The scientific area that our consortium operates covers the biological function of molecules and proteins, leading to enhanced and rationally designed drugs, new and optimised biological functional materials and to inform applications in healthcare and health technology. The tools we focus on and use in our subject domain are:
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Atomistic Molecular Dynamics Molecular Dynamics (MD) is a computational simulation technique that allows researchers to understand the atomic and molecular motion based on structural properties. The most common form of MD solves Newton's equations of motion at fixed time intervals where the forces acting on individual atoms are calculated via structural mechanics forcefields or interatomic potentials. This yields are trajectory where the atoms in the system are in constant motion which represents the dynamical evolution of the system. |
video contributed by Harris research group |
Multiscale Modelling
Multiscale Modelling refers to a simulation regime where a system is described using more than one model and often using different scales or different physics. This quite commonly done when looking at enzyme activity for example, where conformational changes are still very important but the chemical activity within the active site cannot be described by MD alone. Typically in this sort of application, researchers would describe the larger part of the system using Molecular Dynamics/Mechanics (MD/MM). Whilst the much smaller active site area would be described using Quantum Mechanics which would capture chemical bond breaking/formation, this hybrid approach is often known as QM/MM. There are other forms of multiscale simulation and the correct approach should always be chosen based on the research problem being studied.
Coarse-Grain and Mesoscale Modelling
Biology is packed full of extremely large molecular systems that are often difficult to simulate using atomistic methods directly due to the computational load becoming extremely burdensome. Researchers often use modelling methodologies such as Coarse-Graining where they will use basic physics used in MD software but change the structural mechanical forcefield to one specialised in treating larger structural motifs as beads rather than representing atoms. This allows researchers to study much large biological structures without significantly increasing the computational expense, a commonly found example within the field is the Martini forcefield.
Other approaches for modelling the dynamics of large biological structures is to change the physics entirely, instead of using Newtonian Mechanics other approaches make use of for example Continuum Dynamics, Brownian Dynamics or even Lattice-Boltzmann to name just a few of the possibilities.
Talk Slides
From Mona Sarter's talk - "Complementary approaches to obtaining thermodynamic parameters from protein ligand systems: challenges and opportunities and a case for neutrons" 11 September 2024
