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

Supervisors: Clare McCabe 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 and materials simulations, including methods for creating coarse-grained models of complex biomolecules and applying forcefields. 

This project involves developing new capabilities for MoSDeF inspired by the needs of biological and materials simulations and integrating with other relevant open-source tools. 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.

A typical MoSDeF project in our group involves resolving an outstanding scientific/engineering problem while developing the new capabilities for MoSDeF needed in the research. Thus, the student will:

-        develop new capabilities for performing biological and materials 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 and materials systems of interest

All applicants must have or expect to have a 1st class BSc, MChem, MPhys, MEng, MSci or equivalent degree by 01/01/25 date in order to allow registration to start in Jan 2024. 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: 30/11/24. All successful candidates must commence studies by 1/5/25

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. Please also provide a summary of why you want to apply for and are suited for the position.

This information will greatly assist us in tracking your application.

For questions about the application process, please contact [Email Address Removed]