# Application of a novel numerical simulation to biochemical reaction systems

## TL;DR

A new simulation method called NNS is introduced to model biochemical reactions more accurately and efficiently.

## Contribution

The novel NNS method provides a unified approach to simulate biochemical reactions using stoichiometric formulas.

## Key findings

- NNS simplifies modeling by treating all molecules equally in simulations.
- The method is effective for simulating diverse reactions like water ionization and gene systems.
- NNS is implemented in Python for scientific and engineering applications.

## Abstract

Recent advancements in omics and single-cell analysis highlight the necessity of numerical methods for managing the complexity of biological data. This paper introduces a simulation program for biochemical reaction systems based on the natural number simulation (NNS) method. This novel approach ensures the equitable treatment of all molecular entities, such as DNA, proteins, H2O, and hydrogen ions (H+), in biological systems. Central to NNS is its use of stoichiometric formulas, simplifying the modeling process and facilitating efficient and accurate simulations of diverse biochemical reactions. The advantage of this method is its ability to manage all molecules uniformly, ensuring a balanced representation in simulations. Detailed in Python, NNS is adept at simulating various reactions, ranging from water ionization to Michaelis–Menten kinetics and complex gene-based systems, making it an effective tool for scientific and engineering research.