Note: All files with extension .TRM are .TXT files and should be opened as such.

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Folder: AFM and SEM

This folder contains: 

> SEM images of the reference array (reflayer_SEM.tif), nitride-capped layer (nitride_SEM.tif), HSQ planarized layer (HSQ_SEM.tif), and the sensing layer (sensinglayer_SEM.tif). 

> AFM profile images of the reference array (reflayer_AFM.tif), nitride-capped layer (nitride_AFM.tif), HSQ planarized layer (HSQ_AFM.tif), and the sensing layer (sensinglayer_AFM.tif).

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Folder: biosensing

This folder contains 3 subfolders
	(1) Avidin_1ug-ml
	(2) Avidin_100ng-ml
	(3) Avidin_100ug-ml
	(4) Avidin_500ug-ml
	(5) BSA_100ug-ml
	
(1 - 5) contain the real-time transmission data of the device from the specific binding of surface-bound biotin to Avidin with concentrations of 1 ug/mL, 100 ng/mL, 100 ug/mL and 500 ug/mL, respectively. After 30 minutes, the surface was regenerated using 20mM NaOH. Measurements were taken every 3.5 seconds.

(5) contains the real-time transmission data of the device from the control experiment of non-specific binding of BSA to the surface. After 30 minutes, the surface was regenerated using 20mM NaOH. Measurements were taken every 3.5 seconds.

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Folder: contour_spectra

This folder contains the raw data of the transmission response of the sensor to  0% (0_sucrose.trm), 5% (5_sucrose.trm), 10% (10_sucrose.trm), 15% (15_sucrose.trm), 20% (20_sucrose.trm), and 50% (50_sucrose.trm) sucrose (w/w) solutions.


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Folder: ellipsometry

This folder contains the measured (n,k) values for the silicon nitride layer and a screenshot of the thickness read out from the ellipsometer.

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Folder: FDTD

This folder contains 3 subfolders:
	(1) full_device
	(2) SiN_thickness
	(3) vertical_distance

(1) contains the finite-difference time-domain (FDTD) simulated response of the full device. 

(2) contains the FDTD simulated response of various plasmonic nanostructure arrays to determine the minimum nitride thickness necessary to isolate the reference region. The .txt files contain the transmission response of each structure and the name of the files give the dimensions of the prism-shaped structures in length by width by height (nm). The .jpg files are the electric field at the wavelength of the resonance peak for the 100 nm x 100 nm x 50 nm simulated structure. The title of the .jpg files indicate the View (XY or XZ) and the slice in Z or Y, respectively.

(3) contains the FDTD simulated response of the 100 nm x 100 nm x 50 nm (L x W x H) nanostructure array to determine the minimum distance between the sensing and reference layer necessary to prevent coupling between the layers. The .txt file contains the transmission response of the simulations. The .jpg files are the electric field in XZ at the centre of the particles in Y at the wavelength of the resonance peaks (given by the numeric value after 'eField' in the filename as measured in nm) for the distance between structures (given by the numeric value after 'D-' in the filename as measured in nm).

The parameters of all the simulations are explained in the supplemental section.

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Folder: HSQ_thickness

This folder contains the results of the experiment to determine minimum HSQ thickness required to planarize the surface. 

The file names are in the following pattern:
	50x50x50_52HSQ
	(size of the nanoparticle)_(thickness of HSQ)


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Folder: sucrose_calibrations

This folder contains 3 subfolders:
	(1) sucrose_run1
	(2) sucrose_run2
	(3) sucrose_run3

(1) contains real-time measurements of the sensor as sucrose concentration is increased from 0% to 5%, 10%, 15%, 20%, and 50% (w/w) in water. Measurements were taken every 7.5 seconds.

(2) contains real-time measurements of the sensor as sucrose concentration is increased from 0% to 0.5%, 1%, 2.5%, 5%, 10%, 15%, and 20% (w/w) in water. Measurements were taken every 7.5 seconds.

(3) contains real-time measurements of the sensor as sucrose concentration is increased from 0% to 5%, 10%, 15%, and 20% (w/w) in water. Measurements were taken every 7.5 seconds. This experiment was run after the sucrose_run2 experiment. For the initial 13 minutes of data measurements, the solution surrounding the plasmonics had not returned to 0% (water).

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