The dataset presented is split into two sections: experimental and simulation.
In the experimental section you will find
a) webcam images used to determine the induction times associated with
each experiment, and
b) FT-IR spectra of the obtained crytals.
Each folder in ~/experimental/ may contain the data associated with one or two experiments as given in the folder names. Experiments that have been performed simultaneously have been combined into one folder.
a) Webcam Images
Webcam images are contained in
FT-IR spectra are contained in
There are 19 different experimental sets labelled a to s.
A readme file is included in folders that contain multiple experiments
to state which vials are associated with each experiment. The webcam
images from each side of the incubator are labelled A or B, and they
are found in folder labelled A or B.
In each side there are either 2 or 4 rows of 10 vials. The numerical labelling
of vials is from left to right, bottom to top. For example, in the
the image is from date 11 Jan 2019 and time 15:15:04,
and the vials are in the visual order:
A31 A32 A33 A34 A35 A36 A37 A38 A39 A40
A21 A22 A23 A24 A25 A26 A27 A28 A29 A30
A11 A12 A13 A14 A15 A16 A17 A18 A19 A20
A1 A2 A3 A4 A5 A6 A7 A8 A9 A10
The readme file connects the vial image to the experimental set.
For example in folder
we can see from the readme file that vials A1-A20 and B1-B20 are for
experimental set b, and vials A21-A40 and B21-B40 are for experimental
b) FT-IR spectra
FT-IR spectra for each vial that has crystallised is given as a text file labeled using the same system as above.
Each file contains two columns: Wavenumber (cm^-1), Absorbance.
IR spectra are not available for vials A7, A12-A14, A19, A22, B5-B6 in experiment a.
IR spectra are not available for experiment g.
The simulation section contains input files used to setup and run the
307 g/kg tridecane-solution interface molecular dynamics simulation. The other simulated systems can be easily reproduced with minor modifications to the files provided.
Files used for setting up the system are in
The system was set up in several steps:
1) generating a layer of tridecane
2) generating a box of glycine and a box of water and combining them
to get glycine aqueous solution
3) combining the glycine aqueous solution with the tridecane layer.
The files in.tridecane and data.tridecane in
will generate one layer of tridecane as data.oil_slab.
The files in.glycine and data.glycine in
will generate a box of glycine molecules.
The files in.spce/data.spce in
will generate a box of water molecules.
These boxes can be combined using in.solution in
The file in.interface in
will then combine the data files (data.solution, data.oil_slab)
produced in Step 2 to give the final oil-solution interface system.
The system is then minimised using in.minimise
The system is then run using the files in ~/simulation/1-run/
This folder contains the files for the equilibration and production run of the 307 g/kg oil-solution interface simulation.
in.equil and data.minimised_interface will run the equilibration step
in.npt and data.equil_interface will run 100 ns of npt production run.
The production run periodically generates new datafiles that can be used to continue the production beyond the 100 ns mark.