Probing the conformational space of biomolecules using large scale molecular dynamics simulation

Abstract

This thesis addresses the topic of peptide structure formation and the computational generation of plausible conformations for these systems. Although the value of this concept may appear self-evident, it has the potential to be applied in a wide range of contexts. Potential avenues for further development include applications in bio-materials, medication, and disease understanding. Given that minor alterations to proteins and peptides can result in markedly disparate chemical and biochemical behaviours, it is beneficial to utilise computational techniques to gain insight into specific behaviours. The selection of an appropriate computational method is often challenging, given the wide range of available options, which differ greatly in terms of accuracy and computational cost. In certain instances, it may not be feasible to sacrifice precision in order to calculate larger molecules. In this thesis, we propose a novel approach to the unification of precision and affordable computational cost.