Implementing a global approach for efficiently simulating molecular dynamics in agent-based models of biological tissue
Summary: This protocol explains how to take an agent-based model (ABM) with molecular dynamics and set it up to solve the molecular dynamics with a global approach. It can be used to speed up simulations significantly while retaining high levels of accuracy with the original ABM. Two options are pre...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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Elsevier
2022-12-01
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| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166722006578 |
| _version_ | 1811292024828067840 |
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| author | Daniel Bergman Trachette L. Jackson |
| author_facet | Daniel Bergman Trachette L. Jackson |
| author_sort | Daniel Bergman |
| collection | DOAJ |
| description | Summary: This protocol explains how to take an agent-based model (ABM) with molecular dynamics and set it up to solve the molecular dynamics with a global approach. It can be used to speed up simulations significantly while retaining high levels of accuracy with the original ABM. Two options are presented for implementing this global approach, depending on the desired spatial variability in molecular concentrations. Both options coarse-grain the molecular dynamics in space by dividing the microenvironment into regions with uniform concentrations.For complete details on the use and execution of this protocol, please refer to Bergman et al. (2022). : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| first_indexed | 2024-04-13T04:39:11Z |
| format | Article |
| id | doaj.art-db837114037d4d57ae5d596b1d7a8728 |
| institution | Directory Open Access Journal |
| issn | 2666-1667 |
| language | English |
| last_indexed | 2024-04-13T04:39:11Z |
| publishDate | 2022-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj.art-db837114037d4d57ae5d596b1d7a87282022-12-22T03:02:05ZengElsevierSTAR Protocols2666-16672022-12-0134101777Implementing a global approach for efficiently simulating molecular dynamics in agent-based models of biological tissueDaniel Bergman0Trachette L. Jackson1Department of Mathematics, University of Michigan, Ann Arbor, MI 48109, USA; Corresponding authorDepartment of Mathematics, University of Michigan, Ann Arbor, MI 48109, USA; Corresponding authorSummary: This protocol explains how to take an agent-based model (ABM) with molecular dynamics and set it up to solve the molecular dynamics with a global approach. It can be used to speed up simulations significantly while retaining high levels of accuracy with the original ABM. Two options are presented for implementing this global approach, depending on the desired spatial variability in molecular concentrations. Both options coarse-grain the molecular dynamics in space by dividing the microenvironment into regions with uniform concentrations.For complete details on the use and execution of this protocol, please refer to Bergman et al. (2022). : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.http://www.sciencedirect.com/science/article/pii/S2666166722006578Systems biologyComputer sciences |
| spellingShingle | Daniel Bergman Trachette L. Jackson Implementing a global approach for efficiently simulating molecular dynamics in agent-based models of biological tissue STAR Protocols Systems biology Computer sciences |
| title | Implementing a global approach for efficiently simulating molecular dynamics in agent-based models of biological tissue |
| title_full | Implementing a global approach for efficiently simulating molecular dynamics in agent-based models of biological tissue |
| title_fullStr | Implementing a global approach for efficiently simulating molecular dynamics in agent-based models of biological tissue |
| title_full_unstemmed | Implementing a global approach for efficiently simulating molecular dynamics in agent-based models of biological tissue |
| title_short | Implementing a global approach for efficiently simulating molecular dynamics in agent-based models of biological tissue |
| title_sort | implementing a global approach for efficiently simulating molecular dynamics in agent based models of biological tissue |
| topic | Systems biology Computer sciences |
| url | http://www.sciencedirect.com/science/article/pii/S2666166722006578 |
| work_keys_str_mv | AT danielbergman implementingaglobalapproachforefficientlysimulatingmoleculardynamicsinagentbasedmodelsofbiologicaltissue AT trachetteljackson implementingaglobalapproachforefficientlysimulatingmoleculardynamicsinagentbasedmodelsofbiologicaltissue |