Hydroxyapatite Surface Simulations for Free-Energy and Mechanical Analysis

A 2.2 GB dataset from 2026 contains equilibrated input structures and simulation scripts for hydroxyapatite (HAp) surfaces. It was created by Mahdi Tavakol at the University of Oxford. The data supports steered molecular dynamics, thermodynamic integration, and uniaxial deformation tests for surfaces at pH 5 and 7.

Use Cases

• Calculate free-energy profiles for surface interactions based on steered molecular dynamics (SMD) pulling scripts.
• Perform thermodynamic integration (TI) calculations using the provided λ-dependent coupling inputs.
• Analyze mechanical properties like stress-strain behavior based on uniaxial deformation test scripts.
• Study the effect of pH and surface orientation on biomaterial properties using equilibrated structures for (001) and (010) surfaces.

Strengths

• Includes simulation scripts for three distinct computational workflows: SMD, TI, and mechanical testing.
• Provides input structures equilibrated under multiple random seeds, which suggests statistical diversity.
• Covers two surface orientations ((001) and (010)) and two pH levels (5 and 7).

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment for certain analyses.
• The 2.2 GB size indicates a medium-scale dataset, which may require significant computational resources to process fully.

Provenance

Source

Mahdi Tavakol, Department of Engineering Science, University of Oxford

Collection Method

Generated via molecular dynamics simulations.

Freshness

Last updated 2026-05-27 07:50:52; freshness should be verified.