Computed Three-Dimensional Atomic Force Microscopy Images of Biopolymers Using the Jarzynski Equality

Area of Science:

• Biophysics
• Materials Science
• Computational Biology

Background:

• Three-dimensional atomic force microscopy (3D-AFM) enables subnanometer resolution of solvent distributions at interfaces.
• 3D-AFM is being adapted for imaging complex biopolymer assemblies like chromosomes and proteins within cells.
• Resolving the three-dimensional structures of biopolymers is a key challenge in molecular biology.

Purpose of the Study:

• To develop a computational method for simulating 3D-AFM images of biopolymers.
• To investigate the capability of 3D-AFM in resolving biopolymer structures.
• To analyze the influence of scanning velocity on 3D-AFM imaging of biopolymers.

Main Methods:

• Development of a computational simulation method based on the Jarzynski equality.
• Simulation of 3D-AFM imaging for various biopolymer structures.
• Analysis of the relationship between vertical scanning velocity and image resolution.

Main Results:

• The computational method successfully simulated 3D-AFM images, resolving parts of the biopolymer fiber structure.
• Optimal vertical scanning velocities were identified for improved 3D-AFM imaging.
• The study clarified that 3D-AFM measures forces in nonequilibrium processes for slow polymer dynamics relative to probe scanning.

Conclusions:

• The developed computational method provides a valuable tool for predicting and interpreting 3D-AFM images of biopolymers.
• 3D-AFM holds significant potential for elucidating the three-dimensional structures of complex biopolymers.
• Understanding the dynamics and scanning parameters is crucial for accurate force measurements and structural determination using 3D-AFM.