# The many roads to the simulation of reaction systems

## TL;DR

This paper compares three algorithms for simulating reaction systems, demonstrating that optimized CPU-based simulations can match GPU performance for real-world biochemical models.

## Contribution

It introduces and evaluates multiple simulation algorithms for reaction systems, highlighting a CPU-based approach that rivals GPU-based methods in efficiency.

## Key findings

- Three different simulation algorithms were compared.
- Optimized CPU simulation can match GPU performance.
- The study provides practical tools for biochemical system modeling.

## Abstract

Reaction systems are a computational model inspired by the bio-chemical reactions that happen inside biological cells. They have been and currently are studied for their many nice theoretical properties. They are also a useful modeling tool for biochemical systems, but in order to be able to employ them effectively in the field the presence of efficient and widely available simulators is essential. Here we explore three different algorithms and implementations of the simulation, comparing them to the current state of the art. We also show that we can obtain performances comparable to GPU-based simulations on real-world systems by using a carefully tuned CPU-based simulator.