PhD Prep¶

Tuesday 22 March¶

So, I’m not currently enrolled and I’ve not received an offer yet as the graduate research office is inundated with paperwork atm, but I am going to start anyway as my commencement date was yesterday. I came in though and the only really did a few clerical things and taught for the afternoon (god it felt good to be back int he teaching labs ), but after a quick chat with Peter I think I know what I need to be doing…

Read Read Read¶

It’s such a mammoth task to think about I feel like a decent methodology would be to:

Start by reviewing my honours thesis
- Go over the IL notes that I put aside when my project pivoted
- Review some key papers that I identified in that work
Start exploring the field more broadly
- What are the papers that I didn’t get around to properly digesting?
- What are some larger reviews that I really need to have read?
- I have a big pile of papers in my “to read” list that I should probably down
To try and read more broadly as well to get a more diverse understanding of the field

I really need to find a good way to be able to keep track of notes though as this is going to explode in detail so much. Perhaps I need a structure on this website to deal with that

What I actually did:¶

Chatted, got into the groove of things and decided to switch from Mendeley to Zotero for organisational reasons

Comment from Katya:

“At the moment you need to focus on literature covering the prediction of kinetics from MD simulations or ab initio MD simulations.”

Wednesday 23 March¶

What I actually did:¶

Today I really just focused on the CHM3911 tutorial and prep. I did also set up a self hosted WebDav server on my little NUC in order to save myself $20 USD on the Zotero storage access, which was ultimately decided by experiencing how incredibly slow Zotero’s paper storage is. Simply put, I can’t justify spending that money to wait for minutes for a 3 MB paper to download.

Friday 1 April¶

Error

Well, It looks like the direction for my PhD has changed drastically after a chat with Katya, which means that I’m starting from scratch.

Meeting Notes¶

Lit review should be no more than 15 pages and the talk should be max 20 mins with a goal of 15 mins. These should focus on snippets of what is already out there in the field.

After much back and forth the new project is going to be something relating to better handling of solvation for UV-vis/Fluorescence spectroscopic predictions by utilising multilayered computational approaches
- Could potentially involve a mix of QM/QM/SE/MM or any combination of theories to better model the solvent effects.
- In contrast to the previous project, this will be far more focused on the application of pre-existing methodologies in new ways, as opposed to the creation of all new methods.

Potential search terms:
- Excited state calculations
- UV-Vis spectroscopic methods (QM, MD, etc.)
  - Predicting these in solvent (explicit, implicit, QM/MM)
- Chromophores/fluorophores
- Potential investigation; Green Fluorescent Protein (GFP)

Literature questions to ask?
- What stops people from predicting chromophores and fluoropohres of interest?
- What systems do they want to be able to predict? (avoid NDIs…)

Researchers of interest:
- Martin Head-Grodon
- Theresa Head-Gordon
- Benedetta Mennicci

Emails to send:
- Toby - seems like a potential co-supervisor, will know more about grand challenges in fluorescence and some ideal fluorophores to investigate
- Rico - to postpone the allocation of a panel
- Tanja - Seems like there may be an interesting side project here to generate a whole bunch of rate constants of radical polymerisation for machine learning purposes

The new project will likely be looking into something along the lines of multilayered (ONIOM-like) approaches to try and better account for solvent effects in excited state calculations, probably for better/more robust determination of fluorosence spectroscopy. This is going to take a lot of reading to get my head around...

Many papers have been found… now to read!