Particle-based simulation of non-elementary bimolecular kinetics.

Area of Science:

• Biochemistry
• Computational Biology
• Chemical Kinetics

Background:

• Particle-based simulations are crucial for biochemical systems, bridging scales between molecular dynamics and reaction-diffusion models.
• Current methods are limited to elementary (mass-action) kinetics, restricting the simulation of complex biological processes.

Purpose of the Study:

• To develop a novel framework for directly simulating non-elementary bimolecular kinetics in particle-based simulations.
• To adapt non-elementary reaction conditions, typically for trimolecular interactions, to biomolecular reactions.

Main Methods:

• Implemented a novel approach using a third implicit reactant to mimic non-elementary kinetics.
• Utilized an event-driven simulation framework.
• Validated the method by reproducing Michaelis-Menten kinetics and simulating the Goldbeter circadian rhythm model.

Main Results:

• Successfully simulated non-elementary bimolecular kinetics without explicitly modeling underlying fast elementary reactions.
• Accurately reproduced Michaelis-Menten kinetics and the Goldbeter model dynamics.
• Significantly reduced computational cost compared to simulating all elementary steps.

Conclusions:

• The developed framework expands the scope of reaction networks accessible to particle-based simulations.
• Offers a practical and computationally efficient alternative for simulating systems with non-elementary kinetics where quasi-steady-state approximations apply.