University of Cambridge
Advisor: Prof. Jonathan Goodman

This repository contains the Ph.D. thesis of Mengman Wei, focused on the development of conformation searching algorithms. The thesis introduces Diamond Energy, a systematic conformation searching method designed to enhance our understanding of molecular structures by efficiently identifying low-energy conformations within a diamond lattice.

Diamond Energy is a Python program based on the assumption that the structures of local minima in molecular conformations resemble a diamond lattice. This innovative approach allows for systematic searching of conformations using integer arithmetic and simplified energy equations to enhance speed and accuracy.

• Systematic Conformational Searching: Capable of exhaustively and accurately performing conformational searches for acyclic alkanes.
• High Performance: Demonstrates significant speed in conformational searching, leveraging optimized computations.
• Extensibility: Initially developed for acyclic alkanes, the program has been extended to include six-membered rings and saccharides.

The scope of Diamond Energy has been broadened through an automatic pipeline that searches for suitable energy evaluation parameters for new atom types. This has facilitated its application to more complex molecular structures.

Utilizing the vast amount of data generated by Diamond Energy, a machine learning pipeline was developed to analyze the geometry distribution of the diamond lattice framework. This integration aids in refining and improving the conformational searching process.

@phdthesis{Wei2024DiamondEnergy,
  title={*Diamond Energy* – a systematic conformation searching method},
  author={Wei, Mengman},
  year={2024},
  school={University of Cambridge}
  doi={https://doi.org/10.17863/CAM.109200}
}