New Biomolecular Forcefields Paper Wins Molecular Physics Young Author Prize

An EMRP-funded paper on new biomolecular forcefields has won the Molecular Physics Young Author Prize for 2013. Given the particularly strong competition, 72 nominations across 23 different countries, the editors decided to award two Young Author prizes, one of which went to Andrew P Jones, University of Edinburgh for: Electronically coarse-grained molecular dynamics using quantum Drude oscillators

Andrew P Jones (University of Edinburgh), J Crain (University of Edinburgh and NPL), F S Cipeigan (University of Edinburgh), V P Sokhan (NPL), M Modani (IBM) and G J Martyna (University of Edinburgh and IBM).

Abstract:

• Standard molecular dynamics (MD) simulations generally make use of a basic description of intermolecular forces which consists of fixed, pairwise, atom-centred Coulomb, van der Waals and short-range repulsive terms. Important interactions such as many-body polarisation and many-body dispersion which are sensitive to changes in the environment are usually neglected, and their effects treated effectively within mean-field approximations to reproduce a single thermodynamic state point or physical environment. This leads to difficulties in modelling the complex interfaces of interest today where the behaviour may be quite different from the regime of parameterisation. Here, we describe the construction and properties of a Gaussian coarse-grained electronic structure, which naturally generates many-body polarisation and dispersion interactions. The electronic structure arises from a fully quantum mechanical treatment of a set of distributed quantum Drude oscillators (QDOs), harmonic atoms which interact with each other and other moieties via electrostatic (Coulomb) interactions; this coarse-grained approach is capable of describing many-body polarisation and dispersion but not short-range interactions which must be parametrised. We describe how on-the-fly forces due to this exchange-free Gaussian model may be generated with linear scale in the number of atoms in the system using an adiabatic path integral molecular dynamics for quantum Drude oscillators technique (APIMD-QDO). We demonstrate the applicability of the QDO approach to realistic systems via a study of the liquid-vapour interface of water.

The work was part funded by the EMRP project HLT10-BiOrigin - Metrology for Biomolecular Origin of Disease. The National Physical Laboratory (NPL) and the University of Edinburgh are partners in this project, which is led by the Physikalisch-Technische Bundesanstalt (PTB) and includeds: IBM; JRC, European Union and the University of Oxford.This project addresses the incompleteness and inconsistency in the details of links between the structure and activity of peptides and the lack of measurands, established reference methodologies and reference materials, particularly those based on peptide folding responses in native environments.

The European Metrology Research Programme (EMRP) funds collaborative research projects to meet Grand Challenges such as Health, Industry, Energy and the Environment, and to progress fundamental measurement science throughout Europe and the rest of the world.

Source: http://www.npl.co.uk/