Project 1: Kinetics of thermal decomposition of lithium formate and lithium acetate clusters.


Questions to answer:


  • How do the rate constants compare from 12-mer to 13mer (same T)?
  • What range of data gives good statistics (short times for parent, longer times for fragment)?
  • Do temperature-dependent k values show expected behavior?
  • Can you determine Ea for each parent? For each major daughter (n=10 for 12; n=11 for 13)?


Project 2: Thermal decomposition molecular dynamics simulations of doubly charged clusters of lithium acetate: Asymmetric fission


Primary experimental reference: doi:10.1002/rcm.7597

Questions to answer:



  • What temperature best corresponds to the experimental normalized collision energy (NCE)?
  • What splitting patterns are observed from each doubly-charged cluster?
  • What is the Rayleigh assumption? When is it valid? Should it be valid for these clusters?

Project 3: Parameterize oxalate for use in TDMD simulations.



  1. Use ChemSpider to grab a structure of oxalate in mol format
  2. Use Openbabel to convert this to mol2 format (see OpenBabel documentation)
  3. Use ParamChem to create a topology/stream file. Change the generic residue name to "OXT" in the file.
  4. Use vmd/psfgen w/ top_all36_cgenff.rtf and file from 3) to create a PSF (see for example this tutorial, pages 6-8)
  5. Test this with a single TDMD simulation to see what happens