Expanding the capabilities of the Molecular Simulation Design Framework (MoSDeF)

Supervisors: Clare M^cCabe and Peter T. Cummings (Heriot-Watt University)

The Molecular Simulation Design Framework (MoSDeF, mosdef.org) is an open-source, extensible Python-based software package designed to facilitate the hierarchical construction of both atomistic and coarse-grained system configurations, the application of classical force fields (i.e., atom-typing), encapsulation of chemical topology information, and the generation of input files for a variety of molecular dynamics and Monte Carlo simulation engines, including LAMMPS, GROMACS, HOOMD-Blue, Cassandra, and GOMC. The use of MoSDeF for developing and running molecular simulations enables the simulations to be reported in a reproducible way, which is becoming an increasingly important requirement for computational science. MoSDeF has many tools that serve the research community performing biological simulations, including methods for creating coarse-grained models of complex biomolecules and applying forcefields used in biosimulations.

This project involves developing new capabilities for MoSDeF inspired by the needs of biological simulations and integrating other open-source tools relevant to biosimulations. MoSDeF has an active worldwide developer community, so coordination with other developers is an important aspect of this project. Multi-developer software creation is done through the public repository GitHub. Students thus gain valuable experience in how to develop software using modern, industry-standard multi-developer tools.

Utilising MoSDeF and open-source simulation engines the student will:

-         develop new capabilities for performing biological simulations with the MoSDeF tool suite

-         examine ways to facilitate and perform multi-scale simulations that span the molecular to meso-scales with easy interoperability

-         perform molecular simulations to test the tools and examine biological systems of interest, with an emphasis on membranes

All applicants must have or expect to have a 1^st class BSc, MChem, MPhys, MEng, MSci or equivalent degree by 01/04/23 date in order to allow registration to start in May 2023. Selection will be based on academic excellence and research potential, and all short-listed applicants will be interviewed (in person or via Teams).

Closing Date: 31/1/23. All successful candidates must commence studies by 1/5/23

How to Apply

Apply Online

When applying through the Heriot-Watt on-line system please ensure you provide the following information:

(a) in ‘Study Option’

You will need to select ‘Edinburgh’ and ‘Postgraduate Research’. ‘Programme’ presents you with a drop-down menu. Choose Bio-engineering and Bio-sciences PhD for study option

(b) in ‘Research Project Information’

You will be provided with a free text box for details of your research project. Enter Title of the project for which you are applying and also enter the supervisor’s name.

This information will greatly assist us in tracking your application.

For questions about the application process, please contact pgr.eps@hw.ac.uk