Pub Date : 2019-01-01DOI: 10.1016/b978-0-12-813370-5.00016-x
B. Zeigler, A. Muzy, E. Kofman
{"title":"Simulators for Basic Formalisms","authors":"B. Zeigler, A. Muzy, E. Kofman","doi":"10.1016/b978-0-12-813370-5.00016-x","DOIUrl":"https://doi.org/10.1016/b978-0-12-813370-5.00016-x","url":null,"abstract":"","PeriodicalId":92297,"journal":{"name":"Symposium on Theory of Modeling & Simulation : DEVS Integrative M&S Symposium (TMS-DEVS). Symposium on Theory of Modeling and Simulation","volume":"36 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84700682","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2019-01-01DOI: 10.1016/B978-0-12-813370-5.00024-9
B. Zeigler, A. Muzy, E. Kofman
{"title":"Parallel and Distributed Discrete Event Simulation","authors":"B. Zeigler, A. Muzy, E. Kofman","doi":"10.1016/B978-0-12-813370-5.00024-9","DOIUrl":"https://doi.org/10.1016/B978-0-12-813370-5.00024-9","url":null,"abstract":"","PeriodicalId":92297,"journal":{"name":"Symposium on Theory of Modeling & Simulation : DEVS Integrative M&S Symposium (TMS-DEVS). Symposium on Theory of Modeling and Simulation","volume":"40 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83395268","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2019-01-01DOI: 10.1016/b978-0-12-813370-5.00026-2
B. Zeigler, A. Muzy, E. Kofman
{"title":"Abstraction: Constructing Model Families","authors":"B. Zeigler, A. Muzy, E. Kofman","doi":"10.1016/b978-0-12-813370-5.00026-2","DOIUrl":"https://doi.org/10.1016/b978-0-12-813370-5.00026-2","url":null,"abstract":"","PeriodicalId":92297,"journal":{"name":"Symposium on Theory of Modeling & Simulation : DEVS Integrative M&S Symposium (TMS-DEVS). Symposium on Theory of Modeling and Simulation","volume":"255 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76340894","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2019-01-01DOI: 10.1016/B978-0-12-813370-5.00029-8
B. Zeigler, A. Muzy, E. Kofman
{"title":"Quantization-Based Simulation of Continuous Time Systems","authors":"B. Zeigler, A. Muzy, E. Kofman","doi":"10.1016/B978-0-12-813370-5.00029-8","DOIUrl":"https://doi.org/10.1016/B978-0-12-813370-5.00029-8","url":null,"abstract":"","PeriodicalId":92297,"journal":{"name":"Symposium on Theory of Modeling & Simulation : DEVS Integrative M&S Symposium (TMS-DEVS). Symposium on Theory of Modeling and Simulation","volume":"12 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74502022","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2019-01-01DOI: 10.1016/B978-0-12-813370-5.00032-8
B. Zeigler, A. Muzy, E. Kofman
{"title":"DEVS Markov Modeling and Simulation","authors":"B. Zeigler, A. Muzy, E. Kofman","doi":"10.1016/B978-0-12-813370-5.00032-8","DOIUrl":"https://doi.org/10.1016/B978-0-12-813370-5.00032-8","url":null,"abstract":"","PeriodicalId":92297,"journal":{"name":"Symposium on Theory of Modeling & Simulation : DEVS Integrative M&S Symposium (TMS-DEVS). Symposium on Theory of Modeling and Simulation","volume":"9 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79499576","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical properties, chemical uptake and secretion, cell differentiation, proliferation, death, and migration. Modeling and simulation of such dynamic phenomena poses a number of computational challenges. A modeling language describing cellular dynamics must naturally represent complex intra and extra-cellular spatial structures and coupled mechanical, chemical and electrical processes. Domain experts will find a modeling language most useful when it is based on concepts, terms and principles native to the problem domain. A compiler must then be able to generate an executable model from this physically motivated description. Finally, an executable model must efficiently calculate the time evolution of such dynamic and inhomogeneous phenomena. We present a spatial hybrid systems modeling language, compiler and mesh-free Lagrangian based simulation engine which will enable domain experts to define models using natural, biologically motivated constructs and to simulate time evolution of coupled cellular, mechanical and chemical processes acting on a time varying number of cells and their environment.
{"title":"A MODELING AND SIMULATION LANGUAGE FOR BIOLOGICAL CELLS WITH COUPLED MECHANICAL AND CHEMICAL PROCESSES.","authors":"Endre Somogyi, James A Glazier","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical properties, chemical uptake and secretion, cell differentiation, proliferation, death, and migration. Modeling and simulation of such dynamic phenomena poses a number of computational challenges. A modeling language describing cellular dynamics must naturally represent complex intra and extra-cellular spatial structures and coupled mechanical, chemical and electrical processes. Domain experts will find a modeling language most useful when it is based on concepts, terms and principles native to the problem domain. A compiler must then be able to generate an executable model from this physically motivated description. Finally, an executable model must efficiently calculate the time evolution of such dynamic and inhomogeneous phenomena. We present a spatial hybrid systems modeling language, compiler and mesh-free Lagrangian based simulation engine which will enable domain experts to define models using natural, biologically motivated constructs and to simulate time evolution of coupled cellular, mechanical and chemical processes acting on a time varying number of cells and their environment.</p>","PeriodicalId":92297,"journal":{"name":"Symposium on Theory of Modeling & Simulation : DEVS Integrative M&S Symposium (TMS-DEVS). Symposium on Theory of Modeling and Simulation","volume":"2017 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5749416/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35710804","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2017-01-02DOI: 10.22360/springsim.2017.tmsdevs.033
Endre T. Somogyi, J. Glazier
Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical properties, chemical uptake and secretion, cell differentiation, proliferation, death, and migration. Modeling and simulation of such dynamic phenomena poses a number of computational challenges. A modeling language describing cellular dynamics must naturally represent complex intra and extra-cellular spatial structures and coupled mechanical, chemical and electrical processes. Domain experts will find a modeling language most useful when it is based on concepts, terms and principles native to the problem domain. A compiler must then be able to generate an executable model from this physically motivated description. Finally, an executable model must efficiently calculate the time evolution of such dynamic and inhomogeneous phenomena. We present a spatial hybrid systems modeling language, compiler and mesh-free Lagrangian based simulation engine which will enable domain experts to define models using natural, biologically motivated constructs and to simulate time evolution of coupled cellular, mechanical and chemical processes acting on a time varying number of cells and their environment.
{"title":"A modeling and simulation language for biological cells with coupled mechanical and chemical processes","authors":"Endre T. Somogyi, J. Glazier","doi":"10.22360/springsim.2017.tmsdevs.033","DOIUrl":"https://doi.org/10.22360/springsim.2017.tmsdevs.033","url":null,"abstract":"Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical properties, chemical uptake and secretion, cell differentiation, proliferation, death, and migration. Modeling and simulation of such dynamic phenomena poses a number of computational challenges. A modeling language describing cellular dynamics must naturally represent complex intra and extra-cellular spatial structures and coupled mechanical, chemical and electrical processes. Domain experts will find a modeling language most useful when it is based on concepts, terms and principles native to the problem domain. A compiler must then be able to generate an executable model from this physically motivated description. Finally, an executable model must efficiently calculate the time evolution of such dynamic and inhomogeneous phenomena. We present a spatial hybrid systems modeling language, compiler and mesh-free Lagrangian based simulation engine which will enable domain experts to define models using natural, biologically motivated constructs and to simulate time evolution of coupled cellular, mechanical and chemical processes acting on a time varying number of cells and their environment.","PeriodicalId":92297,"journal":{"name":"Symposium on Theory of Modeling & Simulation : DEVS Integrative M&S Symposium (TMS-DEVS). Symposium on Theory of Modeling and Simulation","volume":"67 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87799912","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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