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Related Experiment Video

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An Analog Macroscopic Technique for Studying Molecular Hydrodynamic Processes in Dense Gases and Liquids

An Analog Macroscopic Technique for Studying Molecular Hydrodynamic Processes in Dense Gases and Liquids

Published on: December 4, 2017

Recent advances in macromolecular hydrodynamic modeling.

Sergio R Aragon¹

¹Department of Chemistry and Biochemistry, San Francisco State University, 1600 Holloway Avenue, San Francisco 94132, USA. aragons@sfsu.edu

Methods (San Diego, Calif.)

|November 16, 2010

Summary

The boundary element method (BEM) accurately models hydrodynamic properties of molecules. Incorporating molecular dynamics (MD) and validated force fields improves accuracy for proteins and nucleic acids, especially flexible ones.

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Area of Science:

Computational hydrodynamics
Biophysics
Molecular modeling

Background:

The boundary element method (BEM) offers high precision for solving Stokes equations in hydrodynamics.
Accurate modeling of molecular surfaces and solvation is crucial for macromolecular computations.
Discrepancies in hydrodynamic properties of some multimeric proteins require further investigation.

Purpose of the Study:

To review and demonstrate the accuracy of the BEM program BEST for hydrodynamic computations.
To investigate discrepancies in multimeric protein hydrodynamics using Molecular Dynamics (MD) simulations.
To validate protein force fields and MD methods for predicting solution structures and transport properties.

Main Methods:

Review of BEM computations for smooth objects (ellipsoids, cylinders) using the BEST program.
Application of a 1.1Å hydration layer model for protein hydrodynamic computations.
Integration of MD simulations (implicit and explicit water) with validated force fields (ff03, ff99SB) for proteins and nucleic acids.

Main Results:

BEM with BEST achieves high precision for smooth objects and proteins with a 1.1Å hydration layer.
MD simulations and validated force fields accurately predict transport properties and solution structures for proteins (e.g., Trastuzumab) and nucleic acids.
Non-uniform hydration models improve accuracy for DNA oligomers, aligning with X-ray diffraction data.

Conclusions:

The BEM program BEST provides accurate hydrodynamic predictions for various molecules.
MD simulations with validated force fields are reliable for studying solution structures and dynamics of proteins and nucleic acids.
Future improvements to BEST will focus on reducing memory requirements and increasing computational speed.