Abstract
Agent-based modelling and simulation have been effectively applied to the study of complex biological systems, especially when composed of many interacting entities. Representing biomolecules as autonomous agents allows this approach to bring out the global behaviour of biochemical processes as resulting from local molecular interactions. In this paper, we leverage the capabilities of the agent paradigm to construct an in silico replica of the glycolytic pathway; the aim is to detect the role that long-range electrodynamic forces might have on the rate of glucose oxidation. Experimental evidences have shown that random encounters and short-range potentials might not be sufficient to explain the high efficiency of biochemical reactions in living cells. However, while the latest in vitro studies are limited by present-day technology, agent-based simulations provide an in silico support to the outcomes hitherto obtained and shed light on behaviours not yet well understood. Our results grasp properties hard to uncover through other computational methods, such as the effect of electromagnetic potentials on glycolytic oscillations.
Highlights
Agent-based modelling and simulation have been effectively applied to the study of complex biological systems, especially when composed of many interacting entities
We identified in the “Smallbone2013 - Iteration 18”16 a model suitable to serve as a source for the agent-based model (ABM), since it contains a complete set of experimental data on the isoenzymes involved in a well-studied metabolic process, the glycolysis of Saccharomyces cerevisiae
The outcomes of the agent-based simulations detailed above suggest that the two systems reproducing an offresonance situation, where molecular interactions rely only on van der Waals-like potentials or, at least, on electromagnetic forces shorter than the Debye length, are not able to oxidise glucose at a high rate
Summary
Agent-based modelling and simulation have been effectively applied to the study of complex biological systems, especially when composed of many interacting entities. Numerical studies proved that the overall interaction potential U(r) between cognate partners (with r being the intermolecular distance) is generally composed of a short-range term (1 /r6 ) and a resonant long-range term (1 /r3 ), meaning that, when the dipole moments of two molecules oscillate at the same frequency, an attractive resonant potential U(r) ∼ r−3 should be added to the random Brownian force[7]. These phenomena have been lately analysed, theoretically and experimentally, in the interactions among lysozyme molecules and oppositely charged dyes[8]. We construct an agent-based model (ABM) of a well-studied process, the glycolysis of yeasts, to simulate the effect of the long-distance electrodynamic
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