Sustainable research software engineering practices for fluctuating finite element analysis

Research software is often developed with a focus on the output over the software's quality, and made by researchers untrained in formal software development techniques. Conditions such as these lead to an unsustainable environment of rapid software decay, and the wasteful re-invention of software for similar research purposes. The field of research software engineering (RSE) was coined to focus on the development and maintenance of sustainable research software.
Fluctuating Finite Element Analysis (FFEA) is a numerical method and software suite that uses continuum mechanics to simulate mesoscopic biomolecules. As research software, FFEA is subject to the same conditions which threaten software decay. This research applies sustainable RSE principles to FFEA to analyse and mitigate for this threat.
FFEA is evaluated to determine the major bottlenecks in the workflow impairing the software's sustainability. Results show these issues stem from the difficulty and time cost of setting up FFEA experiments, especially due to the current meshing algorithm producing unstable outputs that disrupt setup and frequently terminate FFEA simulations due to physics errors.
Two solutions are developed to attempt to solve these problems. The first extends the features of a new meshing algorithm started by Gravett (2022) which divides voxel representations of molecules into tetrahedra to create a consistent, stable geometry. This research adds new features to the meshing algorithm, and compares it to the previous meshing algorithm to show that it produces meshes more reliably with fewer steps in the process.
The second solution works towards automatic generation of FFEA KOBRA models for rod-shaped biomolecules through using machine learning algorithms to predict the presence of rod structures. Machine learning algorithms were able to categorise isosurface meshes of biomolecules through analysing the curvatures across the surface. This proved the concept and highlights necessary steps required to achieve full automation.