EUROPE school and Erasmus Mundus Master 'Chemical Nanoengineering': Wrocław University of Science and Technology (Politechnika Wrocławska), Wrocłow, Poland

Local organizers Wroclaw University of Science and Technology (Politechnika Wrocławska):

  • prof. Bogdan Kuchta
  • dr Elżbieta (Ela) Zienkiewicz

Organizers and lectures:

  • Dr. David Dubbeldam
  • Prof. Randall Q. Snurr
  • Prof. Sofía Calero
  • Prof. Thijs J.H. Vlugt
Groupphoto School Wroclow 2019

About the school

The school focuses on a practical understanding of molecular simulations of fluids, ionic liquids, and nanoporous materials and applying the RASPA molecular simulation code to practical examples. The duration is 3.5 days, with lectures in the morning and exercises in the afternoon.

Students will learn the theoretical foundations of Molecular Dynamics and Monte Carlo with the aim of understanding the benefits and limitations of the algorithms, as well as the practical side of performing molecular simulations: setting up the system, constructing input files for molecules and frameworks, choosing and setting up a force field, understanding input settings, and analyzing the results. We will use our publicly available code RASPA for the workshop, but the gained knowledge and understanding are also directly applicable to other software.


Monday 1 July 2019

Day 1 TimeLecturerContent
AM Lectures
9.00-10.00Sofia CaleroIntroduction to the course, introduction to the field of molecular simulation. Introduction to simulations: classical simulations, periodic boundary conditions, force fields (electrostatics, VDW interactions, intramolecular interactions).
10.30-11.30Randall SnurrSimulation setup and measuring properties. Introduction to simulation research of nanoporous materials, description of frameworks (IZA, CoRE MOF), simple calculations of pore volume, surface area, blocking pockets.
11.30-12.30David DubbeldamOverview of the RASPA code, showing the manual, demo running RASPA, iRASPA for linux, demo of the linux live-usb environment.
PM Practical Hands-on Exercises
13.30-17.00David DubbeldamMonte Carlo of methane in a box.
Investigating framework structures.
Methane in LTA-type zeolite.
Energy distributions of methane and CO2 in LTA and MFI
Where is the CO2 located in LTA-type zeolite?
Ship cruise on the Odra river and the conference dinner
18.45meeting at the entrance of the Main Building
19.00-19.30ship cruise
20.00-20.30start of the conference dinner at the Marina restaurant

Tuesday 2 July 2019

Day 2 TimeLecturerContent
AM Lectures
9.00-10.00Randall SnurrMolecular dynamics (MD) simulation, solving Newton’s equations of motion, NVE and NVT (thermostats).
10.30-11.30Sofia CaleroNPT-MD and other ensembles, computing dynamic properties (e.g. diffusion), TST-methodology for rare-events.
11.30-12.30David DubbeldamVisualization (for RASPA with VTK), plotting (gnuplot, plotting output of RASPA), and custom input for RASPA.
PM Practical Hands-on Exercises
13.30-17.00David DubbeldamRadial distribution functions (RDF) in a fluid.
Self-diffusion in a fluid.
Self- and collective diffusion of methane in MFI.
Self- and collective diffusion of methane in LTA.
Transition State Theory (TST) for slow diffusion (methane in LTA).

Wednesday 3 July 2019

Day 3 TimeContent
AM Lectures
9.00-10.00Randall SnurrMonte Carlo (MC) simulation, NVT-MC, basic level, Markov chains.
10.30-11.30Thijs VlugtGibbs and grand-canonical MC, computing isotherms, mixtures, converting fugacity and pressure, IAST.
11.30-12.30Thijs VlugtAdvanced MC techniques, CBMC and CFCMC, use of biasing to enhanced sampling for “difficult systems”.
PM Practical Hands-on Exercises
13.30-17.00David DubbeldamGibbs simulation of Vapor-Liquid Equilibrium (VLE) of CO2.
Computing the helium void-fraction.
Computing adsorption isotherm of CO2 in LTA-type zeolite.
Computing adsorption isotherms of CO2 in LTA-type zeolite using advanced methods (CFCMC).
Advanced simulations of ionic liquids.

Thursday 4 July 2019

Day 4 TimeLecturerContent
AM Lectures
9.00-9.45David DubbeldamDemo iRASPA for macOS, GPU-accelerated visualization software for material scientists.
9.45-10.30Thijs VlugtReactive MC in fluids and use of expanded ensembles.
11.00-11.45Sofia CaleroForce field development.
11.45-12.30 Randall SnurrDiffusion in nanoporous materials.
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