An agent-based model of molecular aggregation at the cell membrane

Abstract

Molecular clustering at the plasma membrane has long been identified as a key process and is associated with regulating signalling pathways across cell types. Recent advances in microscopy, in particular the rise of super-resolution, have allowed the experimental observation of nanoscale molecular clusters in the plasma membrane. However, modelling approaches capable of recapitulating these observations are in their infancy, partly because of the extremely complex array of biophysical factors which influence molecular distributions and dynamics in the plasma membrane. We propose here a highly abstracted approach: an agent-based model dedicated to the study of molecular aggregation at the plasma membrane. We show that when molecules are modelled as though they can act (diffuse) in a manner which is influenced by their molecular neighbourhood, many of the distributions observed in cells can be recapitulated, even though such sensing and response is not possible for real membrane molecules. As such, agent-based offers a unique platform which may lead to a new understanding of how molecular clustering in extremely complex molecular environments can be abstracted, simulated and interpreted using simple rules.Author summaryMolecular aggregation in cell membranes is a key component of cellular machinery, involved across cell types in inter-cellular communication and signalling pathway initiation. As such, understanding the underlying mechanisms and molecule cluster characteristics at a more theoretical level is a pre-requisite. Complete descriptive molecular models have proven impossible to realise due to the overall complexity of the processes involved, highlighting the need for novel approaches. While conceptual models have been shown to be powerful tools and are routinely used in other fields with high level of complexity such as social sciences or economics, they are overall lacking from the literature when it comes to cell studies. We suggest in this work that the same principle applies to cell biology and in particular, the study of molecular clustering. We propose here a general model, independent of cell types or signalling pathways: an agent-based model dedicated to molecular clustering in the plasma membrane. We show we are able to recapitulate molecular aggregation similar to observations in cells while new properties are highlighted by our model, for instance, clustering is a digitised process.

Agent-Based Modeling of T Cell Receptor Cooperativity

“…In recent years, agent-based models are extensively used in systems biology and immunology [ 30 , 31 ]. These models range from cellular and molecular aggregation [ 32 , 33 ], receptor–ligand interactions [ 34 , 35 , 36 ], signal transduction in bacteria [ 37 ], and cellular homeostasis in diseases such as multiple sclerosis [ 38 ] to immune responses against tumors [ 39 ]. However, there are no agent-based models studying T cell signaling and consequently TCR cooperativity, to the best of our knowledge.…”