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Systematic Analysis of In Vitro Cell Rolling Using a Multi-well Plate Microfluidic System

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Pressure control using stochastic cell rescaling.

Mattia Bernetti¹, Giovanni Bussi¹

¹Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea 265, Trieste 34136, Italy.

The Journal of Chemical Physics

|September 23, 2020

Summary

This summary is machine-generated.

We introduce stochastic cell rescaling, a new first-order barostat for molecular dynamics simulations. This method accurately samples volume fluctuations at constant pressure, improving simulation reliability.

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Area of Science:

Computational chemistry
Biophysics
Materials science

Background:

Molecular dynamics (MD) simulations require barostats for constant pressure simulations.
Traditional methods use Berendsen barostats for equilibration, but they yield inaccurate volume fluctuations.
Production runs often necessitate switching to more complex barostats like Parrinello-Rahman or Monte Carlo.

Purpose of the Study:

To develop a novel first-order barostat for MD simulations.
To address the issue of incorrect volume fluctuations in existing first-order barostats.
To provide a single barostat algorithm suitable for both equilibration and production phases.

Main Methods:

Introduction of stochastic cell rescaling, a first-order barostat.
Inclusion of a noise term to ensure correct volume fluctuation sampling.
Anisotropic variant tested on membrane simulations.

Main Results:

Stochastic cell rescaling accurately samples volume fluctuations, consistent with the isobaric ensemble.
The anisotropic variant performs well in membrane simulations.
The algorithm is easily integrated into existing simulation software.

Conclusions:

Stochastic cell rescaling offers an accurate and efficient alternative to traditional barostat methods.
This new barostat can be effectively used throughout the entire simulation process, from equilibration to production.
Its straightforward implementation facilitates wider adoption in molecular dynamics research.