In this part of the course, you will be able to set up a model of the system of your choice. I will provide input files to create and set up systems used in my publications and work:
- Amino acids and layered double hydroxides – the study of the prebiotic formation of protobiomolecules.
- Erastova V, Degiacomi MT, Fraser D, Greenwell HC. Mineral surface chemistry control for origin of prebiotic peptides. Nature communications. 2017 Dec 11;8(1):2033.
- Grégoire B, Erastova V, Geatches DL, Clark SJ, Greenwell HC, Fraser DG. Insights into the behaviour of biomolecules on the early Earth: The concentration of aspartate by layered double hydroxide minerals. Geochimica et Cosmochimica Acta. 2016 Mar 1;176:239-58.
- Crude oil components and silicate clays – the study of the effect of soils for the enhanced oil recovery (Big thanks to Tom Underwood who originally set up and validated all the systems).
- Underwood T, Erastova V, Cubillas P, Greenwell HC. Molecular dynamic simulations of montmorillonite–organic interactions under varying salinity: an insight into enhanced oil recovery. The Journal of Physical Chemistry C. 2015 Mar 18;119(13):7282-94.
- Underwood T, Erastova V, Greenwell HC. Wetting effects and molecular adsorption at hydrated kaolinite clay mineral surfaces. The Journal of Physical Chemistry C. 2016 May 19;120(21):11433-49.
- Underwood T, Erastova V, Greenwell HC. Ion Adsorption at Clay-Mineral Surfaces: The Hofmeister Series for Hydrated Smectite Minerals. Clays and Clay Minerals. 2016 Aug 1;64(4):472-87.
- Tian S, Erastova V, Lu S, Greenwell HC, Underwood T, Xue H, Zeng F, Chen G, Wu C, Zhao R. Understanding model crude oil component interactions on kaolinite silicate and aluminol surfaces: towards improved understanding of shale oil recovery. Energy & Fuels. 2017 Dec 18.
- Graphene sheet and crude oil – the study of the effect of asphaltenes deposition on enchanced oil recovery (Big thanks to Shansi Thian for providing the inputs and guidelines).
- Zwitterionic glyphosate molecules and silicate clays – the study of the interactions of herbicides and soils.
- Dynamics withing diamantane crystal – the study of the relation between SS-NMR and MD for the understanding of dynamics in solids.
This practical will span over two sessions: in the first session we will construct the system and submit it to run on the HPC. Calculations can run until the following session. This will provide enough time to complete simulation and analyze data. We will spend the second session finishing analysis, plotting data and discussing results.
NOTE: Since some of the work has not been published yet, set up for systems are available only ON REQUEST.
If you are using these tutorials and our methodologies for setting up research-associated work please cite our relevant papers (above).