Dr. Silvia Chiacchiera
Host beneficiary: Science and Technology Facilities Council, UK
Industrial partner: Unilever, UK
This project concerns the derivation of a realistic model of water to be used in Dissipative Particle Dynamics (DPD) simulations. These are mesoscale particle-based fluid simulations that are suited to describe fluids containing solutes. This approach is intermediate between microscopic molecular dynamics and macroscopic continuum fluid dynamics and is commonly used in some industrial sectors.
A realistic water model must capture, among others, its charge polarizability: this is important to improve the description of electrostatics close to interfaces (relevant, for example, for biomolecular processes and for solutions involving surfactants, as detergents).
A typical system we have in mind is a mixture of water and oil (two fluids with very different dielectric properties) containing ions and (possibly charged) polymers.
This project involves a collaboration between computational scientists (STFC Daresbury), academe (University of Manchester), and industry (Unilever).
The base code for the set of modules listed below is DL_MESO_DPD, the Dissipative Particle Dynamics code from the mesoscopic simulation package DL_MESO, developed by Dr. M. Seaton at Daresbury Laboratory. This open source code is available from STFC under both academic (free) and commercial (paid) licenses.
List of Tasks
1) Developing a realistic water model suitable DPD. The model should have few charges (numerically favorable), and be well described by liquid theory approximations (allows comparisons and faster parameter adjustments). The model should capture: dielectric properties, hydrogen bonding, and hydrophobicity.
2) Developing related utilities for the DL_MESO_DPD code.
List of Modules
Most of the modules produced in the context of this project are related to charge dipole moments properties. The remaining ones are general tools for DL_MESO_DPD (e.g., formatting trajectories, consistency check of input files). The modules apply to DL_MESO second to last released version (2.6, dating November 2015). Variants to be used with its last released version, version 2.7 (released December 2018), will be provided soon.
Description: Analysis of charge dipole moments in DL_MESO_DPD. In the case of a single molecular species, it also computes the Kirkwood number and the relative electric permittivity for this species, together with an estimate for their errors.
Description: Autocorrelation functions of charge dipole moments in DL_MESO_DPD.
Description: Autocorrelation functions of individual charge dipole moments in DL_MESO_DPD.
Description: Formatting the trajectory (HISTORY) files of DL_MESO_DPD. It converts the HISTORY files from unformatted to a human readable form, (optionally) including explicative comments about all the quantities.
Description: Pre-processing utility for DL_MESO_DPD. It checks that the content of the optional configuration (CONFIG) file is consistent with that of the necessary input files (CONTROL and FIELD).
Description: Analysis of local tetrahedral ordering (a feature that is relevant, for example, in water-like system) in DL_MESO_DPD.
Description: This module proposes to use the SIONlib library to write/read the trajectory (HISTORY) files in DL_MESO_DPD.
A manuscript on polarizable fluid models for DPD is in preparation.
E-CAM related work labeled as “Excellent Science” by the EC Innovation Radar Initiative
9 software modules recently delivered in the area of Meso and Multi-scale Modelling
E-CAM Case Study: Mesoscale models for polarisable solvents: application to oil-water interfaces
Improving I/O of DL_MESO_DPD files using SIONlib
New E-CAM modules based on DL_MESO_DPD
Analysis of charge dipole moments in DL_MESO_DPD