ChE-609(4) / 1 credit
Remark: Next time: January 2021
This course will have three components: Molecular Simulation, Electronic Laboratory Notebooks, and Machine learning. The focus of the course is applications to microporous materials (metal organic frameworks, zeolites, covalent organic frameworks) and is aimed at non-computational chemists.
General introduction to eln.epfl.ch The first seminar will focus on the "big picture"
- Store / retrieve original data
- Extract knowledge
- Publish information to Zenodo
1.2.2021: Add a new sample
- Biological sample, material sample.
- Chemical structure, stereochemistry, mixture of isomers.
- Natural or modified peptidic and nucleic sequences.
- Keywords and meta information.
Managing chemical libraries of synthesized products
- Find synthesized chemicals from former colleagues.
- How to create labels for new products (with chemical structure)?
- Define a location and status.
- Update the stock.
1.3.2021: Monoisotopic mass
- Determine possible molecular formula from monoisotopic mass
- Problem of ionization.
- Difference of mass and corresponding molecular formula.
- Pubchem lookup.
15.3.2021: Mass spectrometry of polymers
- Polymer, copolymer, âº and âµ end groups.
- Kendrick chart.
- Advanced reporting.
29.3.2021: Electronic laboratory notebook
- Calculation of quantities.
- Definition of shortcuts.
12.4.2021: Mass spectrometry of natural or non-natural peptides
- How to enter a sequence?
- Fragmentation and internal fragmentation.
- Create a report for publication.
26.4.2021: Image analysis
- Bit depth, mask, ROI, resolution
- Hull, MBR, Ferret min, Ferret max, Compactness
10.5.2021: XRD and PXRD (Kevin Jablonka)
- Find topology of a periodic net
- Predict PXRD patterns / change cell parameters
- Match to pattern in database using Deep Learning
- Look up PXRD patterns form database
23.5.2021: Multiple spectra analysis
- Superimpose hundreds of spectra in one click
- Integration, relative spectra
- Export data for kinetic analysis
7.6.2021: Machine learning on spectra
- Preprocessing and normalization of spectra
- Principal component Analysis (PCA)
- Uniform Manifold Approximation and Projection (UMAP)
21.6.2021: Data exportation
- Create reports
- Export to Zenodo
electronic laboratory notebooks
Basic thermodynamics and some basic knowledge on computational methods (e.g., Matlab or programming)
By the end of the course, the student must be able to:
- Apply and understand some of the computational methods discussed in the course
2021: marked on their contribution to the user guides and suggestions of improvements
In the programs
- Exam form: Project report (session free)
- Subject examined: Computational method in Chemistry and Chemical Engineering-Data in Chemistry and Electronic Lab Notebooks
- Lecture: 7 Hour(s)
- Project: 14 Hour(s)