Dynamic simulation of concentrated macromolecular solutions with screened long-range hydrodynamic interactions:...

Area of Science:

• Computational physics
• Polymer physics
• Biophysics

Background:

• Hydrodynamic interactions significantly influence macromolecular dynamics.
• Concentrated macromolecular solutions may exhibit hydrodynamic screening, similar to polymer solutions or flow in porous media.
• Accurate simulation of macromolecular dynamics is crucial for understanding cellular processes.

Purpose of the Study:

• To investigate the validity of the diagonal approximation for hydrodynamic screening in polydisperse suspensions.
• To evaluate the accuracy and efficiency of this approximation using preconditioned iterative methods.
• To enable large-scale, long-time simulations of concentrated macromolecular systems.

Main Methods:

• Employed Stokesian dynamics (SD) with a diagonal approximation for the far-field hydrodynamic matrix.
• Utilized newly designed preconditioned iterative methods for Brownian force computation and linear system solutions.
• Evaluated the approximation's accuracy in an intracellular-like suspension model.

Main Results:

• The diagonal approximation yields particle diffusivities close to the original Stokesian dynamics method.
• A trade-off exists: the approximation improves computational efficiency at the cost of underestimating intermolecular correlated motions.
• The developed methods facilitate large-scale and long-time simulations with approximated hydrodynamic interactions.

Conclusions:

• The diagonal approximation is a viable method for simulating concentrated macromolecular suspensions, offering significant computational speed-up.
• While it simplifies calculations, researchers must be aware of its limitations regarding correlated motions.
• This approach opens possibilities for more extensive simulations in biophysics and materials science.