# Rejection-free kinetic Monte Carlo simulation of multivalent biomolecular interactions

Source: [Rejection-free kinetic Monte Carlo simulation of multivalent biomolecular interactions](<https://www.sota2.com/research/paper/68fa5e9b1e209131ce9e3cc5>)

Collection index: [llms.txt](<https://www.sota2.com/research/llms.txt>)

Data updated: 2025-10-28T13:56:19.366Z

Authors: Jin Yang, William S. Hlavacek

Published: 2008-12-25T17:19:44.000Z

## Abstract

The system-level dynamics of multivalent biomolecular interactions can be simulated using a rule-based kinetic Monte Carlo method in which a rejection sampling strategy is used to generate reaction events. This method becomes inefficient when simulating aggregation processes with large biomolecular complexes. Here, we present a rejection-free method for determining the kinetics of multivalent biomolecular interactions, and we apply the method to simulate simple models for ligand-receptor interactions. Simulation results show that performance of the rejection-free method is equal to or better than that of the rejection method over wide parameter ranges, and the rejection-free method is more efficient for simulating systems in which aggregation is extensive. The rejection-free method reported here should be useful for simulating a variety of systems in which multisite molecular interactions yield large molecular aggregates.

## Recorded benchmark results

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## Original sources and implementation

[Original paper](<https://arxiv.org/abs/0812.4619>)

[PDF](<https://arxiv.org/pdf/0812.4619.pdf>)