Simulations for the Experimentalists and the Industrialists


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VENUE:Diamond Light Source. Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE
COST: The workshop is free to attend and meals (lunch and evening buffet) will be provided free of charge.
ACCOMMODATION: This is NOT provided with your registration. You are responsible for your own travel and accommodation costs!

Start Date: Tuesday, 6th November 2018
End Date: Wednesday, 7th November 2018

 

EVENT DETAILS

This new introductory modelling meeting is targeted both at industry and academia. The objectives of the course are to demonstrate software used by the CCP5 and CCPBioSim communities, emphasising how to proceed further in what can be a bewildering field to the non-specialist. The course will include overview lectures and some introductory practical sessions on the scope and application of modern simulation methods covering (i) ab initio methods for small molecules and periodic systems, (ii) modern Monte Carlo codes and methods, (iii) modern molecular dynamics simulations and long-timescale techniques, (iv) modern mesoscopic methods (DPD, Lattice -Boltzmann).  Most of the course will centre on the use of DL software (e.g. DL_MONTE, DL_POLY, DL_MESO) largely developed through CCP5.  Case studies will be discussed, tailored as far as possible to meet the needs of the audience.

The course will include both taught (training) modules and sessions to promote discussion between experimentalists and simulation experts. One of the most challenging aspect of modern simulation is the translation of an experimental problem into one that can be tacked by simulation and modelling. Thus, each participant will be given the option/ encouraged to present on their work for 5 minutes followed by 5 minutes of open floor discussion on how simulation can help or to bring a related poster. We anticipate this will, for example, promote more effective cross-disciplinary working with experimentalists at the large facilities such as ISIS or DIAMOND.        

 

COURSE CONTENT
Application of Molecular & Coarse Grain Dynamics
We intend to give an introduction to the basics of how the Molecular Dynamics method works and an overview of what defines and limits its area of its application.  A discussion on the particular strengths, algorithmic functionality and advantages of using DL_POLY will be carried out and demonstrations will complement it with real time code building and application to user cases.  Further discussions will include recommendation on using DL_Software suite with accompanying UI, analytics and visualisation software as tool chain of projects workflows.

Application of Mesoscale Dynamics
Introduction to mesoscale modelling techniques, particularly Dissipative Particle Dynamics (DPD) and the lattice Boltzmann equation (LBE) method. The lecture will cover the advantages of each method and how they can be applied for industrial problems, including basic parameter fitting to represent required phenomena, determination of mesophase structures and rheological behaviour.

Stochastic and beyond MD methods for material simulation
Introduction into the calculation of thermodynamic properties of materials using the Monte Carlo technique. The lecture will cover, amongst others, the calculation of adsorption isotherms and the study of solid solutions and disordered materials. In addition, the application of kinetic Monte for the calculation of diffusion in solid state materials will be discussed.

Electronic Structure Programmes and their use in molecular sciences
Introduction into how these programmes work, what inputs are required and what outputs may be expected. Some insight will be provided to gauge what role these programs have in an industrial environment.

Ab initio modelling of solid state materials
Density functional theory based approaches for simulation of the solid state. The lecture will cover minimisation, density of states, band structure and defect chemistry, with explicit comparison to experimental characterisation techniques. In addition, the ability to predict materials properties will be discussed.

Macromolecule/Biological/multiscale simulations (CCPBiosim)
Introduction to the calculation of properties of macromolecules such as proteins and enzymes using atomistic simulation techniques. The lectures will focus on classical and combined QM/MM methods for protein-ligand modelling, free energy calculations and enzymatic reaction mechanisms.
 

PROGRAM OF EVENTS
NB this is a preliminary program that may change slightly to accommodate the number and needs of the audience.

Day 1 (6 November)
 
10:00-11:00    Registration and coffee          
11.00-12.30    Introduction to Simulation (NLA)
12.30-13.30    Lunch     
13.30-14.15    Application of Molecular & Dissipative Dynamics (ITT)
14.15-15.00    Application of Mesoscale Dynamics (MAS)
15.00-15.45    Stochastic and beyond MD methods for material simulation (AB and/or JAP)
15.45-16.30    Case Studies/Demonstrations/Practical (All)
16.30-17.15    Open floor  (part 1) 5 minute presentations   
17.15-18.00    Open floor  (part 1) 5 minute presentations   
 
Poster session and buffet until 19.30
 
Day 2 (7 November)
 
09.00-09.45    Electronic Structure Programmes and their use in molecular sciences (AS)
09.45-10.30    Looking into molecular properties using Gaussian and GaussView (AS)
10.30-12.30    Open floor Discussion of possible collaborations  (part 2)     
12.30-13.30    Lunch     
13.30-14.15    Macromolecule/Biological/multiscale simulations (CCPBiosim)
14.15-15.00    Macromolecule/Biological/multiscale simulation (CCPBiosim)
15.00-16.00    Ab initio modelling of solid state materials (DS)
16.00-17.00    Ab initio modelling of solid state materials (practical) (DS)
 
Beverages and Biscuits available all the time.
 

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