning, and how the future could look as developers learn to use the emerging capabilities of the Semantic Web. It presents a general understanding of how the Semantic Web will impact education and how games and…

  12. Semantic Extension of Agent-Based Control: The Packing Cell Case Study

    NASA Astrophysics Data System (ADS)

    Vrba, Pavel; Radakovič, Miloslav; Obitko, Marek; Mařík, Vladimír

    The paper reports on the latest R&D activities in the field of agent-based manufacturing control systems. It is documented that this area becomes strongly influenced by the advancements of semantic technologies like the Web Ontology Language. The application of ontologies provides the agents with much more effective means for handling, exchanging and reasoning about the knowledge. The ontology dedicated for semantic description of orders, production processes and material handling tasks in discrete manufacturing domain has been developed. In addition, the framework for integration of this ontology in distributed, agent-based control solutions is given. The Manufacturing Agent Simulation Tool (MAST) is used as a base for pilot implementation of the ontology-powered multiagent control system; the packing cell environment is selected as a case study.

  13. Simulation Framework for Teaching in Modeling and Simulation Areas

    ERIC Educational Resources Information Center

    De Giusti, Marisa Raquel; Lira, Ariel Jorge; Villarreal, Gonzalo Lujan

    2008-01-01

    Simulation is the process of executing a model that describes a system with enough detail; this model has its entities, an internal state, some input and output variables and a list of processes bound to these variables. Teaching a simulation language such as general purpose simulation system (GPSS) is always a challenge, because of the way it…

  14. FDPS: Framework for Developing Particle Simulators

    NASA Astrophysics Data System (ADS)

    Iwasawa, Masaki; Tanikawa, Ataru; Hosono, Natsuki; Nitadori, Keigo; Muranushi, Takayuki; Makino, Junichiro

    2016-04-01

    FDPS provides the necessary functions for efficient parallel execution of particle-based simulations as templates independent of the data structure of particles and the functional form of the interaction. It is used to develop particle-based simulation programs for large-scale distributed-memory parallel supercomputers. FDPS includes templates for domain decomposition, redistribution of particles, and gathering of particle information for interaction calculation. It uses algorithms such as Barnes-Hut tree method for long-range interactions; methods to limit the calculation to neighbor particles are used for short-range interactions. FDPS reduces the time and effort necessary to write a simple, sequential and unoptimized program of O(N^2) calculation cost, and produces compiled programs that will run efficiently on large-scale parallel supercomputers.

  15. A simulation framework for the CMS Track Trigger electronics

    NASA Astrophysics Data System (ADS)

    Amstutz, C.; Magazzù, G.; Weber, M.; Palla, F.

    2015-03-01

    A simulation framework has been developed to test and characterize algorithms, architectures and hardware implementations of the vastly complex CMS Track Trigger for the high luminosity upgrade of the CMS experiment at the Large Hadron Collider in Geneva. High-level SystemC models of all system components have been developed to simulate a portion of the track trigger. The simulation of the system components together with input data from physics simulations allows evaluating figures of merit, like delays or bandwidths, under realistic conditions. The use of SystemC for high-level modelling allows co-simulation with models developed in Hardware Description Languages, e.g. VHDL or Verilog. Therefore, the simulation framework can also be used as a test bench for digital modules developed for the final system.

  16. Software Framework for Advanced Power Plant Simulations

    SciTech Connect

    John Widmann; Sorin Munteanu; Aseem Jain; Pankaj Gupta; Mark Moales; Erik Ferguson; Lewis Collins; David Sloan; Woodrow Fiveland; Yi-dong Lang; Larry Biegler; Michael Locke; Simon Lingard; Jay Yun

    2010-08-01

    This report summarizes the work accomplished during the Phase II development effort of the Advanced Process Engineering Co-Simulator (APECS). The objective of the project is to develop the tools to efficiently combine high-fidelity computational fluid dynamics (CFD) models with process modeling software. During the course of the project, a robust integration controller was developed that can be used in any CAPE-OPEN compliant process modeling environment. The controller mediates the exchange of information between the process modeling software and the CFD software. Several approaches to reducing the time disparity between CFD simulations and process modeling have been investigated and implemented. These include enabling the CFD models to be run on a remote cluster and enabling multiple CFD models to be run simultaneously. Furthermore, computationally fast reduced-order models (ROMs) have been developed that can be 'trained' using the results from CFD simulations and then used directly within flowsheets. Unit operation models (both CFD and ROMs) can be uploaded to a model database and shared between multiple users.

  17. The Uniframe Mobile Agent Based Resource Discovery Service

    DTIC Science & Technology

    2004-06-28

    ABSTRACT see report 15. SUBJECT TERMS 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT Same as Report (SAR) 18 . NUMBER OF PAGES 251...Prescribed by ANSI Std Z39- 18 THE UNIFRAME MOBILE AGENT BASED RESOURCE DISCOVERY SERVICE A Technical Report Report Number TR-CIS... 18 2.1.2.3 The UniFrame System Level Generative Programming Framework (USGPF

  18. Development of an Agent-Based Model (ABM) to Simulate the Immune System and Integration of a Regression Method to Estimate the Key ABM Parameters by Fitting the Experimental Data.

    PubMed

    Tong, Xuming; Chen, Jinghang; Miao, Hongyu; Li, Tingting; Zhang, Le

    2015-01-01

    Agent-based models (ABM) and differential equations (DE) are two commonly used methods for immune system simulation. However, it is difficult for ABM to estimate key parameters of the model by incorporating experimental data, whereas the differential equation model is incapable of describing the complicated immune system in detail. To overcome these problems, we developed an integrated ABM regression model (IABMR). It can combine the advantages of ABM and DE by employing ABM to mimic the multi-scale immune system with various phenotypes and types of cells as well as using the input and output of ABM to build up the Loess regression for key parameter estimation. Next, we employed the greedy algorithm to estimate the key parameters of the ABM with respect to the same experimental data set and used ABM to describe a 3D immune system similar to previous studies that employed the DE model. These results indicate that IABMR not only has the potential to simulate the immune system at various scales, phenotypes and cell types, but can also accurately infer the key parameters like DE model. Therefore, this study innovatively developed a complex system development mechanism that could simulate the complicated immune system in detail like ABM and validate the reliability and efficiency of model like DE by fitting the experimental data.

  19. Development of an Agent-Based Model (ABM) to Simulate the Immune System and Integration of a Regression Method to Estimate the Key ABM Parameters by Fitting the Experimental Data

    PubMed Central

    Tong, Xuming; Chen, Jinghang; Miao, Hongyu; Li, Tingting; Zhang, Le

    2015-01-01

    Agent-based models (ABM) and differential equations (DE) are two commonly used methods for immune system simulation. However, it is difficult for ABM to estimate key parameters of the model by incorporating experimental data, whereas the differential equation model is incapable of describing the complicated immune system in detail. To overcome these problems, we developed an integrated ABM regression model (IABMR). It can combine the advantages of ABM and DE by employing ABM to mimic the multi-scale immune system with various phenotypes and types of cells as well as using the input and output of ABM to build up the Loess regression for key parameter estimation. Next, we employed the greedy algorithm to estimate the key parameters of the ABM with respect to the same experimental data set and used ABM to describe a 3D immune system similar to previous studies that employed the DE model. These results indicate that IABMR not only has the potential to simulate the immune system at various scales, phenotypes and cell types, but can also accurately infer the key parameters like DE model. Therefore, this study innovatively developed a complex system development mechanism that could simulate the complicated immune system in detail like ABM and validate the reliability and efficiency of model like DE by fitting the experimental data. PMID:26535589

  20. Framework for Architecture Trade Study Using MBSE and Performance Simulation

    NASA Technical Reports Server (NTRS)

    Ryan, Jessica; Sarkani, Shahram; Mazzuchim, Thomas

    2012-01-01

    Increasing complexity in modern systems as well as cost and schedule constraints require a new paradigm of system engineering to fulfill stakeholder needs. Challenges facing efficient trade studies include poor tool interoperability, lack of simulation coordination (design parameters) and requirements flowdown. A recent trend toward Model Based System Engineering (MBSE) includes flexible architecture definition, program documentation, requirements traceability and system engineering reuse. As a new domain MBSE still lacks governing standards and commonly accepted frameworks. This paper proposes a framework for efficient architecture definition using MBSE in conjunction with Domain Specific simulation to evaluate trade studies. A general framework is provided followed with a specific example including a method for designing a trade study, defining candidate architectures, planning simulations to fulfill requirements and finally a weighted decision analysis to optimize system objectives.

  1. A Simulation Framework for Exploring Socioecological Dynamics and Sustainability of Settlement Systems Under Stress in Ancient Mesopotamia and Beyond

    NASA Astrophysics Data System (ADS)

    Christiansen, J. H.; Altaweel, M. R.

    2007-12-01

    The presentation will describe an object-oriented, agent-based simulation framework being used to help answer longstanding questions regarding the development trajectories and sustainability of ancient Mesopotamian settlement systems. This multidisciplinary, multi-model framework supports explicit, fine-scale representations of the dynamics of key natural processes such as crop growth, hydrology, and weather, operating concurrently with social processes such as kinship-driven behaviors, farming and herding practices, social stratification, and economic and political activities carried out by social agents that represent individual persons, households, and larger-scale organizations. The framework has allowed us to explore the inherently coupled dynamics of modeled settlements and landscapes that are undergoing diverse social and environmental stresses, both acute and chronic, across multi-generational time spans. The simulation framework was originally used to address single-settlement scenarios, but has recently been extended to begin to address settlement system sustainability issues at sub-regional to regional scale, by introducing a number of new dynamic mechanisms, such as the activities of nomadic communities, that manifest themselves at these larger spatial scales. The framework is flexible and scalable and has broad applicability. It has, for example, recently been adapted to address agroeconomic sustainability of settlement systems in modern rural Thailand, testing the resilience and vulnerability of settled landscapes in the face of such perturbations as large-scale political interventions, global economic shifts, and climate change.

  2. Agent-based power sharing scheme for active hybrid power sources

    NASA Astrophysics Data System (ADS)

    Jiang, Zhenhua

    The active hybridization technique provides an effective approach to combining the best properties of a heterogeneous set of power sources to achieve higher energy density, power density and fuel efficiency. Active hybrid power sources can be used to power hybrid electric vehicles with selected combinations of internal combustion engines, fuel cells, batteries, and/or supercapacitors. They can be deployed in all-electric ships to build a distributed electric power system. They can also be used in a bulk power system to construct an autonomous distributed energy system. An important aspect in designing an active hybrid power source is to find a suitable control strategy that can manage the active power sharing and take advantage of the inherent scalability and robustness benefits of the hybrid system. This paper presents an agent-based power sharing scheme for active hybrid power sources. To demonstrate the effectiveness of the proposed agent-based power sharing scheme, simulation studies are performed for a hybrid power source that can be used in a solar car as the main propulsion power module. Simulation results clearly indicate that the agent-based control framework is effective to coordinate the various energy sources and manage the power/voltage profiles.

  3. Next Generation Simulation Framework for Robotic and Human Space Missions

    NASA Technical Reports Server (NTRS)

    Cameron, Jonathan M.; Balaram, J.; Jain, Abhinandan; Kuo, Calvin; Lim, Christopher; Myint, Steven

    2012-01-01

    The Dartslab team at NASA's Jet Propulsion Laboratory (JPL) has a long history of developing physics-based simulations based on the Darts/Dshell simulation framework that have been used to simulate many planetary robotic missions, such as the Cassini spacecraft and the rovers that are currently driving on Mars. Recent collaboration efforts between the Dartslab team at JPL and the Mission Operations Directorate (MOD) at NASA Johnson Space Center (JSC) have led to significant enhancements to the Dartslab DSENDS (Dynamics Simulator for Entry, Descent and Surface landing) software framework. The new version of DSENDS is now being used for new planetary mission simulations at JPL. JSC is using DSENDS as the foundation for a suite of software known as COMPASS (Core Operations, Mission Planning, and Analysis Spacecraft Simulation) that is the basis for their new human space mission simulations and analysis. In this paper, we will describe the collaborative process with the JPL Dartslab and the JSC MOD team that resulted in the redesign and enhancement of the DSENDS software. We will outline the improvements in DSENDS that simplify creation of new high-fidelity robotic/spacecraft simulations. We will illustrate how DSENDS simulations are assembled and show results from several mission simulations.

  4. Linking MODFLOW with an agent-based land-use model to support decision making

    USGS Publications Warehouse

    Reeves, H.W.; Zellner, M.L.

    2010-01-01

    The U.S. Geological Survey numerical groundwater flow model, MODFLOW, was integrated with an agent-based land-use model to yield a simulator for environmental planning studies. Ultimately, this integrated simulator will be used as a means to organize information, illustrate potential system responses, and facilitate communication within a participatory modeling framework. Initial results show the potential system response to different zoning policy scenarios in terms of the spatial patterns of development, which is referred to as urban form, and consequent impacts on groundwater levels. These results illustrate how the integrated simulator is capable of representing the complexity of the system. From a groundwater modeling perspective, the most important aspect of the integration is that the simulator generates stresses on the groundwater system within the simulation in contrast to the traditional approach that requires the user to specify the stresses through time. Copyright ?? 2010 The Author(s). Journal compilation ?? 2010 National Ground Water Association.

  5. Linking MODFLOW with an agent-based land-use model to support decision making.

    PubMed

    Reeves, Howard W; Zellner, Moira L

    2010-01-01

    The U.S. Geological Survey numerical groundwater flow model, MODFLOW, was integrated with an agent-based land-use model to yield a simulator for environmental planning studies. Ultimately, this integrated simulator will be used as a means to organize information, illustrate potential system responses, and facilitate communication within a participatory modeling framework. Initial results show the potential system response to different zoning policy scenarios in terms of the spatial patterns of development, which is referred to as urban form, and consequent impacts on groundwater levels. These results illustrate how the integrated simulator is capable of representing the complexity of the system. From a groundwater modeling perspective, the most important aspect of the integration is that the simulator generates stresses on the groundwater system within the simulation in contrast to the traditional approach that requires the user to specify the stresses through time.

  6. Frameworks for Assessing the Quality of Modeling and Simulation Capabilities

    NASA Astrophysics Data System (ADS)

    Rider, W. J.

    2012-12-01

    The importance of assuring quality in modeling and simulation has spawned several frameworks for structuring the examination of quality. The format and content of these frameworks provides an emphasis, completeness and flow to assessment activities. I will examine four frameworks that have been developed and describe how they can be improved and applied to a broader set of high consequence applications. Perhaps the first of these frameworks was known as CSAU [Boyack] (code scaling, applicability and uncertainty) used for nuclear reactor safety and endorsed the United States' Nuclear Regulatory Commission (USNRC). This framework was shaped by nuclear safety practice, and the practical structure needed after the Three Mile Island accident. It incorporated the dominant experimental program, the dominant analysis approach, and concerns about the quality of modeling. The USNRC gave it the force of law that made the nuclear industry take it seriously. After the cessation of nuclear weapons' testing the United States began a program of examining the reliability of these weapons without testing. This program utilizes science including theory, modeling, simulation and experimentation to replace the underground testing. The emphasis on modeling and simulation necessitated attention on the quality of these simulations. Sandia developed the PCMM (predictive capability maturity model) to structure this attention [Oberkampf]. PCMM divides simulation into six core activities to be examined and graded relative to the needs of the modeling activity. NASA [NASA] has built yet another framework in response to the tragedy of the space shuttle accidents. Finally, Ben-Haim and Hemez focus upon modeling robustness and predictive fidelity in another approach. These frameworks are similar, and applied in a similar fashion. The adoption of these frameworks at Sandia and NASA has been slow and arduous because the force of law has not assisted acceptance. All existing frameworks are

  7. Introducing FNCS: Framework for Network Co-Simulation

    ScienceCinema

    None

    2016-07-12

    This video provides a basic overview of the PNNL Future Power Grid Initiative-developed Framework for Network Co-Simulation (FNCS). It discusses the increasing amounts of data coming from the power grid, and the need for a tool like FNCS that brings together data, transmission and distribution simulators. Included is a description of the FNCS architecture, and the advantages this new open source tool can bring to grid research and development efforts.

  8. Introducing FNCS: Framework for Network Co-Simulation

    SciTech Connect

    2014-10-23

    This video provides a basic overview of the PNNL Future Power Grid Initiative-developed Framework for Network Co-Simulation (FNCS). It discusses the increasing amounts of data coming from the power grid, and the need for a tool like FNCS that brings together data, transmission and distribution simulators. Included is a description of the FNCS architecture, and the advantages this new open source tool can bring to grid research and development efforts.

  9. Automated numerical simulation of biological pattern formation based on visual feedback simulation framework

    PubMed Central

    Sun, Mingzhu; Xu, Hui; Zeng, Xingjuan; Zhao, Xin

    2017-01-01

    There are various fantastic biological phenomena in biological pattern formation. Mathematical modeling using reaction-diffusion partial differential equation systems is employed to study the mechanism of pattern formation. However, model parameter selection is both difficult and time consuming. In this paper, a visual feedback simulation framework is proposed to calculate the parameters of a mathematical model automatically based on the basic principle of feedback control. In the simulation framework, the simulation results are visualized, and the image features are extracted as the system feedback. Then, the unknown model parameters are obtained by comparing the image features of the simulation image and the target biological pattern. Considering two typical applications, the visual feedback simulation framework is applied to fulfill pattern formation simulations for vascular mesenchymal cells and lung development. In the simulation framework, the spot, stripe, labyrinthine patterns of vascular mesenchymal cells, the normal branching pattern and the branching pattern lacking side branching for lung branching are obtained in a finite number of iterations. The simulation results indicate that it is easy to achieve the simulation targets, especially when the simulation patterns are sensitive to the model parameters. Moreover, this simulation framework can expand to other types of biological pattern formation. PMID:28225811

  10. Hierarchical petascale simulation framework for stress corrosion cracking

    NASA Astrophysics Data System (ADS)

    Vashishta, P.; Kalia, R. K.; Nakano, A.; Kaxiras, E.; Grama, A.; Lu, G.; Eidenbenz, S.; Voter, A. F.; Hood, R. Q.; Moriarty, J. A.; Yang, L. H.

    2008-07-01

    We are developing a scalable parallel and distributed computational framework consisting of methods, algorithms, and integrated software tools for multi-terascle-to-petascale simulations of stress corrosion cracking (SCC) with quantum-level accuracy. We have performed multimillion- to billion-atom molecular dynamics (MD) simulations of deformation, flow, and fracture in amorphous silica with interatomic potentials and forces validated by density functional theory (DFT) calculations. Optimized potentials have been developed to study sulfur embrittlement of nickel with multimillion-to-multibillion atom MD simulations based on DFT and temperature dependent model generalized pseudopotential theory. We have also developed a quasi-continuum method embedded with quantum simulations based on DFT to reach macroscopic length scales and an accelerated molecular dynamics scheme to reach macroscopic time scales in simulations of solid-fluid interfaces that are relevant to SCC. A hybrid MD and mesoscale lattice Boltzmann simulation algorithm is being designed to study fluid flow through cracks.

  11. Introduction of a Framework for Dynamic Knowledge Representation of the Control Structure of Transplant Immunology: Employing the Power of Abstraction with a Solid Organ Transplant Agent-Based Model

    PubMed Central

    An, Gary

    2015-01-01

    Agent-based modeling has been used to characterize the nested control loops and non-linear dynamics associated with inflammatory and immune responses, particularly as a means of visualizing putative mechanistic hypotheses. This process is termed dynamic knowledge representation and serves a critical role in facilitating the ability to test and potentially falsify hypotheses in the current data- and hypothesis-rich biomedical research environment. Importantly, dynamic computational modeling aids in identifying useful abstractions, a fundamental scientific principle that pervades the physical sciences. Recognizing the critical scientific role of abstraction provides an intellectual and methodological counterweight to the tendency in biology to emphasize comprehensive description as the primary manifestation of biological knowledge. Transplant immunology represents yet another example of the challenge of identifying sufficient understanding of the inflammatory/immune response in order to develop and refine clinically effective interventions. Advances in immunosuppressive therapies have greatly improved solid organ transplant (SOT) outcomes, most notably by reducing and treating acute rejection. The end goal of these transplant immune strategies is to facilitate effective control of the balance between regulatory T cells and the effector/cytotoxic T-cell populations in order to generate, and ideally maintain, a tolerant phenotype. Characterizing the dynamics of immune cell populations and the interactive feedback loops that lead to graft rejection or tolerance is extremely challenging, but is necessary if rational modulation to induce transplant tolerance is to be accomplished. Herein is presented the solid organ agent-based model (SOTABM) as an initial example of an agent-based model (ABM) that abstractly reproduces the cellular and molecular components of the immune response to SOT. Despite its abstract nature, the SOTABM is able to qualitatively reproduce acute

  12. Introduction of a Framework for Dynamic Knowledge Representation of the Control Structure of Transplant Immunology: Employing the Power of Abstraction with a Solid Organ Transplant Agent-Based Model.

    PubMed

    An, Gary

    2015-01-01

    Agent-based modeling has been used to characterize the nested control loops and non-linear dynamics associated with inflammatory and immune responses, particularly as a means of visualizing putative mechanistic hypotheses. This process is termed dynamic knowledge representation and serves a critical role in facilitating the ability to test and potentially falsify hypotheses in the current data- and hypothesis-rich biomedical research environment. Importantly, dynamic computational modeling aids in identifying useful abstractions, a fundamental scientific principle that pervades the physical sciences. Recognizing the critical scientific role of abstraction provides an intellectual and methodological counterweight to the tendency in biology to emphasize comprehensive description as the primary manifestation of biological knowledge. Transplant immunology represents yet another example of the challenge of identifying sufficient understanding of the inflammatory/immune response in order to develop and refine clinically effective interventions. Advances in immunosuppressive therapies have greatly improved solid organ transplant (SOT) outcomes, most notably by reducing and treating acute rejection. The end goal of these transplant immune strategies is to facilitate effective control of the balance between regulatory T cells and the effector/cytotoxic T-cell populations in order to generate, and ideally maintain, a tolerant phenotype. Characterizing the dynamics of immune cell populations and the interactive feedback loops that lead to graft rejection or tolerance is extremely challenging, but is necessary if rational modulation to induce transplant tolerance is to be accomplished. Herein is presented the solid organ agent-based model (SOTABM) as an initial example of an agent-based model (ABM) that abstractly reproduces the cellular and molecular components of the immune response to SOT. Despite its abstract nature, the SOTABM is able to qualitatively reproduce acute

  13. Addressing the translational dilemma: dynamic knowledge representation of inflammation using agent-based modeling.

    PubMed

    An, Gary; Christley, Scott

    2012-01-01

    Given the panoply of system-level diseases that result from disordered inflammation, such as sepsis, atherosclerosis, cancer, and autoimmune disorders, understanding and characterizing the inflammatory response is a key target of biomedical research. Untangling the complex behavioral configurations associated with a process as ubiquitous as inflammation represents a prototype of the translational dilemma: the ability to translate mechanistic knowledge into effective therapeutics. A critical failure point in the current research environment is a throughput bottleneck at the level of evaluating hypotheses of mechanistic causality; these hypotheses represent the key step toward the application of knowledge for therapy development and design. Addressing the translational dilemma will require utilizing the ever-increasing power of computers and computational modeling to increase the efficiency of the scientific method in the identification and evaluation of hypotheses of mechanistic causality. More specifically, development needs to focus on facilitating the ability of non-computer trained biomedical researchers to utilize and instantiate their knowledge in dynamic computational models. This is termed "dynamic knowledge representation." Agent-based modeling is an object-oriented, discrete-event, rule-based simulation method that is well suited for biomedical dynamic knowledge representation. Agent-based modeling has been used in the study of inflammation at multiple scales. The ability of agent-based modeling to encompass multiple scales of biological process as well as spatial considerations, coupled with an intuitive modeling paradigm, suggest that this modeling framework is well suited for addressing the translational dilemma. This review describes agent-based modeling, gives examples of its applications in the study of inflammation, and introduces a proposed general expansion of the use of modeling and simulation to augment the generation and evaluation of knowledge

  14. A Computational Framework for Efficient Low Temperature Plasma Simulations

    NASA Astrophysics Data System (ADS)

    Verma, Abhishek Kumar; Venkattraman, Ayyaswamy

    2016-10-01

    Over the past years, scientific computing has emerged as an essential tool for the investigation and prediction of low temperature plasmas (LTP) applications which includes electronics, nanomaterial synthesis, metamaterials etc. To further explore the LTP behavior with greater fidelity, we present a computational toolbox developed to perform LTP simulations. This framework will allow us to enhance our understanding of multiscale plasma phenomenon using high performance computing tools mainly based on OpenFOAM FVM distribution. Although aimed at microplasma simulations, the modular framework is able to perform multiscale, multiphysics simulations of physical systems comprises of LTP. Some salient introductory features are capability to perform parallel, 3D simulations of LTP applications on unstructured meshes. Performance of the solver is tested based on numerical results assessing accuracy and efficiency of benchmarks for problems in microdischarge devices. Numerical simulation of microplasma reactor at atmospheric pressure with hemispherical dielectric coated electrodes will be discussed and hence, provide an overview of applicability and future scope of this framework.

  15. An example-based brain MRI simulation framework

    NASA Astrophysics Data System (ADS)

    He, Qing; Roy, Snehashis; Jog, Amod; Pham, Dzung L.

    2015-03-01

    The simulation of magnetic resonance (MR) images plays an important role in the validation of image analysis algorithms such as image segmentation, due to lack of sufficient ground truth in real MR images. Previous work on MRI simulation has focused on explicitly modeling the MR image formation process. However, because of the overwhelming complexity of MR acquisition these simulations must involve simplifications and approximations that can result in visually unrealistic simulated images. In this work, we describe an example-based simulation framework, which uses an "atlas" consisting of an MR image and its anatomical models derived from the hard segmentation. The relationships between the MR image intensities and its anatomical models are learned using a patch-based regression that implicitly models the physics of the MR image formation. Given the anatomical models of a new brain, a new MR image can be simulated using the learned regression. This approach has been extended to also simulate intensity inhomogeneity artifacts based on the statistical model of training data. Results show that the example based MRI simulation method is capable of simulating different image contrasts and is robust to different choices of atlas. The simulated images resemble real MR images more than simulations produced by a physics-based model.

  16. Applications of Agent Based Approaches in Business (A Three Essay Dissertation)

    ERIC Educational Resources Information Center

    Prawesh, Shankar

    2013-01-01

    The goal of this dissertation is to investigate the enabling role that agent based simulation plays in business and policy. The aforementioned issue has been addressed in this dissertation through three distinct, but related essays. The first essay is a literature review of different research applications of agent based simulation in various…

  17. A Multi-Paradigm Modeling Framework to Simulate Dynamic Reciprocity in a Bioreactor

    PubMed Central

    Kaul, Himanshu; Cui, Zhanfeng; Ventikos, Yiannis

    2013-01-01

    Despite numerous technology advances, bioreactors are still mostly utilized as functional black-boxes where trial and error eventually leads to the desirable cellular outcome. Investigators have applied various computational approaches to understand the impact the internal dynamics of such devices has on overall cell growth, but such models cannot provide a comprehensive perspective regarding the system dynamics, due to limitations inherent to the underlying approaches. In this study, a novel multi-paradigm modeling platform capable of simulating the dynamic bidirectional relationship between cells and their microenvironment is presented. Designing the modeling platform entailed combining and coupling fully an agent-based modeling platform with a transport phenomena computational modeling framework. To demonstrate capability, the platform was used to study the impact of bioreactor parameters on the overall cell population behavior and vice versa. In order to achieve this, virtual bioreactors were constructed and seeded. The virtual cells, guided by a set of rules involving the simulated mass transport inside the bioreactor, as well as cell-related probabilistic parameters, were capable of displaying an array of behaviors such as proliferation, migration, chemotaxis and apoptosis. In this way the platform was shown to capture not only the impact of bioreactor transport processes on cellular behavior but also the influence that cellular activity wields on that very same local mass transport, thereby influencing overall cell growth. The platform was validated by simulating cellular chemotaxis in a virtual direct visualization chamber and comparing the simulation with its experimental analogue. The results presented in this paper are in agreement with published models of similar flavor. The modeling platform can be used as a concept selection tool to optimize bioreactor design specifications. PMID:23555740

  18. In-situ Data Analysis Framework for ACME Land Simulations

    NASA Astrophysics Data System (ADS)

    Wang, D.; Yao, C.; Jia, Y.; Steed, C.; Atchley, S.

    2015-12-01

    The realistic representation of key biogeophysical and biogeochemical functions is the fundamental of process-based ecosystem models. Investigating the behavior of those ecosystem functions within real-time model simulation can be a very challenging due to the complex of both model and software structure of an environmental model, such as the Accelerated Climate Model for Energy (ACME) Land Model (ALM). In this research, author will describe the urgent needs and challenges for in-situ data analysis for ALM simulations, and layouts our methods/strategies to meet these challenges. Specifically, an in-situ data analysis framework is designed to allow users interactively observe the biogeophyical and biogeochemical process during ALM simulation. There are two key components in this framework, automatically instrumented ecosystem simulation, in-situ data communication and large-scale data exploratory toolkit. This effort is developed by leveraging several active projects, including scientific unit testing platform, common communication interface and extreme-scale data exploratory toolkit. Authors believe that, based on advanced computing technologies, such as compiler-based software system analysis, automatic code instrumentation, and in-memory data transport, this software system provides not only much needed capability for real-time observation and in-situ data analytics for environmental model simulation, but also the potentials for in-situ model behavior adjustment via simulation steering.

  19. A hybrid agent-based approach for modeling microbiological systems.

    PubMed

    Guo, Zaiyi; Sloot, Peter M A; Tay, Joc Cing

    2008-11-21

    Models for systems biology commonly adopt Differential Equations or Agent-Based modeling approaches for simulating the processes as a whole. Models based on differential equations presuppose phenomenological intracellular behavioral mechanisms, while models based on Multi-Agent approach often use directly translated, and quantitatively less precise if-then logical rule constructs. We propose an extendible systems model based on a hybrid agent-based approach where biological cells are modeled as individuals (agents) while molecules are represented by quantities. This hybridization in entity representation entails a combined modeling strategy with agent-based behavioral rules and differential equations, thereby balancing the requirements of extendible model granularity with computational tractability. We demonstrate the efficacy of this approach with models of chemotaxis involving an assay of 10(3) cells and 1.2x10(6) molecules. The model produces cell migration patterns that are comparable to laboratory observations.

  20. Symphony: a framework for accurate and holistic WSN simulation.

    PubMed

    Riliskis, Laurynas; Osipov, Evgeny

    2015-02-25

    Research on wireless sensor networks has progressed rapidly over the last decade, and these technologies have been widely adopted for both industrial and domestic uses. Several operating systems have been developed, along with a multitude of network protocols for all layers of the communication stack. Industrial Wireless Sensor Network (WSN) systems must satisfy strict criteria and are typically more complex and larger in scale than domestic systems. Together with the non-deterministic behavior of network hardware in real settings, this greatly complicates the debugging and testing of WSN functionality. To facilitate the testing, validation, and debugging of large-scale WSN systems, we have developed a simulation framework that accurately reproduces the processes that occur inside real equipment, including both hardware- and software-induced delays. The core of the framework consists of a virtualized operating system and an emulated hardware platform that is integrated with the general purpose network simulator ns-3. Our framework enables the user to adjust the real code base as would be done in real deployments and also to test the boundary effects of different hardware components on the performance of distributed applications and protocols. Additionally we have developed a clock emulator with several different skew models and a component that handles sensory data feeds. The new framework should substantially shorten WSN application development cycles.

  1. Symphony: A Framework for Accurate and Holistic WSN Simulation

    PubMed Central

    Riliskis, Laurynas; Osipov, Evgeny

    2015-01-01

    Research on wireless sensor networks has progressed rapidly over the last decade, and these technologies have been widely adopted for both industrial and domestic uses. Several operating systems have been developed, along with a multitude of network protocols for all layers of the communication stack. Industrial Wireless Sensor Network (WSN) systems must satisfy strict criteria and are typically more complex and larger in scale than domestic systems. Together with the non-deterministic behavior of network hardware in real settings, this greatly complicates the debugging and testing of WSN functionality. To facilitate the testing, validation, and debugging of large-scale WSN systems, we have developed a simulation framework that accurately reproduces the processes that occur inside real equipment, including both hardware- and software-induced delays. The core of the framework consists of a virtualized operating system and an emulated hardware platform that is integrated with the general purpose network simulator ns-3. Our framework enables the user to adjust the real code base as would be done in real deployments and also to test the boundary effects of different hardware components on the performance of distributed applications and protocols. Additionally we have developed a clock emulator with several different skew models and a component that handles sensory data feeds. The new framework should substantially shorten WSN application development cycles. PMID:25723144

  2. A Framework for Modeling and Simulation of the Artificial

    DTIC Science & Technology

    2012-01-01

    style of symphonic, folk, or jazz . A musical performance can also therefore have an ensemble of orches- tra, small group, or soloist. With no...constraint m3 :musical-performance (==> (equale (e@ style) jazz ) (or (equale (e@ ensemble) small-group) (equale (e@ ensemble) orchestra)))) (orv (ifv...equale (e@ style) jazz ) (assert! (orv (equale (e@ ensemble) orchestra) (equale (e@ ensemble) small-group))))) A Framework for Modeling and Simulation of

  3. Etomica: an object-oriented framework for molecular simulation.

    PubMed

    Schultz, Andrew J; Kofke, David A

    2015-03-30

    We describe the design of an object-oriented library of software components that are suitable for constructing simulations of systems of interacting particles. The emphasis of the discussion is on the general design of the components and how they interact, and less on details of the programming interface or its implementation. Example code is provided as an aid to understanding object-oriented programming structures and to demonstrate how the framework is applied.

  4. Design and Performance Frameworks for Constructing Problem-Solving Simulations

    PubMed Central

    Stevens, Ron; Palacio-Cayetano, Joycelin

    2003-01-01

    Rapid advancements in hardware, software, and connectivity are helping to shorten the times needed to develop computer simulations for science education. These advancements, however, have not been accompanied by corresponding theories of how best to design and use these technologies for teaching, learning, and testing. Such design frameworks ideally would be guided less by the strengths/limitations of the presentation media and more by cognitive analyses detailing the goals of the tasks, the needs and abilities of students, and the resulting decision outcomes needed by different audiences. This article describes a problem-solving environment and associated theoretical framework for investigating how students select and use strategies as they solve complex science problems. A framework is first described for designing on-line problem spaces that highlights issues of content, scale, cognitive complexity, and constraints. While this framework was originally designed for medical education, it has proven robust and has been successfully applied to learning environments from elementary school through medical school. Next, a similar framework is detailed for collecting student performance and progress data that can provide evidence of students' strategic thinking and that could potentially be used to accelerate student progress. Finally, experimental validation data are presented that link strategy selection and use with other metrics of scientific reasoning and student achievement. PMID:14506505

  5. Agent-based model for the h-index - exact solution

    NASA Astrophysics Data System (ADS)

    Żogała-Siudem, Barbara; Siudem, Grzegorz; Cena, Anna; Gagolewski, Marek

    2016-01-01

    Hirsch's h-index is perhaps the most popular citation-based measure of scientific excellence. In 2013, Ionescu and Chopard proposed an agent-based model describing a process for generating publications and citations in an abstract scientific community [G. Ionescu, B. Chopard, Eur. Phys. J. B 86, 426 (2013)]. Within such a framework, one may simulate a scientist's activity, and - by extension - investigate the whole community of researchers. Even though the Ionescu and Chopard model predicts the h-index quite well, the authors provided a solution based solely on simulations. In this paper, we complete their results with exact, analytic formulas. What is more, by considering a simplified version of the Ionescu-Chopard model, we obtained a compact, easy to compute formula for the h-index. The derived approximate and exact solutions are investigated on a simulated and real-world data sets.

  6. EIC detector simulations in FairRoot framework

    NASA Astrophysics Data System (ADS)

    Kiselev, Alexander; eRHIC task force Team

    2013-10-01

    The long-term RHIC facility upgrade plan foresees the addition of a high-energy electron beam to the existing hadron accelerator complex thus converting RHIC into an Electron-Ion Collider (eRHIC). A dedicated EIC detector, designed to efficiently register and identify deep inelastic electron scattering (DIS) processes in a wide range of center-of-mass energies is one of the key elements of this upgrade. Detailed Monte-Carlo studies are needed to optimize EIC detector components and to fine tune their design. The simulation package foreseen for this purpose (EicRoot) is based on the FairRoot framework developed and maintained at the GSI. A feature of this framework is its level of flexibility, allowing one to switch easily between different geometry (ROOT, GEANT) and transport (GEANT3, GEANT4, FLUKA) models. Apart from providing a convenient simulation environment the framework includes basic tools for visualization and allows for easy sharing of event reconstruction codes between higher level experiment-specific applications. The description of the main EicRoot features and first simulation results will be the main focus of the talk.

  7. A new framework for simulating forced homogeneous buoyant turbulent flows

    NASA Astrophysics Data System (ADS)

    Carroll, Phares L.; Blanquart, Guillaume

    2015-06-01

    This work proposes a new simulation methodology to study variable density turbulent buoyant flows. The mathematical framework, referred to as homogeneous buoyant turbulence, relies on a triply periodic domain and incorporates numerical forcing methods commonly used in simulation studies of homogeneous, isotropic flows. In order to separate the effects due to buoyancy from those due to large-scale gradients, the linear scalar forcing technique is used to maintain the scalar variance at a constant value. Two sources of kinetic energy production are considered in the momentum equation, namely shear via an isotropic forcing term and buoyancy via the gravity term. The simulation framework is designed such that the four dimensionless parameters of importance in buoyant mixing, namely the Reynolds, Richardson, Atwood, and Schmidt numbers, can be independently varied and controlled. The framework is used to interrogate fully non-buoyant, fully buoyant, and partially buoyant turbulent flows. The results show that the statistics of the scalar fields (mixture fraction and density) are not influenced by the energy production mechanism (shear vs. buoyancy). On the other hand, the velocity field exhibits anisotropy, namely a larger variance in the direction of gravity which is associated with a statistical dependence of the velocity component on the local fluid density.

  8. Adding ecosystem function to agent-based land use models

    PubMed Central

    Yadav, V.; Del Grosso, S.J.; Parton, W.J.; Malanson, G.P.

    2015-01-01

    The objective of this paper is to examine issues in the inclusion of simulations of ecosystem functions in agent-based models of land use decision-making. The reasons for incorporating these simulations include local interests in land fertility and global interests in carbon sequestration. Biogeochemical models are needed in order to calculate such fluxes. The Century model is described with particular attention to the land use choices that it can encompass. When Century is applied to a land use problem the combinatorial choices lead to a potentially unmanageable number of simulation runs. Century is also parameter-intensive. Three ways of including Century output in agent-based models, ranging from separately calculated look-up tables to agents running Century within the simulation, are presented. The latter may be most efficient, but it moves the computing costs to where they are most problematic. Concern for computing costs should not be a roadblock. PMID:26191077

  9. Agent-based modeling of host–pathogen systems: The successes and challenges

    PubMed Central

    Bauer, Amy L.; Beauchemin, Catherine A.A.; Perelson, Alan S.

    2009-01-01

    Agent-based models have been employed to describe numerous processes in immunology. Simulations based on these types of models have been used to enhance our understanding of immunology and disease pathology. We review various agent-based models relevant to host–pathogen systems and discuss their contributions to our understanding of biological processes. We then point out some limitations and challenges of agent-based models and encourage efforts towards reproducibility and model validation. PMID:20161146

  10. A Conceptual Framework for Representing Human Behavior Characteristics in a System of Systems Agent-based Survivability Simulation-Intelligent Networks

    DTIC Science & Technology

    2014-10-17

    of their similarity. In equation 11, a node awareness of other nodes in a MANET is the negation of cooperation in the sense that it is the fuzzy...Khatibi, S. & Rohani, R. ( ). Quorum -Based Neighbor Discovery in Self-Organized Cognitive MANET 21st Annual IEEE International Symposium on

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

    SciTech Connect

    Jiang, Yi; He, Kejing; Dong, Shoubin

    2009-01-01

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

  12. Framework Application for Core Edge Transport Simulation (FACETS)

    SciTech Connect

    Krasheninnikov, Sergei; Pigarov, Alexander

    2011-10-15

    The FACETS (Framework Application for Core-Edge Transport Simulations) project of Scientific Discovery through Advanced Computing (SciDAC) Program was aimed at providing a high-fidelity whole-tokamak modeling for the U.S. magnetic fusion energy program and ITER through coupling separate components for each of the core region, edge region, and wall, with realistic plasma particles and power sources and turbulent transport simulation. The project also aimed at developing advanced numerical algorithms, efficient implicit coupling methods, and software tools utilizing the leadership class computing facilities under Advanced Scientific Computing Research (ASCR). The FACETS project was conducted by a multi-discipline, multi-institutional teams, the Lead PI was J.R. Cary (Tech-X Corp.). In the FACETS project, the Applied Plasma Theory Group at the MAE Department of UCSD developed the Wall and Plasma-Surface Interaction (WALLPSI) module, performed its validation against experimental data, and integrated it into the developed framework. WALLPSI is a one-dimensional, coarse grained, reaction/advection/diffusion code applied to each material boundary cell in the common modeling domain for a tokamak. It incorporates an advanced model for plasma particle transport and retention in the solid matter of plasma facing components, simulation of plasma heat power load handling, calculation of erosion/deposition, and simulation of synergistic effects in strong plasma-wall coupling.

  13. Component Framework for Coupled Integrated Fusion Plasma Simulation

    SciTech Connect

    Elwasif, Wael R; Bernholdt, David E; Berry, Lee A; Batchelor, Donald B

    2007-01-01

    Fusion Successful simulation of the complex physics that affect magnetically confined fusion plasma remains an important target milestone towards the development of viable fusion energy. Major advances in the underlying physics formulations, mathematical modeling, and computational tools and techniques are needed to enable a complete fusion simulation on the emerging class of large scale capability parallel computers that are coming on-line in the next few years. Several pilot projects are currently being undertaken to explore different (partial) code integration and coupling problems, and possible solutions that may guide the larger integration endeavor. In this paper, we present the design and implementation details of one such project, a component based approach to couple existing codes to model the interaction between high power radio frequency (RF) electromagnetic waves, and magnetohydrodynamics (MHD) aspects of the burning plasma. The framework and component design utilize a light coupling approach based on high level view of constituent codes that facilitates rapid incorporation of new components into the integrated simulation framework. The work illustrates the viability of the light coupling approach to better understand physics and stand-alone computer code dependencies and interactions, as a precursor to a more tightly coupled integrated simulation environment.

  14. Modeling the Population Dynamics of Antibiotic-Resistant Bacteria:. AN Agent-Based Approach

    NASA Astrophysics Data System (ADS)

    Murphy, James T.; Walshe, Ray; Devocelle, Marc

    The response of bacterial populations to antibiotic treatment is often a function of a diverse range of interacting factors. In order to develop strategies to minimize the spread of antibiotic resistance in pathogenic bacteria, a sound theoretical understanding of the systems of interactions taking place within a colony must be developed. The agent-based approach to modeling bacterial populations is a useful tool for relating data obtained at the molecular and cellular level with the overall population dynamics. Here we demonstrate an agent-based model, called Micro-Gen, which has been developed to simulate the growth and development of bacterial colonies in culture. The model also incorporates biochemical rules and parameters describing the kinetic interactions of bacterial cells with antibiotic molecules. Simulations were carried out to replicate the development of methicillin-resistant S. aureus (MRSA) colonies growing in the presence of antibiotics. The model was explored to see how the properties of the system emerge from the interactions of the individual bacterial agents in order to achieve a better mechanistic understanding of the population dynamics taking place. Micro-Gen provides a good theoretical framework for investigating the effects of local environmental conditions and cellular properties on the response of bacterial populations to antibiotic exposure in the context of a simulated environment.

  15. The PandaRoot framework for simulation, reconstruction and analysis

    NASA Astrophysics Data System (ADS)

    Spataro, Stefano; PANDA Collaboration

    2011-12-01

    The PANDA experiment at the future facility FAIR will study anti-proton proton and anti-proton nucleus collisions in a beam momentum range from 2 GeV/c up to 15 GeV/c. The PandaRoot framework is part of the FairRoot project, a common software framework for the future FAIR experiments, and is currently used to simulate detector performances and to evaluate different detector concepts. It is based on the packages ROOT and Virtual MonteCarlo with Geant3 and Geant4. Different reconstruction algorithms for tracking and particle identification are under development and optimization, in order to achieve the performance requirements of the experiment. In the central tracker a first track fit is performed using a conformal map transformation based on a helix assumption, then the track is used as input for a Kalman Filter (package genfit), using GEANE as track follower. The track is then correlated to the pid detectors (e.g. Cerenkov detectors, EM Calorimeter or Muon Chambers) to evaluate a global particle identification probability, using a Bayesian approach or multivariate methods. Further implemented packages in PandaRoot are: the analysis tools framework Rho, the kinematic fitter package for vertex and mass constraint fits, and a fast simulation code based upon parametrized detector responses. PandaRoot was also tested on an Alien-based GRID infrastructure. The contribution will report about the status of PandaRoot and show some example results for analysis of physics benchmark channels.

  16. Seawater Pervaporation through Zeolitic Imidazolate Framework Membranes: Atomistic Simulation Study.

    PubMed

    Gupta, Krishna M; Qiao, Zhiwei; Zhang, Kang; Jiang, Jianwen

    2016-06-01

    An atomistic simulation study is reported for seawater pervaporation through five zeolitic imidazolate framework (ZIF) membranes including ZIF-8, -93, -95, -97, and -100. Salt rejection in the five ZIFs is predicted to be 100%. With the largest aperture, ZIF-100 possesses the highest water permeability of 5 × 10(-4) kg m/(m(2) h bar), which is substantially higher compared to commercial reverse osmosis membranes, as well as zeolite and graphene oxide pervaporation membranes. In ZIF-8, -93, -95, and -97 with similar aperture size, water flux is governed by framework hydrophobicity/hydrophilicity; in hydrophobic ZIF-8 and -95, water flux is higher than in hydrophilic ZIF-93 and -97. Furthermore, water molecules in ZIF-93 move slowly and remain in the membrane for a long time but undergo to-and-fro motion in ZIF-100. The lifetime of hydrogen bonds in ZIF-93 is found to be longer than in ZIF-100. This simulation study quantitatively elucidates the dynamic and structural properties of water in ZIF membranes, identifies the key governing factors (aperture size and framework hydrophobicity/hydrophilicity), and suggests that ZIF-100 is an intriguing membrane for seawater pervaporation.

  17. Agent-based enterprise integration

    SciTech Connect

    N. M. Berry; C. M. Pancerella

    1998-12-01

    The authors are developing and deploying software agents in an enterprise information architecture such that the agents manage enterprise resources and facilitate user interaction with these resources. The enterprise agents are built on top of a robust software architecture for data exchange and tool integration across heterogeneous hardware and software. The resulting distributed multi-agent system serves as a method of enhancing enterprises in the following ways: providing users with knowledge about enterprise resources and applications; accessing the dynamically changing enterprise; locating enterprise applications and services; and improving search capabilities for applications and data. Furthermore, agents can access non-agents (i.e., databases and tools) through the enterprise framework. The ultimate target of the effort is the user; they are attempting to increase user productivity in the enterprise. This paper describes their design and early implementation and discusses the planned future work.

  18. Agent-based enterprise integration

    SciTech Connect

    N. M. Berry; C. M. Pancerella

    1999-05-01

    The authors are developing and deploying software agents in an enterprise information architecture such that the agents manage enterprise resources and facilitate user interaction with these resources. Their enterprise agents are built on top of a robust software architecture for data exchange and tool integration across heterogeneous hardware and software. The resulting distributed multi-agent system serves as a method of enhancing enterprises in the following ways: providing users with knowledge about enterprise resources and applications; accessing the dynamically changing enterprise; intelligently locating enterprise applications and services; and improving search capabilities for applications and data. Furthermore, agents can access non-agents (i.e., databases and tools) through the enterprise framework. The ultimate target of their effort is the user; they are attempting to increase user productivity in the enterprise. This paper describes their design and early implementation and discusses their planned future work.

  19. A modeling and simulation framework for electrokinetic nanoparticle treatment

    NASA Astrophysics Data System (ADS)

    Phillips, James

    2011-12-01

    The focus of this research is to model and provide a simulation framework for the packing of differently sized spheres within a hard boundary. The novel contributions of this dissertation are the cylinders of influence (COI) method and sectoring method implementations. The impetus for this research stems from modeling electrokinetic nanoparticle (EN) treatment, which packs concrete pores with differently sized nanoparticles. We show an improved speed of the simulation compared to previously published results of EN treatment simulation while obtaining similar porosity reduction results. We mainly focused on readily, commercially available particle sizes of 2 nm and 20 nm particles, but have the capability to model other sizes. Our simulation has graphical capabilities and can provide additional data unobtainable from physical experimentation. The data collected has a median of 0.5750 and a mean of 0.5504. The standard error is 0.0054 at alpha = 0.05 for a 95% confidence interval of 0.5504 +/- 0.0054. The simulation has produced maximum packing densities of 65% and minimum packing densities of 34%. Simulation data are analyzed using linear regression via the R statistical language to obtain two equations: one that describes porosity reduction based on all cylinder and particle characteristics, and another that focuses on describing porosity reduction based on cylinder diameter for 2 and 20 nm particles into pores of 100 nm height. Simulation results are similar to most physical results obtained from MIP and WLR. Some MIP results do not fall within the simulation limits; however, this is expected as MIP has been documented to be an inaccurate measure of pore distribution and porosity of concrete. Despite the disagreement between WLR and MIP, there is a trend that porosity reduction is higher two inches from the rebar as compared to the rebar-concrete interface. The simulation also detects a higher porosity reduction further from the rebar. This may be due to particles

  20. A framework of modeling detector systems for computed tomography simulations

    NASA Astrophysics Data System (ADS)

    Youn, H.; Kim, D.; Kim, S. H.; Kam, S.; Jeon, H.; Nam, J.; Kim, H. K.

    2016-01-01

    Ultimate development in computed tomography (CT) technology may be a system that can provide images with excellent lesion conspicuity with the patient dose as low as possible. Imaging simulation tools have been cost-effectively used for these developments and will continue. For a more accurate and realistic imaging simulation, the signal and noise propagation through a CT detector system has been modeled in this study using the cascaded linear-systems theory. The simulation results are validated in comparisons with the measured results using a laboratory flat-panel micro-CT system. Although the image noise obtained from the simulations at higher exposures is slightly smaller than that obtained from the measurements, the difference between them is reasonably acceptable. According to the simulation results for various exposure levels and additive electronic noise levels, x-ray quantum noise is more dominant than the additive electronic noise. The framework of modeling a CT detector system suggested in this study will be helpful for the development of an accurate and realistic projection simulation model.

  1. Who's your neighbor? neighbor identification for agent-based modeling.

    SciTech Connect

    Macal, C. M.; Howe, T. R.; Decision and Information Sciences; Univ. of Chicago

    2006-01-01

    Agent-based modeling and simulation, based on the cellular automata paradigm, is an approach to modeling complex systems comprised of interacting autonomous agents. Open questions in agent-based simulation focus on scale-up issues encountered in simulating large numbers of agents. Specifically, how many agents can be included in a workable agent-based simulation? One of the basic tenets of agent-based modeling and simulation is that agents only interact and exchange locally available information with other agents located in their immediate proximity or neighborhood of the space in which the agents are situated. Generally, an agent's set of neighbors changes rapidly as a simulation proceeds through time and as the agents move through space. Depending on the topology defined for agent interactions, proximity may be defined by spatial distance for continuous space, adjacency for grid cells (as in cellular automata), or by connectivity in social networks. Identifying an agent's neighbors is a particularly time-consuming computational task and can dominate the computational effort in a simulation. Two challenges in agent simulation are (1) efficiently representing an agent's neighborhood and the neighbors in it and (2) efficiently identifying an agent's neighbors at any time in the simulation. These problems are addressed differently for different agent interaction topologies. While efficient approaches have been identified for agent neighborhood representation and neighbor identification for agents on a lattice with general neighborhood configurations, other techniques must be used when agents are able to move freely in space. Techniques for the analysis and representation of spatial data are applicable to the agent neighbor identification problem. This paper extends agent neighborhood simulation techniques from the lattice topology to continuous space, specifically R2. Algorithms based on hierarchical (quad trees) or non-hierarchical data structures (grid cells) are

  2. Effectiveness of dynamic rescheduling in agent-based flexible manufacturing systems

    NASA Astrophysics Data System (ADS)

    Saad, Ashraf; Biswas, Gautam; Kawamura, Kazuhiko; Johnson, Eric M.

    1997-12-01

    This work has been developed within the framework of agent- based decentralized scheduling for flexible manufacturing systems. In this framework, all workcells comprising the manufacturing system, and the products to be generated, are modeled via intelligent software agents. These agents interact dynamically using a bidding production reservation (BPRS) scheme, based on the Contract Net Protocol, to devise the production schedule for each product unit. Simulation studies of a job shop have demonstrated the gains in performance achieved by this approach over heuristic dispatching rules commonly used in industry. Manufacturing environments are also prone to operational uncertainties such as variations in processing times and machine breakdowns. In order to cope with these uncertainties, the BPRS algorithm has been extended for dynamic rescheduling to also occur in a fully decentralized manner. The resulting multi-agent rescheduling scheme results in decentralized control of flexible manufacturing systems that are capable of responding dynamically to such operational uncertainties, thereby enhancing the robustness and fault tolerance of the proposed scheduling approach. This paper also presents the effects of the proposed agent-based decentralized scheduling approach on the performance of the underlying flexible manufacturing system under a variety of production and scheduling scenarios, including forward and backward scheduling. Future directions for this work include applying the proposed scheduling approach to other advanced manufacturing areas such as agile and holonic manufacturing.

  3. The Integrated Plasma Simulator: A Flexible Python Framework for Coupled Multiphysics Simulation

    SciTech Connect

    Foley, Samantha S; Elwasif, Wael R; Bernholdt, David E

    2011-11-01

    High-fidelity coupled multiphysics simulations are an increasingly important aspect of computational science. In many domains, however, there has been very limited experience with simulations of this sort, therefore research in coupled multiphysics often requires computational frameworks with significant flexibility to respond to the changing directions of the physics and mathematics. This paper presents the Integrated Plasma Simulator (IPS), a framework designed for loosely coupled simulations of fusion plasmas. The IPS provides users with a simple component architecture into which a wide range of existing plasma physics codes can be inserted as components. Simulations can take advantage of multiple levels of parallelism supported in the IPS, and can be controlled by a high-level ``driver'' component, or by other coordination mechanisms, such as an asynchronous event service. We describe the requirements and design of the framework, and how they were implemented in the Python language. We also illustrate the flexibility of the framework by providing examples of different types of simulations that utilize various features of the IPS.

  4. An agent based model of genotype editing

    SciTech Connect

    Rocha, L. M.; Huang, C. F.

    2004-01-01

    This paper presents our investigation on an agent-based model of Genotype Editing. This model is based on several characteristics that are gleaned from the RNA editing system as observed in several organisms. The incorporation of editing mechanisms in an evolutionary agent-based model provides a means for evolving agents with heterogenous post-transcriptional processes. The study of this agent-based genotype-editing model has shed some light into the evolutionary implications of RNA editing as well as established an advantageous evolutionary computation algorithm for machine learning. We expect that our proposed model may both facilitate determining the evolutionary role of RNA editing in biology, and advance the current state of research in agent-based optimization.

  5. Faunus: An object oriented framework for molecular simulation

    PubMed Central

    Lund, Mikael; Trulsson, Martin; Persson, Björn

    2008-01-01

    Background We present a C++ class library for Monte Carlo simulation of molecular systems, including proteins in solution. The design is generic and highly modular, enabling multiple developers to easily implement additional features. The statistical mechanical methods are documented by extensive use of code comments that – subsequently – are collected to automatically build a web-based manual. Results We show how an object oriented design can be used to create an intuitively appealing coding framework for molecular simulation. This is exemplified in a minimalistic C++ program that can calculate protein protonation states. We further discuss performance issues related to high level coding abstraction. Conclusion C++ and the Standard Template Library (STL) provide a high-performance platform for generic molecular modeling. Automatic generation of code documentation from inline comments has proven particularly useful in that no separate manual needs to be maintained. PMID:18241331

  6. A wind turbine hybrid simulation framework considering aeroelastic effects

    NASA Astrophysics Data System (ADS)

    Song, Wei; Su, Weihua

    2015-04-01

    In performing an effective structural analysis for wind turbine, the simulation of turbine aerodynamic loads is of great importance. The interaction between the wake flow and the blades may impact turbine blades loading condition, energy yield and operational behavior. Direct experimental measurement of wind flow field and wind profiles around wind turbines is very helpful to support the wind turbine design. However, with the growth of the size of wind turbines for higher energy output, it is not convenient to obtain all the desired data in wind-tunnel and field tests. In this paper, firstly the modeling of dynamic responses of large-span wind turbine blades will consider nonlinear aeroelastic effects. A strain-based geometrically nonlinear beam formulation will be used for the basic structural dynamic modeling, which will be coupled with unsteady aerodynamic equations and rigid-body rotations of the rotor. Full wind turbines can be modeled by using the multi-connected beams. Then, a hybrid simulation experimental framework is proposed to potentially address this issue. The aerodynamic-dominant components, such as the turbine blades and rotor, are simulated as numerical components using the nonlinear aeroelastic model; while the turbine tower, where the collapse of failure may occur under high level of wind load, is simulated separately as the physical component. With the proposed framework, dynamic behavior of NREL's 5MW wind turbine blades will be studied and correlated with available numerical data. The current work will be the basis of the authors' further studies on flow control and hazard mitigation on wind turbine blades and towers.

  7. An Agent-Based Model of Farmer Decision Making in Jordan

    NASA Astrophysics Data System (ADS)

    Selby, Philip; Medellin-Azuara, Josue; Harou, Julien; Klassert, Christian; Yoon, Jim

    2016-04-01

    We describe an agent based hydro-economic model of groundwater irrigated agriculture in the Jordan Highlands. The model employs a Multi-Agent-Simulation (MAS) framework and is designed to evaluate direct and indirect outcomes of climate change scenarios and policy interventions on farmer decision making, including annual land use, groundwater use for irrigation, and water sales to a water tanker market. Land use and water use decisions are simulated for groups of farms grouped by location and their behavioural and economic similarities. Decreasing groundwater levels, and the associated increase in pumping costs, are important drivers for change within Jordan'S agricultural sector. We describe how this is considered by coupling of agricultural and groundwater models. The agricultural production model employs Positive Mathematical Programming (PMP), a method for calibrating agricultural production functions to observed planted areas. PMP has successfully been used with disaggregate models for policy analysis. We adapt the PMP approach to allow explicit evaluation of the impact of pumping costs, groundwater purchase fees and a water tanker market. The work demonstrates the applicability of agent-based agricultural decision making assessment in the Jordan Highlands and its integration with agricultural model calibration methods. The proposed approach is designed and implemented with software such that it could be used to evaluate a variety of physical and human influences on decision making in agricultural water management.

  8. A Virtual Engineering Framework for Simulating Advanced Power System

    SciTech Connect

    Mike Bockelie; Dave Swensen; Martin Denison; Stanislav Borodai

    2008-06-18

    In this report is described the work effort performed to provide NETL with VE-Suite based Virtual Engineering software and enhanced equipment models to support NETL's Advanced Process Engineering Co-simulation (APECS) framework for advanced power generation systems. Enhancements to the software framework facilitated an important link between APECS and the virtual engineering capabilities provided by VE-Suite (e.g., equipment and process visualization, information assimilation). Model enhancements focused on improving predictions for the performance of entrained flow coal gasifiers and important auxiliary equipment (e.g., Air Separation Units) used in coal gasification systems. In addition, a Reduced Order Model generation tool and software to provide a coupling between APECS/AspenPlus and the GE GateCycle simulation system were developed. CAPE-Open model interfaces were employed where needed. The improved simulation capability is demonstrated on selected test problems. As part of the project an Advisory Panel was formed to provide guidance on the issues on which to focus the work effort. The Advisory Panel included experts from industry and academics in gasification, CO2 capture issues, process simulation and representatives from technology developers and the electric utility industry. To optimize the benefit to NETL, REI coordinated its efforts with NETL and NETL funded projects at Iowa State University, Carnegie Mellon University and ANSYS/Fluent, Inc. The improved simulation capabilities incorporated into APECS will enable researchers and engineers to better understand the interactions of different equipment components, identify weaknesses and processes needing improvement and thereby allow more efficient, less expensive plants to be developed and brought on-line faster and in a more cost-effective manner. These enhancements to APECS represent an important step toward having a fully integrated environment for performing plant simulation and engineering

  9. Framework Application for Core Edge Transport Simulation (FACETS)

    SciTech Connect

    Malony, Allen D; Shende, Sameer S; Huck, Kevin A; Mr. Alan Morris, and Mr. Wyatt Spear

    2012-03-14

    The goal of the FACETS project (Framework Application for Core-Edge Transport Simulations) was to provide a multiphysics, parallel framework application (FACETS) that will enable whole-device modeling for the U.S. fusion program, to provide the modeling infrastructure needed for ITER, the next step fusion confinement device. Through use of modern computational methods, including component technology and object oriented design, FACETS is able to switch from one model to another for a given aspect of the physics in a flexible manner. This enables use of simplified models for rapid turnaround or high-fidelity models that can take advantage of the largest supercomputer hardware. FACETS does so in a heterogeneous parallel context, where different parts of the application execute in parallel by utilizing task farming, domain decomposition, and/or pipelining as needed and applicable. ParaTools, Inc. was tasked with supporting the performance analysis and tuning of the FACETS components and framework in order to achieve the parallel scaling goals of the project. The TAU Performance System® was used for instrumentation, measurement, archiving, and profile / tracing analysis. ParaTools, Inc. also assisted in FACETS performance engineering efforts. Through the use of the TAU Performance System, ParaTools provided instrumentation, measurement, analysis and archival support for the FACETS project. Performance optimization of key components has yielded significant performance speedups. TAU was integrated into the FACETS build for both the full coupled application and the UEDGE component. The performance database provided archival storage of the performance regression testing data generated by the project, and helped to track improvements in the software development.

  10. Particle beam dynamics simulations using the POOMA framework

    SciTech Connect

    Humphrey, W.; Ryne, R.; Cleland, T.; Cummings, J.; Habib, S.; Mark, G.; Ji Qiang

    1998-12-31

    A program for simulation of the dynamics of high intensity charged particle beams in linear particle accelerators has been developed in C++ using the POOMA Framework, for use on serial and parallel architectures. The code models the trajectories of charged particles through a sequence of different accelerator beamline elements such as drift chambers, quadrupole magnets, or RF cavities. An FFT-based particle-in-cell algorithm is used to solve the Poisson equation that models the Coulomb interactions of the particles. The code employs an object-oriented design with software abstractions for the particle beam, accelerator beamline, and beamline elements, using C++ templates to efficiently support both 2D and 3D capabilities in the same code base. The POOMA Framework, which encapsulates much of the effort required for parallel execution, provides particle and field classes, particle-field interaction capabilities, and parallel FFT algorithms. The performance of this application running serially and in parallel is compared to an existing HPF implementation, with the POOMA version seen to run four times faster than the HPF code.

  11. A Hybrid Multiscale Framework for Subsurface Flow and Transport Simulations

    SciTech Connect

    Scheibe, Timothy D.; Yang, Xiaofan; Chen, Xingyuan; Hammond, Glenn E.

    2015-06-01

    -specific and sometimes ad-hoc approaches for model coupling. We are developing a generalized approach to hierarchical model coupling designed for high-performance computational systems, based on the Swift computing workflow framework. In this presentation we will describe the generalized approach and provide two use cases: 1) simulation of a mixing-controlled biogeochemical reaction coupling pore- and continuum-scale models, and 2) simulation of biogeochemical impacts of groundwater – river water interactions coupling fine- and coarse-grid model representations. This generalized framework can be customized for use with any pair of linked models (microscale and macroscale) with minimal intrusiveness to the at-scale simulators. It combines a set of python scripts with the Swift workflow environment to execute a complex multiscale simulation utilizing an approach similar to the well-known Heterogeneous Multiscale Method. User customization is facilitated through user-provided input and output file templates and processing function scripts, and execution within a high-performance computing environment is handled by Swift, such that minimal to no user modification of at-scale codes is required.

  12. A Hybrid Multiscale Framework for Subsurface Flow and Transport Simulations

    DOE PAGES

    Scheibe, Timothy D.; Yang, Xiaofan; Chen, Xingyuan; ...

    2015-06-01

    -specific and sometimes ad-hoc approaches for model coupling. We are developing a generalized approach to hierarchical model coupling designed for high-performance computational systems, based on the Swift computing workflow framework. In this presentation we will describe the generalized approach and provide two use cases: 1) simulation of a mixing-controlled biogeochemical reaction coupling pore- and continuum-scale models, and 2) simulation of biogeochemical impacts of groundwater – river water interactions coupling fine- and coarse-grid model representations. This generalized framework can be customized for use with any pair of linked models (microscale and macroscale) with minimal intrusiveness to the at-scale simulators. It combines a set of python scripts with the Swift workflow environment to execute a complex multiscale simulation utilizing an approach similar to the well-known Heterogeneous Multiscale Method. User customization is facilitated through user-provided input and output file templates and processing function scripts, and execution within a high-performance computing environment is handled by Swift, such that minimal to no user modification of at-scale codes is required.« less

  13. A rigorous framework for multiscale simulation of stochastic cellular networks

    PubMed Central

    Chevalier, Michael W.; El-Samad, Hana

    2009-01-01

    Noise and stochasticity are fundamental to biology and derive from the very nature of biochemical reactions where thermal motion of molecules translates into randomness in the sequence and timing of reactions. This randomness leads to cell-cell variability even in clonal populations. Stochastic biochemical networks are modeled as continuous time discrete state Markov processes whose probability density functions evolve according to a chemical master equation (CME). The CME is not solvable but for the simplest cases, and one has to resort to kinetic Monte Carlo techniques to simulate the stochastic trajectories of the biochemical network under study. A commonly used such algorithm is the stochastic simulation algorithm (SSA). Because it tracks every biochemical reaction that occurs in a given system, the SSA presents computational difficulties especially when there is a vast disparity in the timescales of the reactions or in the number of molecules involved in these reactions. This is common in cellular networks, and many approximation algorithms have evolved to alleviate the computational burdens of the SSA. Here, we present a rigorously derived modified CME framework based on the partition of a biochemically reacting system into restricted and unrestricted reactions. Although this modified CME decomposition is as analytically difficult as the original CME, it can be naturally used to generate a hierarchy of approximations at different levels of accuracy. Most importantly, some previously derived algorithms are demonstrated to be limiting cases of our formulation. We apply our methods to biologically relevant test systems to demonstrate their accuracy and efficiency. PMID:19673546

  14. Agent-based computational model investigates muscle-specific responses to disuse-induced atrophy

    PubMed Central

    Martin, Kyle S.; Peirce, Shayn M.

    2015-01-01

    Skeletal muscle is highly responsive to use. In particular, muscle atrophy attributable to decreased activity is a common problem among the elderly and injured/immobile. However, each muscle does not respond the same way. We developed an agent-based model that generates a tissue-level skeletal muscle response to disuse/immobilization. The model incorporates tissue-specific muscle fiber architecture parameters and simulates changes in muscle fiber size as a result of disuse-induced atrophy that are consistent with published experiments. We created simulations of 49 forelimb and hindlimb muscles of the rat by incorporating eight fiber-type and size parameters to explore how these parameters, which vary widely across muscles, influence sensitivity to disuse-induced atrophy. Of the 49 muscles modeled, the soleus exhibited the greatest atrophy after 14 days of simulated immobilization (51% decrease in fiber size), whereas the extensor digitorum communis atrophied the least (32%). Analysis of these simulations revealed that both fiber-type distribution and fiber-size distribution influence the sensitivity to disuse atrophy even though no single tissue architecture parameter correlated with atrophy rate. Additionally, software agents representing fibroblasts were incorporated into the model to investigate cellular interactions during atrophy. Sensitivity analyses revealed that fibroblast agents have the potential to affect disuse-induced atrophy, albeit with a lesser effect than fiber type and size. In particular, muscle atrophy elevated slightly with increased initial fibroblast population and increased production of TNF-α. Overall, the agent-based model provides a novel framework for investigating both tissue adaptations and cellular interactions in skeletal muscle during atrophy. PMID:25722379

  15. Agent Based Modeling of Air Carrier Behavior for Evaluation of Technology Equipage and Adoption

    NASA Technical Reports Server (NTRS)

    Horio, Brant M.; DeCicco, Anthony H.; Stouffer, Virginia L.; Hasan, Shahab; Rosenbaum, Rebecca L.; Smith, Jeremy C.

    2014-01-01

    As part of ongoing research, the National Aeronautics and Space Administration (NASA) and LMI developed a research framework to assist policymakers in identifying impacts on the U.S. air transportation system (ATS) of potential policies and technology related to the implementation of the Next Generation Air Transportation System (NextGen). This framework, called the Air Transportation System Evolutionary Simulation (ATS-EVOS), integrates multiple models into a single process flow to best simulate responses by U.S. commercial airlines and other ATS stakeholders to NextGen-related policies, and in turn, how those responses impact the ATS. Development of this framework required NASA and LMI to create an agent-based model of airline and passenger behavior. This Airline Evolutionary Simulation (AIRLINE-EVOS) models airline decisions about tactical airfare and schedule adjustments, and strategic decisions related to fleet assignments, market prices, and equipage. AIRLINE-EVOS models its own heterogeneous population of passenger agents that interact with airlines; this interaction allows the model to simulate the cycle of action-reaction as airlines compete with each other and engage passengers. We validated a baseline configuration of AIRLINE-EVOS against Airline Origin and Destination Survey (DB1B) data and subject matter expert opinion, and we verified the ATS-EVOS framework and agent behavior logic through scenario-based experiments. These experiments demonstrated AIRLINE-EVOS's capabilities in responding to an input price shock in fuel prices, and to equipage challenges in a series of analyses based on potential incentive policies for best equipped best served, optimal-wind routing, and traffic management initiative exemption concepts..

  16. Agent-based models of financial markets

    NASA Astrophysics Data System (ADS)

    Samanidou, E.; Zschischang, E.; Stauffer, D.; Lux, T.

    2007-03-01

    This review deals with several microscopic ('agent-based') models of financial markets which have been studied by economists and physicists over the last decade: Kim-Markowitz, Levy-Levy-Solomon, Cont-Bouchaud, Solomon-Weisbuch, Lux-Marchesi, Donangelo-Sneppen and Solomon-Levy-Huang. After an overview of simulation approaches in financial economics, we first give a summary of the Donangelo-Sneppen model of monetary exchange and compare it with related models in economics literature. Our selective review then outlines the main ingredients of some influential early models of multi-agent dynamics in financial markets (Kim-Markowitz, Levy-Levy-Solomon). As will be seen, these contributions draw their inspiration from the complex appearance of investors' interactions in real-life markets. Their main aim is to reproduce (and, thereby, provide possible explanations) for the spectacular bubbles and crashes seen in certain historical episodes, but they lack (like almost all the work before 1998 or so) a perspective in terms of the universal statistical features of financial time series. In fact, awareness of a set of such regularities (power-law tails of the distribution of returns, temporal scaling of volatility) only gradually appeared over the nineties. With the more precise description of the formerly relatively vague characteristics (e.g. moving from the notion of fat tails to the more concrete one of a power law with index around three), it became clear that financial market dynamics give rise to some kind of universal scaling law. Showing similarities with scaling laws for other systems with many interacting sub-units, an exploration of financial markets as multi-agent systems appeared to be a natural consequence. This topic has been pursued by quite a number of contributions appearing in both the physics and economics literature since the late nineties. From the wealth of different flavours of multi-agent models that have appeared up to now, we discuss the Cont

  17. Multiscale Simulation Framework for Coupled Fluid Flow and Mechanical Deformation

    SciTech Connect

    Hou, Thomas; Efendiev, Yalchin; Tchelepi, Hamdi; Durlofsky, Louis

    2016-05-24

    Our work in this project is aimed at making fundamental advances in multiscale methods for flow and transport in highly heterogeneous porous media. The main thrust of this research is to develop a systematic multiscale analysis and efficient coarse-scale models that can capture global effects and extend existing multiscale approaches to problems with additional physics and uncertainties. A key emphasis is on problems without an apparent scale separation. Multiscale solution methods are currently under active investigation for the simulation of subsurface flow in heterogeneous formations. These procedures capture the effects of fine-scale permeability variations through the calculation of specialized coarse-scale basis functions. Most of the multiscale techniques presented to date employ localization approximations in the calculation of these basis functions. For some highly correlated (e.g., channelized) formations, however, global effects are important and these may need to be incorporated into the multiscale basis functions. Other challenging issues facing multiscale simulations are the extension of existing multiscale techniques to problems with additional physics, such as compressibility, capillary effects, etc. In our project, we explore the improvement of multiscale methods through the incorporation of additional (single-phase flow) information and the development of a general multiscale framework for flows in the presence of uncertainties, compressible flow and heterogeneous transport, and geomechanics. We have considered (1) adaptive local-global multiscale methods, (2) multiscale methods for the transport equation, (3) operator-based multiscale methods and solvers, (4) multiscale methods in the presence of uncertainties and applications, (5) multiscale finite element methods for high contrast porous media and their generalizations, and (6) multiscale methods for geomechanics.

  18. Understanding agent-based models of financial markets: A bottom-up approach based on order parameters and phase diagrams

    NASA Astrophysics Data System (ADS)

    Lye, Ribin; Tan, James Peng Lung; Cheong, Siew Ann

    2012-11-01

    We describe a bottom-up framework, based on the identification of appropriate order parameters and determination of phase diagrams, for understanding progressively refined agent-based models and simulations of financial markets. We illustrate this framework by starting with a deterministic toy model, whereby N independent traders buy and sell M stocks through an order book that acts as a clearing house. The price of a stock increases whenever it is bought and decreases whenever it is sold. Price changes are updated by the order book before the next transaction takes place. In this deterministic model, all traders based their buy decisions on a call utility function, and all their sell decisions on a put utility function. We then make the agent-based model more realistic, by either having a fraction fb of traders buy a random stock on offer, or a fraction fs of traders sell a random stock in their portfolio. Based on our simulations, we find that it is possible to identify useful order parameters from the steady-state price distributions of all three models. Using these order parameters as a guide, we find three phases: (i) the dead market; (ii) the boom market; and (iii) the jammed market in the phase diagram of the deterministic model. Comparing the phase diagrams of the stochastic models against that of the deterministic model, we realize that the primary effect of stochasticity is to eliminate the dead market phase.

  19. Multiscale Simulation Framework for Coupled Fluid Flow and Mechanical Deformation

    SciTech Connect

    Tchelepi, Hamdi

    2014-11-14

    A multiscale linear-solver framework for the pressure equation associated with flow in highly heterogeneous porous formations was developed. The multiscale based approach is cast in a general algebraic form, which facilitates integration of the new scalable linear solver in existing flow simulators. The Algebraic Multiscale Solver (AMS) is employed as a preconditioner within a multi-stage strategy. The formulations investigated include the standard MultiScale Finite-Element (MSFE) andMultiScale Finite-Volume (MSFV) methods. The local-stage solvers include incomplete factorization and the so-called Correction Functions (CF) associated with the MSFV approach. Extensive testing of AMS, as an iterative linear solver, indicate excellent convergence rates and computational scalability. AMS compares favorably with advanced Algebraic MultiGrid (AMG) solvers for highly detailed three-dimensional heterogeneous models. Moreover, AMS is expected to be especially beneficial in solving time-dependent problems of coupled multiphase flow and transport in large-scale subsurface formations.

  20. A new framework for magnetohydrodynamic simulations with anisotropic pressure

    NASA Astrophysics Data System (ADS)

    Hirabayashi, Kota; Hoshino, Masahiro; Amano, Takanobu

    2016-12-01

    We describe a new theoretical and numerical framework for magnetohydrodynamic (MHD) simulations with an incorporated anisotropic pressure tensor, which can play an important role in collisionless plasmas. The classical approach to handle the anisotropy is based on application of the double adiabatic approximation, assuming that the pressure tensor is well described only by those components that are oriented parallel and perpendicular to the local magnetic field. This gyrotropic assumption, however, fails around magnetically neutral regions, where the cyclotron period may become comparable to or even longer than the system's dynamical time, which causes a singularity in the mathematical expression. In this paper, we demonstrate that this singularity can be completely removed by direct use of the 2nd-moment of the Vlasov equation, combined with an ingenious gyrotropization model. Numerical tests are used to verify that our model properly reduces to the standard MHD results or the double adiabatic formulation in an asymptotic manner under the limit of fast isotropization and fast gyrotropization, respectively.

  1. A detailed framework to incorporate dust in hydrodynamical simulations

    NASA Astrophysics Data System (ADS)

    Grassi, T.; Bovino, S.; Haugbølle, T.; Schleicher, D. R. G.

    2017-04-01

    Dust plays a key role in the evolution of the interstellar medium and its correct modelling in numerical simulations is therefore fundamental. We present a new and self-consistent model that treats grain thermal coupling with the gas, radiation balance, and surface chemistry for molecular hydrogen self-consistently. This method can be applied to any dust distribution with an arbitrary number of grain types without affecting the overall computational cost. In this paper, we describe in detail the physics and the algorithm behind our approach, and in order to test the methodology, we present some examples of astrophysical interest, namely (i) a one-zone collapse with complete gas chemistry and thermochemical processes, (ii) a 3D model of a low-metallicity collapse of a minihalo starting from cosmological initial conditions, and (iii) a turbulent molecular cloud with H-C-O chemistry (277 reactions), together with self-consistent cooling and heating solved on the fly. Although these examples employ the publicly available code KROME, our approach can easily be integrated into any computational framework.

  2. Agent-Based Collaborative Affective e-Learning Framework

    ERIC Educational Resources Information Center

    Neji, Mahmoud; Ben Ammar, Mohamed

    2007-01-01

    Based on facial expression (FE), this paper explores the possible use of the affective communication in virtual environments (VEs). The attention of affective communication is examined and some research ideas for developing affective communication in virtual environments are proposed. We place an emphasis on communication between virtual entities,…

  3. Creating an Agent Based Framework to Maximize Information Utility

    DTIC Science & Technology

    2008-03-01

    Pecarina graduated from Central High School in San Angelo , Texas. He received his Bachelor of Science in Computer Science from Angelo State...instance, snipers in several building in strategic topographic locations could be setting themselves up for a coordinated jamming attack while enemy...scheduling problem and maps it to the restless bandit problem. The restless bandit problem is formulated, then its complexity is described and an

  4. Agent-Based Deterministic Modeling of the Bone Marrow Homeostasis.

    PubMed

    Kurhekar, Manish; Deshpande, Umesh

    2016-01-01

    Modeling of stem cells not only describes but also predicts how a stem cell's environment can control its fate. The first stem cell populations discovered were hematopoietic stem cells (HSCs). In this paper, we present a deterministic model of bone marrow (that hosts HSCs) that is consistent with several of the qualitative biological observations. This model incorporates stem cell death (apoptosis) after a certain number of cell divisions and also demonstrates that a single HSC can potentially populate the entire bone marrow. It also demonstrates that there is a production of sufficient number of differentiated cells (RBCs, WBCs, etc.). We prove that our model of bone marrow is biologically consistent and it overcomes the biological feasibility limitations of previously reported models. The major contribution of our model is the flexibility it allows in choosing model parameters which permits several different simulations to be carried out in silico without affecting the homeostatic properties of the model. We have also performed agent-based simulation of the model of bone marrow system proposed in this paper. We have also included parameter details and the results obtained from the simulation. The program of the agent-based simulation of the proposed model is made available on a publicly accessible website.

  5. Agent-Based Deterministic Modeling of the Bone Marrow Homeostasis

    PubMed Central

    2016-01-01

    Modeling of stem cells not only describes but also predicts how a stem cell's environment can control its fate. The first stem cell populations discovered were hematopoietic stem cells (HSCs). In this paper, we present a deterministic model of bone marrow (that hosts HSCs) that is consistent with several of the qualitative biological observations. This model incorporates stem cell death (apoptosis) after a certain number of cell divisions and also demonstrates that a single HSC can potentially populate the entire bone marrow. It also demonstrates that there is a production of sufficient number of differentiated cells (RBCs, WBCs, etc.). We prove that our model of bone marrow is biologically consistent and it overcomes the biological feasibility limitations of previously reported models. The major contribution of our model is the flexibility it allows in choosing model parameters which permits several different simulations to be carried out in silico without affecting the homeostatic properties of the model. We have also performed agent-based simulation of the model of bone marrow system proposed in this paper. We have also included parameter details and the results obtained from the simulation. The program of the agent-based simulation of the proposed model is made available on a publicly accessible website. PMID:27340402

  6. Agent based simulations in disease modeling Comment on "Towards a unified approach in the modeling of fibrosis: A review with research perspectives" by Martine Ben Amar and Carlo Bianca

    NASA Astrophysics Data System (ADS)

    Pappalardo, Francesco; Pennisi, Marzio

    2016-07-01

    Fibrosis represents a process where an excessive tissue formation in an organ follows the failure of a physiological reparative or reactive process. Mathematical and computational techniques may be used to improve the understanding of the mechanisms that lead to the disease and to test potential new treatments that may directly or indirectly have positive effects against fibrosis [1]. In this scenario, Ben Amar and Bianca [2] give us a broad picture of the existing mathematical and computational tools that have been used to model fibrotic processes at the molecular, cellular, and tissue levels. Among such techniques, agent based models (ABM) can give a valuable contribution in the understanding and better management of fibrotic diseases.

  7. A Hybrid Sensitivity Analysis Approach for Agent-based Disease Spread Models

    SciTech Connect

    Pullum, Laura L; Cui, Xiaohui

    2012-01-01

    Agent-based models (ABM) have been widely deployed in different fields for studying the collective behavior of large numbers of interacting agents. Of particular interest lately is the application of agent-based and hybrid models to epidemiology, specifically Agent-based Disease Spread Models (ABDSM). Validation (one aspect of the means to achieve dependability) of ABDSM simulation models is extremely important. It ensures that the right model has been built and lends confidence to the use of that model to inform critical decisions. In this report, we describe our preliminary efforts in ABDSM validation by using hybrid model fusion technology.

  8. Multiscale agent-based consumer market modeling.

    SciTech Connect

    North, M. J.; Macal, C. M.; St. Aubin, J.; Thimmapuram, P.; Bragen, M.; Hahn, J.; Karr, J.; Brigham, N.; Lacy, M. E.; Hampton, D.; Decision and Information Sciences; Procter & Gamble Co.

    2010-05-01

    Consumer markets have been studied in great depth, and many techniques have been used to represent them. These have included regression-based models, logit models, and theoretical market-level models, such as the NBD-Dirichlet approach. Although many important contributions and insights have resulted from studies that relied on these models, there is still a need for a model that could more holistically represent the interdependencies of the decisions made by consumers, retailers, and manufacturers. When the need is for a model that could be used repeatedly over time to support decisions in an industrial setting, it is particularly critical. Although some existing methods can, in principle, represent such complex interdependencies, their capabilities might be outstripped if they had to be used for industrial applications, because of the details this type of modeling requires. However, a complementary method - agent-based modeling - shows promise for addressing these issues. Agent-based models use business-driven rules for individuals (e.g., individual consumer rules for buying items, individual retailer rules for stocking items, or individual firm rules for advertizing items) to determine holistic, system-level outcomes (e.g., to determine if brand X's market share is increasing). We applied agent-based modeling to develop a multi-scale consumer market model. We then conducted calibration, verification, and validation tests of this model. The model was successfully applied by Procter & Gamble to several challenging business problems. In these situations, it directly influenced managerial decision making and produced substantial cost savings.

  9. Assurance in Agent-Based Systems

    SciTech Connect

    Gilliom, Laura R.; Goldsmith, Steven Y.

    1999-05-10

    Our vision of the future of information systems is one that includes engineered collectives of software agents which are situated in an environment over years and which increasingly improve the performance of the overall system of which they are a part. At a minimum, the movement of agent and multi-agent technology into National Security applications, including their use in information assurance, is apparent today. The use of deliberative, autonomous agents in high-consequence/high-security applications will require a commensurate level of protection and confidence in the predictability of system-level behavior. At Sandia National Laboratories, we have defined and are addressing a research agenda that integrates the surety (safety, security, and reliability) into agent-based systems at a deep level. Surety is addressed at multiple levels: The integrity of individual agents must be protected by addressing potential failure modes and vulnerabilities to malevolent threats. Providing for the surety of the collective requires attention to communications surety issues and mechanisms for identifying and working with trusted collaborators. At the highest level, using agent-based collectives within a large-scale distributed system requires the development of principled design methods to deliver the desired emergent performance or surety characteristics. This position paper will outline the research directions underway at Sandia, will discuss relevant work being performed elsewhere, and will report progress to date toward assurance in agent-based systems.

  10. Reducing complexity in an agent based reaction model-Benefits and limitations of simplifications in relation to run time and system level output.

    PubMed

    Rhodes, David M; Holcombe, Mike; Qwarnstrom, Eva E

    2016-09-01

    Agent based modelling is a methodology for simulating a variety of systems across a broad spectrum of fields. However, due to the complexity of the systems it is often impossible or impractical to model them at a one to one scale. In this paper we use a simple reaction rate model implemented using the FLAME framework to test the impact of common methods for reducing model complexity such as reducing scale, increasing iteration duration and reducing message overheads. We demonstrate that such approaches can have significant impact on simulation runtime albeit with increasing risk of aberrant system behaviour and errors, as the complexity of the model is reduced.

  11. An Agent Based Model for Social Class Emergence

    NASA Astrophysics Data System (ADS)

    Yang, Xiaoxiang; Rodriguez Segura, Daniel; Lin, Fei; Mazilu, Irina

    We present an open system agent-based model to analyze the effects of education and the society-specific wealth transactions on the emergence of social classes. Building on previous studies, we use realistic functions to model how years of education affect the income level. Numerical simulations show that the fraction of an individual's total transactions that is invested rather than consumed can cause wealth gaps between different income brackets in the long run. In an attempt to incorporate the network effects, we also explore how the probability of interactions among agents depending on the spread of their income brackets affects wealth distribution.

  12. Surgical model-view-controller simulation software framework for local and collaborative applications

    PubMed Central

    Sankaranarayanan, Ganesh; Halic, Tansel; Arikatla, Venkata Sreekanth; Lu, Zhonghua; De, Suvranu

    2010-01-01

    Purpose Surgical simulations require haptic interactions and collaboration in a shared virtual environment. A software framework for decoupled surgical simulation based on a multi-controller and multi-viewer model-view-controller (MVC) pattern was developed and tested. Methods A software framework for multimodal virtual environments was designed, supporting both visual interactions and haptic feedback while providing developers with an integration tool for heterogeneous architectures maintaining high performance, simplicity of implementation, and straightforward extension. The framework uses decoupled simulation with updates of over 1,000 Hz for haptics and accommodates networked simulation with delays of over 1,000 ms without performance penalty. Results The simulation software framework was implemented and was used to support the design of virtual reality-based surgery simulation systems. The framework supports the high level of complexity of such applications and the fast response required for interaction with haptics. The efficacy of the framework was tested by implementation of a minimally invasive surgery simulator. Conclusion A decoupled simulation approach can be implemented as a framework to handle simultaneous processes of the system at the various frame rates each process requires. The framework was successfully used to develop collaborative virtual environments (VEs) involving geographically distributed users connected through a network, with the results comparable to VEs for local users. PMID:20714933

  13. Coupling Agent-Based and Groundwater Modeling to Explore Demand Management Strategies for Shared Resources

    NASA Astrophysics Data System (ADS)

    Al-Amin, S.

    2015-12-01

    Municipal water demands in growing population centers in the arid southwest US are typically met through increased groundwater withdrawals. Hydro-climatic uncertainties attributed to climate change and land use conversions may also alter demands and impact the replenishment of groundwater supply. Groundwater aquifers are not necessarily confined within municipal and management boundaries, and multiple diverse agencies may manage a shared resource in a decentralized approach, based on individual concerns and resources. The interactions among water managers, consumers, and the environment influence the performance of local management strategies and regional groundwater resources. This research couples an agent-based modeling (ABM) framework and a groundwater model to analyze the effects of different management approaches on shared groundwater resources. The ABM captures the dynamic interactions between household-level consumers and policy makers to simulate water demands under climate change and population growth uncertainties. The groundwater model is used to analyze the relative effects of management approaches on reducing demands and replenishing groundwater resources. The framework is applied for municipalities located in the Verde River Basin, Arizona that withdraw groundwater from the Verde Formation-Basin Fill-Carbonate aquifer system. Insights gained through this simulation study can be used to guide groundwater policy-making under changing hydro-climatic scenarios for a long-term planning horizon.

  14. artG4: A Generic Framework for Geant4 Simulations

    SciTech Connect

    Arvanitis, Tasha; Lyon, Adam

    2014-01-01

    A small experiment must devote its limited computing expertise to writing physics code directly applicable to the experiment. A software 'framework' is essential for providing an infrastructure that makes writing the physics-relevant code easy. In this paper, we describe a highly modular and easy to use framework for writing Geant4 based simulations called 'artg4'. This framework is a layer on top of the art framework.

  15. Techniques and Issues in Agent-Based Modeling Validation

    SciTech Connect

    Pullum, Laura L; Cui, Xiaohui

    2012-01-01

    Validation of simulation models is extremely important. It ensures that the right model has been built and lends confidence to the use of that model to inform critical decisions. Agent-based models (ABM) have been widely deployed in different fields for studying the collective behavior of large numbers of interacting agents. However, researchers have only recently started to consider the issues of validation. Compared to other simulation models, ABM has many differences in model development, usage and validation. An ABM is inherently easier to build than a classical simulation, but more difficult to describe formally since they are closer to human cognition. Using multi-agent models to study complex systems has attracted criticisms because of the challenges involved in their validation [1]. In this report, we describe the challenge of ABM validation and present a novel approach we recently developed for an ABM system.

  16. A framework for web browser-based medical simulation using WebGL.

    PubMed

    Halic, Tansel; Ahn, Woojin; De, Suvranu

    2012-01-01

    This paper presents a web browser-based software framework that provides accessibility, portability, and platform independence for medical simulation. Typical medical simulation systems are restricted to the underlying platform and device, which limits widespread use. Our framework allows realistic and efficient medical simulation using only the web browser for anytime anywhere access using a variety of platforms ranging from desktop PCs to tablets. The framework consists of visualization, simulation, and hardware integration modules that are fundamental components for multimodal interactive simulation. Benchmark tests are performed to validate the rendering and computing performance of our framework with latest web browsers including Chrome and Firefox. The results are quite promising opening up the possibility of developing web-based medical simulation technology.

  17. An agent-based microsimulation of critical infrastructure systems

    SciTech Connect

    BARTON,DIANNE C.; STAMBER,KEVIN L.

    2000-03-29

    US infrastructures provide essential services that support the economic prosperity and quality of life. Today, the latest threat to these infrastructures is the increasing complexity and interconnectedness of the system. On balance, added connectivity will improve economic efficiency; however, increased coupling could also result in situations where a disturbance in an isolated infrastructure unexpectedly cascades across diverse infrastructures. An understanding of the behavior of complex systems can be critical to understanding and predicting infrastructure responses to unexpected perturbation. Sandia National Laboratories has developed an agent-based model of critical US infrastructures using time-dependent Monte Carlo methods and a genetic algorithm learning classifier system to control decision making. The model is currently under development and contains agents that represent the several areas within the interconnected infrastructures, including electric power and fuel supply. Previous work shows that agent-based simulations models have the potential to improve the accuracy of complex system forecasting and to provide new insights into the factors that are the primary drivers of emergent behaviors in interdependent systems. Simulation results can be examined both computationally and analytically, offering new ways of theorizing about the impact of perturbations to an infrastructure network.

  18. Educational Validity of Business Gaming Simulation: A Research Methodology Framework

    ERIC Educational Resources Information Center

    Stainton, Andrew J.; Johnson, Johnnie E.; Borodzicz, Edward P.

    2010-01-01

    Many past educational validity studies of business gaming simulation, and more specifically total enterprise simulation, have been inconclusive. Studies have focused on the weaknesses of business gaming simulation; which is often regarded as an educational medium that has limitations regarding learning effectiveness. However, no attempts have been…

  19. Extending the FairRoot framework to allow for simulation and reconstruction of free streaming data

    NASA Astrophysics Data System (ADS)

    Al-Turany, M.; Klein, D.; Manafov, A.; Rybalchenko, A.; Uhlig, F.

    2014-06-01

    The FairRoot framework is the standard framework for simulation, reconstruction and data analysis for the FAIR experiments. The framework is designed to optimise the accessibility for beginners and developers, to be flexible and to cope with future developments. FairRoot enhances the synergy between the different physics experiments. As a first step toward simulation of free streaming data, the time based simulation was introduced to the framework. The next step is the event source simulation. This is achieved via a client server system. After digitization the so called "samplers" can be started, where sampler can read the data of the corresponding detector from the simulation files and make it available for the reconstruction clients. The system makes it possible to develop and validate the online reconstruction algorithms. In this work, the design and implementation of the new architecture and the communication layer will be described.

  20. NEVESIM: event-driven neural simulation framework with a Python interface.

    PubMed

    Pecevski, Dejan; Kappel, David; Jonke, Zeno

    2014-01-01

    NEVESIM is a software package for event-driven simulation of networks of spiking neurons with a fast simulation core in C++, and a scripting user interface in the Python programming language. It supports simulation of heterogeneous networks with different types of neurons and synapses, and can be easily extended by the user with new neuron and synapse types. To enable heterogeneous networks and extensibility, NEVESIM is designed to decouple the simulation logic of communicating events (spikes) between the neurons at a network level from the implementation of the internal dynamics of individual neurons. In this paper we will present the simulation framework of NEVESIM, its concepts and features, as well as some aspects of the object-oriented design approaches and simulation strategies that were utilized to efficiently implement the concepts and functionalities of the framework. We will also give an overview of the Python user interface, its basic commands and constructs, and also discuss the benefits of integrating NEVESIM with Python. One of the valuable capabilities of the simulator is to simulate exactly and efficiently networks of stochastic spiking neurons from the recently developed theoretical framework of neural sampling. This functionality was implemented as an extension on top of the basic NEVESIM framework. Altogether, the intended purpose of the NEVESIM framework is to provide a basis for further extensions that support simulation of various neural network models incorporating different neuron and synapse types that can potentially also use different simulation strategies.

  1. NEVESIM: event-driven neural simulation framework with a Python interface

    PubMed Central

    Pecevski, Dejan; Kappel, David; Jonke, Zeno

    2014-01-01

    NEVESIM is a software package for event-driven simulation of networks of spiking neurons with a fast simulation core in C++, and a scripting user interface in the Python programming language. It supports simulation of heterogeneous networks with different types of neurons and synapses, and can be easily extended by the user with new neuron and synapse types. To enable heterogeneous networks and extensibility, NEVESIM is designed to decouple the simulation logic of communicating events (spikes) between the neurons at a network level from the implementation of the internal dynamics of individual neurons. In this paper we will present the simulation framework of NEVESIM, its concepts and features, as well as some aspects of the object-oriented design approaches and simulation strategies that were utilized to efficiently implement the concepts and functionalities of the framework. We will also give an overview of the Python user interface, its basic commands and constructs, and also discuss the benefits of integrating NEVESIM with Python. One of the valuable capabilities of the simulator is to simulate exactly and efficiently networks of stochastic spiking neurons from the recently developed theoretical framework of neural sampling. This functionality was implemented as an extension on top of the basic NEVESIM framework. Altogether, the intended purpose of the NEVESIM framework is to provide a basis for further extensions that support simulation of various neural network models incorporating different neuron and synapse types that can potentially also use different simulation strategies. PMID:25177291

  2. A New Simulation Framework for Autonomy in Robotic Missions

    NASA Technical Reports Server (NTRS)

    Flueckiger, Lorenzo; Neukom, Christian

    2003-01-01

    Autonomy is a key factor in remote robotic exploration and there is significant activity addressing the application of autonomy to remote robots. It has become increasingly important to have simulation tools available to test the autonomy algorithms. While indus1;rial robotics benefits from a variety of high quality simulation tools, researchers developing autonomous software are still dependent primarily on block-world simulations. The Mission Simulation Facility I(MSF) project addresses this shortcoming with a simulation toolkit that will enable developers of autonomous control systems to test their system s performance against a set of integrated, standardized simulations of NASA mission scenarios. MSF provides a distributed architecture that connects the autonomous system to a set of simulated components replacing the robot hardware and its environment.

  3. A Runtime Verification Framework for Control System Simulation

    SciTech Connect

    Ciraci, Selim; Fuller, Jason C.; Daily, Jeffrey A.; Makhmalbaf, Atefe; Callahan, Charles D.

    2014-08-02

    n a standard workflow for the validation of a control system, the control system is implemented as an extension to a simulator. Such simulators are complex software systems, and engineers may unknowingly violate constraints a simulator places on extensions. As such, errors may be introduced in the implementation of either the control system or the simulator leading to invalid simulation results. This paper presents a novel runtime verification approach for verifying control system implementations within simulators. The major contribution of the approach is the two-tier specification process. In the first tier, engineers model constraints using a domain-specific language tailored to modeling a controller’s response to changes in its input. The language is high-level and effectively hides the implementation details of the simulator, allowing engineers to specify design-level constraints independent of low-level simulator interfaces. In the second tier, simulator developers provide mapping rules for mapping design-level constraints to the implementation of the simulator. Using the rules, an automated tool transforms the design-level specifications into simulator-specific runtime verification specifications and generates monitoring code which is injected into the implementation of the simulator. During simulation, these monitors observe the input and output variables of the control system and report changes to the verifier. The verifier checks whether these changes follow the constraints of the control system. We describe application of this approach to the verification of the constraints of an HVAC control system implemented with the power grid simulator GridLAB-D.

  4. Agent based modeling of "crowdinforming" as a means of load balancing at emergency departments.

    PubMed

    Neighbour, Ryan; Oppenheimer, Luis; Mukhi, Shamir N; Friesen, Marcia R; McLeod, Robert D

    2010-01-01

    This work extends ongoing development of a framework for modeling the spread of contact-transmission infectious diseases. The framework is built upon Agent Based Modeling (ABM), with emphasis on urban scale modelling integrated with institutional models of hospital emergency departments. The method presented here includes ABM modeling an outbreak of influenza-like illness (ILI) with concomitant surges at hospital emergency departments, and illustrates the preliminary modeling of 'crowdinforming' as an intervention. 'Crowdinforming', a component of 'crowdsourcing', is characterized as the dissemination of collected and processed information back to the 'crowd' via public access. The objective of the simulation is to allow for effective policy evaluation to better inform the public of expected wait times as part of their decision making process in attending an emergency department or clinic. In effect, this is a means of providing additional decision support garnered from a simulation, prior to real world implementation. The conjecture is that more optimal service delivery can be achieved under balanced patient loads, compared to situations where some emergency departments are overextended while others are underutilized. Load balancing optimization is a common notion in many operations, and the simulation illustrates that 'crowdinforming' is a potential tool when used as a process control parameter to balance the load at emergency departments as well as serving as an effective means to direct patients during an ILI outbreak with temporary clinics deployed. The information provided in the 'crowdinforming' model is readily available in a local context, although it requires thoughtful consideration in its interpretation. The extension to a wider dissemination of information via a web service is readily achievable and presents no technical obstacles, although political obstacles may be present. The 'crowdinforming' simulation is not limited to arrivals of patients at

  5. An agent-based hydroeconomic model to evaluate water policies in Jordan

    NASA Astrophysics Data System (ADS)

    Yoon, J.; Gorelick, S.

    2014-12-01

    Modern water systems can be characterized by a complex network of institutional and private actors that represent competing sectors and interests. Identifying solutions to enhance water security in such systems calls for analysis that can adequately account for this level of complexity and interaction. Our work focuses on the development of a hierarchical, multi-agent, hydroeconomic model that attempts to realistically represent complex interactions between hydrologic and multi-faceted human systems. The model is applied to Jordan, one of the most water-poor countries in the world. In recent years, the water crisis in Jordan has escalated due to an ongoing drought and influx of refugees from regional conflicts. We adopt a modular approach in which biophysical modules simulate natural and engineering phenomena, and human modules represent behavior at multiple scales of decision making. The human modules employ agent-based modeling, in which agents act as autonomous decision makers at the transboundary, state, organizational, and user levels. A systematic nomenclature and conceptual framework is used to characterize model agents and modules. Concepts from the Unified Modeling Language (UML) are adopted to promote clear conceptualization of model classes and process sequencing, establishing a foundation for full deployment of the integrated model in a scalable object-oriented programming environment. Although the framework is applied to the Jordanian water context, it is generalizable to other regional human-natural freshwater supply systems.

  6. Combining Bayesian Networks and Agent Based Modeling to develop a decision-support model in Vietnam

    NASA Astrophysics Data System (ADS)

    Nong, Bao Anh; Ertsen, Maurits; Schoups, Gerrit

    2016-04-01

    Complexity and uncertainty in natural resources management have been focus themes in recent years. Within these debates, with the aim to define an approach feasible for water management practice, we are developing an integrated conceptual modeling framework for simulating decision-making processes of citizens, in our case in the Day river area, Vietnam. The model combines Bayesian Networks (BNs) and Agent-Based Modeling (ABM). BNs are able to combine both qualitative data from consultants / experts / stakeholders, and quantitative data from observations on different phenomena or outcomes from other models. Further strengths of BNs are that the relationship between variables in the system is presented in a graphical interface, and that components of uncertainty are explicitly related to their probabilistic dependencies. A disadvantage is that BNs cannot easily identify the feedback of agents in the system once changes appear. Hence, ABM was adopted to represent the reaction among stakeholders under changes. The modeling framework is developed as an attempt to gain better understanding about citizen's behavior and factors influencing their decisions in order to reduce uncertainty in the implementation of water management policy.

  7. Integrated Modeling, Mapping, and Simulation (IMMS) framework for planning exercises.

    SciTech Connect

    Friedman-Hill, Ernest J.; Plantenga, Todd D.

    2010-06-01

    The Integrated Modeling, Mapping, and Simulation (IMMS) program is designing and prototyping a simulation and collaboration environment for linking together existing and future modeling and simulation tools to enable analysts, emergency planners, and incident managers to more effectively, economically, and rapidly prepare, analyze, train, and respond to real or potential incidents. When complete, the IMMS program will demonstrate an integrated modeling and simulation capability that supports emergency managers and responders with (1) conducting 'what-if' analyses and exercises to address preparedness, analysis, training, operations, and lessons learned, and (2) effectively, economically, and rapidly verifying response tactics, plans and procedures.

  8. An agent-based approach to financial stylized facts

    NASA Astrophysics Data System (ADS)

    Shimokawa, Tetsuya; Suzuki, Kyoko; Misawa, Tadanobu

    2007-06-01

    An important challenge of the financial theory in recent years is to construct more sophisticated models which have consistencies with as many financial stylized facts that cannot be explained by traditional models. Recently, psychological studies on decision making under uncertainty which originate in Kahneman and Tversky's research attract a lot of interest as key factors which figure out the financial stylized facts. These psychological results have been applied to the theory of investor's decision making and financial equilibrium modeling. This paper, following these behavioral financial studies, would like to propose an agent-based equilibrium model with prospect theoretical features of investors. Our goal is to point out a possibility that loss-averse feature of investors explains vast number of financial stylized facts and plays a crucial role in price formations of financial markets. Price process which is endogenously generated through our model has consistencies with, not only the equity premium puzzle and the volatility puzzle, but great kurtosis, asymmetry of return distribution, auto-correlation of return volatility, cross-correlation between return volatility and trading volume. Moreover, by using agent-based simulations, the paper also provides a rigorous explanation from the viewpoint of a lack of market liquidity to the size effect, which means that small-sized stocks enjoy excess returns compared to large-sized stocks.

  9. Agent based modeling in tactical wargaming

    NASA Astrophysics Data System (ADS)

    James, Alex; Hanratty, Timothy P.; Tuttle, Daniel C.; Coles, John B.

    2016-05-01

    Army staffs at division, brigade, and battalion levels often plan for contingency operations. As such, analysts consider the impact and potential consequences of actions taken. The Army Military Decision-Making Process (MDMP) dictates identification and evaluation of possible enemy courses of action; however, non-state actors often do not exhibit the same level and consistency of planned actions that the MDMP was originally designed to anticipate. The fourth MDMP step is a particular challenge, wargaming courses of action within the context of complex social-cultural behaviors. Agent-based Modeling (ABM) and its resulting emergent behavior is a potential solution to model terrain in terms of the human domain and improve the results and rigor of the traditional wargaming process.

  10. A modular simulation framework for colonoscopy using a new haptic device.

    PubMed

    Hellier, David; Samur, Evren; Passenger, Josh; Spälter, Ulrich; Frimmel, Hans; Appleyard, Mark; Bleuler, Hannes; Ourselin, Sébastien

    2008-01-01

    We have developed a multi-threaded framework for colonoscopy simulation utilising OpenGL with an interface to a real-time prototype colonoscopy haptic device. A modular framework has enabled us to support multiple haptic devices and efficiently integrate new research into physically based modelling of the colonoscope, colon and surrounding organs. The framework supports GPU accelerated algorithms as runtime modules, allowing the real-time calculations required for haptic feedback.

  11. Developing and Implementing a Framework of Participatory Simulation for Mobile Learning Using Scaffolding

    ERIC Educational Resources Information Center

    Yin, Chengjiu; Song, Yanjie; Tabata, Yoshiyuki; Ogata, Hiroaki; Hwang, Gwo-Jen

    2013-01-01

    This paper proposes a conceptual framework, scaffolding participatory simulation for mobile learning (SPSML), used on mobile devices for helping students learn conceptual knowledge in the classroom. As the pedagogical design, the framework adopts an experiential learning model, which consists of five sequential but cyclic steps: the initial stage,…

  12. NetSim-Steer: A Runtime Steering Framework for Network Simulators

    SciTech Connect

    Ciraci, Selim; Akyol, Bora A.

    2012-08-07

    This paper presents NetSim-Steer, a runtime steering framework for network simulators. With this framework, users can specify execution constraints for the network protocols and network models. In addition to this, users can implement steering rules to be executed when a constraint is violated. These rules allows users to alter the parameters of the protocols/models during the simulation so that they stay within the boundaries of the constraints.

  13. NetSim Steer: A Runtime Steering Framework for Network Simulators

    SciTech Connect

    Ciraci, Selim; Akyol, Bora A.

    2012-08-09

    This paper presents NetSim-Steer, a runtime steering framework for network simulators. With this framework, users can specify execution constraints for the network protocols and network models. In addition to this, users can implement steering rules to be executed when a constraint is violated. These rules allows users to alter the parameters of the protocols/models during the simulation so that they stay within the boundaries of the constraints.

  14. An Agent-Based Model for Studying Child Maltreatment and Child Maltreatment Prevention

    NASA Astrophysics Data System (ADS)

    Hu, Xiaolin; Puddy, Richard W.

    This paper presents an agent-based model that simulates the dynamics of child maltreatment and child maltreatment prevention. The developed model follows the principles of complex systems science and explicitly models a community and its families with multi-level factors and interconnections across the social ecology. This makes it possible to experiment how different factors and prevention strategies can affect the rate of child maltreatment. We present the background of this work and give an overview of the agent-based model and show some simulation results.

  15. Framework Application for Core-Edge Transport Simulations

    SciTech Connect

    2007-06-13

    FACETS is a whole-device model for magnetic-fusion experiments (including ITER) combining physics effects from sources & sinks, wall effects, edge effects, and core effects in an advanced parallel framework which manages allocation of parallel resources, performs runtime performance analysis, and provides tools for interactive steering and visualization. FACETS will be used by fusion researchers to design experimental campaigns, predict and model fusion experimental phenomena, and design and optimize future machines.

  16. High performance computing for three-dimensional agent-based molecular models.

    PubMed

    Pérez-Rodríguez, G; Pérez-Pérez, M; Fdez-Riverola, F; Lourenço, A

    2016-07-01

    Agent-based simulations are increasingly popular in exploring and understanding cellular systems, but the natural complexity of these systems and the desire to grasp different modelling levels demand cost-effective simulation strategies and tools. In this context, the present paper introduces novel sequential and distributed approaches for the three-dimensional agent-based simulation of individual molecules in cellular events. These approaches are able to describe the dimensions and position of the molecules with high accuracy and thus, study the critical effect of spatial distribution on cellular events. Moreover, two of the approaches allow multi-thread high performance simulations, distributing the three-dimensional model in a platform independent and computationally efficient way. Evaluation addressed the reproduction of molecular scenarios and different scalability aspects of agent creation and agent interaction. The three approaches simulate common biophysical and biochemical laws faithfully. The distributed approaches show improved performance when dealing with large agent populations while the sequential approach is better suited for small to medium size agent populations. Overall, the main new contribution of the approaches is the ability to simulate three-dimensional agent-based models at the molecular level with reduced implementation effort and moderate-level computational capacity. Since these approaches have a generic design, they have the major potential of being used in any event-driven agent-based tool.

  17. Agent-based model to rural urban migration analysis

    NASA Astrophysics Data System (ADS)

    Silveira, Jaylson J.; Espíndola, Aquino L.; Penna, T. J. P.

    2006-05-01

    In this paper, we analyze the rural-urban migration phenomenon as it is usually observed in economies which are in the early stages of industrialization. The analysis is conducted by means of a statistical mechanics approach which builds a computational agent-based model. Agents are placed on a lattice and the connections among them are described via an Ising-like model. Simulations on this computational model show some emergent properties that are common in developing economies, such as a transitional dynamics characterized by continuous growth of urban population, followed by the equalization of expected wages between rural and urban sectors (Harris-Todaro equilibrium condition), urban concentration and increasing of per capita income.

  18. Climate Shocks and Migration: An Agent-Based Modeling Approach.

    PubMed

    Entwisle, Barbara; Williams, Nathalie E; Verdery, Ashton M; Rindfuss, Ronald R; Walsh, Stephen J; Malanson, George P; Mucha, Peter J; Frizzelle, Brian G; McDaniel, Philip M; Yao, Xiaozheng; Heumann, Benjamin W; Prasartkul, Pramote; Sawangdee, Yothin; Jampaklay, Aree

    2016-09-01

    This is a study of migration responses to climate shocks. We construct an agent-based model that incorporates dynamic linkages between demographic behaviors, such as migration, marriage, and births, and agriculture and land use, which depend on rainfall patterns. The rules and parameterization of our model are empirically derived from qualitative and quantitative analyses of a well-studied demographic field site, Nang Rong district, Northeast Thailand. With this model, we simulate patterns of migration under four weather regimes in a rice economy: 1) a reference, 'normal' scenario; 2) seven years of unusually wet weather; 3) seven years of unusually dry weather; and 4) seven years of extremely variable weather. Results show relatively small impacts on migration. Experiments with the model show that existing high migration rates and strong selection factors, which are unaffected by climate change, are likely responsible for the weak migration response.

  19. Validating agent based models through virtual worlds.

    SciTech Connect

    Lakkaraju, Kiran; Whetzel, Jonathan H.; Lee, Jina; Bier, Asmeret Brooke; Cardona-Rivera, Rogelio E.; Bernstein, Jeremy Ray Rhythm

    2014-01-01

    As the US continues its vigilance against distributed, embedded threats, understanding the political and social structure of these groups becomes paramount for predicting and dis- rupting their attacks. Agent-based models (ABMs) serve as a powerful tool to study these groups. While the popularity of social network tools (e.g., Facebook, Twitter) has provided extensive communication data, there is a lack of ne-grained behavioral data with which to inform and validate existing ABMs. Virtual worlds, in particular massively multiplayer online games (MMOG), where large numbers of people interact within a complex environ- ment for long periods of time provide an alternative source of data. These environments provide a rich social environment where players engage in a variety of activities observed between real-world groups: collaborating and/or competing with other groups, conducting battles for scarce resources, and trading in a market economy. Strategies employed by player groups surprisingly re ect those seen in present-day con icts, where players use diplomacy or espionage as their means for accomplishing their goals. In this project, we propose to address the need for ne-grained behavioral data by acquiring and analyzing game data a commercial MMOG, referred to within this report as Game X. The goals of this research were: (1) devising toolsets for analyzing virtual world data to better inform the rules that govern a social ABM and (2) exploring how virtual worlds could serve as a source of data to validate ABMs established for analogous real-world phenomena. During this research, we studied certain patterns of group behavior to compliment social modeling e orts where a signi cant lack of detailed examples of observed phenomena exists. This report outlines our work examining group behaviors that underly what we have termed the Expression-To-Action (E2A) problem: determining the changes in social contact that lead individuals/groups to engage in a particular behavior

  20. Abdominal surgery process modeling framework for simulation using spreadsheets.

    PubMed

    Boshkoska, Biljana Mileva; Damij, Talib; Jelenc, Franc; Damij, Nadja

    2015-08-01

    We provide a continuation of the existing Activity Table Modeling methodology with a modular spreadsheets simulation. The simulation model developed is comprised of 28 modeling elements for the abdominal surgery cycle process. The simulation of a two-week patient flow in an abdominal clinic with 75 beds demonstrates the applicability of the methodology. The simulation does not include macros, thus programming experience is not essential for replication or upgrading the model. Unlike the existing methods, the proposed solution employs a modular approach for modeling the activities that ensures better readability, the possibility of easily upgrading the model with other activities, and its easy extension and connectives with other similar models. We propose a first-in-first-served approach for simulation of servicing multiple patients. The uncertain time duration of the activities is modeled using the function "rand()". The patients movements from one activity to the next one is tracked with nested "if()" functions, thus allowing easy re-creation of the process without the need of complex programming.

  1. Hierarchical Petascale Simulation Framework for Stress Corrosion Cracking

    SciTech Connect

    Vashishta, Priya

    2014-12-01

    Reaction Dynamics in Energetic Materials: Detonation is a prototype of mechanochemistry, in which mechanically and thermally induced chemical reactions far from equilibrium exhibit vastly different behaviors. It is also one of the hardest multiscale physics problems, in which diverse length and time scales play important roles. The CACS group has performed multimillion-atom reactive MD simulations to reveal a novel two-stage reaction mechanism during the detonation of cyclotrimethylenetrinitramine (RDX) crystal. Rapid production of N2 and H2O within ~10 ps is followed by delayed production of CO molecules within ~ 1 ns. They found that further decomposition towards the final products is inhibited by the formation of large metastable C- and O-rich clusters with fractal geometry. The CACS group has also simulated the oxidation dynamics of close-packed aggregates of aluminum nanoparticles passivated by oxide shells. Their simulation results suggest an unexpectedly active role of the oxide shell as a nanoreactor.

  2. Agent-based modeling in ecological economics.

    PubMed

    Heckbert, Scott; Baynes, Tim; Reeson, Andrew

    2010-01-01

    Interconnected social and environmental systems are the domain of ecological economics, and models can be used to explore feedbacks and adaptations inherent in these systems. Agent-based modeling (ABM) represents autonomous entities, each with dynamic behavior and heterogeneous characteristics. Agents interact with each other and their environment, resulting in emergent outcomes at the macroscale that can be used to quantitatively analyze complex systems. ABM is contributing to research questions in ecological economics in the areas of natural resource management and land-use change, urban systems modeling, market dynamics, changes in consumer attitudes, innovation, and diffusion of technology and management practices, commons dilemmas and self-governance, and psychological aspects to human decision making and behavior change. Frontiers for ABM research in ecological economics involve advancing the empirical calibration and validation of models through mixed methods, including surveys, interviews, participatory modeling, and, notably, experimental economics to test specific decision-making hypotheses. Linking ABM with other modeling techniques at the level of emergent properties will further advance efforts to understand dynamics of social-environmental systems.

  3. Agent Based Model of Livestock Movements

    NASA Astrophysics Data System (ADS)

    Miron, D. J.; Emelyanova, I. V.; Donald, G. E.; Garner, G. M.

    The modelling of livestock movements within Australia is of national importance for the purposes of the management and control of exotic disease spread, infrastructure development and the economic forecasting of livestock markets. In this paper an agent based model for the forecasting of livestock movements is presented. This models livestock movements from farm to farm through a saleyard. The decision of farmers to sell or buy cattle is often complex and involves many factors such as climate forecast, commodity prices, the type of farm enterprise, the number of animals available and associated off-shore effects. In this model the farm agent's intelligence is implemented using a fuzzy decision tree that utilises two of these factors. These two factors are the livestock price fetched at the last sale and the number of stock on the farm. On each iteration of the model farms choose either to buy, sell or abstain from the market thus creating an artificial supply and demand. The buyers and sellers then congregate at the saleyard where livestock are auctioned using a second price sealed bid. The price time series output by the model exhibits properties similar to those found in real livestock markets.

  4. Maestro: An Orchestration Framework for Large-Scale WSN Simulations

    PubMed Central

    Riliskis, Laurynas; Osipov, Evgeny

    2014-01-01

    Contemporary wireless sensor networks (WSNs) have evolved into large and complex systems and are one of the main technologies used in cyber-physical systems and the Internet of Things. Extensive research on WSNs has led to the development of diverse solutions at all levels of software architecture, including protocol stacks for communications. This multitude of solutions is due to the limited computational power and restrictions on energy consumption that must be accounted for when designing typical WSN systems. It is therefore challenging to develop, test and validate even small WSN applications, and this process can easily consume significant resources. Simulations are inexpensive tools for testing, verifying and generally experimenting with new technologies in a repeatable fashion. Consequently, as the size of the systems to be tested increases, so does the need for large-scale simulations. This article describes a tool called Maestro for the automation of large-scale simulation and investigates the feasibility of using cloud computing facilities for such task. Using tools that are built into Maestro, we demonstrate a feasible approach for benchmarking cloud infrastructure in order to identify cloud Virtual Machine (VM)instances that provide an optimal balance of performance and cost for a given simulation. PMID:24647123

  5. Maestro: an orchestration framework for large-scale WSN simulations.

    PubMed

    Riliskis, Laurynas; Osipov, Evgeny

    2014-03-18

    Contemporary wireless sensor networks (WSNs) have evolved into large and complex systems and are one of the main technologies used in cyber-physical systems and the Internet of Things. Extensive research on WSNs has led to the development of diverse solutions at all levels of software architecture, including protocol stacks for communications. This multitude of solutions is due to the limited computational power and restrictions on energy consumption that must be accounted for when designing typical WSN systems. It is therefore challenging to develop, test and validate even small WSN applications, and this process can easily consume significant resources. Simulations are inexpensive tools for testing, verifying and generally experimenting with new technologies in a repeatable fashion. Consequently, as the size of the systems to be tested increases, so does the need for large-scale simulations. This article describes a tool called Maestro for the automation of large-scale simulation and investigates the feasibility of using cloud computing facilities for such task. Using tools that are built into Maestro, we demonstrate a feasible approach for benchmarking cloud infrastructure in order to identify cloud Virtual Machine (VM)instances that provide an optimal balance of performance and cost for a given simulation.

  6. A Framework to Simulate Semiconductor Devices Using Parallel Computer Architecture

    NASA Astrophysics Data System (ADS)

    Kumar, Gaurav; Singh, Mandeep; Bulusu, Anand; Trivedi, Gaurav

    2016-10-01

    Device simulations have become an integral part of semiconductor technology to address many issues (short channel effects, narrow width effects, hot-electron effect) as it goes into nano regime, helping us to continue further with the Moore's Law. TCAD provides a simulation environment to design and develop novel devices, thus a leap forward to study their electrical behaviour in advance. In this paper, a parallel 2D simulator for semiconductor devices using Discontinuous Galerkin Finite Element Method (DG-FEM) is presented. Discontinuous Galerkin (DG) method is used to discretize essential device equations and later these equations are analyzed by using a suitable methodology to find the solution. DG method is characterized to provide more accurate solution as it efficiently conserve the flux and easily handles complex geometries. OpenMP is used to parallelize solution of device equations on manycore processors and a speed of 1.4x is achieved during assembly process of discretization. This study is important for more accurate analysis of novel devices (such as FinFET, GAAFET etc.) on a parallel computing platform and will help us to develop a parallel device simulator which will be able to address this issue efficiently. A case study of PN junction diode is presented to show the effectiveness of proposed approach.

  7. [Simulation in health care, an overview and framework for development].

    PubMed

    Herbreteau, Francine; Granry, Jean-Claude

    2017-03-01

    Following the example of Anglo-Saxon countries, which have been using it for some thirty years, simulation in health care is growing rapidly in France. The development of this challenging pedagogical method is guided by several documents published by the French National Health Authority.

  8. Simulation toolkit with CMOS detector in the framework of hadrontherapy

    NASA Astrophysics Data System (ADS)

    Rescigno, R.; Finck, Ch.; Juliani, D.; Baudot, J.; Dauvergne, D.; Dedes, G.; Krimmer, J.; Ray, C.; Reithinger, V.; Rousseau, M.; Testa, E.; Winter, M.

    2014-03-01

    Proton imaging can be seen as a powerful technique for on-line monitoring of ion range during carbon ion therapy irradiation. The protons detection technique uses, as three-dimensional tracking system, a set of CMOS sensor planes. A simulation toolkit based on GEANT4 and ROOT is presented including detector response and reconstruction algorithm.

  9. Design and Performance Frameworks for Constructing Problem-Solving Simulations

    ERIC Educational Resources Information Center

    Stevens, Rons; Palacio-Cayetano, Joycelin

    2003-01-01

    Rapid advancements in hardware, software, and connectivity are helping to shorten the times needed to develop computer simulations for science education. These advancements, however, have not been accompanied by corresponding theories of how best to design and use these technologies for teaching, learning, and testing. Such design frameworks…

  10. Power grid simulation applications developed using the GridPACK™ high performance computing framework

    SciTech Connect

    Jin, Shuangshuang; Chen, Yousu; Diao, Ruisheng; Huang, Zhenyu; Perkins, William; Palmer, Bruce

    2016-12-01

    This paper describes the GridPACK™ software framework for developing power grid simulations that can run on high performance computing platforms, with several example applications (dynamic simulation, static contingency analysis, and dynamic contingency analysis) that have been developed using GridPACK.

  11. Designing a Virtual Olympic Games Framework by Using Simulation in Web 2.0 Technologies

    ERIC Educational Resources Information Center

    Stoilescu, Dorian

    2013-01-01

    Instructional simulation had major difficulties in the past for offering limited possibilities in practice and learning. This article proposes a link between instructional simulation and Web 2.0 technologies. More exactly, I present the design of the Virtual Olympic Games Framework (VOGF), as a significant demonstration of how interactivity in…

  12. Agent based models for testing city evacuation strategies under a flood event as strategy to reduce flood risk

    NASA Astrophysics Data System (ADS)

    Medina, Neiler; Sanchez, Arlex; Nokolic, Igor; Vojinovic, Zoran

    2016-04-01

    This research explores the uses of Agent Based Models (ABM) and its potential to test large scale evacuation strategies in coastal cities at risk from flood events due to extreme hydro-meteorological events with the final purpose of disaster risk reduction by decreasing human's exposure to the hazard. The first part of the paper corresponds to the theory used to build the models such as: Complex adaptive systems (CAS) and the principles and uses of ABM in this field. The first section outlines the pros and cons of using AMB to test city evacuation strategies at medium and large scale. The second part of the paper focuses on the central theory used to build the ABM, specifically the psychological and behavioral model as well as the framework used in this research, specifically the PECS reference model is cover in this section. The last part of this section covers the main attributes or characteristics of human beings used to described the agents. The third part of the paper shows the methodology used to build and implement the ABM model using Repast-Symphony as an open source agent-based modelling and simulation platform. The preliminary results for the first implementation in a region of the island of Sint-Maarten a Dutch Caribbean island are presented and discussed in the fourth section of paper. The results obtained so far, are promising for a further development of the model and its implementation and testing in a full scale city

  13. Hybrid framework for the simulation of stochastic chemical kinetics

    NASA Astrophysics Data System (ADS)

    Duncan, Andrew; Erban, Radek; Zygalakis, Konstantinos

    2016-12-01

    Stochasticity plays a fundamental role in various biochemical processes, such as cell regulatory networks and enzyme cascades. Isothermal, well-mixed systems can be modelled as Markov processes, typically simulated using the Gillespie Stochastic Simulation Algorithm (SSA) [25]. While easy to implement and exact, the computational cost of using the Gillespie SSA to simulate such systems can become prohibitive as the frequency of reaction events increases. This has motivated numerous coarse-grained schemes, where the "fast" reactions are approximated either using Langevin dynamics or deterministically. While such approaches provide a good approximation when all reactants are abundant, the approximation breaks down when one or more species exist only in small concentrations and the fluctuations arising from the discrete nature of the reactions become significant. This is particularly problematic when using such methods to compute statistics of extinction times for chemical species, as well as simulating non-equilibrium systems such as cell-cycle models in which a single species can cycle between abundance and scarcity. In this paper, a hybrid jump-diffusion model for simulating well-mixed stochastic kinetics is derived. It acts as a bridge between the Gillespie SSA and the chemical Langevin equation. For low reactant reactions the underlying behaviour is purely discrete, while purely diffusive when the concentrations of all species are large, with the two different behaviours coexisting in the intermediate region. A bound on the weak error in the classical large volume scaling limit is obtained, and three different numerical discretisations of the jump-diffusion model are described. The benefits of such a formalism are illustrated using computational examples.

  14. A framework for service enterprise workflow simulation with multi-agents cooperation

    NASA Astrophysics Data System (ADS)

    Tan, Wenan; Xu, Wei; Yang, Fujun; Xu, Lida; Jiang, Chuanqun

    2013-11-01

    Process dynamic modelling for service business is the key technique for Service-Oriented information systems and service business management, and the workflow model of business processes is the core part of service systems. Service business workflow simulation is the prevalent approach to be used for analysis of service business process dynamically. Generic method for service business workflow simulation is based on the discrete event queuing theory, which is lack of flexibility and scalability. In this paper, we propose a service workflow-oriented framework for the process simulation of service businesses using multi-agent cooperation to address the above issues. Social rationality of agent is introduced into the proposed framework. Adopting rationality as one social factor for decision-making strategies, a flexible scheduling for activity instances has been implemented. A system prototype has been developed to validate the proposed simulation framework through a business case study.

  15. A geostatistical extreme-value framework for fast simulation of natural hazard events.

    PubMed

    Youngman, Benjamin D; Stephenson, David B

    2016-05-01

    We develop a statistical framework for simulating natural hazard events that combines extreme value theory and geostatistics. Robust generalized additive model forms represent generalized Pareto marginal distribution parameters while a Student's t-process captures spatial dependence and gives a continuous-space framework for natural hazard event simulations. Efficiency of the simulation method allows many years of data (typically over 10 000) to be obtained at relatively little computational cost. This makes the model viable for forming the hazard module of a catastrophe model. We illustrate the framework by simulating maximum wind gusts for European windstorms, which are found to have realistic marginal and spatial properties, and validate well against wind gust measurements.

  16. The Unified Behavior Framework for the Simulation of Autonomous Agents

    DTIC Science & Technology

    2015-03-01

    architectures. Brooks built more complex behaviors on top of the lower-level “instincts,” so that the robot could explore by wandering throughout its...time has passed. With this in mind , every entity in the simulation has a method that re-calculates the state of that entity, and is called every time...making, a much more accurate representation of the pilots mind could be obtained with the UBF tree. In addition to the mental model fidelity, complexity

  17. A Framework for the Measurement of Simulated Behavior Performance

    DTIC Science & Technology

    2011-03-24

    takes professional soccer team recordings to aid Robocup team tactics development, measuring success through goal tracking [5]. With interest in...Cloning for Simulator Validation”. Ubbo Visser, Fernando Ribeiro, Takeshi Ohashi, and Frank Dellaert (editors), RoboCup 2007: Robot Soccer World Cup...XI, volume 5001 of Lecture Notes in Computer Science, 329–336. Springer Berlin / Heidelberg, 2008. URL http://dx.doi.org/10. 1007/978-3-540-68847-1_32

  18. Extensible Modeling and Simulation Framework (XMSF) 2004 Project Summary Report

    DTIC Science & Technology

    2007-11-02

    common solution is the use of metamodels. We recommend starting work on a common layered metamodel to organize and map the proposed standards, very...process; e.g., one (or more) describing the natural environment, one (or more) describing military and non-military forces to be represented in the...simulation. Markup languages based on XML, Internet technologies, and Web services are combining to enable a new generation of distributed M&S

  19. A Modular Simulation Framework for Assessing Swarm Search Models

    DTIC Science & Technology

    2014-09-01

    Autonomous Agents and Multiagent Systems. Bologna, Italy: ACM, 2002, pp. 449–450. [22] J. E. Kline, “Red Dragon at Sea Scenario 2025,” unpublished. [23...different target module, the United States Coast Guard could simulate search and rescue operations for personnel lost at sea , or the searcher module could...natural gas and oil deposits in the East China Sea comes at a critical time for the country. China immediately claims sovereignty over these natural

  20. A compressible multiphase framework for simulating supersonic atomization

    NASA Astrophysics Data System (ADS)

    Regele, Jonathan D.; Garrick, Daniel P.; Hosseinzadeh-Nik, Zahra; Aslani, Mohamad; Owkes, Mark

    2016-11-01

    The study of atomization in supersonic combustors is critical in designing efficient and high performance scramjets. Numerical methods incorporating surface tension effects have largely focused on the incompressible regime as most atomization applications occur at low Mach numbers. Simulating surface tension effects in high speed compressible flow requires robust numerical methods that can handle discontinuities caused by both material interfaces and shocks. A shock capturing/diffused interface method is developed to simulate high-speed compressible gas-liquid flows with surface tension effects using the five-equation model. This includes developments that account for the interfacial pressure jump that occurs in the presence of surface tension. A simple and efficient method for computing local interface curvature is developed and an acoustic non-dimensional scaling for the surface tension force is proposed. The method successfully captures a variety of droplet breakup modes over a range of Weber numbers and demonstrates the impact of surface tension in countering droplet deformation in both subsonic and supersonic cross flows.

  1. Turbulent Simulations of Divertor Detachment Based On BOUT + + Framework

    NASA Astrophysics Data System (ADS)

    Chen, Bin; Xu, Xueqiao; Xia, Tianyang; Ye, Minyou

    2015-11-01

    China Fusion Engineering Testing Reactor is under conceptual design, acting as a bridge between ITER and DEMO. The detached divertor operation offers great promise for a reduction of heat flux onto divertor target plates for acceptable erosion. Therefore, a density scan is performed via an increase of D2 gas puffing rates in the range of 0 . 0 ~ 5 . 0 ×1023s-1 by using the B2-Eirene/SOLPS 5.0 code package to study the heat flux control and impurity screening property. As the density increases, it shows a gradually change of the divertor operation status, from low-recycling regime to high-recycling regime and finally to detachment. Significant radiation loss inside the confined plasma in the divertor region during detachment leads to strong parallel density and temperature gradients. Based on the SOLPS simulations, BOUT + + simulations will be presented to investigate the stability and turbulent transport under divertor plasma detachment, particularly the strong parallel gradient driven instabilities and enhanced plasma turbulence to spread heat flux over larger surface areas. The correlation between outer mid-plane and divertor turbulence and the related transport will be analyzed. Prepared by LLNL under Contract DE-AC52-07NA27344. LLNL-ABS-675075.

  2. Improving Agent Based Models and Validation through Data Fusion

    PubMed Central

    Laskowski, Marek; Demianyk, Bryan C.P.; Friesen, Marcia R.; McLeod, Robert D.; Mukhi, Shamir N.

    2011-01-01

    This work is contextualized in research in modeling and simulation of infection spread within a community or population, with the objective to provide a public health and policy tool in assessing the dynamics of infection spread and the qualitative impacts of public health interventions. This work uses the integration of real data sources into an Agent Based Model (ABM) to simulate respiratory infection spread within a small municipality. Novelty is derived in that the data sources are not necessarily obvious within ABM infection spread models. The ABM is a spatial-temporal model inclusive of behavioral and interaction patterns between individual agents on a real topography. The agent behaviours (movements and interactions) are fed by census / demographic data, integrated with real data from a telecommunication service provider (cellular records) and person-person contact data obtained via a custom 3G Smartphone application that logs Bluetooth connectivity between devices. Each source provides data of varying type and granularity, thereby enhancing the robustness of the model. The work demonstrates opportunities in data mining and fusion that can be used by policy and decision makers. The data become real-world inputs into individual SIR disease spread models and variants, thereby building credible and non-intrusive models to qualitatively simulate and assess public health interventions at the population level. PMID:23569606

  3. Using Agent Base Models to Optimize Large Scale Network for Large System Inventories

    NASA Technical Reports Server (NTRS)

    Shameldin, Ramez Ahmed; Bowling, Shannon R.

    2010-01-01

    The aim of this paper is to use Agent Base Models (ABM) to optimize large scale network handling capabilities for large system inventories and to implement strategies for the purpose of reducing capital expenses. The models used in this paper either use computational algorithms or procedure implementations developed by Matlab to simulate agent based models in a principal programming language and mathematical theory using clusters, these clusters work as a high performance computational performance to run the program in parallel computational. In both cases, a model is defined as compilation of a set of structures and processes assumed to underlie the behavior of a network system.

  4. Agent-Based Modeling of Cancer Stem Cell Driven Solid Tumor Growth.

    PubMed

    Poleszczuk, Jan; Macklin, Paul; Enderling, Heiko

    2016-01-01

    Computational modeling of tumor growth has become an invaluable tool to simulate complex cell-cell interactions and emerging population-level dynamics. Agent-based models are commonly used to describe the behavior and interaction of individual cells in different environments. Behavioral rules can be informed and calibrated by in vitro assays, and emerging population-level dynamics may be validated with both in vitro and in vivo experiments. Here, we describe the design and implementation of a lattice-based agent-based model of cancer stem cell driven tumor growth.

  5. A Distributed Platform for Global-Scale Agent-Based Models of Disease Transmission

    PubMed Central

    Parker, Jon; Epstein, Joshua M.

    2013-01-01

    The Global-Scale Agent Model (GSAM) is presented. The GSAM is a high-performance distributed platform for agent-based epidemic modeling capable of simulating a disease outbreak in a population of several billion agents. It is unprecedented in its scale, its speed, and its use of Java. Solutions to multiple challenges inherent in distributing massive agent-based models are presented. Communication, synchronization, and memory usage are among the topics covered in detail. The memory usage discussion is Java specific. However, the communication and synchronization discussions apply broadly. We provide benchmarks illustrating the GSAM’s speed and scalability. PMID:24465120

  6. A configurable distributed high-performance computing framework for satellite's TDI-CCD imaging simulation

    NASA Astrophysics Data System (ADS)

    Xue, Bo; Mao, Bingjing; Chen, Xiaomei; Ni, Guoqiang

    2010-11-01

    This paper renders a configurable distributed high performance computing(HPC) framework for TDI-CCD imaging simulation. It uses strategy pattern to adapt multi-algorithms. Thus, this framework help to decrease the simulation time with low expense. Imaging simulation for TDI-CCD mounted on satellite contains four processes: 1) atmosphere leads degradation, 2) optical system leads degradation, 3) electronic system of TDI-CCD leads degradation and re-sampling process, 4) data integration. Process 1) to 3) utilize diversity data-intensity algorithms such as FFT, convolution and LaGrange Interpol etc., which requires powerful CPU. Even uses Intel Xeon X5550 processor, regular series process method takes more than 30 hours for a simulation whose result image size is 1500 * 1462. With literature study, there isn't any mature distributing HPC framework in this field. Here we developed a distribute computing framework for TDI-CCD imaging simulation, which is based on WCF[1], uses Client/Server (C/S) layer and invokes the free CPU resources in LAN. The server pushes the process 1) to 3) tasks to those free computing capacity. Ultimately we rendered the HPC in low cost. In the computing experiment with 4 symmetric nodes and 1 server , this framework reduced about 74% simulation time. Adding more asymmetric nodes to the computing network, the time decreased namely. In conclusion, this framework could provide unlimited computation capacity in condition that the network and task management server are affordable. And this is the brand new HPC solution for TDI-CCD imaging simulation and similar applications.

  7. Using a scalable modeling and simulation framework to evaluate the benefits of intelligent transportation systems.

    SciTech Connect

    Ewing, T.; Tentner, A.

    2000-03-21

    A scalable, distributed modeling and simulation framework has been developed at Argonne National Laboratory to study Intelligent Transportation Systems. The framework can run on a single-processor workstation, or run distributed on a multiprocessor computer or network of workstations. The framework is modular and supports plug-in models, hardware, and live data sources. The initial set of models currently includes road network and traffic flow, probe and smart vehicles, traffic management centers, communications between vehicles and centers, in-vehicle navigation systems, roadway traffic advisories. The modeling and simulation capability has been used to examine proposed ITS concepts. Results are presented from modeling scenarios from the Advanced Driver and Vehicle Advisory Navigation Concept (ADVANCE) experimental program to demonstrate how the framework can be used to evaluate the benefits of ITS and to plan future ITS operational tests and deployment initiatives.

  8. A conceptual modeling framework for discrete event simulation using hierarchical control structures

    PubMed Central

    Furian, N.; O’Sullivan, M.; Walker, C.; Vössner, S.; Neubacher, D.

    2015-01-01

    Conceptual Modeling (CM) is a fundamental step in a simulation project. Nevertheless, it is only recently that structured approaches towards the definition and formulation of conceptual models have gained importance in the Discrete Event Simulation (DES) community. As a consequence, frameworks and guidelines for applying CM to DES have emerged and discussion of CM for DES is increasing. However, both the organization of model-components and the identification of behavior and system control from standard CM approaches have shortcomings that limit CM’s applicability to DES. Therefore, we discuss the different aspects of previous CM frameworks and identify their limitations. Further, we present the Hierarchical Control Conceptual Modeling framework that pays more attention to the identification of a models’ system behavior, control policies and dispatching routines and their structured representation within a conceptual model. The framework guides the user step-by-step through the modeling process and is illustrated by a worked example. PMID:26778940

  9. A conceptual modeling framework for discrete event simulation using hierarchical control structures.

    PubMed

    Furian, N; O'Sullivan, M; Walker, C; Vössner, S; Neubacher, D

    2015-08-01

    Conceptual Modeling (CM) is a fundamental step in a simulation project. Nevertheless, it is only recently that structured approaches towards the definition and formulation of conceptual models have gained importance in the Discrete Event Simulation (DES) community. As a consequence, frameworks and guidelines for applying CM to DES have emerged and discussion of CM for DES is increasing. However, both the organization of model-components and the identification of behavior and system control from standard CM approaches have shortcomings that limit CM's applicability to DES. Therefore, we discuss the different aspects of previous CM frameworks and identify their limitations. Further, we present the Hierarchical Control Conceptual Modeling framework that pays more attention to the identification of a models' system behavior, control policies and dispatching routines and their structured representation within a conceptual model. The framework guides the user step-by-step through the modeling process and is illustrated by a worked example.

  10. Creating a Software Framework for Simulating Satellite Geolocation

    SciTech Connect

    Koch, Daniel B

    2011-01-01

    It is hard to imagine life these days without having some sort of electronic indication of one's current location. Whether the purpose is for business, personal, or emergency use, utilizing smart cell phones, in-vehicle navigation systems, or location beacons, dependence on the Global Positioning System (GPS) is pervasive. Yet the availability of the GPS should not be taken for granted. Both environmental (e.g., terrain, weather) and intentional interference (i.e., jamming) can reduce or deny satellite access. In order to investigate these and other issues, as well as to explore possible alternative satellite constellations, an application called the Satellite Simulation Toolkit (SatSim) was created. This paper presents a high-level overview of SatSim and an example of how it may be used to study geolocation.

  11. Simulation Framework for Rapid Entry, Descent, and Landing (EDL) Analysis, Phase 2 Results

    NASA Technical Reports Server (NTRS)

    Murri, Daniel G.

    2011-01-01

    The NASA Engineering and Safety Center (NESC) was requested to establish the Simulation Framework for Rapid Entry, Descent, and Landing (EDL) Analysis assessment, which involved development of an enhanced simulation architecture using the Program to Optimize Simulated Trajectories II simulation tool. The assessment was requested to enhance the capability of the Agency to provide rapid evaluation of EDL characteristics in systems analysis studies, preliminary design, mission development and execution, and time-critical assessments. Many of the new simulation framework capabilities were developed to support the Agency EDL-Systems Analysis (SA) team that is conducting studies of the technologies and architectures that are required to enable human and higher mass robotic missions to Mars. The findings, observations, and recommendations from the NESC are provided in this report.

  12. Simulation Framework for Rapid Entry, Descent, and Landing (EDL) Analysis. Volume 1

    NASA Technical Reports Server (NTRS)

    Murri, Daniel G.

    2010-01-01

    The NASA Engineering and Safety Center (NESC) was requested to establish the Simulation Framework for Rapid Entry, Descent, and Landing (EDL) Analysis assessment, which involved development of an enhanced simulation architecture using the Program to Optimize Simulated Trajectories II (POST2) simulation tool. The assessment was requested to enhance the capability of the Agency to provide rapid evaluation of EDL characteristics in systems analysis studies, preliminary design, mission development and execution, and time-critical assessments. Many of the new simulation framework capabilities were developed to support the Agency EDL Systems Analysis (EDL-SA) team, that is conducting studies of the technologies and architectures that are required to enable higher mass robotic and human mission to Mars. The findings of the assessment are contained in this report.

  13. Simulation Framework for Rapid Entry, Descent, and Landing (EDL) Analysis. Volume 2; Appendices

    NASA Technical Reports Server (NTRS)

    Murri, Daniel G.

    2010-01-01

    The NASA Engineering and Safety Center (NESC) was requested to establish the Simulation Framework for Rapid Entry, Descent, and Landing (EDL) Analysis assessment, which involved development of an enhanced simulation architecture using the Program to Optimize Simulated Trajectories II (POST2) simulation tool. The assessment was requested to enhance the capability of the Agency to provide rapid evaluation of EDL characteristics in systems analysis studies, preliminary design, mission development and execution, and time-critical assessments. Many of the new simulation framework capabilities were developed to support the Agency EDL Systems Analysis (EDL-SA) team, that is conducting studies of the technologies and architectures that are required to enable higher mass robotic and human mission to Mars. The appendices to the original report are contained in this document.

  14. Demeter, persephone, and the search for emergence in agent-based models.

    SciTech Connect

    North, M. J.; Howe, T. R.; Collier, N. T.; Vos, J. R.; Decision and Information Sciences; Univ. of Chicago; PantaRei Corp.; Univ. of Illinois

    2006-01-01

    In Greek mythology, the earth goddess Demeter was unable to find her daughter Persephone after Persephone was abducted by Hades, the god of the underworld. Demeter is said to have embarked on a long and frustrating, but ultimately successful, search to find her daughter. Unfortunately, long and frustrating searches are not confined to Greek mythology. In modern times, agent-based modelers often face similar troubles when searching for agents that are to be to be connected to one another and when seeking appropriate target agents while defining agent behaviors. The result is a 'search for emergence' in that many emergent or potentially emergent behaviors in agent-based models of complex adaptive systems either implicitly or explicitly require search functions. This paper considers a new nested querying approach to simplifying such agent-based modeling and multi-agent simulation search problems.

  15. An Evaluation of the High Level Architecture (HLA) as a Framework for NASA Modeling and Simulation

    NASA Technical Reports Server (NTRS)

    Reid, Michael R.; Powers, Edward I. (Technical Monitor)

    2000-01-01

    The High Level Architecture (HLA) is a current US Department of Defense and an industry (IEEE-1516) standard architecture for modeling and simulations. It provides a framework and set of functional rules and common interfaces for integrating separate and disparate simulators into a larger simulation. The goal of the HLA is to reduce software costs by facilitating the reuse of simulation components and by providing a runtime infrastructure to manage the simulations. In order to evaluate the applicability of the HLA as a technology for NASA space mission simulations, a Simulations Group at Goddard Space Flight Center (GSFC) conducted a study of the HLA and developed a simple prototype HLA-compliant space mission simulator. This paper summarizes the prototyping effort and discusses the potential usefulness of the HLA in the design and planning of future NASA space missions with a focus on risk mitigation and cost reduction.

  16. Providing conceptual framework support for distributed Web-based simulation within the high-level architecture

    NASA Astrophysics Data System (ADS)

    Page, Ernest H.; Griffin, Sean P.; Rother, S. L.

    1998-08-01

    Web-based simulation, a subject of increasing interest to both simulation researchers and practitioners, has the potential to significantly influence the application and availability of simulation as a problem-solving technique. Web technologies also portend cost-effective distributed modeling and simulation. These applications will require solutions to the systems interoperability problem similar to the DoD High Level Architecture (HLA). The suitability of the HLA to serve 'mainstream' simulation is examined.Approaches for incorporating discrete event simulation conceptual frameworks within the HLA are described and ongoing research in this area noted. Issues raised include a discussion of the appropriate roles for a simulation-support language and a simulation-support architecture.

  17. Consentaneous Agent-Based and Stochastic Model of the Financial Markets

    PubMed Central

    Gontis, Vygintas; Kononovicius, Aleksejus

    2014-01-01

    We are looking for the agent-based treatment of the financial markets considering necessity to build bridges between microscopic, agent based, and macroscopic, phenomenological modeling. The acknowledgment that agent-based modeling framework, which may provide qualitative and quantitative understanding of the financial markets, is very ambiguous emphasizes the exceptional value of well defined analytically tractable agent systems. Herding as one of the behavior peculiarities considered in the behavioral finance is the main property of the agent interactions we deal with in this contribution. Looking for the consentaneous agent-based and macroscopic approach we combine two origins of the noise: exogenous one, related to the information flow, and endogenous one, arising form the complex stochastic dynamics of agents. As a result we propose a three state agent-based herding model of the financial markets. From this agent-based model we derive a set of stochastic differential equations, which describes underlying macroscopic dynamics of agent population and log price in the financial markets. The obtained solution is then subjected to the exogenous noise, which shapes instantaneous return fluctuations. We test both Gaussian and q-Gaussian noise as a source of the short term fluctuations. The resulting model of the return in the financial markets with the same set of parameters reproduces empirical probability and spectral densities of absolute return observed in New York, Warsaw and NASDAQ OMX Vilnius Stock Exchanges. Our result confirms the prevalent idea in behavioral finance that herding interactions may be dominant over agent rationality and contribute towards bubble formation. PMID:25029364

  18. Consentaneous agent-based and stochastic model of the financial markets.

    PubMed

    Gontis, Vygintas; Kononovicius, Aleksejus

    2014-01-01

    We are looking for the agent-based treatment of the financial markets considering necessity to build bridges between microscopic, agent based, and macroscopic, phenomenological modeling. The acknowledgment that agent-based modeling framework, which may provide qualitative and quantitative understanding of the financial markets, is very ambiguous emphasizes the exceptional value of well defined analytically tractable agent systems. Herding as one of the behavior peculiarities considered in the behavioral finance is the main property of the agent interactions we deal with in this contribution. Looking for the consentaneous agent-based and macroscopic approach we combine two origins of the noise: exogenous one, related to the information flow, and endogenous one, arising form the complex stochastic dynamics of agents. As a result we propose a three state agent-based herding model of the financial markets. From this agent-based model we derive a set of stochastic differential equations, which describes underlying macroscopic dynamics of agent population and log price in the financial markets. The obtained solution is then subjected to the exogenous noise, which shapes instantaneous return fluctuations. We test both Gaussian and q-Gaussian noise as a source of the short term fluctuations. The resulting model of the return in the financial markets with the same set of parameters reproduces empirical probability and spectral densities of absolute return observed in New York, Warsaw and NASDAQ OMX Vilnius Stock Exchanges. Our result confirms the prevalent idea in behavioral finance that herding interactions may be dominant over agent rationality and contribute towards bubble formation.

  19. SIMPEG: An open source framework for simulation and gradient based parameter estimation in geophysical applications

    NASA Astrophysics Data System (ADS)

    Cockett, Rowan; Kang, Seogi; Heagy, Lindsey J.; Pidlisecky, Adam; Oldenburg, Douglas W.

    2015-12-01

    Inverse modeling is a powerful tool for extracting information about the subsurface from geophysical data. Geophysical inverse problems are inherently multidisciplinary, requiring elements from the relevant physics, numerical simulation, and optimization, as well as knowledge of the geologic setting, and a comprehension of the interplay between all of these elements. The development and advancement of inversion methodologies can be enabled by a framework that supports experimentation, is flexible and extensible, and allows the knowledge generated to be captured and shared. The goal of this paper is to propose a framework that supports many different types of geophysical forward simulations and deterministic inverse problems. Additionally, we provide an open source implementation of this framework in Python called SIMPEG (Simulation and Parameter Estimation in Geophysics,

  20. An Implicit Solution Framework for Reactor Fuel Performance Simulation

    SciTech Connect

    Glen Hansen; Chris Newman; Derek Gaston; Cody Permann

    2009-08-01

    The simulation of nuclear reactor fuel performance involves complex thermomechanical processes between fuel pellets, made of fissile material, and the protective cladding that surrounds the pellets. An important design goal for a fuel is to maximize the life of the cladding thereby allowing the fuel to remain in the reactor for a longer period of time to achieve higher degrees of burnup. This presentation presents an initial approach for modeling the thermomechanical response of reactor fuel, and details of the solution method employed within INL's fuel performance code, BISON. The code employs advanced methods for solving coupled partial differential equation systems that describe multidimensional fuel thermomechanics, heat generation, and oxygen transport within the fuel. This discussion explores the effectiveness of a JFNK-based solution of a problem involving three dimensional fully coupled, nonlinear transient heat conduction and that includes pellet displacement and oxygen diffusion effects. These equations are closed using empirical data that is a function of temperature, density, and oxygen hyperstoichiometry. The method appears quite effective for the fuel pellet / cladding configurations examined, with excellent nonlinear convergence properties exhibited on the combined system. In closing, fully coupled solutions of three dimensional thermomechanics coupled with oxygen diffusion appear quite attractive using the JFNK approach described here, at least for configurations similar to those examined in this report.

  1. Synthesized Population Databases: A US Geospatial Database for Agent-Based Models.

    PubMed

    Wheaton, William D; Cajka, James C; Chasteen, Bernadette M; Wagener, Diane K; Cooley, Philip C; Ganapathi, Laxminarayana; Roberts, Douglas J; Allpress, Justine L

    2009-05-01

    Agent-based models simulate large-scale social systems. They assign behaviors and activities to "agents" (individuals) within the population being modeled and then allow the agents to interact with the environment and each other in complex simulations. Agent-based models are frequently used to simulate infectious disease outbreaks, among other uses.RTI used and extended an iterative proportional fitting method to generate a synthesized, geospatially explicit, human agent database that represents the US population in the 50 states and the District of Columbia in the year 2000. Each agent is assigned to a household; other agents make up the household occupants.For this database, RTI developed the methods for generating synthesized households and personsassigning agents to schools and workplaces so that complex interactions among agents as they go about their daily activities can be taken into accountgenerating synthesized human agents who occupy group quarters (military bases, college dormitories, prisons, nursing homes).In this report, we describe both the methods used to generate the synthesized population database and the final data structure and data content of the database. This information will provide researchers with the information they need to use the database in developing agent-based models.Portions of the synthesized agent database are available to any user upon request. RTI will extract a portion (a county, region, or state) of the database for users who wish to use this database in their own agent-based models.

  2. Bayesian uncertainty quantification and propagation in molecular dynamics simulations: A high performance computing framework

    NASA Astrophysics Data System (ADS)

    Angelikopoulos, Panagiotis; Papadimitriou, Costas; Koumoutsakos, Petros

    2012-10-01

    We present a Bayesian probabilistic framework for quantifying and propagating the uncertainties in the parameters of force fields employed in molecular dynamics (MD) simulations. We propose a highly parallel implementation of the transitional Markov chain Monte Carlo for populating the posterior probability distribution of the MD force-field parameters. Efficient scheduling algorithms are proposed to handle the MD model runs and to distribute the computations in clusters with heterogeneous architectures. Furthermore, adaptive surrogate models are proposed in order to reduce the computational cost associated with the large number of MD model runs. The effectiveness and computational efficiency of the proposed Bayesian framework is demonstrated in MD simulations of liquid and gaseous argon.

  3. Bayesian uncertainty quantification and propagation in molecular dynamics simulations: a high performance computing framework.

    PubMed

    Angelikopoulos, Panagiotis; Papadimitriou, Costas; Koumoutsakos, Petros

    2012-10-14

    We present a Bayesian probabilistic framework for quantifying and propagating the uncertainties in the parameters of force fields employed in molecular dynamics (MD) simulations. We propose a highly parallel implementation of the transitional Markov chain Monte Carlo for populating the posterior probability distribution of the MD force-field parameters. Efficient scheduling algorithms are proposed to handle the MD model runs and to distribute the computations in clusters with heterogeneous architectures. Furthermore, adaptive surrogate models are proposed in order to reduce the computational cost associated with the large number of MD model runs. The effectiveness and computational efficiency of the proposed Bayesian framework is demonstrated in MD simulations of liquid and gaseous argon.

  4. Agent-Based Mapping of Credit Risk for Sustainable Microfinance

    PubMed Central

    Lee, Joung-Hun; Jusup, Marko; Podobnik, Boris; Iwasa, Yoh

    2015-01-01

    By drawing analogies with independent research areas, we propose an unorthodox framework for mapping microfinance credit risk---a major obstacle to the sustainability of lenders outreaching to the poor. Specifically, using the elements of network theory, we constructed an agent-based model that obeys the stylized rules of microfinance industry. We found that in a deteriorating economic environment confounded with adverse selection, a form of latent moral hazard may cause a regime shift from a high to a low loan payment probability. An after-the-fact recovery, when possible, required the economic environment to improve beyond that which led to the shift in the first place. These findings suggest a small set of measurable quantities for mapping microfinance credit risk and, consequently, for balancing the requirements to reasonably price loans and to operate on a fully self-financed basis. We illustrate how the proposed mapping works using a 10-year monthly data set from one of the best-known microfinance representatives, Grameen Bank in Bangladesh. Finally, we discuss an entirely new perspective for managing microfinance credit risk based on enticing spontaneous cooperation by building social capital. PMID:25945790

  5. Agent-based mapping of credit risk for sustainable microfinance.

    PubMed

    Lee, Joung-Hun; Jusup, Marko; Podobnik, Boris; Iwasa, Yoh

    2015-01-01

    By drawing analogies with independent research areas, we propose an unorthodox framework for mapping microfinance credit risk--a major obstacle to the sustainability of lenders outreaching to the poor. Specifically, using the elements of network theory, we constructed an agent-based model that obeys the stylized rules of microfinance industry. We found that in a deteriorating economic environment confounded with adverse selection, a form of latent moral hazard may cause a regime shift from a high to a low loan payment probability. An after-the-fact recovery, when possible, required the economic environment to improve beyond that which led to the shift in the first place. These findings suggest a small set of measurable quantities for mapping microfinance credit risk and, consequently, for balancing the requirements to reasonably price loans and to operate on a fully self-financed basis. We illustrate how the proposed mapping works using a 10-year monthly data set from one of the best-known microfinance representatives, Grameen Bank in Bangladesh. Finally, we discuss an entirely new perspective for managing microfinance credit risk based on enticing spontaneous cooperation by building social capital.

  6. An Advanced Computational Approach to System of Systems Analysis & Architecting Using Agent-Based Behavioral Model

    DTIC Science & Technology

    2012-09-30

    The Wave Process Model provides a framework for an agent-based modeling methodology, which is used to abstract the non- utopian behavioral aspects...that SoS participants exhibit nominal behavior ( utopian behavior), but deviation from nominal motivation leads to complications and disturbances in... characteristics . Figure 2 outlines the agent architecture components and flow of information among components. Own Process Control (OPC) Cooperation

  7. E-laboratories : agent-based modeling of electricity markets.

    SciTech Connect

    North, M.; Conzelmann, G.; Koritarov, V.; Macal, C.; Thimmapuram, P.; Veselka, T.

    2002-05-03

    Electricity markets are complex adaptive systems that operate under a wide range of rules that span a variety of time scales. These rules are imposed both from above by society and below by physics. Many electricity markets are undergoing or are about to undergo a transition from centrally regulated systems to decentralized markets. Furthermore, several electricity markets have recently undergone this transition with extremely unsatisfactory results, most notably in California. These high stakes transitions require the introduction of largely untested regulatory structures. Suitable laboratories that can be used to test regulatory structures before they are applied to real systems are needed. Agent-based models can provide such electronic laboratories or ''e-laboratories.'' To better understand the requirements of an electricity market e-laboratory, a live electricity market simulation was created. This experience helped to shape the development of the Electricity Market Complex Adaptive Systems (EMCAS) model. To explore EMCAS' potential as an e-laboratory, several variations of the live simulation were created. These variations probed the possible effects of changing power plant outages and price setting rules on electricity market prices.

  8. FNCS: A Framework for Power System and Communication Networks Co-Simulation

    SciTech Connect

    Ciraci, Selim; Daily, Jeffrey A.; Fuller, Jason C.; Fisher, Andrew R.; Marinovici, Laurentiu D.; Agarwal, Khushbu

    2014-04-13

    This paper describes the Fenix framework that uses a federated approach for integrating power grid and communication network simulators. Compared existing approaches, Fenix al- lows co-simulation of both transmission and distribution level power grid simulators with the communication network sim- ulator. To reduce the performance overhead of time synchro- nization, Fenix utilizes optimistic synchronization strategies that make speculative decisions about when the simulators are going to exchange messages. GridLAB-D (a distribution simulator), PowerFlow (a transmission simulator), and ns-3 (a telecommunication simulator) are integrated with the frame- work and are used to illustrate the enhanced performance pro- vided by speculative multi-threading on a smart grid applica- tion. Our speculative multi-threading approach achieved on average 20% improvement over the existing synchronization methods

  9. A framework-based approach to designing simulation-augmented surgical education and training programs.

    PubMed

    Cristancho, Sayra M; Moussa, Fuad; Dubrowski, Adam

    2011-09-01

    The goal of simulation-based medical education and training is to help trainees acquire and refine the technical and cognitive skills necessary to perform clinical procedures. When designers incorporate simulation into programs, their efforts should be in line with training needs, rather than technology. Designers of simulation-augmented surgical training programs, however, face particular problems related to identifying a framework that guides the curricular design activity to fulfill the particular requirements of such training programs. These problems include the lack of (1) an objective identification of training needs, (2) a systematic design methodology to match training objectives with simulation resources, (3) structured assessments of performance, and (4) a research-centered view to evaluate and validate systematically the educational effectiveness of the program. In this report, we present a process called "Aim - FineTune - FollowThrough" to enable the connection of the identified problems to solutions, using frameworks from psychology, motor learning, education and experimental design.

  10. Development of a Computational Framework on Fluid-Solid Mixture Flow Simulations for the COMPASS Code

    NASA Astrophysics Data System (ADS)

    Zhang, Shuai; Morita, Koji; Shirakawa, Noriyuki; Yamamoto, Yuichi

    The COMPASS code is designed based on the moving particle semi-implicit method to simulate various complex mesoscale phenomena relevant to core disruptive accidents of sodium-cooled fast reactors. In this study, a computational framework for fluid-solid mixture flow simulations was developed for the COMPASS code. The passively moving solid model was used to simulate hydrodynamic interactions between fluid and solids. Mechanical interactions between solids were modeled by the distinct element method. A multi-time-step algorithm was introduced to couple these two calculations. The proposed computational framework for fluid-solid mixture flow simulations was verified by the comparison between experimental and numerical studies on the water-dam break with multiple solid rods.

  11. A Framework for Simulating Turbine-Based Combined-Cycle Inlet Mode-Transition

    NASA Technical Reports Server (NTRS)

    Le, Dzu K.; Vrnak, Daniel R.; Slater, John W.; Hessel, Emil O.

    2012-01-01

    A simulation framework based on the Memory-Mapped-Files technique was created to operate multiple numerical processes in locked time-steps and send I/O data synchronously across to one-another to simulate system-dynamics. This simulation scheme is currently used to study the complex interactions between inlet flow-dynamics, variable-geometry actuation mechanisms, and flow-controls in the transition from the supersonic to hypersonic conditions and vice-versa. A study of Mode-Transition Control for a high-speed inlet wind-tunnel model with this MMF-based framework is presented to illustrate this scheme and demonstrate its usefulness in simulating supersonic and hypersonic inlet dynamics and controls or other types of complex systems.

  12. Agent-based modeling of complex infrastructures

    SciTech Connect

    North, M. J.

    2001-06-01

    Complex Adaptive Systems (CAS) can be applied to investigate complex infrastructures and infrastructure interdependencies. The CAS model agents within the Spot Market Agent Research Tool (SMART) and Flexible Agent Simulation Toolkit (FAST) allow investigation of the electric power infrastructure, the natural gas infrastructure and their interdependencies.

  13. Investigating Ground Swarm Robotics Using Agent Based Simulation

    DTIC Science & Technology

    2006-12-01

    sensors and explosive detectors. These will be laid out further in Chapter II. Swarm robotics has attracted much attention because of the numerous key... attractive and repulsive force fields, which then control the dispersion and coverage of the swarm. Last but not least, Batalin and Sukhatme (2002) focused...of animals such as cockroaches , crickets, snakes and even lobsters (Ayers et al., 2002). Each of these species is highly efficient in mobility in

  14. Plan Validation Using DES and Agent-based Simulation

    DTIC Science & Technology

    2008-12-01

    a lock on A301 because in the model, a SAM site is only able to acquire a lock on one aircraft at a time, and since A302 and A301 are flying in...disengaged A302 and was assigned a new target A301 when A302 flies out of the gun’s firing range. The gun is behaving correctly. Target’s flight path Gun’s...A302 and starts to engage A301 . The gun is behaving correctly. Figure 39 Scenario for Target Switching When a Target is Killed A302 A301

  15. A Semantic Web Service and Simulation Framework to Intelligent Distributed Manufacturing

    SciTech Connect

    Son, Young Jun; Kulvatunyou, Boonserm; Cho, Hyunbo; Feng, Shaw

    2005-11-01

    To cope with today's fluctuating markets, a virtual enterprise (VE) concept can be employed to achieve the cooperation among independently operating enterprises. The success of VE depends on reliable interoperation among trading partners. This paper proposes a framework based on semantic web of manufacturing and simulation services to enable business and engineering collaborations between VE partners, particularly a design house and manufacturing suppliers.

  16. A Framework for the Design of Computer-Assisted Simulation Training for Complex Police Situations

    ERIC Educational Resources Information Center

    Söderström, Tor; Åström, Jan; Anderson, Greg; Bowles, Ron

    2014-01-01

    Purpose: The purpose of this paper is to report progress concerning the design of a computer-assisted simulation training (CAST) platform for developing decision-making skills in police students. The overarching aim is to outline a theoretical framework for the design of CAST to facilitate police students' development of search techniques in…

  17. A framework of knowledge creation processes in participatory simulation of hospital work systems.

    PubMed

    Andersen, Simone Nyholm; Broberg, Ole

    2017-04-01

    Participatory simulation (PS) is a method to involve workers in simulating and designing their own future work system. Existing PS studies have focused on analysing the outcome, and minimal attention has been devoted to the process of creating this outcome. In order to study this process, we suggest applying a knowledge creation perspective. The aim of this study was to develop a framework describing the process of how ergonomics knowledge is created in PS. Video recordings from three projects applying PS of hospital work systems constituted the foundation of process mining analysis. The analysis resulted in a framework revealing the sources of ergonomics knowledge creation as sequential relationships between the activities of simulation participants sharing work experiences; experimenting with scenarios; and reflecting on ergonomics consequences. We argue that this framework reveals the hidden steps of PS that are essential when planning and facilitating PS that aims at designing work systems. Practitioner Summary: When facilitating participatory simulation (PS) in work system design, achieving an understanding of the PS process is essential. By applying a knowledge creation perspective and process mining, we investigated the knowledge-creating activities constituting the PS process. The analysis resulted in a framework of the knowledge-creating process in PS.

  18. Agent Based Modeling of “Crowdinforming” as a Means of Load Balancing at Emergency Departments

    PubMed Central

    Neighbour, Ryan; Oppenheimer, Luis; Mukhi, Shamir N.; Friesen, Marcia R.; McLeod, Robert D.

    2010-01-01

    This work extends ongoing development of a framework for modeling the spread of contact-transmission infectious diseases. The framework is built upon Agent Based Modeling (ABM), with emphasis on urban scale modelling integrated with institutional models of hospital emergency departments. The method presented here includes ABM modeling an outbreak of influenza-like illness (ILI) with concomitant surges at hospital emergency departments, and illustrates the preliminary modeling of ‘crowdinforming’ as an intervention. ‘Crowdinforming’, a component of ‘crowdsourcing’, is characterized as the dissemination of collected and processed information back to the ‘crowd’ via public access. The objective of the simulation is to allow for effective policy evaluation to better inform the public of expected wait times as part of their decision making process in attending an emergency department or clinic. In effect, this is a means of providing additional decision support garnered from a simulation, prior to real world implementation. The conjecture is that more optimal service delivery can be achieved under balanced patient loads, compared to situations where some emergency departments are overextended while others are underutilized. Load balancing optimization is a common notion in many operations, and the simulation illustrates that ‘crowdinforming’ is a potential tool when used as a process control parameter to balance the load at emergency departments as well as serving as an effective means to direct patients during an ILI outbreak with temporary clinics deployed. The information provided in the ‘crowdinforming’ model is readily available in a local context, although it requires thoughtful consideration in its interpretation. The extension to a wider dissemination of information via a web service is readily achievable and presents no technical obstacles, although political obstacles may be present. The ‘crowdinforming’ simulation is not limited to

  19. A Framework for Determining the Return on Investment of Simulation-Based Training in Health Care.

    PubMed

    Bukhari, Hatim; Andreatta, Pamela; Goldiez, Brian; Rabelo, Luis

    2017-01-01

    This article describes a framework that has been developed to monetize the real value of simulation-based training in health care. A significant consideration has been given to the incorporation of the intangible and qualitative benefits, not only the tangible and quantitative benefits of simulation-based training in health care. The framework builds from three works: the value measurement methodology (VMM) used by several departments of the US Government, a methodology documented in several books by Dr Jack Phillips to monetize various training approaches, and a traditional return on investment methodology put forth by Frost and Sullivan, and Immersion Medical. All 3 source materials were adapted to create an integrated methodology that can be readily implemented. This article presents details on each of these methods and how they can be integrated and presents a framework that integrates the previous methods. In addition to that, it describes the concept and the application of the developed framework. As a test of the applicability of the framework, a real case study has been used to demonstrate the application of the framework. This case study provides real data related to the correlation between the pediatric patient cardiopulmonary arrest (CPA) survival rates and a simulation-based mock codes at the University of Michigan tertiary care academic medical center. It is important to point out that the proposed framework offers the capability to consider a wide range of benefits and values, but on the other hand, there are several limitations that has been discussed and need to be taken in consideration.

  20. A generalized framework for interactive dynamic simulation for MultiRigid bodies.

    PubMed

    Son, Wookho; Kim, Kyunghwan; Amato, Nancy M; Trinkle, Jeffrey C

    2004-04-01

    This paper presents a generalized framework for dynamic simulation realized in a prototype simulator called the Interactive Generalized Motion Simulator (I-GMS), which can simulate motions of multirigid-body systems with contact interaction in virtual environments. I-GMS is designed to meet two important goals: generality and interactivity. By generality, we mean a dynamic simulator which can easily support various systems of rigid bodies, ranging from a single free-flying rigid object to complex linkages such as those needed for robotic systems or human body simulation. To provide this generality, we have developed I-GMS in an object-oriented framework. The user interactivity is supported through a haptic interface for articulated bodies, introducing interactive dynamic simulation schemes. This user-interaction is achieved by performing push and pull operations via the PHANToM haptic device, which runs as an integrated part of I-GMS. Also, a hybrid scheme was used for simulating internal contacts (between bodies in the multirigid-body system) in the presence of friction, which could avoid the nonexistent solution problem often faced when solving contact problems with Coulomb friction. In our hybrid scheme, two impulse-based methods are exploited so that different methods are applied adaptively, depending on whether the current contact situation is characterized as "bouncing" or "steady." We demonstrate the user-interaction capability of I-GMS through on-line editing of trajectories of a 6-degree of freedom (dof) articulated structure.

  1. Investigating mathematical models of immuno-interactions with early-stage cancer under an agent-based modelling perspective

    PubMed Central

    2013-01-01

    Many advances in research regarding immuno-interactions with cancer were developed with the help of ordinary differential equation (ODE) models. These models, however, are not effectively capable of representing problems involving individual localisation, memory and emerging properties, which are common characteristics of cells and molecules of the immune system. Agent-based modelling and simulation is an alternative paradigm to ODE models that overcomes these limitations. In this paper we investigate the potential contribution of agent-based modelling and simulation when compared to ODE modelling and simulation. We seek answers to the following questions: Is it possible to obtain an equivalent agent-based model from the ODE formulation? Do the outcomes differ? Are there any benefits of using one method compared to the other? To answer these questions, we have considered three case studies using established mathematical models of immune interactions with early-stage cancer. These case studies were re-conceptualised under an agent-based perspective and the simulation results were then compared with those from the ODE models. Our results show that it is possible to obtain equivalent agent-based models (i.e. implementing the same mechanisms); the simulation output of both types of models however might differ depending on the attributes of the system to be modelled. In some cases, additional insight from using agent-based modelling was obtained. Overall, we can confirm that agent-based modelling is a useful addition to the tool set of immunologists, as it has extra features that allow for simulations with characteristics that are closer to the biological phenomena. PMID:23734575

  2. Investigating mathematical models of immuno-interactions with early-stage cancer under an agent-based modelling perspective.

    PubMed

    Figueredo, Grazziela P; Siebers, Peer-Olaf; Aickelin, Uwe

    2013-01-01

    Many advances in research regarding immuno-interactions with cancer were developed with the help of ordinary differential equation (ODE) models. These models, however, are not effectively capable of representing problems involving individual localisation, memory and emerging properties, which are common characteristics of cells and molecules of the immune system. Agent-based modelling and simulation is an alternative paradigm to ODE models that overcomes these limitations. In this paper we investigate the potential contribution of agent-based modelling and simulation when compared to ODE modelling and simulation. We seek answers to the following questions: Is it possible to obtain an equivalent agent-based model from the ODE formulation? Do the outcomes differ? Are there any benefits of using one method compared to the other? To answer these questions, we have considered three case studies using established mathematical models of immune interactions with early-stage cancer. These case studies were re-conceptualised under an agent-based perspective and the simulation results were then compared with those from the ODE models. Our results show that it is possible to obtain equivalent agent-based models (i.e. implementing the same mechanisms); the simulation output of both types of models however might differ depending on the attributes of the system to be modelled. In some cases, additional insight from using agent-based modelling was obtained. Overall, we can confirm that agent-based modelling is a useful addition to the tool set of immunologists, as it has extra features that allow for simulations with characteristics that are closer to the biological phenomena.

  3. Simulating the Household Plug-in Hybrid Electric Vehicle Distribution and its Electric Distribution Network Impacts

    SciTech Connect

    Cui, Xiaohui; Kim, Hoe Kyoung; Liu, Cheng; Kao, Shih-Chieh; Bhaduri, Budhendra L

    2012-01-01

    This paper presents a multi agent-based simulation framework for modeling spatial distribution of plug-in hybrid electric vehicle ownership at local residential level, discovering plug-in hybrid electric vehicle hot zones where ownership may quickly increase in the near future, and estimating the impacts of the increasing plug-in hybrid electric vehicle ownership on the local electric distribution network with different charging strategies. We use Knox County, Tennessee as a case study to highlight the simulation results of the agent-based simulation framework.

  4. NISAC Agent Based Laboratory for Economics

    SciTech Connect

    Downes, Paula; Davis, Chris; Eidson, Eric; Ehlen, Mark; Gieseler, Charles; Harris, Richard

    2006-10-11

    The software provides large-scale microeconomic simulation of complex economic and social systems (such as supply chain and market dynamics of businesses in the US economy) and their dependence on physical infrastructure systems. The system is based on Agent simulation, where each entity of inteest in the system to be modeled (for example, a Bank, individual firms, Consumer households, etc.) is specified in a data-driven sense to be individually repreented by an Agent. The Agents interact using rules of interaction appropriate to their roles, and through those interactions complex economic and social dynamics emerge. The software is implemented in three tiers, a Java-based visualization client, a C++ control mid-tier, and a C++ computational tier.

  5. Optimization and Control of Agent-Based Models in Biology: A Perspective.

    PubMed

    An, G; Fitzpatrick, B G; Christley, S; Federico, P; Kanarek, A; Neilan, R Miller; Oremland, M; Salinas, R; Laubenbacher, R; Lenhart, S

    2017-01-01

    Agent-based models (ABMs) have become an increasingly important mode of inquiry for the life sciences. They are particularly valuable for systems that are not understood well enough to build an equation-based model. These advantages, however, are counterbalanced by the difficulty of analyzing and using ABMs, due to the lack of the type of mathematical tools available for more traditional models, which leaves simulation as the primary approach. As models become large, simulation becomes challenging. This paper proposes a novel approach to two mathematical aspects of ABMs, optimization and control, and it presents a few first steps outlining how one might carry out this approach. Rather than viewing the ABM as a model, it is to be viewed as a surrogate for the actual system. For a given optimization or control problem (which may change over time), the surrogate system is modeled instead, using data from the ABM and a modeling framework for which ready-made mathematical tools exist, such as differential equations, or for which control strategies can explored more easily. Once the optimization problem is solved for the model of the surrogate, it is then lifted to the surrogate and tested. The final step is to lift the optimization solution from the surrogate system to the actual system. This program is illustrated with published work, using two relatively simple ABMs as a demonstration, Sugarscape and a consumer-resource ABM. Specific techniques discussed include dimension reduction and approximation of an ABM by difference equations as well systems of PDEs, related to certain specific control objectives. This demonstration illustrates the very challenging mathematical problems that need to be solved before this approach can be realistically applied to complex and large ABMs, current and future. The paper outlines a research program to address them.

  6. Numerical validation framework for micromechanical simulations based on synchrotron 3D imaging

    NASA Astrophysics Data System (ADS)

    Buljac, Ante; Shakoor, Modesar; Neggers, Jan; Bernacki, Marc; Bouchard, Pierre-Olivier; Helfen, Lukas; Morgeneyer, Thilo F.; Hild, François

    2017-03-01

    A combined computational-experimental framework is introduced herein to validate numerical simulations at the microscopic scale. It is exemplified for a flat specimen with central hole made of cast iron and imaged via in-situ synchrotron laminography at micrometer resolution during a tensile test. The region of interest in the reconstructed volume, which is close to the central hole, is analyzed by digital volume correlation (DVC) to measure kinematic fields. Finite element (FE) simulations, which account for the studied material microstructure, are driven by Dirichlet boundary conditions extracted from DVC measurements. Gray level residuals for DVC measurements and FE simulations are assessed for validation purposes.

  7. Measure of Landscape Heterogeneity by Agent-Based Methodology

    NASA Astrophysics Data System (ADS)

    Wirth, E.; Szabó, Gy.; Czinkóczky, A.

    2016-06-01

    With the rapid increase of the world's population, the efficient food production is one of the key factors of the human survival. Since biodiversity and heterogeneity is the basis of the sustainable agriculture, the authors tried to measure the heterogeneity of a chosen landscape. The EU farming and subsidizing policies (EEA, 2014) support landscape heterogeneity and diversity, nevertheless exact measurements and calculations apart from statistical parameters (standard deviation, mean), do not really exist. In the present paper the authors' goal is to find an objective, dynamic method that measures landscape heterogeneity. It is achieved with the so called agent-based modelling, where randomly dispatched dynamic scouts record the observed land cover parameters and sum up the features of a new type of land. During the simulation the agents collect a Monte Carlo integral as a diversity landscape potential which can be considered as the unit of the `greening' measure. As a final product of the ABM method, a landscape potential map is obtained that can serve as a tool for objective decision making to support agricultural diversity.

  8. Evaluating Water Demand Using Agent-Based Modeling

    NASA Astrophysics Data System (ADS)

    Lowry, T. S.

    2004-12-01

    The supply and demand of water resources are functions of complex, inter-related systems including hydrology, climate, demographics, economics, and policy. To assess the safety and sustainability of water resources, planners often rely on complex numerical models that relate some or all of these systems using mathematical abstractions. The accuracy of these models relies on how well the abstractions capture the true nature of the systems interactions. Typically, these abstractions are based on analyses of observations and/or experiments that account only for the statistical mean behavior of each system. This limits the approach in two important ways: 1) It cannot capture cross-system disruptive events, such as major drought, significant policy change, or terrorist attack, and 2) it cannot resolve sub-system level responses. To overcome these limitations, we are developing an agent-based water resources model that includes the systems of hydrology, climate, demographics, economics, and policy, to examine water demand during normal and extraordinary conditions. Agent-based modeling (ABM) develops functional relationships between systems by modeling the interaction between individuals (agents), who behave according to a probabilistic set of rules. ABM is a "bottom-up" modeling approach in that it defines macro-system behavior by modeling the micro-behavior of individual agents. While each agent's behavior is often simple and predictable, the aggregate behavior of all agents in each system can be complex, unpredictable, and different than behaviors observed in mean-behavior models. Furthermore, the ABM approach creates a virtual laboratory where the effects of policy changes and/or extraordinary events can be simulated. Our model, which is based on the demographics and hydrology of the Middle Rio Grande Basin in the state of New Mexico, includes agent groups of residential, agricultural, and industrial users. Each agent within each group determines its water usage

  9. A Collective Case Study of Secondary Students' Model-Based Inquiry on Natural Selection through Programming in an Agent-Based Modeling Environment

    ERIC Educational Resources Information Center

    Xiang, Lin

    2011-01-01

    This is a collective case study seeking to develop detailed descriptions of how programming an agent-based simulation influences a group of 8th grade students' model-based inquiry (MBI) by examining students' agent-based programmable modeling (ABPM) processes and the learning outcomes. The context of the present study was a biology unit on…

  10. A hierarchical Bayesian framework for force field selection in molecular dynamics simulations.

    PubMed

    Wu, S; Angelikopoulos, P; Papadimitriou, C; Moser, R; Koumoutsakos, P

    2016-02-13

    We present a hierarchical Bayesian framework for the selection of force fields in molecular dynamics (MD) simulations. The framework associates the variability of the optimal parameters of the MD potentials under different environmental conditions with the corresponding variability in experimental data. The high computational cost associated with the hierarchical Bayesian framework is reduced by orders of magnitude through a parallelized Transitional Markov Chain Monte Carlo method combined with the Laplace Asymptotic Approximation. The suitability of the hierarchical approach is demonstrated by performing MD simulations with prescribed parameters to obtain data for transport coefficients under different conditions, which are then used to infer and evaluate the parameters of the MD model. We demonstrate the selection of MD models based on experimental data and verify that the hierarchical model can accurately quantify the uncertainty across experiments; improve the posterior probability density function estimation of the parameters, thus, improve predictions on future experiments; identify the most plausible force field to describe the underlying structure of a given dataset. The framework and associated software are applicable to a wide range of nanoscale simulations associated with experimental data with a hierarchical structure.

  11. Agent Based Intelligence in a Tetrahedral Rover

    NASA Technical Reports Server (NTRS)

    Phelps, Peter; Truszkowski, Walt

    2007-01-01

    A tetrahedron is a 4-node 6-strut pyramid structure which is being used by the NASA - Goddard Space Flight Center as the basic building block for a new approach to robotic motion. The struts are extendable; it is by the sequence of activities: strut-extension, changing the center of gravity and falling that the tetrahedron "moves". Currently, strut-extension is handled by human remote control. There is an effort underway to make the movement of the tetrahedron autonomous, driven by an attempt to achieve a goal. The approach being taken is to associate an intelligent agent with each node. Thus, the autonomous tetrahedron is realized as a constrained multi-agent system, where the constraints arise from the fact that between any two agents there is an extendible strut. The hypothesis of this work is that, by proper composition of such automated tetrahedra, robotic structures of various levels of complexity can be developed which will support more complex dynamic motions. This is the basis of the new approach to robotic motion which is under investigation. A Java-based simulator for the single tetrahedron, realized as a constrained multi-agent system, has been developed and evaluated. This paper reports on this project and presents a discussion of the structure and dynamics of the simulator.

  12. Agent-Based Modeling of Growth Processes

    ERIC Educational Resources Information Center

    Abraham, Ralph

    2014-01-01

    Growth processes abound in nature, and are frequently the target of modeling exercises in the sciences. In this article we illustrate an agent-based approach to modeling, in the case of a single example from the social sciences: bullying.

  13. AGENT-BASED MODELS IN EMPIRICAL SOCIAL RESEARCH*

    PubMed Central

    Bruch, Elizabeth; Atwell, Jon

    2014-01-01

    Agent-based modeling has become increasingly popular in recent years, but there is still no codified set of recommendations or practices for how to use these models within a program of empirical research. This article provides ideas and practical guidelines drawn from sociology, biology, computer science, epidemiology, and statistics. We first discuss the motivations for using agent-based models in both basic science and policy-oriented social research. Next, we provide an overview of methods and strategies for incorporating data on behavior and populations into agent-based models, and review techniques for validating and testing the sensitivity of agent-based models. We close with suggested directions for future research. PMID:25983351

  14. Users' Perception of Medical Simulation Training: A Framework for Adopting Simulator Technology

    ERIC Educational Resources Information Center

    Green, Leili Hayati

    2014-01-01

    Users play a key role in many training strategies, yet some organizations often fail to understand the users' perception after a simulation training implementation, their attitude about acceptance or rejection of and integration of emerging simulation technology in medical training (Gaba, 2007, and Topol, 2012). Several factors are considered to…

  15. Smell Detection Agent Based Optimization Algorithm

    NASA Astrophysics Data System (ADS)

    Vinod Chandra, S. S.

    2016-09-01

    In this paper, a novel nature-inspired optimization algorithm has been employed and the trained behaviour of dogs in detecting smell trails is adapted into computational agents for problem solving. The algorithm involves creation of a surface with smell trails and subsequent iteration of the agents in resolving a path. This algorithm can be applied in different computational constraints that incorporate path-based problems. Implementation of the algorithm can be treated as a shortest path problem for a variety of datasets. The simulated agents have been used to evolve the shortest path between two nodes in a graph. This algorithm is useful to solve NP-hard problems that are related to path discovery. This algorithm is also useful to solve many practical optimization problems. The extensive derivation of the algorithm can be enabled to solve shortest path problems.

  16. Flexible simulation framework to couple processes in complex 3D models for subsurface utilization assessment

    NASA Astrophysics Data System (ADS)

    Kempka, Thomas; Nakaten, Benjamin; De Lucia, Marco; Nakaten, Natalie; Otto, Christopher; Pohl, Maik; Tillner, Elena; Kühn, Michael

    2016-04-01

    Utilization of the geological subsurface for production and storage of hydrocarbons, chemical energy and heat as well as for waste disposal requires the quantification and mitigation of environmental impacts as well as the improvement of georesources utilization in terms of efficiency and sustainability. The development of tools for coupled process simulations is essential to tackle these challenges, since reliable assessments are only feasible by integrative numerical computations. Coupled processes at reservoir to regional scale determine the behaviour of reservoirs, faults and caprocks, generally demanding for complex 3D geological models to be considered besides available monitoring and experimenting data in coupled numerical simulations. We have been developing a flexible numerical simulation framework that provides efficient workflows for integrating the required data and software packages to carry out coupled process simulations considering, e.g., multiphase fluid flow, geomechanics, geochemistry and heat. Simulation results are stored in structured data formats to allow for an integrated 3D visualization and result interpretation as well as data archiving and its provision to collaborators. The main benefits in using the flexible simulation framework are the integration of data geological and grid data from any third party software package as well as data export to generic 3D visualization tools and archiving formats. The coupling of the required process simulators in time and space is feasible, while different spatial dimensions in the coupled simulations can be integrated, e.g., 0D batch with 3D dynamic simulations. User interaction is established via high-level programming languages, while computational efficiency is achieved by using low-level programming languages. We present three case studies on the assessment of geological subsurface utilization based on different process coupling approaches and numerical simulations.

  17. Agent-Based vs. Equation-based Epidemiological Models:A Model Selection Case Study

    SciTech Connect

    Sukumar, Sreenivas R; Nutaro, James J

    2012-01-01

    This paper is motivated by the need to design model validation strategies for epidemiological disease-spread models. We consider both agent-based and equation-based models of pandemic disease spread and study the nuances and complexities one has to consider from the perspective of model validation. For this purpose, we instantiate an equation based model and an agent based model of the 1918 Spanish flu and we leverage data published in the literature for our case- study. We present our observations from the perspective of each implementation and discuss the application of model-selection criteria to compare the risk in choosing one modeling paradigm to another. We conclude with a discussion of our experience and document future ideas for a model validation framework.

  18. Formalizing the role of agent-based modeling in causal inference and epidemiology.

    PubMed

    Marshall, Brandon D L; Galea, Sandro

    2015-01-15

    Calls for the adoption of complex systems approaches, including agent-based modeling, in the field of epidemiology have largely centered on the potential for such methods to examine complex disease etiologies, which are characterized by feedback behavior, interference, threshold dynamics, and multiple interacting causal effects. However, considerable theoretical and practical issues impede the capacity of agent-based methods to examine and evaluate causal effects and thus illuminate new areas for intervention. We build on this work by describing how agent-based models can be used to simulate counterfactual outcomes in the presence of complexity. We show that these models are of particular utility when the hypothesized causal mechanisms exhibit a high degree of interdependence between multiple causal effects and when interference (i.e., one person's exposure affects the outcome of others) is present and of intrinsic scientific interest. Although not without challenges, agent-based modeling (and complex systems methods broadly) represent a promising novel approach to identify and evaluate complex causal effects, and they are thus well suited to complement other modern epidemiologic methods of etiologic inquiry.

  19. Ensuring congruency in multiscale modeling: towards linking agent based and continuum biomechanical models of arterial adaptation.

    PubMed

    Hayenga, Heather N; Thorne, Bryan C; Peirce, Shayn M; Humphrey, Jay D

    2011-11-01

    There is a need to develop multiscale models of vascular adaptations to understand tissue-level manifestations of cellular level mechanisms. Continuum-based biomechanical models are well suited for relating blood pressures and flows to stress-mediated changes in geometry and properties, but less so for describing underlying mechanobiological processes. Discrete stochastic agent-based models are well suited for representing biological processes at a cellular level, but not for describing tissue-level mechanical changes. We present here a conceptually new approach to facilitate the coupling of continuum and agent-based models. Because of ubiquitous limitations in both the tissue- and cell-level data from which one derives constitutive relations for continuum models and rule-sets for agent-based models, we suggest that model verification should enforce congruency across scales. That is, multiscale model parameters initially determined from data sets representing different scales should be refined, when possible, to ensure that common outputs are consistent. Potential advantages of this approach are illustrated by comparing simulated aortic responses to a sustained increase in blood pressure predicted by continuum and agent-based models both before and after instituting a genetic algorithm to refine 16 objectively bounded model parameters. We show that congruency-based parameter refinement not only yielded increased consistency across scales, it also yielded predictions that are closer to in vivo observations.

  20. Understanding Group/Party Affiliation Using Social Networks and Agent-Based Modeling

    NASA Technical Reports Server (NTRS)

    Campbell, Kenyth

    2012-01-01

    The dynamics of group affiliation and group dispersion is a concept that is most often studied in order for political candidates to better understand the most efficient way to conduct their campaigns. While political campaigning in the United States is a very hot topic that most politicians analyze and study, the concept of group/party affiliation presents its own area of study that producers very interesting results. One tool for examining party affiliation on a large scale is agent-based modeling (ABM), a paradigm in the modeling and simulation (M&S) field perfectly suited for aggregating individual behaviors to observe large swaths of a population. For this study agent based modeling was used in order to look at a community of agents and determine what factors can affect the group/party affiliation patterns that are present. In the agent-based model that was used for this experiment many factors were present but two main factors were used to determine the results. The results of this study show that it is possible to use agent-based modeling to explore group/party affiliation and construct a model that can mimic real world events. More importantly, the model in the study allows for the results found in a smaller community to be translated into larger experiments to determine if the results will remain present on a much larger scale.

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

    NASA Astrophysics Data System (ADS)

    Hong, Weijia; Wang, Jun

    2015-03-01

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

  2. Using Model Replication to Improve the Reliability of Agent-Based Models

    NASA Astrophysics Data System (ADS)

    Zhong, Wei; Kim, Yushim

    The basic presupposition of model replication activities for a computational model such as an agent-based model (ABM) is that, as a robust and reliable tool, it must be replicable in other computing settings. This assumption has recently gained attention in the community of artificial society and simulation due to the challenges of model verification and validation. Illustrating the replication of an ABM representing fraudulent behavior in a public service delivery system originally developed in the Java-based MASON toolkit for NetLogo by a different author, this paper exemplifies how model replication exercises provide unique opportunities for model verification and validation process. At the same time, it helps accumulate best practices and patterns of model replication and contributes to the agenda of developing a standard methodological protocol for agent-based social simulation.

  3. Generic framework for mining cellular automata models on protein-folding simulations.

    PubMed

    Diaz, N; Tischer, I

    2016-05-13

    Cellular automata model identification is an important way of building simplified simulation models. In this study, we describe a generic architectural framework to ease the development process of new metaheuristic-based algorithms for cellular automata model identification in protein-folding trajectories. Our framework was developed by a methodology based on design patterns that allow an improved experience for new algorithms development. The usefulness of the proposed framework is demonstrated by the implementation of four algorithms, able to obtain extremely precise cellular automata models of the protein-folding process with a protein contact map representation. Dynamic rules obtained by the proposed approach are discussed, and future use for the new tool is outlined.

  4. Integrated Modeling, Mapping, and Simulation (IMMS) Framework for Exercise and Response Planning

    NASA Technical Reports Server (NTRS)

    Mapar, Jalal; Hoette, Trisha; Mahrous, Karim; Pancerella, Carmen M.; Plantenga, Todd; Yang, Christine; Yang, Lynn; Hopmeier, Michael

    2011-01-01

    EmergenCy management personnel at federal, stale, and local levels can benefit from the increased situational awareness and operational efficiency afforded by simulation and modeling for emergency preparedness, including planning, training and exercises. To support this goal, the Department of Homeland Security's Science & Technology Directorate is funding the Integrated Modeling, Mapping, and Simulation (IMMS) program to create an integrating framework that brings together diverse models for use by the emergency response community. SUMMIT, one piece of the IMMS program, is the initial software framework that connects users such as emergency planners and exercise developers with modeling resources, bridging the gap in expertise and technical skills between these two communities. SUMMIT was recently deployed to support exercise planning for National Level Exercise 2010. Threat, casualty. infrastructure, and medical surge models were combined within SUMMIT to estimate health care resource requirements for the exercise ground truth.

  5. Agent-based model for rural-urban migration: A dynamic consideration

    NASA Astrophysics Data System (ADS)

    Cai, Ning; Ma, Hai-Ying; Khan, M. Junaid

    2015-10-01

    This paper develops a dynamic agent-based model for rural-urban migration, based on the previous relevant works. The model conforms to the typical dynamic linear multi-agent systems model concerned extensively in systems science, in which the communication network is formulated as a digraph. Simulations reveal that consensus of certain variable could be harmful to the overall stability and should be avoided.

  6. Agent Based Study of Surprise Attacks:. Roles of Surveillance, Prompt Reaction and Intelligence

    NASA Astrophysics Data System (ADS)

    Shanahan, Linda; Sen, Surajit

    Defending a confined territory from a surprise attack is seldom possible. We use molecular dynamics and statistical physics inspired agent-based simulations to explore the evolution and outcome of such attacks. The study suggests robust emergent behavior, which emphasizes the importance of accurate surveillance, automated and powerful attack response, building layout, and sheds light on the role of communication restrictions in defending such territories.

  7. An Adaptive Simulation Framework for the Exploration of Extreme and Unexpected Events in Dynamic Engineered Systems.

    PubMed

    Turati, Pietro; Pedroni, Nicola; Zio, Enrico

    2017-01-01

    The end states reached by an engineered system during an accident scenario depend not only on the sequences of the events composing the scenario, but also on their timing and magnitudes. Including these additional features within an overarching framework can render the analysis infeasible in practical cases, due to the high dimension of the system state-space and the computational effort correspondingly needed to explore the possible system evolutions in search of the interesting (and very rare) ones of failure. To tackle this hurdle, in this article we introduce a framework for efficiently probing the space of event sequences of a dynamic system by means of a guided Monte Carlo simulation. Such framework is semi-automatic and allows embedding the analyst's prior knowledge about the system and his/her objectives of analysis. Specifically, the framework allows adaptively and intelligently allocating the simulation efforts preferably on those sequences leading to outcomes of interest for the objectives of the analysis, e.g., typically those that are more safety-critical (and/or rare). The emerging diversification in the filling of the state-space by the preference-guided exploration allows also the retrieval of critical system features, which can be useful to analysts and designers for taking appropriate means of prevention and mitigation of dangerous and/or unexpected consequences. A dynamic system for gas transmission is considered as a case study to demonstrate the application of the method.

  8. Coupling LAMMPS and the vl3 Framework for Co-Visualization of Atomistic Simulations

    SciTech Connect

    Rizzi, Silvio; Hereld, Mark; Insley, Joseph; Malakar, Preeti; Papka, Michael E.; Uram, Thomas; Vishwanath, Venkatram

    2016-01-01

    In this work we perform in-situ visualization of molecular dynamics simulations, which can help scientists to visualize simulation output on-the-fly, without incurring storage overheads. We present a case study to couple LAMMPS, the large-scale molecular dynamics simulation code with vl3, our parallel framework for large-scale visualization and analysis. Our motivation is to identify effective approaches for covisualization and exploration of large-scale atomistic simulations at interactive frame rates.We propose a system of coupled libraries and describe its architecture, with an implementation that runs on GPU-based clusters. We present the results of strong and weak scalability experiments, as well as future research avenues based on our results.

  9. An extendable simulation framework for benchmarking EEG-based brain connectivity estimation methodologies.

    PubMed

    Haufe, Stefan

    2015-01-01

    Due to its high temporal resolution, electroencephalography (EEG) is a promising research tool for studying functional and effective brain interaction. Yet, it is rather uncommon for researchers to validate their connectivity estimation methodologies prior to applying them to real data, even though problems have been pointed out regarding the validity of some of the predominant approaches. We here provide an extendable simulation framework that enables researchers to test their analysis pipelines on customizable realistically simulated EEG data. We define three simple criteria to measure source localization, connectivity detection and directionality estimation performance. All data and code needed to generate pseudo-EEG data and to benchmark a method's estimation performance are provided.

  10. Microworlds, Simulators, and Simulation: Framework for a Benchmark of Human Reliability Data Sources

    SciTech Connect

    Ronald Boring; Dana Kelly; Carol Smidts; Ali Mosleh; Brian Dyre

    2012-06-01

    In this paper, we propose a method to improve the data basis of human reliability analysis (HRA) by extending the data sources used to inform HRA methods. Currently, most HRA methods are based on limited empirical data, and efforts to enhance the empirical basis behind HRA methods have not yet yielded significant new data. Part of the reason behind this shortage of quality data is attributable to the data sources used. Data have been derived from unrelated industries, from infrequent risk-significant events, or from costly control room simulator studies. We propose a benchmark of four data sources: a simplified microworld simulator using unskilled student operators, a full-scope control room simulator using skilled student operators, a full-scope control room simulator using licensed commercial operators, and a human performance modeling and simulation system using virtual operators. The goal of this research is to compare findings across the data sources to determine to what extent data may be used and generalized from cost effective sources.

  11. An Integrated Qualitative and Quantitative Biochemical Model Learning Framework Using Evolutionary Strategy and Simulated Annealing.

    PubMed

    Wu, Zujian; Pang, Wei; Coghill, George M

    Both qualitative and quantitative model learning frameworks for biochemical systems have been studied in computational systems biology. In this research, after introducing two forms of pre-defined component patterns to represent biochemical models, we propose an integrative qualitative and quantitative modelling framework for inferring biochemical systems. In the proposed framework, interactions between reactants in the candidate models for a target biochemical system are evolved and eventually identified by the application of a qualitative model learning approach with an evolution strategy. Kinetic rates of the models generated from qualitative model learning are then further optimised by employing a quantitative approach with simulated annealing. Experimental results indicate that our proposed integrative framework is feasible to learn the relationships between biochemical reactants qualitatively and to make the model replicate the behaviours of the target system by optimising the kinetic rates quantitatively. Moreover, potential reactants of a target biochemical system can be discovered by hypothesising complex reactants in the synthetic models. Based on the biochemical models learned from the proposed framework, biologists can further perform experimental study in wet laboratory. In this way, natural biochemical systems can be better understood.

  12. A 3D MPI-Parallel GPU-accelerated framework for simulating ocean wave energy converters

    NASA Astrophysics Data System (ADS)

    Pathak, Ashish; Raessi, Mehdi

    2015-11-01

    We present an MPI-parallel GPU-accelerated computational framework for studying the interaction between ocean waves and wave energy converters (WECs). The computational framework captures the viscous effects, nonlinear fluid-structure interaction (FSI), and breaking of waves around the structure, which cannot be captured in many potential flow solvers commonly used for WEC simulations. The full Navier-Stokes equations are solved using the two-step projection method, which is accelerated by porting the pressure Poisson equation to GPUs. The FSI is captured using the numerically stable fictitious domain method. A novel three-phase interface reconstruction algorithm is used to resolve three phases in a VOF-PLIC context. A consistent mass and momentum transport approach enables simulations at high density ratios. The accuracy of the overall framework is demonstrated via an array of test cases. Numerical simulations of the interaction between ocean waves and WECs are presented. Funding from the National Science Foundation CBET-1236462 grant is gratefully acknowledged.

  13. Ximpol: a new X-ray polarimetry observation-simulation and analysis framework

    NASA Astrophysics Data System (ADS)

    Baldini, Luca; Muleri, Fabio; Soffitta, Paolo; Omodei, Nicola; Pesce-Rollins, Melissa; Sgro, Carmelo; Latronico, Luca; Spada, Francesca; Manfreda, Alberto; Di Lalla, Niccolo

    2016-07-01

    We present a new simulation framework, ximpol, based on the Python programming language and the Scipy stack, specifically developed for X-ray polarimetric applications. ximpol is designed to produce fast and yet realistic observation-simulations, given as basic inputs: (i) an arbitrary source model including morphological, temporal, spectral and polarimetric information, and (ii) the response functions of the detector under study, i.e., the effective area, the energy dispersion, the point-spread function and the modulation factor. The format of the response files is OGIP compliant, and the framework has the capability of producing output files that can be directly fed into the standard visualization and analysis tools used by the X-ray community, including XSPEC---which make it a useful tool not only for simulating observations of astronomical sources, but also to develop and test end-to-end analysis chains. In this contribution we shall give an overview of the basic architecture of the software. Although in principle the framework is not tied to any specific mission or instrument design we shall present a few physically interesting case studies in the context of the XIPE mission phase study.

  14. A Framework for Simulation of Aircraft Flyover Noise Through a Non-Standard Atmosphere

    NASA Technical Reports Server (NTRS)

    Arntzen, Michael; Rizzi, Stephen A.; Visser, Hendrikus G.; Simons, Dick G.

    2012-01-01

    This paper describes a new framework for the simulation of aircraft flyover noise through a non-standard atmosphere. Central to the framework is a ray-tracing algorithm which defines multiple curved propagation paths, if the atmosphere allows, between the moving source and listener. Because each path has a different emission angle, synthesis of the sound at the source must be performed independently for each path. The time delay, spreading loss and absorption (ground and atmosphere) are integrated along each path, and applied to each synthesized aircraft noise source to simulate a flyover. A final step assigns each resulting signal to its corresponding receiver angle for the simulation of a flyover in a virtual reality environment. Spectrograms of the results from a straight path and a curved path modeling assumption are shown. When the aircraft is at close range, the straight path results are valid. Differences appear especially when the source is relatively far away at shallow elevation angles. These differences, however, are not significant in common sound metrics. While the framework used in this work performs off-line processing, it is conducive to real-time implementation.

  15. A modelling framework to simulate foliar fungal epidemics using functional–structural plant models

    PubMed Central

    Garin, Guillaume; Fournier, Christian; Andrieu, Bruno; Houlès, Vianney; Robert, Corinne; Pradal, Christophe

    2014-01-01

    Background and Aims Sustainable agriculture requires the identification of new, environmentally responsible strategies of crop protection. Modelling of pathosystems can allow a better understanding of the major interactions inside these dynamic systems and may lead to innovative protection strategies. In particular, functional–structural plant models (FSPMs) have been identified as a means to optimize the use of architecture-related traits. A current limitation lies in the inherent complexity of this type of modelling, and thus the purpose of this paper is to provide a framework to both extend and simplify the modelling of pathosystems using FSPMs. Methods Different entities and interactions occurring in pathosystems were formalized in a conceptual model. A framework based on these concepts was then implemented within the open-source OpenAlea modelling platform, using the platform's general strategy of modelling plant–environment interactions and extending it to handle plant interactions with pathogens. New developments include a generic data structure for representing lesions and dispersal units, and a series of generic protocols to communicate with objects representing the canopy and its microenvironment in the OpenAlea platform. Another development is the addition of a library of elementary models involved in pathosystem modelling. Several plant and physical models are already available in OpenAlea and can be combined in models of pathosystems using this framework approach. Key Results Two contrasting pathosystems are implemented using the framework and illustrate its generic utility. Simulations demonstrate the framework's ability to simulate multiscaled interactions within pathosystems, and also show that models are modular components within the framework and can be extended. This is illustrated by testing the impact of canopy architectural traits on fungal dispersal. Conclusions This study provides a framework for modelling a large number of pathosystems

  16. SMART: A New Semi-distributed Hydrologic Modelling Framework for Soil Moisture and Runoff Simulations

    NASA Astrophysics Data System (ADS)

    Ajami, Hoori; Sharma, Ashish

    2016-04-01

    A new GIS-based semi-distributed hydrological modelling framework is developed based upon the delineation of contiguous and topologically connected Hydrologic Response Units (HRUs). The Soil Moisture and Runoff simulation Toolkit (SMART) performs topographic and geomorphic analysis of a catchment and delineates HRUs in each first order sub-basin. This HRU delineation approach maintains lateral flow dynamics in first order sub-basins and therefore it is suited for simulating runoff in upland catchments. Simulation elements in SMART are distributed cross sections or equivalent cross sections (ECS) in each first order sub-basin to represent hillslope hydrologic processes. Delineation of ECSs in SMART is performed by weighting the topographic and physiographic properties of the part or entire first-order sub-basin and has the advantage of reducing computational time/effort while maintaining reasonable accuracy in simulated hydrologic state and fluxes (e.g. soil moisture, evapotranspiration and runoff). SMART workflow is written in MATLAB to automate the HRU and cross section delineations, model simulations across multiple cross sections, and post-processing of model outputs to visualize the results. The MATLAB Parallel Processing Toolbox is used for simultaneous simulations of cross sections and is further reduced computational time. SMART workflow tasks are: 1) delineation of first order sub-basins of a catchment using a digital elevation model, 2) hillslope delineation, 3) landform delineation in every first order sub-basin based on topographic and geomorphic properties of a group of sub-basins or the entire catchment, 4) formulation of cross sections as well as equivalent cross sections in every first order sub-basin, and 5) deriving vegetation and soil parameters from spatially distributed land cover and soil information. The current version of SMART uses a 2-d distributed hydrological model based on the Richards' equation. However, any hydrologic model can be

  17. A framework for simulating ultrasound imaging based on first order nonlinear pressure-velocity relations.

    PubMed

    Du, Yigang; Fan, Rui; Li, Yong; Chen, Siping; Jensen, Jørgen Arendt

    2016-07-01

    An ultrasound imaging framework modeled with the first order nonlinear pressure-velocity relations (NPVR) and implemented by a half-time staggered solution and pseudospectral method is presented in this paper. The framework is capable of simulating linear and nonlinear ultrasound propagation and reflections in a heterogeneous medium with different sound speeds and densities. It can be initialized with arbitrary focus, excitation and apodization for multiple individual channels in both 2D and 3D spatial fields. The simulated channel data can be generated using this framework, and ultrasound image can be obtained by beamforming the simulated channel data. Various results simulated by different algorithms are illustrated for comparisons. The root mean square (RMS) errors for each compared pulses are calculated. The linear propagation is validated by an angular spectrum approach (ASA) with a RMS error of 3% at the focal point for a 2D field, and Field II with RMS errors of 0.8% and 1.5% at the electronic and the elevation focuses for 3D fields, respectively. The accuracy for the NPVR based nonlinear propagation is investigated by comparing with the Abersim simulation for pulsed fields and with the nonlinear ASA for monochromatic fields. The RMS errors of the nonlinear pulses calculated by the NPVR and Abersim are respectively 2.4%, 7.4%, 17.6% and 36.6% corresponding to initial pressure amplitudes of 50kPa, 200kPa, 500kPa and 1MPa at the transducer. By increasing the sampling frequency for the strong nonlinearity, the RMS error for 1MPa initial pressure amplitude is reduced from 36.6% to 27.3%.

  18. Simulation-optimization framework for multi-site multi-season hybrid stochastic streamflow modeling

    NASA Astrophysics Data System (ADS)

    Srivastav, Roshan; Srinivasan, K.; Sudheer, K. P.

    2016-11-01

    A simulation-optimization (S-O) framework is developed for the hybrid stochastic modeling of multi-site multi-season streamflows. The multi-objective optimization model formulated is the driver and the multi-site, multi-season hybrid matched block bootstrap model (MHMABB) is the simulation engine within this framework. The multi-site multi-season simulation model is the extension of the existing single-site multi-season simulation model. A robust and efficient evolutionary search based technique, namely, non-dominated sorting based genetic algorithm (NSGA - II) is employed as the solution technique for the multi-objective optimization within the S-O framework. The objective functions employed are related to the preservation of the multi-site critical deficit run sum and the constraints introduced are concerned with the hybrid model parameter space, and the preservation of certain statistics (such as inter-annual dependence and/or skewness of aggregated annual flows). The efficacy of the proposed S-O framework is brought out through a case example from the Colorado River basin. The proposed multi-site multi-season model AMHMABB (whose parameters are obtained from the proposed S-O framework) preserves the temporal as well as the spatial statistics of the historical flows. Also, the other multi-site deficit run characteristics namely, the number of runs, the maximum run length, the mean run sum and the mean run length are well preserved by the AMHMABB model. Overall, the proposed AMHMABB model is able to show better streamflow modeling performance when compared with the simulation based SMHMABB model, plausibly due to the significant role played by: (i) the objective functions related to the preservation of multi-site critical deficit run sum; (ii) the huge hybrid model parameter space available for the evolutionary search and (iii) the constraint on the preservation of the inter-annual dependence. Split-sample validation results indicate that the AMHMABB model is

  19. Pain expressiveness and altruistic behavior: an exploration using agent-based modeling.

    PubMed

    de C Williams, Amanda C; Gallagher, Elizabeth; Fidalgo, Antonio R; Bentley, Peter J

    2016-03-01

    Predictions which invoke evolutionary mechanisms are hard to test. Agent-based modeling in artificial life offers a way to simulate behaviors and interactions in specific physical or social environments over many generations. The outcomes have implications for understanding adaptive value of behaviors in context. Pain-related behavior in animals is communicated to other animals that might protect or help, or might exploit or predate. An agent-based model simulated the effects of displaying or not displaying pain (expresser/nonexpresser strategies) when injured and of helping, ignoring, or exploiting another in pain (altruistic/nonaltruistic/selfish strategies). Agents modeled in MATLAB interacted at random while foraging (gaining energy); random injury interrupted foraging for a fixed time unless help from an altruistic agent, who paid an energy cost, speeded recovery. Environmental and social conditions also varied, and each model ran for 10,000 iterations. Findings were meaningful in that, in general, contingencies that evident from experimental work with a variety of mammals, over a few interactions, were replicated in the agent-based model after selection pressure over many generations. More energy-demanding expression of pain reduced its frequency in successive generations, and increasing injury frequency resulted in fewer expressers and altruists. Allowing exploitation of injured agents decreased expression of pain to near zero, but altruists remained. Decreasing costs or increasing benefits of helping hardly changed its frequency, whereas increasing interaction rate between injured agents and helpers diminished the benefits to both. Agent-based modeling allows simulation of complex behaviors and environmental pressures over evolutionary time.

  20. An Object-Oriented Finite Element Framework for Multiphysics Phase Field Simulations

    SciTech Connect

    Michael R Tonks; Derek R Gaston; Paul C Millett; David Andrs; Paul Talbot

    2012-01-01

    The phase field approach is a powerful and popular method for modeling microstructure evolution. In this work, advanced numerical tools are used to create a phase field framework that facilitates rapid model development. This framework, called MARMOT, is based on Idaho National Laboratory's finite element Multiphysics Object-Oriented Simulation Environment. In MARMOT, the system of phase field partial differential equations (PDEs) are solved simultaneously with PDEs describing additional physics, such as solid mechanics and heat conduction, using the Jacobian-Free Newton Krylov Method. An object-oriented architecture is created by taking advantage of commonalities in phase fields models to facilitate development of new models with very little written code. In addition, MARMOT provides access to mesh and time step adaptivity, reducing the cost for performing simulations with large disparities in both spatial and temporal scales. In this work, phase separation simulations are used to show the numerical performance of MARMOT. Deformation-induced grain growth and void growth simulations are included to demonstrate the muliphysics capability.

  1. A framework for WRF to WRF-IBM grid nesting to enable multiscale simulations

    SciTech Connect

    Wiersema, David John; Lundquist, Katherine A.; Chow, Fotini Katapodes

    2016-09-29

    With advances in computational power, mesoscale models, such as the Weather Research and Forecasting (WRF) model, are often pushed to higher resolutions. As the model’s horizontal resolution is refined, the maximum resolved terrain slope will increase. Because WRF uses a terrain-following coordinate, this increase in resolved terrain slopes introduces additional grid skewness. At high resolutions and over complex terrain, this grid skewness can introduce large numerical errors that require methods, such as the immersed boundary method, to keep the model accurate and stable. Our implementation of the immersed boundary method in the WRF model, WRF-IBM, has proven effective at microscale simulations over complex terrain. WRF-IBM uses a non-conforming grid that extends beneath the model’s terrain. Boundary conditions at the immersed boundary, the terrain, are enforced by introducing a body force term to the governing equations at points directly beneath the immersed boundary. Nesting between a WRF parent grid and a WRF-IBM child grid requires a new framework for initialization and forcing of the child WRF-IBM grid. This framework will enable concurrent multi-scale simulations within the WRF model, improving the accuracy of high-resolution simulations and enabling simulations across a wide range of scales.

  2. gadfly: A pandas-based Framework for Analyzing GADGET Simulation Data

    NASA Astrophysics Data System (ADS)

    Hummel, Jacob A.

    2016-11-01

    We present the first public release (v0.1) of the open-source gadget Dataframe Library: gadfly. The aim of this package is to leverage the capabilities of the broader python scientific computing ecosystem by providing tools for analyzing simulation data from the astrophysical simulation codes gadget and gizmo using pandas, a thoroughly documented, open-source library providing high-performance, easy-to-use data structures that is quickly becoming the standard for data analysis in python. Gadfly is a framework for analyzing particle-based simulation data stored in the HDF5 format using pandas DataFrames. The package enables efficient memory management, includes utilities for unit handling, coordinate transformations, and parallel batch processing, and provides highly optimized routines for visualizing smoothed-particle hydrodynamics data sets.

  3. Diversity and Community: The Role of Agent-Based Modeling.

    PubMed

    Stivala, Alex

    2017-03-13

    Community psychology involves several dialectics between potentially opposing ideals, such as theory and practice, rights and needs, and respect for human diversity and sense of community. Some recent papers in the American Journal of Community Psychology have examined the diversity-community dialectic, some with the aid of agent-based modeling and concepts from network science. This paper further elucidates these concepts and suggests that research in community psychology can benefit from a useful dialectic between agent-based modeling and the real-world concerns of community psychology.

  4. Deterministic Agent-Based Path Optimization by Mimicking the Spreading of Ripples.

    PubMed

    Hu, Xiao-Bing; Wang, Ming; Leeson, Mark S; Di Paolo, Ezequiel A; Liu, Hao

    2016-01-01

    Inspirations from nature have contributed fundamentally to the development of evolutionary computation. Learning from the natural ripple-spreading phenomenon, this article proposes a novel ripple-spreading algorithm (RSA) for the path optimization problem (POP). In nature, a ripple spreads at a constant speed in all directions, and the node closest to the source is the first to be reached. This very simple principle forms the foundation of the proposed RSA. In contrast to most deterministic top-down centralized path optimization methods, such as Dijkstra's algorithm, the RSA is a bottom-up decentralized agent-based simulation model. Moreover, it is distinguished from other agent-based algorithms, such as genetic algorithms and ant colony optimization, by being a deterministic method that can always guarantee the global optimal solution with very good scalability. Here, the RSA is specifically applied to four different POPs. The comparative simulation results illustrate the advantages of the RSA in terms of effectiveness and efficiency. Thanks to the agent-based and deterministic features, the RSA opens new opportunities to attack some problems, such as calculating the exact complete Pareto front in multiobjective optimization and determining the kth shortest project time in project management, which are very difficult, if not impossible, for existing methods to resolve. The ripple-spreading optimization principle and the new distinguishing features and capacities of the RSA enrich the theoretical foundations of evolutionary computation.

  5. A generalized mathematical framework for stochastic simulation and forecast of hydrologic time series

    NASA Astrophysics Data System (ADS)

    Koutsoyiannis, Demetris

    2000-02-01

    A generalized framework for single-variate and multivariate simulation and forecasting problems in stochastic hydrology is proposed. It is appropriate for short-term or long-term memory processes and preserves the Hurst coefficient even in multivariate processes with a different Hurst coefficient in each location. Simultaneously, it explicitly preserves the coefficients of skewness of the processes. The proposed framework incorporates short-memory (autoregressive moving average) and long-memory (fractional Gaussian noise) models, considering them as special instances of a parametrically defined generalized autocovariance function, more comprehensive than those used in these classes of models. The generalized autocovariance function is then implemented in a generalized moving average generating scheme that yields a new time-symmetric (backward-forward) representation, whose advantages are studied. Fast algorithms for computation of internal parameters of the generating scheme are developed, appropriate for problems including even thousands of such parameters. The proposed generating scheme is also adapted through a generalized methodology to perform in forecast mode, in addition to simulation mode. Finally, a specific form of the model for problems where the autocorrelation function can be defined only for a certain finite number of lags is also studied. Several illustrations are included to clarify the features and the performance of the components of the proposed framework.

  6. Doing It In The SWMF Way: From Separate Space Physics Simulation Programs To The Framework For Space Weather Simulation.

    NASA Astrophysics Data System (ADS)

    Volberg, O.; Toth, G.; Sokolov, I.; Ridley, A. J.; Gombosi, T. I.; de Zeeuw, D. C.; Hansen, K. C.; Chesney, D. R.; Stout, Q. F.; Powell, K. G.; Kane, K. J.; Oehmke, R. C.

    2003-12-01

    The NASA-funded Space Weather Modeling Framework (SWMF) is developed to provide "plug and play" type Sun-to-Earth simulation capabilities serving the space physics modeling community. In its fully developed form, the SWMF will comprise a series of interoperating models of physics domains, ranging from the surface of the Sun to the upper atmosphere of the Earth. In its current form the SWMF links together five models: Global Magnetosphere, Inner Heliosphere, Ionosphere Electrodynamics, Upper Atmosphere, and Inner Magnetosphere. The framework permits to switch models of any type. The SWMF is a structured collection of software building blocks that can be used or customized to develop Sun-Earth system modeling components, and to assemble them into application. The SWMF consist of utilities and data structures for creating model components and coupling them. The SWMF contains Control Model, which controls initialization and execution of the components. It is responsible for component registration, processor layout for each component and coupling schedules. A component is created from the user-supplied physics code by adding a wrapper, which provides the control functions and coupling interface to perform the data exchange with other components. Both the wrapper and coupling interface are constructed from the building blocks provided by the framework itself. The current SWMF implementation is based on the latest component technology and uses many important concepts of Object-Oriented Programming emulated in Fortran 90. Currently it works on Linux Beowulf clusters, SGI Origin 2000 and Compaq ES45 machines.

  7. Evaluation of a performance appraisal framework for radiation therapists in planning and simulation

    SciTech Connect

    Becker, Jillian; Bridge, Pete; Brown, Elizabeth; Lusk, Ryan; Ferrari-Anderson, Janet

    2015-06-15

    Constantly evolving technology and techniques within radiation therapy require practitioners to maintain a continuous approach to professional development and training. Systems of performance appraisal and adoption of regular feedback mechanisms are vital to support this development yet frequently lack structure and rely on informal peer support. A Radiation Therapy Performance Appraisal Framework (RT-PAF) for radiation therapists in planning and simulation was developed to define expectations of practice and promote a supportive and objective culture of performance and skills appraisal. Evaluation of the framework was conducted via an anonymous online survey tool. Nine peer reviewers and fourteen recipients provided feedback on its effectiveness and the challenges and limitations of the approach. Findings from the evaluation were positive and suggested that both groups gained benefit from and expressed a strong interest in embedding the approach more routinely. Respondents identified common challenges related to the limited ability to implement suggested development strategies; this was strongly associated with time and rostering issues. This framework successfully defined expectations for practice and provided a fair and objective feedback process that focussed on skills development. It empowered staff to maintain their skills and reach their professional potential. Management support, particularly in regard to provision of protected time was highlighted as critical to the framework's ongoing success. The demonstrated benefits arising in terms of staff satisfaction and development highlight the importance of this commitment to the modern radiation therapy workforce.

  8. Architectural considerations for agent-based national scale policy models : LDRD final report.

    SciTech Connect

    Backus, George A.; Strip, David R.

    2007-09-01

    The need to anticipate the consequences of policy decisions becomes ever more important as the magnitude of the potential consequences grows. The multiplicity of connections between the components of society and the economy makes intuitive assessments extremely unreliable. Agent-based modeling has the potential to be a powerful tool in modeling policy impacts. The direct mapping between agents and elements of society and the economy simplify the mapping of real world functions into the world of computation assessment. Our modeling initiative is motivated by the desire to facilitate informed public debate on alternative policies for how we, as a nation, provide healthcare to our population. We explore the implications of this motivation on the design and implementation of a model. We discuss the choice of an agent-based modeling approach and contrast it to micro-simulation and systems dynamics approaches.

  9. Towards strength and stability : agent-based modeling of infrastructure markets.

    SciTech Connect

    North, M. J.; Decision and Information Sciences

    2001-01-01

    Complex Adaptive Systems (CASs) can be applied to investigate complex infrastructures and infrastructure interdependencies. Agent-based modeling (ABM) is a new CAS-based approach to the construction of models. The CAS agents within the Spot Market Agent Research Tool (SMART) and Flexible Agent Simulation Toolkit (FAST) ABMs allow investigation of the electric power infrastructure, the natural gas infrastructure, and their interdependencies. The Swarm-based SMART models use sets of agents and interconnections to represent electric power and natural gas systems. A prototype virtual reality (VR) interface has also been constructed for a version of the SMART model. This tool is intended to explore the use of advanced interactive three-dimensional visualization in agent-based modeling. The Java-based FAST model is currently under construction. FAST is a complete redesign of the SMART models that includes improvements in the modeling environment, model detail, and representational fidelity. Developing ABMs is difficult but can be rewarding.

  10. A unified framework for spiking and gap-junction interactions in distributed neuronal network simulations

    PubMed Central

    Hahne, Jan; Helias, Moritz; Kunkel, Susanne; Igarashi, Jun; Bolten, Matthias; Frommer, Andreas; Diesmann, Markus

    2015-01-01

    Contemporary simulators for networks of point and few-compartment model neurons come with a plethora of ready-to-use neuron and synapse models and support complex network topologies. Recent technological advancements have broadened the spectrum of application further to the efficient simulation of brain-scale networks on supercomputers. In distributed network simulations the amount of spike data that accrues per millisecond and process is typically low, such that a common optimization strategy is to communicate spikes at relatively long intervals, where the upper limit is given by the shortest synaptic transmission delay in the network. This approach is well-suited for simulations that employ only chemical synapses but it has so far impeded the incorporation of gap-junction models, which require instantaneous neuronal interactions. Here, we present a numerical algorithm based on a waveform-relaxation technique which allows for network simulations with gap junctions in a way that is compatible with the delayed communication strategy. Using a reference implementation in the NEST simulator, we demonstrate that the algorithm and the required data structures can be smoothly integrated with existing code such that they complement the infrastructure for spiking connections. To show that the unified framework for gap-junction and spiking interactions achieves high performance and delivers high accuracy in the presence of gap junctions, we present benchmarks for workstations, clusters, and supercomputers. Finally, we discuss limitations of the novel technology. PMID:26441628

  11. Introducing FACETS, the Framework Application for Core-Edge Transport Simulations

    NASA Astrophysics Data System (ADS)

    Cary, J. R.; Candy, J.; Cohen, R. H.; Krasheninnikov, S.; McCune, D. C.; Estep, D. J.; Larson, J.; Malony, A. D.; Worley, P. H.; Carlsson, J. A.; Hakim, A. H.; Hamill, P.; Kruger, S.; Muzsala, S.; Pletzer, A.; Shasharina, S.; Wade-Stein, D.; Wang, N.; McInnes, L.; Wildey, T.; Casper, T.; Diachin, L.; Epperly, T.; Rognlien, T. D.; Fahey, M. R.; Kuehn, J. A.; Morris, A.; Shende, S.; Feibush, E.; Hammett, G. W.; Indireshkumar, K.; Ludescher, C.; Randerson, L.; Stotler, D.; Pigarov, A. Yu; Bonoli, P.; Chang, C. S.; D'Ippolito, D. A.; Colella, P.; Keyes, D. E.; Bramley, R.; Myra, J. R.

    2007-07-01

    The FACETS (Framework Application for Core-Edge Transport Simulations) project began in January 2007 with the goal of providing core to wall transport modeling of a tokamak fusion reactor. This involves coupling previously separate computations for the core, edge, and wall regions. Such a coupling is primarily through connection regions of lower dimensionality. The project has started developing a component-based coupling framework to bring together models for each of these regions. In the first year, the core model will be a 1 ½ dimensional model (1D transport across flux surfaces coupled to a 2D equilibrium) with fixed equilibrium. The initial edge model will be the fluid model, UEDGE, but inclusion of kinetic models is planned for the out years. The project also has an embedded Scientific Application Partnership that is examining embedding a full-scale turbulence model for obtaining the crosssurface fluxes into a core transport code.

  12. A dynamic hybrid subgrid-scale modeling framework for large eddy simulations

    NASA Astrophysics Data System (ADS)

    Maulik, Romit; San, Omer

    2016-11-01

    We put forth a dynamic modeling framework for sub-grid parameterization of large eddy simulation of turbulent flows based upon the use of the approximate deconvolution (AD) procedure to compute the eddy viscosity constant self-adaptively from the resolved flow quantities. In our proposed framework, the test filtering process of the standard dynamic model is replaced by the AD procedure and a posteriori error analysis is performed. The robustness of the model has been tested considering the Burgers, Kraichnan, Kolmogorov turbulence problems. Our numerical assessments for solving these canonical decaying turbulence problems show that the proposed approach could be used as a viable tool to address the turbulence closure problem due to its flexibility.

  13. The ADAQ framework: An integrated toolkit for data acquisition and analysis with real and simulated radiation detectors

    NASA Astrophysics Data System (ADS)

    Hartwig, Zachary S.

    2016-04-01

    The ADAQ framework is a collection of software tools that is designed to streamline the acquisition and analysis of radiation detector data produced in modern digital data acquisition (DAQ) systems and in Monte Carlo detector simulations. The purpose of the framework is to maximize user scientific productivity by minimizing the effort and expertise required to fully utilize radiation detectors in a variety of scientific and engineering disciplines. By using a single set of tools to span the real and simulation domains, the framework eliminates redundancy and provides an integrated workflow for high-fidelity comparison between experimental and simulated detector performance. Built on the ROOT data analysis framework, the core of the ADAQ framework is a set of C++ and Python libraries that enable high-level control of digital DAQ systems and detector simulations with data stored into standardized binary ROOT files for further analysis. Two graphical user interface programs utilize the libraries to create powerful tools: ADAQAcquisition handles control and readout of real-world DAQ systems and ADAQAnalysis provides data analysis and visualization methods for experimental and simulated data. At present, the ADAQ framework supports digital DAQ hardware from CAEN S.p.A. and detector simulations performed in Geant4; however, the modular design will facilitate future extension to other manufacturers and simulation platforms.

  14. Toward an Agent-Based Model of Socially Optimal Water Rights Markets

    NASA Astrophysics Data System (ADS)

    Ehlen, M. A.

    2004-12-01

    There has been considerable interest lately in using public markets for buying and selling the rights to local water usage. Such water rights markets, if designed correctly, should be socially optimal, that is, should sell rights at prices that reflect the true value of water in the region, taking into account that water rights buyers and sellers represent a disparate group of private industry, public authorities, and private users, each having different water needs and different priority to local government. Good market design, however, is hard. As was experienced in California short-run electric power markets, a market design that on paper looks reasonable but in practice is mal-constructed can have devastating effects: firms can learn to manipulate prices by `playing' both sides of the market, and sellers can under-provide so as to create exorbitant prices which buyers have no choice but to pay. Economic theory provides several frameworks for developing a good water rights market design; for example, the structure-conduct-performance paradigm (SCPP) suggests that, among other things, the number and types of buyers and sellers (structure), and transaction clearing rules and government policies (conduct) affect in very particular ways the prices and quantities (performance) in the market. In slow-moving or static markets, SCPP has been a useful predictor of market performance; in faster markets the market dynamics that endogenously develop over time are often too complex to predict with SCPP or other existing modeling techniques. New, more sophisticated combinations of modeling and simulation are needed. Toward developing a good (i.e., socially optimal) water rights market design that can take into account the dynamics inherent in the water sector, we are developing an agent-based model of water rights markets. The model serves two purposes: first, it provides an SCPP-based framework of water rights markets that takes into account the particular structure of

  15. A Methodology for Doctrine in Modeling and Simulation: Battle Management Language (BML) and the Mission to Means Framework (MMF)

    DTIC Science & Technology

    2004-09-01

    and Means Framework (MMF - a framework for explicitly specifying the military mission and quantitatively evaluating the mission utility of alternative...In collaboration with the US Army and selected US Naval and US Air Force projects, the Defense Modeling and Simulation Office developed the Missions

  16. The Application of Modeling and Simulation in Capacity Management within the ITIL Framework

    NASA Technical Reports Server (NTRS)

    Rahmani, Sonya; vonderHoff, Otto

    2010-01-01

    Tightly integrating modeling and simulation techniques into Information Technology Infrastructure Library (ITIL) practices can be one of the driving factors behind a successful and cost-effective capacity management effort for any Information Technology (IT) system. ITIL is a best practices framework for managing IT infrastructure, development and operations. Translating ITIL theory into operational reality can be a challenge. This paper aims to highlight how to best integrate modeling and simulation into an ITIL implementation. For cases where the project team initially has difficulty gaining consensus on investing in modeling and simulation resources, a clear definition for M&S implementation into the ITIL framework, specifically its role in supporting Capacity Management, is critical to gaining the support required to garner these resources. This implementation should also help to clearly define M&S support to the overall system mission. This paper will describe the development of an integrated modeling approach and how best to tie M&S to definitive goals for evaluating system capacity and performance requirements. Specifically the paper will discuss best practices for implementing modeling and simulation into ITIL. These practices hinge on implementing integrated M&S methods that 1) encompass at least two or more predictive modeling techniques, 2) complement each one's respective strengths and weaknesses to support the validation of predicted results, and 3) are tied to the system's performance and workload monitoring efforts. How to structure two forms of modeling: statistical and simUlation in the development of "As Is" and "To Be" efforts will be used to exemplify the integrated M&S methods. The paper will show how these methods can better support the project's overall capacity management efforts.

  17. An Agent-Based Interface to Terrestrial Ecological Forecasting

    NASA Technical Reports Server (NTRS)

    Golden, Keith; Nemani, Ramakrishna; Pang, Wan-Lin; Votava, Petr; Etzioni, Oren

    2004-01-01

    This paper describes a flexible agent-based ecological forecasting system that combines multiple distributed data sources and models to provide near-real-time answers to questions about the state of the Earth system We build on novel techniques in automated constraint-based planning and natural language interfaces to automatically generate data products based on descriptions of the desired data products.

  18. Agent-based services for B2B electronic commerce

    NASA Astrophysics Data System (ADS)

    Fong, Elizabeth; Ivezic, Nenad; Rhodes, Tom; Peng, Yun

    2000-12-01

    The potential of agent-based systems has not been realized yet, in part, because of the lack of understanding of how the agent technology supports industrial needs and emerging standards. The area of business-to-business electronic commerce (b2b e-commerce) is one of the most rapidly developing sectors of industry with huge impact on manufacturing practices. In this paper, we investigate the current state of agent technology and the feasibility of applying agent-based computing to b2b e-commerce in the circuit board manufacturing sector. We identify critical tasks and opportunities in the b2b e-commerce area where agent-based services can best be deployed. We describe an implemented agent-based prototype system to facilitate the bidding process for printed circuit board manufacturing and assembly. These activities are taking place within the Internet Commerce for Manufacturing (ICM) project, the NIST- sponsored project working with industry to create an environment where small manufacturers of mechanical and electronic components may participate competitively in virtual enterprises that manufacture printed circuit assemblies.

  19. Modeling civil violence: An agent-based computational approach

    PubMed Central

    Epstein, Joshua M.

    2002-01-01

    This article presents an agent-based computational model of civil violence. Two variants of the civil violence model are presented. In the first a central authority seeks to suppress decentralized rebellion. In the second a central authority seeks to suppress communal violence between two warring ethnic groups. PMID:11997450

  20. Global Climate Simulation in a Multi-scale Modeling Framework: Sensitivity to GCM- Resolution

    NASA Astrophysics Data System (ADS)

    Duffy, P. B.; Bala, G.; Gleckler, P. J.; Taylor, K. E.; Mirin, A. A.; Wickett, M. E.

    2006-12-01

    We investigate sensitivity of the simulated climate in the NCAR CAM3 atmospheric climate model to increases in horizontal spatial resolution, and to use an alternative representation of unresolved motions. In the Multi-scale Modeling Framework (MMF), cloud parameterizations in are replaced by a two-dimensional Cloud System Resolving Model (CSRM) that is embedded in each column of the general circulation model (GCM. Here we investigate both the resolution-sensitivity of the baseline version (that employing parameterizations) of the CAM3 atmospheric model as well as the sensitivity to decreasing the horizontal grid size of the GCM in an MMF version of the same model. Generally speaking, climate quantities related to clouds, precipitation, and radiative fluxes are more sensitive to treatment of subgrid scale processes than to GCM grid size. Simulated top-of-atmosphere cloud radiative forcings and related radiative fluxes are substantially improved in the MMF simulations; aspects of simulated precipitation and the simulated MJO are also substantially improved. In both the MMF and parameterized simulations, the large-scale climate shows less sensitivity to GCM resolution than has been seen in some other models, particularly the NCAR CCM3, a predecessor to CAM3. However, comparison to published simulations using CAM3 with Eulerian spectral dynamics indicates that that CAM3 configuration has very similar sensitivities to horizontal resolution as the Finite Volume dynamics version used here; comparison to MMF simulations with different GCM grid sizes confirms that parameterized physics influences resolution-sensitivity more than dynamical formulation does. Because the MMF is based more closely on first-principles physics than parameterizations are, one need not retune model parameters when the horizontal resolution of the GCM is changed in the MMF.

  1. Development of a Dynamically Configurable, Object-Oriented Framework for Distributed, Multi-modal Computational Aerospace Systems Simulation

    NASA Technical Reports Server (NTRS)

    Afjeh, Abdollah A.; Reed, John A.

    2003-01-01

    The following reports are presented on this project:A first year progress report on: Development of a Dynamically Configurable,Object-Oriented Framework for Distributed, Multi-modal Computational Aerospace Systems Simulation; A second year progress report on: Development of a Dynamically Configurable, Object-Oriented Framework for Distributed, Multi-modal Computational Aerospace Systems Simulation; An Extensible, Interchangeable and Sharable Database Model for Improving Multidisciplinary Aircraft Design; Interactive, Secure Web-enabled Aircraft Engine Simulation Using XML Databinding Integration; and Improving the Aircraft Design Process Using Web-based Modeling and Simulation.

  2. Review of Molecular Simulations of Methane Storage in Metal-Organic Frameworks.

    PubMed

    Lee, Seung-Joon; Bae, Youn-Sang

    2016-05-01

    Methane storage in porous materials is one of the hot issues because it can replace dangerous high-pressure compressed natural gas (CNG) tanks in natural gas vehicles. Among the diverse adsorbents, metal-organic frameworks (MOFs) are considered to be promising due to their extremely high surface areas and low crystal densities. Molecular simulation has been considered as an important tool for finding an appropriate MOF for methane storage. We review several important roles of molecular modeling for the studies of methane adsorption in MOFs.

  3. The dynamic information architecture system : an advanced simulation framework for military and civilian applications.

    SciTech Connect

    Campbell, A. P.; Hummel, J. R.

    1998-01-08

    DIAS, the Dynamic Information Architecture System, is an object-oriented simulation system that was designed to provide an integrating framework in which new or legacy software applications can operate in a context-driven frame of reference. DIAS provides a flexible and extensible mechanism to allow disparate, and mixed language, software applications to interoperate. DIAS captures the dynamic interplay between different processes or phenomena in the same frame of reference. Finally, DIAS accommodates a broad range of analysis contexts, with widely varying spatial and temporal resolutions and fidelity.

  4. Framework for the construction of a Monte Carlo simulated brain PET-MR image database

    NASA Astrophysics Data System (ADS)

    Thomas, B. A.; Erlandsson, K.; Drobnjak, I.; Pedemonte, S.; Vunckx, K.; Bousse, A.; Reilhac-Laborde, A.; Ourselin, S.; Hutton, B. F.

    2014-01-01

    Simultaneous PET-MR acquisition reduces the possibility of registration mismatch between the two modalities. This facilitates the application of techniques, either during reconstruction or post-reconstruction, that aim to improve the PET resolution by utilising structural information provided by MR. However, in order to validate such methods for brain PET-MR studies it is desirable to evaluate the performance using data where the ground truth is known. In this work, we present a framework for the production of datasets where simulations of both the PET and MR, based on real data, are generated such that reconstruction and post-reconstruction approaches can be fairly compared.

  5. Using Uncertainty and Sensitivity Analyses in Socioecological Agent-Based Models to Improve Their Analytical Performance and Policy Relevance

    PubMed Central

    Ligmann-Zielinska, Arika; Kramer, Daniel B.; Spence Cheruvelil, Kendra; Soranno, Patricia A.

    2014-01-01

    Agent-based models (ABMs) have been widely used to study socioecological systems. They are useful for studying such systems because of their ability to incorporate micro-level behaviors among interacting agents, and to understand emergent phenomena due to these interactions. However, ABMs are inherently stochastic and require proper handling of uncertainty. We propose a simulation framework based on quantitative uncertainty and sensitivity analyses to build parsimonious ABMs that serve two purposes: exploration of the outcome space to simulate low-probability but high-consequence events that may have significant policy implications, and explanation of model behavior to describe the system with higher accuracy. The proposed framework is applied to the problem of modeling farmland conservation resulting in land use change. We employ output variance decomposition based on quasi-random sampling of the input space and perform three computational experiments. First, we perform uncertainty analysis to improve model legitimacy, where the distribution of results informs us about the expected value that can be validated against independent data, and provides information on the variance around this mean as well as the extreme results. In our last two computational experiments, we employ sensitivity analysis to produce two simpler versions of the ABM. First, input space is reduced only to inputs that produced the variance of the initial ABM, resulting in a model with output distribution similar to the initial model. Second, we refine the value of the most influential input, producing a model that maintains the mean of the output of initial ABM but with less spread. These simplifications can be used to 1) efficiently explore model outcomes, including outliers that may be important considerations in the design of robust policies, and 2) conduct explanatory analysis that exposes the smallest number of inputs influencing the steady state of the modeled system. PMID:25340764

  6. Examining the Pathogenesis of Breast Cancer Using a Novel Agent-Based Model of Mammary Ductal Epithelium Dynamics

    PubMed Central

    Chapa, Joaquin; Bourgo, Ryan J.; Greene, Geoffrey L.; Kulkarni, Swati; An, Gary

    2013-01-01

    The study of the pathogenesis of breast cancer is challenged by the long time-course of the disease process and the multi-factorial nature of generating oncogenic insults. The characterization of the longitudinal pathogenesis of malignant transformation from baseline normal breast duct epithelial dynamics may provide vital insight into the cascading systems failure that leads to breast cancer. To this end, extensive information on the baseline behavior of normal mammary epithelium and breast cancer oncogenesis was integrated into a computational model termed the Ductal Epithelium Agent-Based Model (DEABM). The DEABM is composed of computational agents that behave according to rules established from published cellular and molecular mechanisms concerning breast duct epithelial dynamics and oncogenesis. The DEABM implements DNA damage and repair, cell division, genetic inheritance and simulates the local tissue environment with hormone excretion and receptor signaling. Unrepaired DNA damage impacts the integrity of the genome within individual cells, including a set of eight representative oncogenes and tumor suppressors previously implicated in breast cancer, with subsequent consequences on successive generations of cells. The DEABM reproduced cellular population dynamics seen during the menstrual cycle and pregnancy, and demonstrated the oncogenic effect of known genetic factors associated with breast cancer, namely TP53 and Myc, in simulations spanning ∼40 years of simulated time. Simulations comparing normal to BRCA1-mutant breast tissue demonstrated rates of invasive cancer development similar to published epidemiologic data with respect to both cumulative incidence over time and estrogen-receptor status. Investigation of the modeling of ERα-positive (ER+) tumorigenesis led to a novel hypothesis implicating the transcription factor and tumor suppressor RUNX3. These data suggest that the DEABM can serve as a potentially valuable framework to augment the

  7. Examining the pathogenesis of breast cancer using a novel agent-based model of mammary ductal epithelium dynamics.

    PubMed

    Chapa, Joaquin; Bourgo, Ryan J; Greene, Geoffrey L; Kulkarni, Swati; An, Gary

    2013-01-01

    The study of the pathogenesis of breast cancer is challenged by the long time-course of the disease process and the multi-factorial nature of generating oncogenic insults. The characterization of the longitudinal pathogenesis of malignant transformation from baseline normal breast duct epithelial dynamics may provide vital insight into the cascading systems failure that leads to breast cancer. To this end, extensive information on the baseline behavior of normal mammary epithelium and breast cancer oncogenesis was integrated into a computational model termed the Ductal Epithelium Agent-Based Model (DEABM). The DEABM is composed of computational agents that behave according to rules established from published cellular and molecular mechanisms concerning breast duct epithelial dynamics and oncogenesis. The DEABM implements DNA damage and repair, cell division, genetic inheritance and simulates the local tissue environment with hormone excretion and receptor signaling. Unrepaired DNA damage impacts the integrity of the genome within individual cells, including a set of eight representative oncogenes and tumor suppressors previously implicated in breast cancer, with subsequent consequences on successive generations of cells. The DEABM reproduced cellular population dynamics seen during the menstrual cycle and pregnancy, and demonstrated the oncogenic effect of known genetic factors associated with breast cancer, namely TP53 and Myc, in simulations spanning ∼40 years of simulated time. Simulations comparing normal to BRCA1-mutant breast tissue demonstrated rates of invasive cancer development similar to published epidemiologic data with respect to both cumulative incidence over time and estrogen-receptor status. Investigation of the modeling of ERα-positive (ER+) tumorigenesis led to a novel hypothesis implicating the transcription factor and tumor suppressor RUNX3. These data suggest that the DEABM can serve as a potentially valuable framework to augment the

  8. Development of an evaluation framework suitable for assessing humanitarian workforce competencies during crisis simulation exercises.

    PubMed

    Cranmer, Hilarie; Chan, Jennifer L; Kayden, Stephanie; Musani, Altaf; Gasquet, Philippe E; Walker, Peter; Burkle, Frederick M; Johnson, Kirsten

    2014-02-01

    The need to provide a professionalization process for the humanitarian workforce is well established. Current competency-based curricula provided by existing academically affiliated training centers in North America, the United Kingdom, and the European Union provide a route toward certification. Simulation exercises followed by timely evaluation is one way to mimic the field deployment process, test knowledge of core competences, and ensure that a competent workforce can manage the inevitable emergencies and crises they will face. Through a 2011 field-based exercise that simulated a humanitarian crisis, delivered under the auspices of the World Health Organization (WHO), a competency-based framework and evaluation tool is demonstrated as a model for future training and evaluation of humanitarian providers.

  9. A proposed simulation optimization model framework for emergency department problems in public hospital

    NASA Astrophysics Data System (ADS)

    Ibrahim, Ireen Munira; Liong, Choong-Yeun; Bakar, Sakhinah Abu; Ahmad, Norazura; Najmuddin, Ahmad Farid

    2015-12-01

    The Emergency Department (ED) is a very complex system with limited resources to support increase in demand. ED services are considered as good quality if they can meet the patient's expectation. Long waiting times and length of stay is always the main problem faced by the management. The management of ED should give greater emphasis on their capacity of resources in order to increase the quality of services, which conforms to patient satisfaction. This paper is a review of work in progress of a study being conducted in a government hospital in Selangor, Malaysia. This paper proposed a simulation optimization model framework which is used to study ED operations and problems as well as to find an optimal solution to the problems. The integration of simulation and optimization is hoped can assist management in decision making process regarding their resource capacity planning in order to improve current and future ED operations.

  10. Simulating collisions of thick nuclei in the color glass condensate framework

    NASA Astrophysics Data System (ADS)

    Gelfand, Daniil; Ipp, Andreas; Müller, David

    2016-07-01

    We present our work on the simulation of the early stages of heavy-ion collisions with finite longitudinal thickness in the laboratory frame in 3 +1 dimensions. In particular we study the effects of nuclear thickness on the production of a glasma state in the McLerran-Venugopalan model within the color glass condensate framework. A finite thickness enables us to describe nuclei at lower energies, but forces us to abandon boost invariance. As a consequence, random classical color sources within the nuclei have to be included in the simulation, which is achieved by using the colored particle-in-cell method. We show that the description in the laboratory frame agrees with boost-invariant approaches as a limiting case. Furthermore we investigate collisions beyond boost invariance, in particular the pressure anisotropy in the glasma.

  11. Design of a framework for modeling, integration and simulation of physiological models.

    PubMed

    Erson, E; Cavusoglu, M

    2010-01-01

    Modeling and simulation of physiological processes deal with the challenges of multiscale models in which coupling is very high within and among scales. Information technology approaches together with related analytical and computational tools will help to deal with these challenges. Physiological Model Simulation, Integration and Modeling Framework, Phy-SIM, provides the modeling environment which will help to cultivate various approaches to deal with the inherent problem of multiscale modeling of physiological systems. In this paper, we present the modular design of Phy-SIM. The proposed layered design of Phy-SIM, separates structure from function in physiological processes advocating modular thinking in developing and integrating physiological models. Moreover, the ontology based architecture will improve the modeling process by the mechanisms to attach anatomical and physiological ontological information to the models. The ultimate aim of the proposed approaches is to enhance the physiological model development and integration processes by providing the tools and mechanisms in Phy-SIM.

  12. A Two-Stage Multi-Agent Based Assessment Approach to Enhance Students' Learning Motivation through Negotiated Skills Assessment

    ERIC Educational Resources Information Center

    Chadli, Abdelhafid; Bendella, Fatima; Tranvouez, Erwan

    2015-01-01

    In this paper we present an Agent-based evaluation approach in a context of Multi-agent simulation learning systems. Our evaluation model is based on a two stage assessment approach: (1) a Distributed skill evaluation combining agents and fuzzy sets theory; and (2) a Negotiation based evaluation of students' performance during a training…

  13. Exploring Tradeoffs in Demand-side and Supply-side Management of Urban Water Resources using Agent-based Modeling and Evolutionary Computation

    NASA Astrophysics Data System (ADS)

    Kanta, L.; Berglund, E. Z.

    2015-12-01

    Urban water supply systems may be managed through supply-side and demand-side strategies, which focus on water source expansion and demand reductions, respectively. Supply-side strategies bear infrastructure and energy costs, while demand-side strategies bear costs of implementation and inconvenience to consumers. To evaluate the performance of demand-side strategies, the participation and water use adaptations of consumers should be simulated. In this study, a Complex Adaptive Systems (CAS) framework is developed to simulate consumer agents that change their consumption to affect the withdrawal from the water supply system, which, in turn influences operational policies and long-term resource planning. Agent-based models are encoded to represent consumers and a policy maker agent and are coupled with water resources system simulation models. The CAS framework is coupled with an evolutionary computation-based multi-objective methodology to explore tradeoffs in cost, inconvenience to consumers, and environmental impacts for both supply-side and demand-side strategies. Decisions are identified to specify storage levels in a reservoir that trigger (1) increases in the volume of water pumped through inter-basin transfers from an external reservoir and (2) drought stages, which restrict the volume of water that is allowed for residential outdoor uses. The proposed methodology is demonstrated for Arlington, Texas, water supply system to identify non-dominated strategies for an historic drought decade. Results demonstrate that pumping costs associated with maximizing environmental reliability exceed pumping costs associated with minimizing restrictions on consumer water use.

  14. A Probabilistic Framework for the Validation and Certification of Computer Simulations

    NASA Technical Reports Server (NTRS)

    Ghanem, Roger; Knio, Omar

    2000-01-01

    The paper presents a methodology for quantifying, propagating, and managing the uncertainty in the data required to initialize computer simulations of complex phenomena. The purpose of the methodology is to permit the quantitative assessment of a certification level to be associated with the predictions from the simulations, as well as the design of a data acquisition strategy to achieve a target level of certification. The value of a methodology that can address the above issues is obvious, specially in light of the trend in the availability of computational resources, as well as the trend in sensor technology. These two trends make it possible to probe physical phenomena both with physical sensors, as well as with complex models, at previously inconceivable levels. With these new abilities arises the need to develop the knowledge to integrate the information from sensors and computer simulations. This is achieved in the present work by tracing both activities back to a level of abstraction that highlights their commonalities, thus allowing them to be manipulated in a mathematically consistent fashion. In particular, the mathematical theory underlying computer simulations has long been associated with partial differential equations and functional analysis concepts such as Hilbert spares and orthogonal projections. By relying on a probabilistic framework for the modeling of data, a Hilbert space framework emerges that permits the modeling of coefficients in the governing equations as random variables, or equivalently, as elements in a Hilbert space. This permits the development of an approximation theory for probabilistic problems that parallels that of deterministic approximation theory. According to this formalism, the solution of the problem is identified by its projection on a basis in the Hilbert space of random variables, as opposed to more traditional techniques where the solution is approximated by its first or second-order statistics. The present

  15. An agent-based model of signal transduction in bacterial chemotaxis.

    PubMed

    Miller, Jameson; Parker, Miles; Bourret, Robert B; Giddings, Morgan C

    2010-05-13

    We report the application of agent-based modeling to examine the signal transduction network and receptor arrays for chemotaxis in Escherichia coli, which are responsible for regulating swimming behavior in response to environmental stimuli. Agent-based modeling is a stochastic and bottom-up approach, where individual components of the modeled system are explicitly represented, and bulk properties emerge from their movement and interactions. We present the Chemoscape model: a collection of agents representing both fixed membrane-embedded and mobile cytoplasmic proteins, each governed by a set of rules representing knowledge or hypotheses about their function. When the agents were placed in a simulated cellular space and then allowed to move and interact stochastically, the model exhibited many properties similar to the biological system including adaptation, high signal gain, and wide dynamic range. We found the agent based modeling approach to be both powerful and intuitive for testing hypotheses about biological properties such as self-assembly, the non-linear dynamics that occur through cooperative protein interactions, and non-uniform distributions of proteins in the cell. We applied the model to explore the role of receptor type, geometry and cooperativity in the signal gain and dynamic range of the chemotactic response to environmental stimuli. The model provided substantial qualitative evidence that the dynamic range of chemotactic response can be traced to both the heterogeneity of receptor types present, and the modulation of their cooperativity by their methylation state.

  16. A multi-fidelity framework for physics based rotor blade simulation and optimization

    NASA Astrophysics Data System (ADS)

    Collins, Kyle Brian

    with lower fidelity models. This thesis documents the development of automated low and high fidelity physics based rotor simulation frameworks. The low fidelity framework uses a comprehensive code with simplified aerodynamics. The high fidelity model uses a parallel processor capable CFD/CSD methodology. Both low and high fidelity frameworks include an aeroacoustic simulation for prediction of noise. A synergistic process is developed that uses both the low and high fidelity frameworks together to build approximate models of important high fidelity metrics as functions of certain design variables. To test the process, a 4-bladed hingeless rotor model is used as a baseline. The design variables investigated include tip geometry and spanwise twist distribution. Approximation models are built for metrics related to rotor efficiency and vibration using the results from 60+ high fidelity (CFD/CSD) experiments and 400+ low fidelity experiments. Optimization using the approximation models found the Pareto Frontier anchor points, or the design having maximum rotor efficiency and the design having minimum vibration. Various Pareto generation methods are used to find designs on the frontier between these two anchor designs. When tested in the high fidelity framework, the Pareto anchor designs are shown to be very good designs when compared with other designs from the high fidelity database. This provides evidence that the process proposed has merit. Ultimately, this process can be utilized by industry rotor designers with their existing tools to bring high fidelity analysis into the preliminary design stage of rotors. In conclusion, the methods developed and documented in this thesis have made several novel contributions. First, an automated high fidelity CFD based forward flight simulation framework has been built for use in preliminary design optimization. The framework was built around an integrated, parallel processor capable CFD/CSD/AA process. Second, a novel method of

  17. Structure simulation with calculated NMR parameters - integrating COSMOS into the CCPN framework.

    PubMed

    Schneider, Olaf; Fogh, Rasmus H; Sternberg, Ulrich; Klenin, Konstantin; Kondov, Ivan

    2012-01-01

    The Collaborative Computing Project for NMR (CCPN) has build a software framework consisting of the CCPN data model (with APIs) for NMR related data, the CcpNmr Analysis program and additional tools like CcpNmr FormatConverter. The open architecture allows for the integration of external software to extend the abilities of the CCPN framework with additional calculation methods. Recently, we have carried out the first steps for integrating our software Computer Simulation of Molecular Structures (COSMOS) into the CCPN framework. The COSMOS-NMR force field unites quantum chemical routines for the calculation of molecular properties with a molecular mechanics force field yielding the relative molecular energies. COSMOS-NMR allows introducing NMR parameters as constraints into molecular mechanics calculations. The resulting infrastructure will be made available for the NMR community. As a first application we have tested the evaluation of calculated protein structures using COSMOS-derived 13C Cα and Cβ chemical shifts. In this paper we give an overview of the methodology and a roadmap for future developments and applications.

  18. Agent-based modeling: a systematic assessment of use cases and requirements for enhancing pharmaceutical research and development productivity.

    PubMed

    Hunt, C Anthony; Kennedy, Ryan C; Kim, Sean H J; Ropella, Glen E P

    2013-01-01

    A crisis continues to brew within the pharmaceutical research and development (R&D) enterprise: productivity continues declining as costs rise, despite ongoing, often dramatic scientific and technical advances. To reverse this trend, we offer various suggestions for both the expansion and broader adoption of modeling and simulation (M&S) methods. We suggest strategies and scenarios intended to enable new M&S use cases that directly engage R&D knowledge generation and build actionable mechanistic insight, thereby opening the door to enhanced productivity. What M&S requirements must be satisfied to access and open the door, and begin reversing the productivity decline? Can current methods and tools fulfill the requirements, or are new methods necessary? We draw on the relevant, recent literature to provide and explore answers. In so doing, we identify essential, key roles for agent-based and other methods. We assemble a list of requirements necessary for M&S to meet the diverse needs distilled from a collection of research, review, and opinion articles. We argue that to realize its full potential, M&S should be actualized within a larger information technology framework--a dynamic knowledge repository--wherein models of various types execute, evolve, and increase in accuracy over time. We offer some details of the issues that must be addressed for such a repository to accrue the capabilities needed to reverse the productivity decline.

  19. Liquid chromatographic separation in metal-organic framework MIL-101: a molecular simulation study.

    PubMed

    Hu, Zhongqiao; Chen, Yifei; Jiang, Jianwen

    2013-02-05

    A molecular simulation study is reported to investigate liquid chromatographic separation in metal-organic framework MIL-101. Two mixtures are considered: three amino acids (Arg, Phe, and Trp) in aqueous solution and three xylene isomers (p-, m-, and o-xylene) dissolved in hexane. For the first mixture, the elution order is found to be Arg > Phe > Trp. The hydrophilic Arg has the strongest interaction with the polar mobile phase (water) and the weakest interaction with the stationary phase (MIL-101), and thus transports at the fastest velocity. Furthermore, Arg forms the largest number of hydrogen bonds with water and possesses the largest hydrophilic solvent-accessible surface area. For the second mixture, the elution order is p-xylene > m-xylene > o-xylene, consistent with available experimental observation. With the largest polarity as compared to p- and m-xylenes, o-xylene interacts the most strongly with the stationary phase and exhibits the slowest transport velocity. For both mixtures, the underlying separation mechanism is elucidated from detailed energetic and structural analysis. It is revealed that the separation can be attributed to the cooperative solute-solvent and solute-framework interactions. This simulation study, for the first time, provides molecular insight into liquid chromatographic separation in a MOF and suggests that MIL-101 might be an interesting material for the separation of industrially important liquid mixtures.

  20. PHAISTOS: a framework for Markov chain Monte Carlo simulation and inference of protein structure.

    PubMed

    Boomsma, Wouter; Frellsen, Jes; Harder, Tim; Bottaro, Sandro; Johansson, Kristoffer E; Tian, Pengfei; Stovgaard, Kasper; Andreetta, Christian; Olsson, Simon; Valentin, Jan B; Antonov, Lubomir D; Christensen, Anders S; Borg, Mikael; Jensen, Jan H; Lindorff-Larsen, Kresten; Ferkinghoff-Borg, Jesper; Hamelryck, Thomas

    2013-07-15

    We present a new software framework for Markov chain Monte Carlo sampling for simulation, prediction, and inference of protein structure. The software package contains implementations of recent advances in Monte Carlo methodology, such as efficient local updates and sampling from probabilistic models of local protein structure. These models form a probabilistic alternative to the widely used fragment and rotamer libraries. Combined with an easily extendible software architecture, this makes PHAISTOS well suited for Bayesian inference of protein structure from sequence and/or experimental data. Currently, two force-fields are available within the framework: PROFASI and OPLS-AA/L, the latter including the generalized Born surface area solvent model. A flexible command-line and configuration-file interface allows users quickly to set up simulations with the desired configuration. PHAISTOS is released under the GNU General Public License v3.0. Source code and documentation are freely available from http://phaistos.sourceforge.net. The software is implemented in C++ and has been tested on Linux and OSX platforms.

  1. A Component-Based FPGA Design Framework for Neuronal Ion Channel Dynamics Simulations

    PubMed Central

    Mak, Terrence S. T.; Rachmuth, Guy; Lam, Kai-Pui; Poon, Chi-Sang

    2008-01-01

    Neuron-machine interfaces such as dynamic clamp and brain-implantable neuroprosthetic devices require real-time simulations of neuronal ion channel dynamics. Field Programmable Gate Array (FPGA) has emerged as a high-speed digital platform ideal for such application-specific computations. We propose an efficient and flexible component-based FPGA design framework for neuronal ion channel dynamics simulations, which overcomes certain limitations of the recently proposed memory-based approach. A parallel processing strategy is used to minimize computational delay, and a hardware-efficient factoring approach for calculating exponential and division functions in neuronal ion channel models is used to conserve resource consumption. Performances of the various FPGA design approaches are compared theoretically and experimentally in corresponding implementations of the AMPA and NMDA synaptic ion channel models. Our results suggest that the component-based design framework provides a more memory economic solution as well as more efficient logic utilization for large word lengths, whereas the memory-based approach may be suitable for time-critical applications where a higher throughput rate is desired. PMID:17190033

  2. Multiscale Simulation as a Framework for the Enhanced Design of Nanodiamond-Polyethylenimine-based Gene Delivery

    PubMed Central

    Kim, Hansung; Man, Han Bin; Saha, Biswajit; Kopacz, Adrian M.; Lee, One-Sun; Schatz, George C.; Ho, Dean; Liu, Wing Kam

    2012-01-01

    Nanodiamonds (NDs) are emerging carbon platforms with promise as gene/drug delivery vectors for cancer therapy. Specifically, NDs functionalized with the polymer polyethylenimine (PEI) can transfect small interfering RNAs (siRNA) in vitro with high efficiency and low cytotoxicity. Here we present a modeling framework to accurately guide the design of ND-PEI gene platforms and elucidate binding mechanisms between ND, PEI, and siRNA. This is among the first ND simulations to comprehensively account for ND size, charge distribution, surface functionalization, and graphitization. The simulation results are compared with our experimental results both for PEI loading onto NDs and for siRNA (C-myc) loading onto ND-PEI for various mixing ratios. Remarkably, the model is able to predict loading trends and saturation limits for PEI and siRNA, while confirming the essential role of ND surface functionalization in mediating ND-PEI interactions. These results demonstrate that this robust framework can be a powerful tool in ND platform development, with the capacity to realistically treat other nanoparticle systems. PMID:23304428

  3. EEG-fMRI Bayesian framework for neural activity estimation: a simulation study

    NASA Astrophysics Data System (ADS)

    Croce, Pierpaolo; Basti, Alessio; Marzetti, Laura; Zappasodi, Filippo; Del Gratta, Cosimo

    2016-12-01

    Objective. Due to the complementary nature of electroencephalography (EEG) and functional magnetic resonance imaging (fMRI), and given the possibility of simultaneous acquisition, the joint data analysis can afford a better understanding of the underlying neural activity estimation. In this simulation study we want to show the benefit of the joint EEG-fMRI neural activity estimation in a Bayesian framework. Approach. We built a dynamic Bayesian framework in order to perform joint EEG-fMRI neural activity time course estimation. The neural activity is originated by a given brain area and detected by means of both measurement techniques. We have chosen a resting state neural activity situation to address the worst case in terms of the signal-to-noise ratio. To infer information by EEG and fMRI concurrently we used a tool belonging to the sequential Monte Carlo (SMC) methods: the particle filter (PF). Main results. First, despite a high computational cost, we showed the feasibility of such an approach. Second, we obtained an improvement in neural activity reconstruction when using both EEG and fMRI measurements. Significance. The proposed simulation shows the improvements in neural activity reconstruction with EEG-fMRI simultaneous data. The application of such an approach to real data allows a better comprehension of the neural dynamics.

  4. Multivariate simulation framework reveals performance of multi-trait GWAS methods

    PubMed Central

    Porter, Heather F.; O’Reilly, Paul F.

    2017-01-01

    Burgeoning availability of genome-wide association study (GWAS) results and national biobank data has led to growing interest in performing multi-trait genetic analyses. Numerous multi-trait GWAS methods that exploit either summary statistics or individual-level data have been developed, but their relative performance is unclear. Here we develop a simulation framework to model the complex networks underlying multivariate genetic epidemiology, enabling the vast model space of genetic effects on multiple correlated traits to be explored systematically. We perform a comprehensive comparison of the leading multi-trait GWAS methods, finding: (1) method performance is highly sensitive to the specific combination of genetic effects and phenotypic correlations, (2) most of the current multivariate methods have remarkably similar statistical power, and (3) multivariate methods may offer a substantial increase in the discovery of genetic variants over the standard univariate approach. We believe our findings offer the clearest picture to date of the relative performance of multi-trait GWAS methods and act as a guide for method selection. We provide a web application and open-source software program implementing our simulation framework, for: (i) further benchmarking of multivariate GWAS methods, (ii) power calculations for multivariate genetic studies, and (iii) generating data for testing any multivariate method in genetic epidemiology. PMID:28287610

  5. Global Simulation of Bioenergy Crop Productivity: Analytical Framework and Case Study for Switchgrass

    SciTech Connect

    Kang, Shujiang; Kline, Keith L; Nair, S. Surendran; Nichols, Dr Jeff A; Post, Wilfred M; Brandt, Craig C; Wullschleger, Stan D; Wei, Yaxing; Singh, Nagendra

    2013-01-01

    A global energy crop productivity model that provides geospatially explicit quantitative details on biomass potential and factors affecting sustainability would be useful, but does not exist now. This study describes a modeling platform capable of meeting many challenges associated with global-scale agro-ecosystem modeling. We designed an analytical framework for bioenergy crops consisting of six major components: (i) standardized natural resources datasets, (ii) global field-trial data and crop management practices, (iii) simulation units and management scenarios, (iv) model calibration and validation, (v) high-performance computing (HPC) simulation, and (vi) simulation output processing and analysis. The HPC-Environmental Policy Integrated Climate (HPC-EPIC) model simulated a perennial bioenergy crop, switchgrass (Panicum virgatum L.), estimating feedstock production potentials and effects across the globe. This modeling platform can assess soil C sequestration, net greenhouse gas (GHG) emissions, nonpoint source pollution (e.g., nutrient and pesticide loss), and energy exchange with the atmosphere. It can be expanded to include additional bioenergy crops (e.g., miscanthus, energy cane, and agave) and food crops under different management scenarios. The platform and switchgrass field-trial dataset are available to support global analysis of biomass feedstock production potential and corresponding metrics of sustainability.

  6. Global Simulation of Bioenergy Crop Productivity: Analytical framework and Case Study for Switchgrass

    SciTech Connect

    Nair, S. Surendran; Nichols, Jeff A. {Cyber Sciences}; Post, Wilfred M; Wang, Dali; Wullschleger, Stan D; Kline, Keith L; Wei, Yaxing; Singh, Nagendra; Kang, Shujiang

    2014-01-01

    Contemporary global assessments of the deployment potential and sustainability aspects of biofuel crops lack quantitative details. This paper describes an analytical framework capable of meeting the challenges associated with global scale agro-ecosystem modeling. We designed a modeling platform for bioenergy crops, consisting of five major components: (i) standardized global natural resources and management data sets, (ii) global simulation unit and management scenarios, (iii) model calibration and validation, (iv) high-performance computing (HPC) modeling, and (v) simulation output processing and analysis. A case study with the HPC- Environmental Policy Integrated Climate model (HPC-EPIC) to simulate a perennial bioenergy crop, switchgrass (Panicum virgatum L.) and global biomass feedstock analysis on grassland demonstrates the application of this platform. The results illustrate biomass feedstock variability of switchgrass and provide insights on how the modeling platform can be expanded to better assess sustainable production criteria and other biomass crops. Feedstock potentials on global grasslands and within different countries are also shown. Future efforts involve developing databases of productivity, implementing global simulations for other bioenergy crops (e.g. miscanthus, energycane and agave), and assessing environmental impacts under various management regimes. We anticipated this platform will provide an exemplary tool and assessment data for international communities to conduct global analysis of biofuel biomass feedstocks and sustainability.

  7. A GIS/Simulation Framework for Assessing Change in Water Yield over Large Spatial Scales

    SciTech Connect

    Graham, R.; Hargrove, W.W.; Huff, D.D.; Nikolov, N.; Tharp, M.L.

    1999-11-13

    Recent legislation to,initiate vegetation management in the Central Sierra hydrologic region of California includes a focus on corresponding changes in water yield. This served as the impetus for developing a combined geographic information system (GIS) and simulation assessment framework. Using the existing vegetation density condition, together with proposed rules for thinning to reduce fire risk, a set of simulation model inputs were generated for examining the impact of the thinning scenario on water yield. The approach allows results to be expressed as the mean and standard deviation of change in water yield for each 1 km2 map cell that is treated. Values for groups of cells are aggregated for typical watershed units using area-weighted averaging. Wet, dry and average precipitation years were simulated over a large region. Where snow plays an important role in hydrologic processes, the simulated change in water yield was less than 0.5% of expected annual runoff for a typical water shed. Such small changes would be undetectable in the field using conventional stream flow analysis. These results suggest that use of water yield increases to help justify forest-thinning activities or offset their cost will be difficult.

  8. Distributed geant4 simulation in medical and space science applications using DIANE framework and the GRID

    NASA Astrophysics Data System (ADS)

    Mościcki, Jakub T.; Guatelli, Susanna; Mantero, Alfonso; Pia, M. G.

    2003-09-01

    Distributed computing is one of the most important trends in IT which has recently gained significance for large-scale scientific applications. Distributed Analysis Environment (DIANE) [1] is a R&D study, focusing on semi-interactive parallel and remote data analysis and simulation, which has been conducted at CERN. DIANE provides necessary software infrastructure for parallel scientific applications in the master-worker model. Advanced error recovery policies, automatic book-keeping of distributed jobs and on-line monitoring and control tools are provided. DIANE makes a transparent use of a number of different middleware implementations such as load balancing service (LSF, PBS, GRID Resource Broker, Condor) and security service (GSI, Kerberos, openssh). A number of distributed Geant 4 simulations have been deployed and tested, ranging from interactive radiotherapy treatment planning using dedicated clusters in hospitals, to globally-distributed simulations of astrophysics experiments using the European Data Grid middleware. This paper describes the general concepts behind the DIANE framework and results of the first tests with distributed Geant 4 simulations.

  9. Flexible and modular MPI simulation framework and its use in modelling a μMPI

    PubMed Central

    Straub, Marcel; Lammers, Twan; Kiessling, Fabian; Schulz, Volkmar

    2014-01-01

    The availability of thorough system simulations for detailed and accurate performance prediction and optimization of existing and future designs for a new modality such as magnetic particle imaging (MPI) are very important. Our framework aims to simulate a complete MPI system by providing a description of all (drive and receive) coils, permanent magnet configurations, magnetic nanoparticle (MNP) distributions, and characteristics of the signal processing chain. The simulation is performed on a user defined spatial and temporal discrete grid. The magnetization of the MNP is modelled by either the Langevin theory or as ideal particles with infinite steepness and ideal saturation. The magnetic fields are approximated in first order by calculating the Biot-Savart integral. Additionally the coupling constants between the excitation coils (e.g. drive field coils) and the receive coils can be determined. All coils can be described by an XML description language based on primitive geometric shapes. First simulations of a modelled μMPI system are shown. In this regard μMPI refers to a small one dimensional system for samples of a size of a few tens of a cubic millimeter and a spatial resolution of about 200 μm. PMID:25892744

  10. A GIS/simulation framework for assessing change in water yield over large spatial scales.

    PubMed

    Huff, Dale D; Hargrove, William W; Graham, Robin; Nikolov, Ned; Tharp, M Lynn

    2002-02-01

    Recent legislation to initiate vegetation management in the Central Sierra hydrologic region of California includes a focus on corresponding changes in water yield. This served as the impetus for developing a combined geographic information system (GIS) and simulation assessment framework. Using the existing vegetation density condition, together with proposed rules for thinning to reduce fire risk, a set of simulation model inputs were generated for examining the impact of the thinning scenario on water yield. The approach allows results to be expressed as the mean and standard deviation of change in water yield for each 1-km2 map cell that is thinned. Values for groups of cells are aggregated for typical watershed units using area-weighted averaging. Wet, dry, and average precipitation years were simulated over a large region. Where snow plays an important role in hydrologic processes, the simulated change in water yield was less than 0.5% of expected annual runoff for a typical watershed. Such small changes would be undetectable in the field using conventional stream flow analysis. These results suggest that use of water yield increases to help justify forest-thinning activities or offset their cost will be difficult.

  11. SimPEG: An open-source framework for geophysical simulations and inverse problems

    NASA Astrophysics Data System (ADS)

    Cockett, R.; Kang, S.; Heagy, L.

    2014-12-01

    Geophysical surveys are powerful tools for obtaining information about the subsurface. Inverse modelling provides a mathematical framework for constructing a model of physical property distributions that are consistent with the data collected by these surveys. The geosciences are increasingly moving towards the integration of geological, geophysical, and hydrological information to better characterize the subsurface. This integration must span disciplines and is not only challenging scientifically, but the inconsistencies between conventions often makes implementations complicated, non-reproducible, or inefficient. We have developed an open source software package for Simulation and Parameter Estimation in Geophysics (SimPEG), which provides a generalized framework for solving geophysical forward and inverse problems. SimPEG is written entirely in Python with minimal dependencies in the hopes that it can be used both as a research tool and for education. SimPEG includes finite volume discretizations on structured and unstructured meshes, interfaces to standard numerical solver packages, convex optimization algorithms, model parameterizations, and tailored visualization routines. The framework is modular and object-oriented, which promotes real time experimentation and combination of geophysical problems and inversion methodologies. In this presentation, we will highlight a few geophysical examples, including direct-current resistivity and electromagnetics, and discuss some of the challenges and successes we encountered in developing a flexible and extensible framework. Throughout development of SimPEG we have focused on simplicity, usability, documentation, and extensive testing. By embracing a fully open source development paradigm, we hope to encourage reproducible research, cooperation, and communication to help tackle some of the inherently multidisciplinary problems that face integrated geophysical methods.

  12. URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries

    PubMed Central

    2012-01-01

    Background Experiments in silico using stochastic reaction-diffusion models have emerged as an important tool in molecular systems biology. Designing computational software for such applications poses several challenges. Firstly, realistic lattice-based modeling for biological applications requires a consistent way of handling complex geometries, including curved inner- and outer boundaries. Secondly, spatiotemporal stochastic simulations are computationally expensive due to the fast time scales of individual reaction- and diffusion events when compared to the biological phenomena of actual interest. We therefore argue that simulation software needs to be both computationally efficient, employing sophisticated algorithms, yet in the same time flexible in order to meet present and future needs of increasingly complex biological modeling. Results We have developed URDME, a flexible software framework for general stochastic reaction-transport modeling and simulation. URDME uses Unstructured triangular and tetrahedral meshes to resolve general geometries, and relies on the Reaction-Diffusion Master Equation formalism to model the processes under study. An interface to a mature geometry and mesh handling external software (Comsol Multiphysics) provides for a stable and interactive environment for model construction. The core simulation routines are logically separated from the model building interface and written in a low-level language for computational efficiency. The connection to the geometry handling software is realized via a Matlab interface which facilitates script computing, data management, and post-processing. For practitioners, the software therefore behaves much as an interactive Matlab toolbox. At the same time, it is possible to modify and extend URDME with newly developed simulation routines. Since the overall design effectively hides the complexity of managing the geometry and meshes, this means that newly developed methods may be tested in a realistic

  13. The fractional volatility model: An agent-based interpretation

    NASA Astrophysics Data System (ADS)

    Vilela Mendes, R.

    2008-06-01

    Based on the criteria of mathematical simplicity and consistency with empirical market data, a model with volatility driven by fractional noise has been constructed which provides a fairly accurate mathematical parametrization of the data. Here, some features of the model are reviewed and extended to account for leverage effects. Using agent-based models, one tries to find which agent strategies and (or) properties of the financial institutions might be responsible for the features of the fractional volatility model.

  14. Scalable, distributed data mining using an agent based architecture

    SciTech Connect

    Kargupta, H.; Hamzaoglu, I.; Stafford, B.

    1997-05-01

    Algorithm scalability and the distributed nature of both data and computation deserve serious attention in the context of data mining. This paper presents PADMA (PArallel Data Mining Agents), a parallel agent based system, that makes an effort to address these issues. PADMA contains modules for (1) parallel data accessing operations, (2) parallel hierarchical clustering, and (3) web-based data visualization. This paper describes the general architecture of PADMA and experimental results.

  15. Final Report for Project "Framework Application for Core-Edge Transport Simulations (FACETS)"

    SciTech Connect

    Estep, Donald

    2014-01-17

    This is the final report for the Colorado State University Component of the FACETS Project. FACETS was focused on the development of a multiphysics, parallel framework application that could provide the capability to enable whole-device fusion reactor modeling and, in the process, the development of the modeling infrastructure and computational understanding needed for ITER. It was intended that FACETS be highly flexible, through the use of modern computational methods, including component technology and object oriented design, to facilitate switching from one model to another for a given aspect of the physics, and making it possible to use simplified models for rapid turnaround or high-fidelity models that will take advantage of the largest supercomputer hardware. FACETS was designed in a heterogeneous parallel context, where different parts of the application can take advantage through parallelism based on task farming, domain decomposition, and/or pipelining as needed and applicable. As with all fusion simulations, an integral part of the FACETS project was treatment of the coupling of different physical processes at different scales interacting closely. A primary example for the FACETS project is the coupling of existing core and edge simulations, with the transport and wall interactions described by reduced models. However, core and edge simulations themselves involve significant coupling of different processes with large scale differences. Numerical treatment of coupling is impacted by a number of factors including, scale differences, form of information transferred between processes, implementation of solvers for different codes, and high performance computing concerns. Operator decomposition involving the computation of the individual processes individually using appropriate simulation codes and then linking/synchronizing the component simulations at regular points in space and time, is the defacto approach to high performance simulation of multiphysics

  16. A Harris-Todaro Agent-Based Model to Rural-Urban Migration

    NASA Astrophysics Data System (ADS)

    Espíndola, Aquino L.; Silveira, Jaylson J.; Penna, T. J. P.

    2006-09-01

    The Harris-Todaro model of the rural-urban migration process is revisited under an agent-based approach. The migration of the workers is interpreted as a process of social learning by imitation, formalized by a computational model. By simulating this model, we observe a transitional dynamics with continuous growth of the urban fraction of overall population toward an equilibrium. Such an equilibrium is characterized by stabilization of rural-urban expected wages differential (generalized Harris-Todaro equilibrium condition), urban concentration and urban unemployment. These classic results obtained originally by Harris and Todaro are emergent properties of our model.

  17. Finding shared decisions in stakeholder networks: An agent-based approach

    NASA Astrophysics Data System (ADS)

    Le Pira, Michela; Inturri, Giuseppe; Ignaccolo, Matteo; Pluchino, Alessandro; Rapisarda, Andrea

    2017-01-01

    We address the problem of a participatory decision-making process where a shared priority list of alternatives has to be obtained while avoiding inconsistent decisions. An agent-based model (ABM) is proposed to mimic this process in different social networks of stakeholders who interact according to an opinion dynamics model. Simulations' results show the efficacy of interaction in finding a transitive and, above all, shared decision. These findings are in agreement with real participation experiences regarding transport planning decisions and can give useful suggestions on how to plan an effective participation process for sustainable policy-making based on opinion consensus.

  18. Genetic Algorithms for Agent-Based Infrastructure Interdependency Modeling and Analysis

    SciTech Connect

    May Permann

    2007-03-01

    Today’s society relies greatly upon an array of complex national and international infrastructure networks such as transportation, electric power, telecommunication, and financial networks. This paper describes initial research combining agent-based infrastructure modeling software and genetic algorithms (GAs) to help optimize infrastructure protection and restoration decisions. This research proposes to apply GAs to the problem of infrastructure modeling and analysis in order to determine the optimum assets to restore or protect from attack or other disaster. This research is just commencing and therefore the focus of this paper is the integration of a GA optimization method with a simulation through the simulation’s agents.

  19. Agent Based Modeling of Collaboration and Work Practices Onboard the International Space Station

    NASA Technical Reports Server (NTRS)

    Acquisti, Alessandro; Sierhuis, Maarten; Clancey, William J.; Bradshaw, Jeffrey M.; Shaffo, Mike (Technical Monitor)

    2002-01-01

    The International Space Station is one the most complex projects ever, with numerous interdependent constraints affecting productivity and crew safety. This requires planning years before crew expeditions, and the use of sophisticated scheduling tools. Human work practices, however, are difficult to study and represent within traditional planning tools. We present an agent-based model and simulation of the activities and work practices of astronauts onboard the ISS based on an agent-oriented approach. The model represents 'a day in the life' of the ISS crew and is developed in Brahms, an agent-oriented, activity-based language used to model knowledge in situated action and learning in human activities.

  20. GeNN: a code generation framework for accelerated brain simulations

    NASA Astrophysics Data System (ADS)

    Yavuz, Esin; Turner, James; Nowotny, Thomas

    2016-01-01

    Large-scale numerical simulations of detailed brain circuit models are important for identifying hypotheses on brain functions and testing their consistency and plausibility. An ongoing challenge for simulating realistic models is, however, computational speed. In this paper, we present the GeNN (GPU-enhanced Neuronal Networks) framework, which aims to facilitate the use of graphics accelerators for computational models of large-scale neuronal networks to address this challenge. GeNN is an open source library that generates code to accelerate the execution of network simulations on NVIDIA GPUs, through a flexible and extensible interface, which does not require in-depth technical knowledge from the users. We present performance benchmarks showing that 200-fold speedup compared to a single core of a CPU can be achieved for a network of one million conductance based Hodgkin-Huxley neurons but that for other models the speedup can differ. GeNN is available for Linux, Mac OS X and Windows platforms. The source code, user manual, tutorials, Wiki, in-depth example projects and all other related information can be found on the project website http://genn-team.github.io/genn/.

  1. Understanding virulence mechanisms in M. tuberculosis infection via a circuit-based simulation framework.

    SciTech Connect

    May, Elebeoba Eni; Oprea, Tudor I.; Joo, Jaewook; Misra, Milind; Leitao, Andrei; Faulon, Jean-Loup Michel

    2008-08-01

    Tuberculosis (TB), caused by the bacterium Mycobacterium tuberculosis (Mtb), is a growing international health crisis. Mtb is able to persist in host tissues in a non-replicating persistent (NRP) or latent state. This presents a challenge in the treatment of TB. Latent TB can re-activate in 10% of individuals with normal immune systems, higher for those with compromised immune systems. A quantitative understanding of latency-associated virulence mechanisms may help researchers develop more effective methods to battle the spread and reduce TB associated fatalities. Leveraging BioXyce's ability to simulate whole-cell and multi-cellular systems we are developing a circuit-based framework to investigate the impact of pathogenicity-associated pathways on the latency/reactivation phase of tuberculosis infection. We discuss efforts to simulate metabolic pathways that potentially impact the ability of Mtb to persist within host immune cells. We demonstrate how simulation studies can provide insight regarding the efficacy of potential anti-TB agents on biological networks critical to Mtb pathogenicity using a systems chemical biology approach

  2. Reservoir Modeling by Data Integration via Intermediate Spaces and Artificial Intelligence Tools in MPS Simulation Frameworks

    SciTech Connect

    Ahmadi, Rouhollah; Khamehchi, Ehsan

    2013-12-15

    Conditioning stochastic simulations are very important in many geostatistical applications that call for the introduction of nonlinear and multiple-point data in reservoir modeling. Here, a new methodology is proposed for the incorporation of different data types into multiple-point statistics (MPS) simulation frameworks. Unlike the previous techniques that call for an approximate forward model (filter) for integration of secondary data into geologically constructed models, the proposed approach develops an intermediate space where all the primary and secondary data are easily mapped onto. Definition of the intermediate space, as may be achieved via application of artificial intelligence tools like neural networks and fuzzy inference systems, eliminates the need for using filters as in previous techniques. The applicability of the proposed approach in conditioning MPS simulations to static and geologic data is verified by modeling a real example of discrete fracture networks using conventional well-log data. The training patterns are well reproduced in the realizations, while the model is also consistent with the map of secondary data.

  3. a Suggestion of Simulation Framework for Verifing PLC Program & Application in Automotive Production Line

    NASA Astrophysics Data System (ADS)

    Lee, Kang-Gu; Koo, Lock-Jo; Park, Sang-Chul; Wang, Gi-Nam

    2009-08-01

    Proposed in this paper is a framework of virtual plant model for verification of PLC program by conducting the virtual plant modeling and simulation. The proposed virtual plant model consists of three types of objects: the virtual device model (object model), the intermediary transfer model (functional model) and PLC program (dynamic model). For the implementation of the proposed virtual plant model, this paper employs the I/O model which is based on Automata and Discrete Event System Specifications (DEVS) formalism. By applying an example of the automotive assembly line, nine errors in the PLC code are found and have been revised. With the proposed approach, it will be helpful to reduce the ramp up or down time of the automated manufacturing system.

  4. A novel finite element framework for numerical simulation of fluidization processes and multiphase granular flow

    NASA Astrophysics Data System (ADS)

    Percival, James; Xie, Zhihua; Pavlidis, Dimitrios; Gomes, Jefferson; Pain, Christopher; Matar, Omar

    2013-11-01

    We present results from a new formulation of a numerical model for direct simulation of bed fluidization and multiphase granular flow. The model is based on a consistent application of continuous-discontinuous mixed control volume finite element methods applied to fully unstructured meshes. The unstructured mesh framework allows for both a mesh adaptive capability, modifying the computational geometry in order to bound the error in the numerical solution while maximizing computational efficiency, and a simple scripting interface embedded in the model which allows fast prototyping of correlation models and parameterizations in intercomparison experiments. The model is applied to standard test problems for fluidized beds. EPSRC Programme Grant EP/K003976/1.

  5. A framework to quantify uncertainty in simulations of oil transport in the ocean

    NASA Astrophysics Data System (ADS)

    Gonçalves, Rafael C.; Iskandarani, Mohamed; Srinivasan, Ashwanth; Thacker, W. Carlisle; Chassignet, Eric; Knio, Omar M.

    2016-04-01

    An uncertainty quantification framework is developed for the DeepC Oil Model based on a nonintrusive polynomial chaos method. This allows the model's output to be presented in a probabilistic framework so that the model's predictions reflect the uncertainty in the model's input data. The new capability is illustrated by simulating the far-field dispersal of oil in a Deepwater Horizon blowout scenario. The uncertain input consisted of ocean current and oil droplet size data and the main model output analyzed is the ensuing oil concentration in the Gulf of Mexico. A 1331 member ensemble was used to construct a surrogate for the model which was then mined for statistical information. The mean and standard deviations in the oil concentration were calculated for up to 30 days, and the total contribution of each input parameter to the model's uncertainty was quantified at different depths. Also, probability density functions of oil concentration were constructed by sampling the surrogate and used to elaborate probabilistic hazard maps of oil impact. The performance of the surrogate was constantly monitored in order to demarcate the space-time zones where its estimates are reliable.

  6. Implementation and performance of FDPS: a framework for developing parallel particle simulation codes

    NASA Astrophysics Data System (ADS)

    Iwasawa, Masaki; Tanikawa, Ataru; Hosono, Natsuki; Nitadori, Keigo; Muranushi, Takayuki; Makino, Junichiro

    2016-08-01

    We present the basic idea, implementation, measured performance, and performance model of FDPS (Framework for Developing Particle Simulators). FDPS is an application-development framework which helps researchers to develop simulation programs using particle methods for large-scale distributed-memory parallel supercomputers. A particle-based simulation program for distributed-memory parallel computers needs to perform domain decomposition, exchange of particles which are not in the domain of each computing node, and gathering of the particle information in other nodes which are necessary for interaction calculation. Also, even if distributed-memory parallel computers are not used, in order to reduce the amount of computation, algorithms such as the Barnes-Hut tree algorithm or the Fast Multipole Method should be used in the case of long-range interactions. For short-range interactions, some methods to limit the calculation to neighbor particles are required. FDPS provides all of these functions which are necessary for efficient parallel execution of particle-based simulations as "templates," which are independent of the actual data structure of particles and the functional form of the particle-particle interaction. By using FDPS, researchers can write their programs with the amount of work necessary to write a simple, sequential and unoptimized program of O(N2) calculation cost, and yet the program, once compiled with FDPS, will run efficiently on large-scale parallel supercomputers. A simple gravitational N-body program can be written in around 120 lines. We report the actual performance of these programs and the performance model. The weak scaling performance is very good, and almost linear speed-up was obtained for up to the full system of the K computer. The minimum calculation time per timestep is in the range of 30 ms (N = 107) to 300 ms (N = 109). These are currently limited by the time for the calculation of the domain decomposition and communication

  7. Simulation of the neutral beam deposition within integrated tokamak modelling frameworks

    NASA Astrophysics Data System (ADS)

    Schneider, M.; Eriksson, L.-G.; Jenkins, I.; Artaud, J. F.; Basiuk, V.; Imbeaux, F.; Oikawa, T.; contributors, JET-EFDA; contributors, ITM-TF

    2011-06-01

    The NEMO (NEutral beam MOdelling) code for simulating neutral beam ionization during neutral beam injection (NBI) in tokamak plasmas has been developed for implementation in integrated modelling frameworks and is presented. Integrated modelling of fusion plasmas is becoming increasingly important, both for preparation and analysis of experiments in large devices. Moreover, it should play a crucial role for the design of future fusion reactors. In a modern context, integrated modelling requires codes that are (i) flexible in terms of their interfaces, i.e. can be adapted for different simulation environments, (ii) machine independent; i.e. they should not contain hard coded information on a particular device to be simulated; (iii) optimized for speed of execution, (iv) verified and validated. The NEMO code has been specially designed to meet these requirements. The code is based on the physics concept outlined by Feng et al (1995 Comput. Phys. Commun. 88 161-72) and is a completely modular program: it works with any input NBI geometry and can be coupled to any external Fokker-Planck calculation for evaluating the distribution function of the injected species, i.e. it can provide source terms for both Monte Carlo codes and codes using finite difference/elements methods. The NEMO code has already been integrated with the CRONOS integrated modelling suite (Artaud et al 2010 Nucl. Fusion 50 043001) and the European Integrated Tokamak Modelling Task Force (ITM-TF)b https://www.efda-itm.eu/index.html. The basics of the code are described in this paper along with an illustration of its integration in the ITM-TF simulation platform. A crucial aspect is the verification of the code, the results of benchmarks carried out with other NBI codes for JET and ITER discharges are thereby presented.

  8. Molecular dynamics simulation of framework flexibility effects on noble gas diffusion in HKUST-1 and ZIF-8

    SciTech Connect

    Parkes, Marie V.; Demir, Hakan; Teich-McGoldrick, Stephanie L.; Sholl, David S.; Greathouse, Jeffery A.; Allendorf, Mark D.

    2014-03-28

    Molecular dynamics simulations were used to investigate trends in noble gas (Ar, Kr, Xe) diffusion in the metal-organic frameworks HKUST-1 and ZIF-8. Diffusion occurs primarily through inter-cage jump events, with much greater diffusion of guest atoms in HKUST-1 compared to ZIF-8 due to the larger cage and window sizes in the former. We compare diffusion coefficients calculated for both rigid and flexible frameworks. For rigid framework simulations, in which the framework atoms were held at their crystallographic or geometry optimized coordinates, sometimes dramatic differences in guest diffusion were seen depending on the initial framework structure or the choice of framework force field parameters. When framework flexibility effects were included, argon and krypton diffusion increased significantly compared to rigid-framework simulations using general force field parameters. Additionally, for argon and krypton in ZIF-8, guest diffusion increased with loading, demonstrating that guest-guest interactions between cages enhance inter-cage diffusion. No inter-cage jump events were seen for xenon atoms in ZIF-8 regardless of force field or initial structure, and the loading dependence of xenon diffusion in HKUST-1 is different for rigid and flexible frameworks. Diffusion of krypton and xenon in HKUST-1 depends on two competing effects: the steric effect that decreases diffusion as loading increases, and the “small cage effect” that increases diffusion as loading increases. Finally, a detailed analysis of the window size in ZIF-8 reveals that the window increases beyond its normal size to permit passage of a (nominally) larger krypton atom.

  9. Progress report for FACETS (Framework Application for Core-Edge Transport Simulations): C.S. SAP

    SciTech Connect

    Epperly, T W

    2008-10-01

    The mission of the Computer Science Scientific Application Partnership (C.S. SAP) at LLNL is to develop and apply leading-edge scientific component technology to FACETS software. Contributions from LLNL's fusion energy program staff towards the underlying physics modules are described in a separate report. FACETS uses component technology to combine selectively multiple physics and solver software modules written in different languages by different institutions together in an tightly-integrated, parallel computing framework for Tokamak reactor modeling. In the past fiscal year, the C.S. SAP has focused on two primary tasks: applying Babel to connect UEDGE into the FACETS framework through UEDGE's existing Python interface and developing a next generation componentization strategy for UEDGE which avoids the use of Python. The FACETS project uses Babel to solve its language interoperability challenges. Specific accomplishments for the year include: (1) Refined SIDL interfaces for UEDGE to meet satisfy the standard interfaces required by FACETS for all physics modules. This required consensus building between framework and UEDGE developers. (2) Wrote prototype C++ driver for UEDGE to demonstrate how UEDGE can be called from C++ using Babel. (3) Supported the FACETS project by adding new features to Babel such as release number tagging, porting to new machines, and adding new configuration options. Babel modifications were delivered to FACETS by testing and publishing development snapshots in the projects software repository. (4) Assisted Tech-X Corporation in testing and debugging of a high level build system for the complete FACETS tool chain--the complete list of third-party software libraries that FACETS depends on directly or indirectly (e.g., MPI, HDF5, PACT, etc.). (5) Designed and implemented a new approach to wrapping UEDGE as a FACETS component without requiring Python. To get simulation results as soon as possible, our initial connection from the FACETS

  10. Innovative framework to simulate the fate and transport of nonconservative constituents in urban combined sewer catchments

    NASA Astrophysics Data System (ADS)

    Morales, V. M.; Quijano, J. C.; Schmidt, A.; Garcia, M. H.

    2016-11-01

    We have developed a probabilistic model to simulate the fate and transport of nonconservative constituents in urban watersheds. The approach implemented here extends previous studies that rely on the geomorphological instantaneous unit hydrograph concept to include nonconservative constituents. This is implemented with a factor χ that affects the transfer functions and therefore accounts for the loss (gain) of mass associated with the constituent as it travels through the watershed. Using this framework, we developed an analytical solution for the dynamics of dissolved oxygen (DO) and biochemical oxygen demand (BOD) in urban networks based on the Streeter and Phelps model. This model breaks down the catchment into a discreet number of possible flow paths through the system, requiring less data and implementation effort than well-established deterministic models. Application of the model to one sewer catchment in the Chicago area with available BOD information proved its ability to predict the BOD concentration observed in the measurements. In addition, comparison of the model with a calibrated Storm Water Management Model (SWMM) of another sewer catchment from the Chicago area showed that the model predicted the BOD concentration as well as the widely accepted SWMM. The developed model proved to be a suitable alternative to simulate the fate and transport of constituents in urban catchments with limited and uncertain input data.

  11. A discrete element based simulation framework to investigate particulate spray deposition processes

    SciTech Connect

    Mukherjee, Debanjan Zohdi, Tarek I.

    2015-06-01

    This work presents a computer simulation framework based on discrete element method to analyze manufacturing processes that comprise a loosely flowing stream of particles in a carrier fluid being deposited on a target surface. The individual particulate dynamics under the combined action of particle collisions, fluid–particle interactions, particle–surface contact and adhesive interactions is simulated, and aggregated to obtain global system behavior. A model for deposition which incorporates the effect of surface energy, impact velocity and particle size, is developed. The fluid–particle interaction is modeled using appropriate spray nozzle gas velocity distributions and a one-way coupling between the phases. It is found that the particle response times and the release velocity distribution of particles have a combined effect on inter-particle collisions during the flow along the spray. It is also found that resolution of the particulate collisions close to the target surface plays an important role in characterizing the trends in the deposit pattern. Analysis of the deposit pattern using metrics defined from the particle distribution on the target surface is provided to characterize the deposition efficiency, deposit size, and scatter due to collisions.

  12. A framework for stochastic simulation of distribution practices for hotel reservations

    SciTech Connect

    Halkos, George E.; Tsilika, Kyriaki D.

    2015-03-10

    The focus of this study is primarily on the Greek hotel industry. The objective is to design and develop a framework for stochastic simulation of reservation requests, reservation arrivals, cancellations and hotel occupancy with a planning horizon of a tourist season. In Greek hospitality industry there have been two competing policies for reservation planning process up to 2003: reservations coming directly from customers and a reservations management relying on tour operator(s). Recently the Internet along with other emerging technologies has offered the potential to disrupt enduring distribution arrangements. The focus of the study is on the choice of distribution intermediaries. We present an empirical model for the hotel reservation planning process that makes use of a symbolic simulation, Monte Carlo method, as, requests for reservations, cancellations, and arrival rates are all sources of uncertainty. We consider as a case study the problem of determining the optimal booking strategy for a medium size hotel in Skiathos Island, Greece. Probability distributions and parameters estimation result from the historical data available and by following suggestions made in the relevant literature. The results of this study may assist hotel managers define distribution strategies for hotel rooms and evaluate the performance of the reservations management system.

  13. Population genetics and molecular evolution of DNA sequences in transposable elements. I. A simulation framework.

    PubMed

    Kijima, T E; Innan, Hideki

    2013-11-01

    A population genetic simulation framework is developed to understand the behavior and molecular evolution of DNA sequences of transposable elements. Our model incorporates random transposition and excision of transposable element (TE) copies, two modes of selection against TEs, and degeneration of transpositional activity by point mutations. We first investigated the relationships between the behavior of the copy number of TEs and these parameters. Our results show that when selection is weak, the genome can maintain a relatively large number of TEs, but most of them are less active. In contrast, with strong selection, the genome can maintain only a limited number of TEs but the proportion of active copies is large. In such a case, there could be substantial fluctuations of the copy number over generations. We also explored how DNA sequences of TEs evolve through the simulations. In general, active copies form clusters around the original sequence, while less active copies have long branches specific to themselves, exhibiting a star-shaped phylogeny. It is demonstrated that the phylogeny of TE sequences could be informative to understand the dynamics of TE evolution.

  14. A heterogeneous and parallel computing framework for high-resolution hydrodynamic simulations

    NASA Astrophysics Data System (ADS)

    Smith, Luke; Liang, Qiuhua

    2015-04-01

    Shock-capturing hydrodynamic models are now widely applied in the context of flood risk assessment and forecasting, accurately capturing the behaviour of surface water over ground and within rivers. Such models are generally explicit in their numerical basis, and can be computationally expensive; this has prohibited full use of high-resolution topographic data for complex urban environments, now easily obtainable through airborne altimetric surveys (LiDAR). As processor clock speed advances have stagnated in recent years, further computational performance gains are largely dependent on the use of parallel processing. Heterogeneous computing architectures (e.g. graphics processing units or compute accelerator cards) provide a cost-effective means of achieving high throughput in cases where the same calculation is performed with a large input dataset. In recent years this technique has been applied successfully for flood risk mapping, such as within the national surface water flood risk assessment for the United Kingdom. We present a flexible software framework for hydrodynamic simulations across multiple processors of different architectures, within multiple computer systems, enabled using OpenCL and Message Passing Interface (MPI) libraries. A finite-volume Godunov-type scheme is implemented using the HLLC approach to solving the Riemann problem, with optional extension to second-order accuracy in space and time using the MUSCL-Hancock approach. The framework is successfully applied on personal computers and a small cluster to provide considerable improvements in performance. The most significant performance gains were achieved across two servers, each containing four NVIDIA GPUs, with a mix of K20, M2075 and C2050 devices. Advantages are found with respect to decreased parametric sensitivity, and thus in reducing uncertainty, for a major fluvial flood within a large catchment during 2005 in Carlisle, England. Simulations for the three-day event could be performed

  15. Agent-based modeling: case study in cleavage furrow models.

    PubMed

    Mogilner, Alex; Manhart, Angelika

    2016-11-07

    The number of studies in cell biology in which quantitative models accompany experiments has been growing steadily. Roughly, mathematical and computational techniques of these models can be classified as "differential equation based" (DE) or "agent based" (AB). Recently AB models have started to outnumber DE models, but understanding of AB philosophy and methodology is much less widespread than familiarity with DE techniques. Here we use the history of modeling a fundamental biological problem-positioning of the cleavage furrow in dividing cells-to explain how and why DE and AB models are used. We discuss differences, advantages, and shortcomings of these two approaches.

  16. Agent-Based Distributed Data Mining: A Survey

    NASA Astrophysics Data System (ADS)

    Moemeng, Chayapol; Gorodetsky, Vladimir; Zuo, Ziye; Yang, Yong; Zhang, Chengqi

    Distributed data mining is originated from the need of mining over decentralised data sources. Data mining techniques involving in such complex environment must encounter great dynamics due to changes in the system can affect the overall performance of the system. Agent computing whose aim is to deal with complex systems has revealed opportunities to improve distributed data mining systems in a number of ways. This paper surveys the integration of multi-agent system and distributed data mining, also known as agent-based distributed data mining, in terms of significance, system overview, existing systems, and research trends.

  17. Network Interventions on Physical Activity in an Afterschool Program: An Agent-Based Social Network Study

    PubMed Central

    Zhang, Jun; Shoham, David A.; Tesdahl, Eric

    2015-01-01

    Objectives. We studied simulated interventions that leveraged social networks to increase physical activity in children. Methods. We studied a real-world social network of 81 children (average age = 7.96 years) who lived in low socioeconomic status neighborhoods, and attended public schools and 1 of 2 structured afterschool programs. The sample was ethnically diverse, and 44% were overweight or obese. We used social network analysis and agent-based modeling simulations to test whether implementing a network intervention would increase children’s physical activity. We tested 3 intervention strategies. Results. The intervention that targeted opinion leaders was effective in increasing the average level of physical activity across the entire network. However, the intervention that targeted the most sedentary children was the best at increasing their physical activity levels. Conclusions. Which network intervention to implement depends on whether the goal is to shift the entire distribution of physical activity or to influence those most adversely affected by low physical activity. Agent-based modeling could be an important complement to traditional project planning tools, analogous to sample size and power analyses, to help researchers design more effective interventions for increasing children’s physical activity. PMID:25689202

  18. Agent-based modeling of osteogenic differentiation of mesenchymal stem cells in porous biomaterials.

    PubMed

    Bayrak, Elif S; Mehdizadeh, Hamidreza; Akar, Banu; Somo, Sami I; Brey, Eric M; Cinar, Ali

    2014-01-01

    Mesenchymal stem cells (MSC) have shown promise in tissue engineering applications due to their potential for differentiating into mesenchymal tissues such as osteocytes, chondrocytes, and adipocytes and releasing proteins to promote tissue regeneration. One application involves seeding MSCs in biomaterial scaffolds to promote osteogenesis in the repair of bone defects following implantation. However, predicting in vivo survival and differentiation of MSCs in biomaterials is challenging. Rapid and stable vascularization of scaffolds is required to supply nutrients and oxygen that MSCs need to survive as well as to go through osteogenic differentiation. The objective of this study is to develop an agent-based model and simulator that can be used to investigate the effects of using gradient growth factors on survival and differentiation of MSCs seeded in scaffolds. An agent-based model is developed to simulate the MSC behavior. The effect of vascular endothelial growth factor (VEGF) and bone morphogenic protein-2 (BMP-2) on both survival and osteogenic differentiation is studied. Results showed that the survival ratio of MSCs can be enhanced by increasing VEGF concentration. BMP-2 caused a slight increase on survival ratio. Osteogenesis strongly depends on the VEGF concentration as well because of its effect on vascularization. BMP-2 increased the osteogenic differentiation of MSCs.

  19. An agent-based model for domestic water management in Valladolid metropolitan area

    NASA Astrophysics Data System (ADS)

    GaláN, José M.; López-Paredes, Adolfo; Del Olmo, Ricardo

    2009-05-01

    In this work we demonstrate that the combination of agent-based modeling and simulation constitutes a useful methodological approach to dealing with the complexity derived from multiple factors with influence in the domestic water management in emergent metropolitan areas. In particular, we adapt and integrate different social submodels, models of urban dynamics, water consumption, and technological and opinion diffusion, in an agent-based model that is, in turn, linked with a geographic information system. The result is a computational environment that enables simulating and comparing various water demand scenarios. We have parameterized our general model for the metropolitan area of Valladolid (Spain).The model shows the influence of urban dynamics (e.g., intrapopulation movements, residence typology, and changes in the territorial model) and other socio-geographic effects (technological and opinion dynamics) in domestic water demand. The conclusions drawn in this way would have been difficult to obtain using other approaches, such as conventional forecasting methods, given the need to integrate different socioeconomic and geographic aspects in one single model. We illustrate that the described methodology can complement conventional approaches, providing descriptive and formal additional insights into domestic water demand management problems.

  20. EHSMu: a new conceptual model for hourly discharge simulation under ecohydrological framework in urban areas

    NASA Astrophysics Data System (ADS)

    Viola, Francesco; Noto, Leonardo V.; Pumo, Dario; La Loggia, Goffredo

    2013-04-01

    a linear function of soil moisture. The model has been calibrated using Montecarlo simulations on an urban catchment in the United States. This method allows to adapt the conceptual model framework to the catchment characteristics and at the same time to obtain the set of parameters with the higher efficiency in reproducing historical discharge at the outlet. The proposed model gives reliable estimate of runoff, soil moisture traces and evapotranspiration fluxes. Model outputs could be very useful for urban ecohydrology, because they allow for the simulation of vegetation water stress and consequently the design of sustainable urban green spaces. At the same time the model structure allows to simulate the effects of stormwater management best practices for achieving the hydraulic invariance.

  1. Molecular dynamics simulation of framework flexibility effects on noble gas diffusion in HKUST-1 and ZIF-8

    DOE PAGES

    Parkes, Marie V.; Demir, Hakan; Teich-McGoldrick, Stephanie L.; ...

    2014-03-28

    Molecular dynamics simulations were used to investigate trends in noble gas (Ar, Kr, Xe) diffusion in the metal-organic frameworks HKUST-1 and ZIF-8. Diffusion occurs primarily through inter-cage jump events, with much greater diffusion of guest atoms in HKUST-1 compared to ZIF-8 due to the larger cage and window sizes in the former. We compare diffusion coefficients calculated for both rigid and flexible frameworks. For rigid framework simulations, in which the framework atoms were held at their crystallographic or geometry optimized coordinates, sometimes dramatic differences in guest diffusion were seen depending on the initial framework structure or the choice of frameworkmore » force field parameters. When framework flexibility effects were included, argon and krypton diffusion increased significantly compared to rigid-framework simulations using general force field parameters. Additionally, for argon and krypton in ZIF-8, guest diffusion increased with loading, demonstrating that guest-guest interactions between cages enhance inter-cage diffusion. No inter-cage jump events were seen for xenon atoms in ZIF-8 regardless of force field or initial structure, and the loading dependence of xenon diffusion in HKUST-1 is different for rigid and flexible frameworks. Diffusion of krypton and xenon in HKUST-1 depends on two competing effects: the steric effect that decreases diffusion as loading increases, and the “small cage effect” that increases diffusion as loading increases. Finally, a detailed analysis of the window size in ZIF-8 reveals that the window increases beyond its normal size to permit passage of a (nominally) larger krypton atom.« less

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

    NASA Astrophysics Data System (ADS)

    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.

  3. Modelling of robotic work cells using agent based-approach

    NASA Astrophysics Data System (ADS)

    Sękala, A.; Banaś, W.; Gwiazda, A.; Monica, Z.; Kost, G.; Hryniewicz, P.

    2016-08-01

    In the case of modern manufacturing systems the requirements, both according the scope and according characteristics of technical procedures are dynamically changing. This results in production system organization inability to keep up with changes in a market demand. Accordingly, there is a need for new design methods, characterized, on the one hand with a high efficiency and on the other with the adequate level of the generated organizational solutions. One of the tools that could be used for this purpose is the concept of agent systems. These systems are the tools of artificial intelligence. They allow assigning to agents the proper domains of procedures and knowledge so that they represent in a self-organizing system of an agent environment, components of a real system. The agent-based system for modelling robotic work cell should be designed taking into consideration many limitations considered with the characteristic of this production unit. It is possible to distinguish some grouped of structural components that constitute such a system. This confirms the structural complexity of a work cell as a specific production system. So it is necessary to develop agents depicting various aspects of the work cell structure. The main groups of agents that are used to model a robotic work cell should at least include next pattern representatives: machine tool agents, auxiliary equipment agents, robots agents, transport equipment agents, organizational agents as well as data and knowledge bases agents. In this way it is possible to create the holarchy of the agent-based system.

  4. Using an Agent-Based Model to Examine the Role of Dynamic Bacterial Virulence Potential in the Pathogenesis of Surgical Site Infection

    PubMed Central

    Gopalakrishnan, Vissagan; Kim, Moses; An, Gary

    2013-01-01

    Objective Despite clinical advances, surgical site infections (SSIs) remain a problem. The development of SSIs involves a complex interplay between the cellular and molecular mechanisms of wound healing and contaminating bacteria, and here, we utilize an agent-based model (ABM) to investigate the role of bacterial virulence potential in the pathogenesis of SSI. Approach The Muscle Wound ABM (MWABM) incorporates muscle cells, neutrophils, macrophages, myoblasts, abstracted blood vessels, and avirulent/virulent bacteria to simulate the pathogenesis of SSIs. Simulated bacteria with virulence potential can mutate to possess resistance to reactive oxygen species and increased invasiveness. Simulated experiments (t=7 days) involved parameter sweeps of initial wound size to identify transition zones between healed and nonhealed wounds/SSIs, and to evaluate the effect of avirulent/virulent bacteria. Results The MWABM reproduced the dynamics of normal successful healing, including a transition zone in initial wound size beyond which healing was significantly impaired. Parameter sweeps with avirulent bacteria demonstrated that smaller wound sizes were associated with healing failure. This effect was even more pronounced with the addition of virulence potential to the contaminating bacteria. Innovation The MWABM integrates the myriad factors involved in the healing of a normal wound and the pathogenesis of SSIs. This type of model can serve as a useful framework into which more detailed mechanistic knowledge can be embedded. Conclusion Future work will involve more comprehensive representation of host factors, and especially the ability of those host factors to activate virulence potential in the microbes involved. PMID:24761337

  5. A spatial web/agent-based model to support stakeholders' negotiation regarding land development.

    PubMed

    Pooyandeh, Majeed; Marceau, Danielle J

    2013-11-15

    Decision making in land management can be greatly enhanced if the perspectives of concerned stakeholders are taken into consideration. This often implies negotiation in order to reach an agreement based on the examination of multiple alternatives. This paper describes a spatial web/agent-based modeling system that was developed to support the negotiation process of stakeholders regarding land development in southern Alberta, Canada. This system integrates a fuzzy analytic hierarchy procedure within an agent-based model in an interactive visualization environment provided through a web interface to facilitate the learning and negotiation of the stakeholders. In the pre-negotiation phase, the stakeholders compare their evaluation criteria using linguistic expressions. Due to the uncertainty and fuzzy nature of such comparisons, a fuzzy Analytic Hierarchy Process is then used to prioritize the criteria. The negotiation starts by a development plan being submitted by a user (stakeholder) through the web interface. An agent called the proposer, which represents the proposer of the plan, receives this plan and starts negotiating with all other agents. The negotiation is conducted in a step-wise manner where the agents change their attitudes by assigning a new set of weights to their criteria. If an agreement is not achieved, a new location for development is proposed by the proposer agent. This process is repeated until a location is found that satisfies all agents to a certain predefined degree. To evaluate the performance of the model, the negotiation was simulated with four agents, one of which being the proposer agent, using two hypothetical development plans. The first plan was selected randomly; the other one was chosen in an area that is of high importance to one of the agents. While the agents managed to achieve an agreement about the location of the land development after three rounds of negotiation in the first scenario, seven rounds were required in the second

  6. Unprecedentedly high selective adsorption of gas mixtures in rho zeolite-like metal-organic framework: a molecular simulation study.

    PubMed

    Babarao, Ravichandar; Jiang, Jianwen

    2009-08-19

    We report a molecular simulation study for the separation of industrially important gas mixtures (CO(2)/H(2), CO(2)/CH(4), and CO(2)/N(2)) in rho zeolite-like metal-organic framework (rho-ZMOF). Rho-ZMOF contains a wide-open anionic framework and charge-balancing extraframework Na(+) ions. Two types of binding sites for Na(+) ions are identified in the framework. Site I is in the single eight-membered ring, whereas site II is in the alpha-cage. Na(+) ions at site I have a stronger affinity for the framework and thus a smaller mobility. The binding sites in rho-ZMOF resemble those in its inorganic counterpart rho-zeolite. CO(2) is adsorbed predominantly over other gases because of its strong electrostatic interactions with the charged framework and the presence of Na(+) ions acting as additional adsorption sites. At ambient temperature and pressure, the CO(2) selectivities are 1800 for the CO(2)/H(2) mixture, 80 for the CO(2)/CH(4) mixture, and 500 for the CO(2)/N(2) mixture. Compared with other MOFs and nanoporous materials reported to date, rho-ZMOF exhibits unprecedentedly high selective adsorption for these gas mixtures. This work represents the first simulation study to characterize extraframework ions and examine gas separation in a charged ZMOF. The simulation results reveal that rho-ZMOF is a promising candidate for the separation of syngas, natural gas, and flue gas.

  7. Simulating mesoscale coastal evolution for decadal coastal management: A new framework integrating multiple, complementary modelling approaches

    NASA Astrophysics Data System (ADS)

    van Maanen, Barend; Nicholls, Robert J.; French, Jon R.; Barkwith, Andrew; Bonaldo, Davide; Burningham, Helene; Brad Murray, A.; Payo, Andres; Sutherland, James; Thornhill, Gillian; Townend, Ian H.; van der Wegen, Mick; Walkden, Mike J. A.

    2016-03-01

    Coastal and shoreline management increasingly needs to consider morphological change occurring at decadal to centennial timescales, especially that related to climate change and sea-level rise. This requires the development of morphological models operating at a mesoscale, defined by time and length scales of the order 101 to 102 years and 101 to 102 km. So-called 'reduced complexity' models that represent critical processes at scales not much smaller than the primary scale of interest, and are regulated by capturing the critical feedbacks that govern landform behaviour, are proving effective as a means of exploring emergent coastal behaviour at a landscape scale. Such models tend to be computationally efficient and are thus easily applied within a probabilistic framework. At the same time, reductionist models, built upon a more detailed description of hydrodynamic and sediment transport processes, are capable of application at increasingly broad spatial and temporal scales. More qualitative modelling approaches are also emerging that can guide the development and deployment of quantitative models, and these can be supplemented by varied data-driven modelling approaches that can achieve new explanatory insights from observational datasets. Such disparate approaches have hitherto been pursued largely in isolation by mutually exclusive modelling communities. Brought together, they have the potential to facilitate a step change in our ability to simulate the evolution of coastal morphology at scales that are most relevant to managing erosion and flood risk. Here, we advocate and outline a new integrated modelling framework that deploys coupled mesoscale reduced complexity models, reductionist coastal area models, data-driven approaches, and qualitative conceptual models. Integration of these heterogeneous approaches gives rise to model compositions that can potentially resolve decadal- to centennial-scale behaviour of diverse coupled open coast, estuary and inner

  8. A model framework to represent plant-physiology and rhizosphere processes in soil profile simulation models

    NASA Astrophysics Data System (ADS)

    Vanderborght, J.; Javaux, M.; Couvreur, V.; Schröder, N.; Huber, K.; Abesha, B.; Schnepf, A.; Vereecken, H.

    2013-12-01

    of plant transpiration by root-zone produced plant hormones, and (iv) the impact of salt accumulation at the soil-root interface on root water uptake. We further propose a framework how this process knowledge could be implemented in root zone simulation models that do not resolve small scale processes.

  9. Computational Research on Mobile Pastoralism Using Agent-Based Modeling and Satellite Imagery

    PubMed Central

    Sakamoto, Takuto

    2016-01-01

    Dryland pastoralism has long attracted considerable attention from researchers in diverse fields. However, rigorous formal study is made difficult by the high level of mobility of pastoralists as well as by the sizable spatio-temporal variability of their environment. This article presents a new computational approach for studying mobile pastoralism that overcomes these issues. Combining multi-temporal satellite images and agent-based modeling allows a comprehensive examination of pastoral resource access over a realistic dryland landscape with unpredictable ecological dynamics. The article demonstrates the analytical potential of this approach through its application to mobile pastoralism in northeast Nigeria. Employing more than 100 satellite images of the area, extensive simulations are conducted under a wide array of circumstances, including different land-use constraints. The simulation results reveal complex dependencies of pastoral resource access on these circumstances along with persistent patterns of seasonal land use observed at the macro level. PMID:26963526

  10. Re-Examining of Moffitt's Theory of Delinquency through Agent Based Modeling.

    PubMed

    Leaw, Jia Ning; Ang, Rebecca P; Huan, Vivien S; Chan, Wei Teng; Cheong, Siew Ann

    2015-01-01

    Moffitt's theory of delinquency suggests that at-risk youths can be divided into two groups, the adolescence- limited group and the life-course-persistent group, predetermined at a young age, and social interactions between these two groups become important during the adolescent years. We built an agent-based model based on the microscopic interactions Moffitt described: (i) a maturity gap that dictates (ii) the cost and reward of antisocial behavior, and (iii) agents imitating the antisocial behaviors of others more successful than themselves, to find indeed the two groups emerging in our simulations. Moreover, through an intervention simulation where we moved selected agents from one social network to another, we also found that the social network plays an important role in shaping the life course outcome.

  11. Computational Research on Mobile Pastoralism Using Agent-Based Modeling and Satellite Imagery.

    PubMed

    Sakamoto, Takuto

    2016-01-01

    Dryland pastoralism has long attracted considerable attention from researchers in diverse fields. However, rigorous formal study is made difficult by the high level of mobility of pastoralists as well as by the sizable spatio-temporal variability of their environment. This article presents a new computational approach for studying mobile pastoralism that overcomes these issues. Combining multi-temporal satellite images and agent-based modeling allows a comprehensive examination of pastoral resource access over a realistic dryland landscape with unpredictable ecological dynamics. The article demonstrates the analytical potential of this approach through its application to mobile pastoralism in northeast Nigeria. Employing more than 100 satellite images of the area, extensive simulations are conducted under a wide array of circumstances, including different land-use constraints. The simulation results reveal complex dependencies of pastoral resource access on these circumstances along with persistent patterns of seasonal land use observed at the macro level.

  12. Re-Examining of Moffitt’s Theory of Delinquency through Agent Based Modeling

    PubMed Central

    Leaw, Jia Ning; Ang, Rebecca P.; Huan, Vivien S.; Chan, Wei Teng; Cheong, Siew Ann

    2015-01-01

    Moffitt’s theory of delinquency suggests that at-risk youths can be divided into two groups, the adolescence- limited group and the life-course-persistent group, predetermined at a young age, and social interactions between these two groups become important during the adolescent years. We built an agent-based model based on the microscopic interactions Moffitt described: (i) a maturity gap that dictates (ii) the cost and reward of antisocial behavior, and (iii) agents imitating the antisocial behaviors of others more successful than themselves, to find indeed the two groups emerging in our simulations. Moreover, through an intervention simulation where we moved selected agents from one social network to another, we also found that the social network plays an important role in shaping the life course outcome. PMID:26062022

  13. An ancilla-based quantum simulation framework for non-unitary matrices

    NASA Astrophysics Data System (ADS)

    Daskin, Ammar; Kais, Sabre

    2017-01-01

    The success probability in an ancilla-based circuit generally decreases exponentially in the number of qubits consisted in the ancilla. Although the probability can be amplified through the amplitude amplification process, the input dependence of the amplitude amplification makes difficult to sequentially combine two or more ancilla-based circuits. A new version of the amplitude amplification known as the oblivious amplitude amplification runs independently of the input to the system register. This allows us to sequentially combine two or more ancilla-based circuits. However, this type of the amplification only works when the considered system is unitary or non-unitary but somehow close to a unitary. In this paper, we present a general framework to simulate non-unitary processes on ancilla-based quantum circuits in which the success probability is maximized by using the oblivious amplitude amplification. In particular, we show how to extend a non-unitary matrix to an almost unitary matrix. We then employ the extended matrix by using an ancilla-based circuit design along with the oblivious amplitude amplification. Measuring the distance of the produced matrix to the closest unitary matrix, a lower bound for the fidelity of the final state obtained from the oblivious amplitude amplification process is presented. Numerical simulations for random matrices of different sizes show that independent of the system size, the final amplified probabilities are generally around 0.75 and the fidelity of the final state is mostly high and around 0.95. Furthermore, we discuss the complexity analysis and show that combining two such ancilla-based circuits, a matrix product can be implemented. This may lead us to efficiently implement matrix functions represented as infinite matrix products on quantum computers.

  14. Dielectric spectroscopy and simulation of cryptophane and metal-organic framework crystals containing internal molecular rotors

    NASA Astrophysics Data System (ADS)

    Winston, Erick B.

    With recent advances in chemistry and crystal engineering, it is now possible to flexibly synthesize stable crystals with internal molecular electric dipole rotors. This represents a nanoscale design approach to the creation of new materials. Potential applications of such systems include electro-optic materials, new ferroelectrics and dielectrics, and perhaps even information storage. In this thesis, the rotational dynamics of molecular rotors in single crystals is investigated by dielectric spectroscopy. Using X-ray crystallography in combination with molecular mechanics or ab initio calculations, the influence of the local crystal environment on the observed dynamics is ascertained. Additionally, the atomic coordinates from the X-ray structure, and molecular dipole moments determined from ab initio calculations, are used to create an approximate model for a Monte Carlo study of the significance of the dipole-dipole interactions among the rotors. The systems studied here represent two different families of synthetic approaches to creating molecular rotors in crystals. One approach consists of synthesizing inclusion compounds in which molecular crystals have internal cavities capable of hosting small molecular guests. Specifically, we look at the globular cryptophane complexes and find that iodomethane rotates in cryptophane-A with remarkably low barriers near 2 kcal·mol-1 (1000 K), in agreement with the molecular mechanics calculations. The other approach consists of synthesizing covalent crystals where the rotor elements are themselves part of the covalently bonded network. We study metal-organic open frameworks (MOFs), in particular IRMOF-2, and find rotation with a single barrier near 7 kcal·mol-1 (3500 K). The barrier is in approximate agreement with ab initio calculations. Statistical analysis of an MC simulation of IRMOF-2 suggests a dipolar phase change at lower temperatures. The residual dielectric effects of the dipole-dipole interaction above the

  15. A simulation framework for estimating wall stress distribution of abdominal aortic aneurysm.

    PubMed

    Qin, Jing; Zhang, Jing; Chui, Chee-Kong; Huang, Wei-Min; Yang, Tao; Pang, Wai-Man; Sudhakar, Venkatesh; Chang, Stephen

    2011-01-01

    Abdominal aortic aneurysm (AAA) rupture is believed to occur when the mechanical stress acting on the wall exceeds the strength of the wall tissue. In endovascular aneurysm repair, a stent-graft in a catheter is released at the aneurysm site to form a new blood vessel and protect the weakened AAA wall from the pulsatile pressure and, hence, possible rupture. In this paper, we propose a framework to estimate the wall stress distribution of non-stented/stented AAA based on fluid-structure interaction, which is utilized in a surgical simulation system (IRAS). The 3D geometric model of AAA is reconstructed from computed tomography angiographic (CTA) images. Based on our experiments, a combined logarithm and polynomial strain energy equation is applied to model the elastic properties of arterial wall. The blood flow is modeled as laminar, incompressible, and non-Newtonian flow by applying Navier-Stokes equation. The obtained pressure of blood flow is applied as load on the AAA meshes with and without stent-graft and the wall stress distribution is calculated by fluid-structure interaction (FSI) solver equipped in ANSYS. Experiments demonstrate that our analytical results are consistent with clinical observations.

  16. Autogenerator-Based Modelling Framework for Development of Strategic Games Simulations: Rational Pigs Game Extended

    PubMed Central

    Magdalenić, Ivan

    2014-01-01

    When considering strategic games from the conceptual perspective that focuses on the questions of participants' decision-making rationality, the very issues of modelling and simulation are rarely discussed. The well-known Rational Pigs matrix game has been relatively intensively analyzed in terms of reassessment of the logic of two players involved in asymmetric situations as gluttons that differ significantly by their attributes. This paper presents a successful attempt of using autogenerator for creating the framework of the game, including the predefined scenarios and corresponding payoffs. Autogenerator offers flexibility concerning the specification of game parameters, which consist of variations in the number of simultaneous players and their features and game objects and their attributes as well as some general game characteristics. In the proposed approach the model of autogenerator was upgraded so as to enable program specification updates. For the purpose of treatment of more complex strategic scenarios, we created the Rational Pigs Game Extended (RPGE), in which the introduction of a third glutton entails significant structural changes. In addition, due to the existence of particular attributes of the new player, “the tramp,” one equilibrium point from the original game is destabilized which has an influence on the decision-making of rational players. PMID:25254228

  17. Development of a Lattice Boltzmann Framework for Numerical Simulation of Thrombosis

    NASA Astrophysics Data System (ADS)

    Harrison, S. E.; Bernsdorf, J.; Hose, D. R.; Lawford, P. V.

    The interacting factors relating to thrombogenesis were defined by Virchow in 1856 to be abnormalities of blood chemistry, the vessel wall and haemodynamics. Together, these factors are known as Virchow's triad. Many attempts have been made to simulate numerically certain aspects of the complex phenomena of thrombosis, but a comprehensive model, which includes the biochemical and physical aspects of Virchow's triad, and is capable of predicting thrombus development within physiological geometries has not yet been developed. Such a model would consider the role of platelets and the coagulation cascade along with the properties of the flow in the chosen vessel. A lattice Boltzmann thrombosis framework has been developed, on top of an existing flow solver, to model the formation of thrombi resulting from platelet activation and initiation of the coagulation cascade by one or more of the strands of Virchow's triad. Both processes then act in parallel, to restore homeostasis as the deposited thrombus disturbs the flow. Results are presented in a model of deep vein thrombosis (DVT), resulting from hypoxia and associated endothelial damage.

  18. Linking agent-based models and stochastic models of financial markets.

    PubMed

    Feng, Ling; Li, Baowen; Podobnik, Boris; Preis, Tobias; Stanley, H Eugene

    2012-05-29

    It is well-known that financial asset returns exhibit fat-tailed distributions and long-term memory. These empirical features are the main objectives of modeling efforts using (i) stochastic processes to quantitatively reproduce these features and (ii) agent-based simulations to understand the underlying microscopic interactions. After reviewing selected empirical and theoretical evidence documenting the behavior of traders, we construct an agent-based model to quantitatively demonstrate that "fat" tails in return distributions arise when traders share similar technical trading strategies and decisions. Extending our behavioral model to a stochastic model, we derive and explain a set of quantitative scaling relations of long-term memory from the empirical behavior of individual market participants. Our analysis provides a behavioral interpretation of the long-term memory of absolute and squared price returns: They are directly linked to the way investors evaluate their investments by applying technical strategies at different investment horizons, and this quantitative relationship is in agreement with empirical findings. Our approach provides a possible behavioral explanation for stochastic models for financial systems in general and provides a method to parameterize such models from market data rather than from statistical fitting.

  19. Combining agent-based modeling and life cycle assessment for the evaluation of mobility policies.

    PubMed

    Florent, Querini; Enrico, Benetto

    2015-02-03

    This article presents agent-based modeling (ABM) as a novel approach for consequential life cycle assessment (C-LCA) of large scale policies, more specifically mobility-related policies. The approach is validated at the Luxembourgish level (as a first case study). The agent-based model simulates the car market (sales, use, and dismantling) of the population of users in the period 2013-2020, following the implementation of different mobility policies and available electric vehicles. The resulting changes in the car fleet composition as well as the hourly uses of the vehicles are then used to derive consistent LCA results, representing the consequences of the policies. Policies will have significant environmental consequences: when using ReCiPe2008, we observe a decrease of global warming, fossil depletion, acidification, ozone depletion, and photochemical ozone formation and an increase of metal depletion, ionizing radiations, marine eutrophication, and particulate matter formation. The study clearly shows that the extrapolation of LCA results for the circulating fleet at national scale following the introduction of the policies from the LCAs of single vehicles by simple up-scaling (using hypothetical deployment scenarios) would be flawed. The inventory has to be directly conducted at full scale and to this aim, ABM is indeed a promising approach, as it allows identifying and quantifying emerging effects while modeling the Life Cycle Inventory of vehicles at microscale through the concept of agents.

  20. Linking agent-based models and stochastic models of financial markets

    PubMed Central

    Feng, Ling; Li, Baowen; Podobnik, Boris; Preis, Tobias; Stanley, H. Eugene

    2012-01-01

    It is well-known that financial asset returns exhibit fat-tailed distributions and long-term memory. These empirical features are the main objectives of modeling efforts using (i) stochastic processes to quantitatively reproduce these features and (ii) agent-based simulations to understand the underlying microscopic interactions. After reviewing selected empirical and theoretical evidence documenting the behavior of traders, we construct an agent-based model to quantitatively demonstrate that “fat” tails in return distributions arise when traders share similar technical trading strategies and decisions. Extending our behavioral model to a stochastic model, we derive and explain a set of quantitative scaling relations of long-term memory from the empirical behavior of individual market participants. Our analysis provides a behavioral interpretation of the long-term memory of absolute and squared price returns: They are directly linked to the way investors evaluate their investments by applying technical strategies at different investment horizons, and this quantitative relationship is in agreement with empirical findings. Our approach provides a possible behavioral explanation for stochastic models for financial systems in general and provides a method to parameterize such models from market data rather than from statistical fitting. PMID:22586086