Poster
Reference
An Agent-Based Model for Collective Behaviors of Social Amoeba Dictyostelium discoideum Morphogenesis: Aggregation Phase
PARHIZKAR, Mohammad, DI MARZO SERUGENDO, Giovanna
PARHIZKAR, Mohammad, DI MARZO SERUGENDO, Giovanna. An Agent-Based Model for Collective Behaviors of Social Amoeba Dictyostelium discoideum Morphogenesis: Aggregation Phase. In: Dicty 2017, Chavannes-de-Bogis, Switzerland, 24 August 2017, 2017
Available at:
http://archive-ouverte.unige.ch/unige:113000
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Mohammad Parhizkar
Centre Universitaire d’Informatique (CUI) University of Geneva, Switzerland
Email: mohammad.parhizkar@etu.unige.ch
Giovanna Di Marzo Serugendo
Centre Universitaire d’Informatique (CUI) University of Geneva, Switzerland
Email: giovanna.dimarzo@unige.ch
An Agent-Based Model for Collective Behaviors of Social Amoeba Dictyostelium discoideum Morphogenesis: Aggregation Phase
Research domain Method
• Focus on the aggregation phase of Dictyostelium discoideum.
• An agent-based model, which exhibits a series of individual, collective behaviors and emergent properties of social amoeba Dictyostelium discoideum.
• The key character of our model is the cells’ self-assessment and self-generated gradients arising from six chemical factors: PSF, CMF, Adenosine, cAMP, PDE and CF released by each individual amoeba.
• Understand, simulate and visualize the individual and intercellular activities of cells (growth, division, movement, secretion, differentiation, etc.)
• Modeling and simulating of slug formation phase
• Appealing to inspire the engineering of swarm robotics
Short-term Objectives
Conclusion
starvation
t = 0
PSF CMF
t = 5 hr
adenosine, (cAMP + PDE) , CF
t = 12 hr
aggregation
We extended Mackay’s model with:
• Dynamic center self-selection: first centers appear based on cells’ age, high concentration of CMF and low Adenosine. During streams formation, late centers appear when cells’ density is too high (CF high, cAMP high, and Adenosine low).
• Three levels of quorum sensing: the 6 signals provide gradients for collective decentralized decisions:
1. Pre-aggregation: PSF and CMF concentrations trigger identification of starvation and aggregation;
2. Aggregation: CF, cAMP concentrations lead to late centers formation;
3. Density and territory size: cells measure density levels through CF;
trigger more PDE regulating territory size.
• Chemotaxis: cAMP concentration causes cells to move towards centers and form streams, following:
1. Cells follow Michaelis-Menten equation enzyme kinetics (for cAMP and PDE);
2. Three cAMP levels: late center formation, relay response, chemotaxis response;
3. cAMP and PDE secretion depends on cells density.
Long- term Objectives
• Implemented an agent-based model to simulate the formation of cell aggregation using 6 different chemical factors.
• Our model follows a completely decentralized and self-organizing process.
• Simulations show multicellular behaviors, such as stream formation, homogeneous size territories, late centers and centers inhibition.
• This model considers D. discoideum amoeba populations composed of a single cell type without differentiation between pre-stalk and pre-spore.
• The formation of aggregates consisting of two or more cell types and sorting process during the aggregation is also a point of interest for future works. Future work will consider models for the remaining phases of D.
discoideum behaviour, and translation of this model into artificial systems, such as swarms or micro-robots.
Model
Dictyostelium life cycle- The simulations of the red arc
• Second and higher-order emergence
• Swarm robotics
Relaying threshold Chemotaxis threshold cAMP concentration level
for a regular cell C
B
A New center threshold
Different levels of cAMP threshold
Effect of adenosine – The number the centers in 5000 cells
Diffusion of cAMP – 2 centers through 1000 regular cells
Times of continuously synthesizing factors before/after starvation
Result
Future Works
Mohammad Parhizkar
Centre Universitaire d’Informatique (CUI) University of Geneva, Switzerland
Email: mohammad.parhizkar@etu.unige.ch
Giovanna Di Marzo Serugendo
Centre Universitaire d’Informatique (CUI) University of Geneva, Switzerland
Email: giovanna.dimarzo@unige.ch
An Agent-Based Model for Collective Behaviors of Social Amoeba Dictyostelium discoideum Morphogenesis: Aggregation Phase
Cells are seeded in a 2D surface, initially populated uniformly at random within the domain. The simulation is updated at discrete time intervals, using the 6 different chemical factors concentration rules.
Our results show a series of behavior close to individual and collective behavior of living Dictyostelium discoideum.:
1. Dynamic center selection process and centers inhibition: at the beginning of the simulation, 10% of the population has the ability to become an autonomous center. According to the role of PSF, CMF and Adenosine only a few of them actually release autonomous pulses. At the end of the pre-aggregation phase we already observed approximate locations for potential centers. At later stages, based on CF and cAMP concentration, we observe regular cells turning into centers, thus splitting large aggregation territories into smaller ones.
2. Streams formation: without any consideration of other mechanisms, such as incorporating cell adhesion, cell death; we observed the movement of the cells in the stream manner towards the source of cAMP.
3. Homogeneous aggregation territories size: CF and cAMP combination helps the cells to locate the best aggregation field around them. Center formation was stated to be maximal at a cell density of 200 myxamebas per square millimeter and we observed at the end of simulations an homogeneous ratio of centers to cells of approximately 1 : 2100. In over-crowded populations the aggregation process runs fasters with more interesting results.
Conclusion
a.1 a.2 a.3 a.4 a.5
b.1 b.2 b.3 b.4 b.5
c.1 c.2 c.3 c.4 c.5
(a) (b)
(c) (d)
Publications
Comparison: Same aggregation territory size- three different Simulation class with 3000, 4000,7500 self-organized cells
Self-appearance of new centers- simulation start with 5,000 regular cells, 2 autonomous centers. The 3rd center has appeared at time step 5000.
• M. Parhizkar and G. D. M. Serugendo, 2015 IEEE 9th International Conference on Self-Adaptive and Self-Organizing Systems, Social Amoeba Dictyostelium Discoideum as an Inspiration for Swarm Robotics.
• M. Parhizkar and G. D. M. Serugendo, SWARM 2017: The 2nd International Symposium on Swarm Behavior and Bio-Inspired Robotics, An Agent-Based Model for Collective Behaviors of Social Amoeba Dictyostelium discoideum Morphogenesis: Aggregation Phase
• Modeling, simulating and validating the different phases of the D. discoideum
• Higher-order emergence
• Translating the models and mechanisms to the simulation of the swarms of robots
