Dataset for "Interfacial Physics of Field-Effect Biosensors"
Dataset for "Interfacial Physics of Field-Effect Biosensors"
Supporting Data for:
Lowe, Benjamin (2016). Interfacial Physics of Field-Effect Biosensors. University of Southampton, Doctoral Thesis.
See attached README.txt for more details and acknowledgements.
The results of the thesis begin from Chapter 4 onwards and data is included for each Chapter as described below:
Chapter 4: Charging at the Silica-Water Interface.
In the folder "silica_water_DFT" are the results of the convergence study of DFT calculations can be found.
Supplementary Data for these DFT simulations of silica-water interactions can be found with the corresponding paper, or at doi:10.5258/SOTON/401050
Chapter 5: Kinetic Monte Carlo Model of Dynamic Surface Charging.
The folder "KMC": Contains input and output files for the Kinetic Monte Carlo simulations found in Chapter 5 of the thesis. Simulated using the Zacros version 1.01 software.
Chapter 6: Modelling the Net Charge of Proteins
The folder "modelling_net_charges" contains the pH titration results for TNF_alpha and Streptavidin calculated using MOE 2013.8 and PROPKA.
Chapter 7: Electrical Double Layer Dynamics at the Silica-Water Interface
Supplementary Data for these MD simulations of silica-water-biomolecules interactions can be found with the corresponding paper, or at doi:10.5258/SOTON/401018
Chapter 8: Quantitative Analysis of FET-Sensor Literature Data: From pH Sensing to Biosensing
The folder "streptavidin_meta_analysis" contains the summarised quantitative data used to plot the results. The plots were peformed using iPython and can be found in an iPython notebook file "streptavidin_notebook.ipynb"
"Surface Charge Calculations.ipynb" contains general calculations relating to estimating the surface charge density using the Poisson Boltzman equation (linearised vs non linearised). This was used to help choose the surface potential in the Gouy-Chapman-Stern model of Chapter 7.
The archive onetepconv.zip contains the OnetepConv software discussed in Chapter 4, and available online at: https://github.com/holyone2/onetepconv
University of Southampton
Lowe, Benjamin, Mark
69b560bf-d230-4b2a-b103-8e2b485c58a7
Green, Nicolas
d9b47269-c426-41fd-a41d-5f4579faa581
Skylaris, Chris-Kriton
8f593d13-3ace-4558-ba08-04e48211af61
Lowe, Benjamin, Mark
69b560bf-d230-4b2a-b103-8e2b485c58a7
Green, Nicolas
d9b47269-c426-41fd-a41d-5f4579faa581
Skylaris, Chris-Kriton
8f593d13-3ace-4558-ba08-04e48211af61
Lowe, Benjamin, Mark, Green, Nicolas and Skylaris, Chris-Kriton
(2018)
Dataset for "Interfacial Physics of Field-Effect Biosensors".
University of Southampton
doi:10.5258/SOTON/403915
[Dataset]
Abstract
Supporting Data for:
Lowe, Benjamin (2016). Interfacial Physics of Field-Effect Biosensors. University of Southampton, Doctoral Thesis.
See attached README.txt for more details and acknowledgements.
The results of the thesis begin from Chapter 4 onwards and data is included for each Chapter as described below:
Chapter 4: Charging at the Silica-Water Interface.
In the folder "silica_water_DFT" are the results of the convergence study of DFT calculations can be found.
Supplementary Data for these DFT simulations of silica-water interactions can be found with the corresponding paper, or at doi:10.5258/SOTON/401050
Chapter 5: Kinetic Monte Carlo Model of Dynamic Surface Charging.
The folder "KMC": Contains input and output files for the Kinetic Monte Carlo simulations found in Chapter 5 of the thesis. Simulated using the Zacros version 1.01 software.
Chapter 6: Modelling the Net Charge of Proteins
The folder "modelling_net_charges" contains the pH titration results for TNF_alpha and Streptavidin calculated using MOE 2013.8 and PROPKA.
Chapter 7: Electrical Double Layer Dynamics at the Silica-Water Interface
Supplementary Data for these MD simulations of silica-water-biomolecules interactions can be found with the corresponding paper, or at doi:10.5258/SOTON/401018
Chapter 8: Quantitative Analysis of FET-Sensor Literature Data: From pH Sensing to Biosensing
The folder "streptavidin_meta_analysis" contains the summarised quantitative data used to plot the results. The plots were peformed using iPython and can be found in an iPython notebook file "streptavidin_notebook.ipynb"
"Surface Charge Calculations.ipynb" contains general calculations relating to estimating the surface charge density using the Poisson Boltzman equation (linearised vs non linearised). This was used to help choose the surface potential in the Gouy-Chapman-Stern model of Chapter 7.
The archive onetepconv.zip contains the OnetepConv software discussed in Chapter 4, and available online at: https://github.com/holyone2/onetepconv
Archive
onetepconv.zip
- Software
Archive
Supplementary_Data.zip
- Dataset
More information
Published date: 2018
Organisations:
Electronics & Computer Science, Nanoelectronics and Nanotechnology, Computational Systems Chemistry
Identifiers
Local EPrints ID: 421382
URI: http://eprints.soton.ac.uk/id/eprint/421382
PURE UUID: a349884f-5221-4c0b-aaf9-34d1daca4043
Catalogue record
Date deposited: 06 Jun 2018 16:31
Last modified: 05 Nov 2023 02:41
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Contributors
Creator:
Benjamin, Mark Lowe
Creator:
Nicolas Green
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