Free Diffusion Simulation Analysis

Quickly obtain molecular migration speed in specific environments, analyze diffusion paths and energy barriers, and assist in predicting material properties and structural design

Migration Speed Diffusion Path Energy Barrier Calculation

Technical Overview

Free diffusion simulation is an important method for studying molecular movement behavior in unconstrained or specific environments. By tracking molecular movement trajectories, we can quantitatively analyze key parameters such as diffusion coefficients and migration rates. These data are of great significance for understanding material transport properties, optimizing separation processes, and designing new functional materials.

QuantA Molecule's free diffusion simulation service adopts advanced molecular dynamics methods combined with high-performance computing technology. It can efficiently simulate the diffusion behavior of various molecules under different temperature and pressure conditions, providing customers with accurate and reliable data analysis results.

Simulation Results Display

Molecular Structure and Adsorption Analysis

Molecular Structure and Adsorption Analysis

The figure above shows the adsorption behavior of molecules in Metal-Organic Framework (MOF) materials. By calculating the binding energy (Eads) at different adsorption sites, we can predict the main adsorption positions and strengths of molecules in the material. The binding energies of two different adsorption sites in the figure are -3.803 kcal·mol-1 and -6.807 kcal·mol-1, indicating that the red molecule has stronger binding ability at the right site.

These adsorption data are crucial for understanding the initial state and diffusion starting point of molecules in materials, directly affecting the calculation results of subsequent diffusion paths and energy barriers.

Diffusion Trajectory and MSD Analysis

Diffusion Trajectory and MSD Analysis

The right part of the figure shows the diffusion trajectory of molecules at different time points (0 ps, 4 ps, 8 ps, 12 ps), clearly presenting how molecules migrate through material channels. The left MSD (Mean Square Displacement) curve provides quantitative analysis, with the red curve representing ZIF-67 material loaded with Ir metal and the green curve representing pure ZIF-67 material.

It can be seen from the MSD curve that the molecular diffusion rate in Ir-loaded materials is significantly higher than that in pure materials, indicating that metal modification can effectively improve the transport properties of materials. The diffusion coefficient can be calculated through the slope of the MSD curve, providing important basis for material performance optimization.

Detailed Data Display

Diffusion Kinetics Analysis

Material Type Binding Energy (kcal·mol-1) Diffusion Coefficient (×10-8 cm2/s) Migration Rate Improvement
ZIF-67 (Pure Material) -3.803 2.4 Reference
Ir@ZIF-67 (Metal-Loaded) -6.807 3.8 +58.3%

Analysis Result Explanation

  • After loading Ir metal, the binding ability of the material to molecules is significantly enhanced, with the binding energy decreasing from -3.803 kcal·mol-1 to -6.807 kcal·mol-1
  • Despite the enhanced binding ability, the diffusion coefficient of molecules increases by 58.3%, indicating that metal sites can act as springboards for molecular transport, promoting molecular diffusion
  • The linear relationship of the MSD curve (R2>0.99) indicates that molecular diffusion behavior conforms to Fick's law, and the simulation results are reliable

Application Cases

Drug Molecule Diffusion in Cell Membranes

Through free diffusion simulation, we successfully predicted the path and energy barrier of drug molecules passing through cell membranes, providing an important basis for drug design. The simulation results show that drug molecules mainly diffuse through membrane protein channels rather than directly passing through the phospholipid bilayer.

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Water Molecule Diffusion in Proton Exchange Membranes

For fuel cell proton exchange membranes, we simulated the diffusion mechanism of water molecules under different humidity conditions. The study found that the formation of water channels is the key to improving proton conductivity, which provides new ideas for designing high-performance fuel cell membrane materials.

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Technical Parameters

Calculation Method

Classical Molecular Dynamics (MD) simulation, using COMPASS force field

Simulation Time

Up to 100 nanoseconds (ns) to ensure sufficient sampling

Output Data

Diffusion coefficient, MSD curve, radial distribution function (RDF), trajectory files, etc.

Environmental Conditions

Supports simulations under different temperature (273-473K) and pressure conditions

Related Technologies

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