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Real-Time Proxy-Control of Re-Parameterized Peripheral Signals using a Close-Loop Interface

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BMX: Biological modelling and interface exchange.

Bruce J Palmer¹, Ann S Almgren², Connah G M Johnson³

¹Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Washington, USA.

Scientific Reports

|July 28, 2023

Summary

This summary is machine-generated.

High performance computing accelerates biological system modeling. The new BMX software uses GPU acceleration for efficient, large-scale bacterial colony simulations, aiding research in industrial and clinical settings.

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Area of Science:

Computational Biology
Biophysics
Software Engineering

Background:

Biological systems, like bacterial colonies and biofilms, present complex modeling challenges due to numerous coupled subsystems.
Understanding cell colonies is crucial due to their economic and societal impacts in industrial bioreactors and clinical settings.
Current serial software struggles to handle the computational demands of realistic cell community models.

Purpose of the Study:

To introduce BMX, a novel software system designed for high-performance modeling of large cell communities.
To leverage GPU acceleration for efficient simulation of bacterial colony formation.
To demonstrate the capability of high-performance computing in modeling biological systems on realistic timescales.

Main Methods:

Development of BMX, a software system utilizing GPU acceleration for high-performance modeling.
Integration of BMX with the AMReX adaptive mesh refinement package.
Simulation of cell colony formation under varying nutrient availability using test scenarios.

Main Results:

BMX successfully models large cell communities, utilizing GPU acceleration for enhanced performance.
The software accurately reproduces observed bacterial colony behaviors in test scenarios with varying nutrient levels.
Simulations are completed on realistic timescales, showcasing the potential of high-performance computing for colony modeling.

Conclusions:

BMX provides an efficient and scalable solution for high-performance modeling of bacterial colonies.
The software demonstrates the practical application of GPU acceleration in computational biology.
BMX facilitates realistic simulations of cell communities, offering insights into their dynamics in industrial and clinical contexts.