Article

A Comparison of System Dynamics and Agent-Based Simulation Applied to the Study of Cellular Receptor Dynamics

Authors:

Wayne W. Wakeland,

Edward J. Gallaher,

Louis M. Macovsky,

C. Athena AktipisAuthors Info & Claims

HICSS '04: Proceedings of the Proceedings of the 37th Annual Hawaii International Conference on System Sciences (HICSS'04) - Track 3 - Volume 3

Page 30086.2

Published: 05 January 2004 Publication History

Publisher Site

Abstract

Cellular receptor dynamics are often analyzed using differential equations, making system dynamics (SD) a candidate methodology. In some cases it may be useful to model the phenomena at the biomolecular level, especially when concentrations and reaction probabilities are low and might lead to unexpected behavior modes. In such cases, agent-based simulation (ABS) may be useful. We show the application of both SD and ABS to simulate non-equilibrium ligand-receptor dynamics over a broad range of concentrations, where the probability of interaction varies from low to very low. Both approaches offer much to the researcher and are complementary. We did not find a clear demarcation indicating when one paradigm or the other would be strongly preferred, although SD is an obvious choice when studying systems at a high level of aggregation and abstraction, and ABS is well suited to studying phenomena at the level of individual receptors and molecules.

Cited By

View all

Nemiche MM'hamdi A(2018)Bottom-Up and Top-Down Approaches to Simulate Complex Social PhenomenaInternational Journal of Applied Evolutionary Computation10.4018/IJAEC.20180401019:2(1-16)Online publication date: 1-Apr-2018
https://dl.acm.org/doi/10.4018/IJAEC.2018040101
Djanatliev AGerman R(2015)Towards a guide to domain-specific hybrid simulationProceedings of the 2015 Winter Simulation Conference10.5555/2888619.2888801(1609-1620)Online publication date: 6-Dec-2015
https://dl.acm.org/doi/10.5555/2888619.2888801
Heath SBuss ABrailsford SMacal C(2011)Cross-paradigm simulation modelingProceedings of the Winter Simulation Conference10.5555/2431518.2431850(2788-2802)Online publication date: 11-Dec-2011
https://dl.acm.org/doi/10.5555/2431518.2431850
Show More Cited By

Index Terms

A Comparison of System Dynamics and Agent-Based Simulation Applied to the Study of Cellular Receptor Dynamics
1. Applied computing
  1. Life and medical sciences
2. Computing methodologies
  1. Artificial intelligence
    1. Distributed artificial intelligence
      1. Intelligent agents
  2. Modeling and simulation

Recommendations

Molecular dynamics study-based mechanism of nefiracetam-induced NMDA receptor potentiation

Display Omitted Nefiracetam-induced N-methyl-d-aspartic acid (NMDA) receptor signaling was investigated.Nefiracetam-induces NMDA receptor ligand binding domain conformation which favors glycine dissociation.Nefiracetam replaces glycine within glycine-...
Discovering novel inhibitors of P2Y₁₂ receptor using structure-based virtual screening, molecular dynamics simulation and MMPBSA approaches
Abstract
P2Y₁₂, a G-protein coupled receptor is involved in platelets plug formation and it amplifies and maintains the process of platelet aggregation. P2Y₁₂ is considered as a potent target to inhibit platelet aggregation in thrombotic and cardiac ...
Graphical abstract

Display Omitted
Highlights
- P2Y12 receptor is considered as a potential drug target in thrombotic and cardiac emergencies.
- Structure-based virtual screening techniques including pharmacophore modeling and molecular docking were employed to screen drug-like ...
An investigation of molecular dynamics simulation and molecular docking: Interaction of citrus flavonoids and bovine β-lactoglobulin in focus

Citrus flavonoids are natural compounds with important health benefits. The study of their interaction with a transport protein, such as bovine @b-lactoglobulin (BLG), at the atomic level could be a valuable factor to control their transport to ...

Comments

Please enable JavaScript to view thecomments powered by Disqus.

Information & Contributors

Information

Published In

HICSS '04: Proceedings of the Proceedings of the 37th Annual Hawaii International Conference on System Sciences (HICSS'04) - Track 3 - Volume 3

January 2004

ISBN:0769520561

Publisher

IEEE Computer Society

United States

Publication History

Published: 05 January 2004

Qualifiers

Article

Contributors

Other Metrics

View Article Metrics

Bibliometrics & Citations

Bibliometrics

Article Metrics

11
Total Citations
View Citations
0
Total Downloads

Downloads (Last 12 months)0
Downloads (Last 6 weeks)0

Reflects downloads up to 06 Jan 2025

Other Metrics

View Author Metrics

Citations

Cited By

View all

Nemiche MM'hamdi A(2018)Bottom-Up and Top-Down Approaches to Simulate Complex Social PhenomenaInternational Journal of Applied Evolutionary Computation10.4018/IJAEC.20180401019:2(1-16)Online publication date: 1-Apr-2018
https://dl.acm.org/doi/10.4018/IJAEC.2018040101
Djanatliev AGerman R(2015)Towards a guide to domain-specific hybrid simulationProceedings of the 2015 Winter Simulation Conference10.5555/2888619.2888801(1609-1620)Online publication date: 6-Dec-2015
https://dl.acm.org/doi/10.5555/2888619.2888801
Heath SBuss ABrailsford SMacal C(2011)Cross-paradigm simulation modelingProceedings of the Winter Simulation Conference10.5555/2431518.2431850(2788-2802)Online publication date: 11-Dec-2011
https://dl.acm.org/doi/10.5555/2431518.2431850
Figueredo GAickelin UKropf P(2011)Comparing system dynamics and agent-based simulation for tumour growth and its interactions with effector cellsProceedings of the 2011 Summer Computer Simulation Conference10.5555/2348196.2348204(52-59)Online publication date: 27-Jun-2011
https://dl.acm.org/doi/10.5555/2348196.2348204
Macal CYücesan E(2010)To agent-based simulation from system dynamicsProceedings of the Winter Simulation Conference10.5555/2433508.2433551(371-382)Online publication date: 5-Dec-2010
https://dl.acm.org/doi/10.5555/2433508.2433551
Figueredo GAickelin U(2010)Investigating immune system agingProceedings of the 2010 Summer Computer Simulation Conference10.5555/1999416.1999437(174-181)Online publication date: 11-Jul-2010
https://dl.acm.org/doi/10.5555/1999416.1999437
Hester PTolk AMcGraw RImsand EChinni M(2010)Applying methods of the M&S spectrum for complex systems engineeringProceedings of the 2010 Spring Simulation Multiconference10.1145/1878537.1878615(1-8)Online publication date: 11-Apr-2010
https://dl.acm.org/doi/10.1145/1878537.1878615
Lättilä LHilletofth PLin B(2010)Hybrid simulation models - When, Why, How?Expert Systems with Applications: An International Journal10.1016/j.eswa.2010.04.03937:12(7969-7975)Online publication date: 1-Dec-2010
https://dl.acm.org/doi/10.1016/j.eswa.2010.04.039
Majid MAickelin USiebers P(2009)Comparing simulation output accuracy of discrete event and agent based modelsProceedings of the 2009 Summer Computer Simulation Conference10.5555/2349508.2349532(177-184)Online publication date: 13-Jul-2009
https://dl.acm.org/doi/10.5555/2349508.2349532
Thompson K(2008)The value of multiple representations for learning about complex systemsProceedings of the 8th international conference on International conference for the learning sciences - Volume 210.5555/1599871.1599921(398-406)Online publication date: 24-Jun-2008
https://dl.acm.org/doi/10.5555/1599871.1599921
Show More Cited By

Abstract

Cited By

Index Terms

Recommendations

Molecular dynamics study-based mechanism of nefiracetam-induced NMDA receptor potentiation

Discovering novel inhibitors of P2Y12 receptor using structure-based virtual screening, molecular dynamics simulation and MMPBSA approaches

An investigation of molecular dynamics simulation and molecular docking: Interaction of citrus flavonoids and bovine β-lactoglobulin in focus

Comments

Information

Published In

Publisher

Publication History

Qualifiers

Contributors

Other Metrics

Bibliometrics

Article Metrics

Other Metrics

Citations

Cited By

View options

Figures

Other

Share

Share this Publication link

Share on social media

Affiliations

Discovering novel inhibitors of P2Y₁₂ receptor using structure-based virtual screening, molecular dynamics simulation and MMPBSA approaches