ENBIOS-1D Lab

By Paolo Scarbolo1, Federico Pittino2, Matteo 2, Andrea Cossettini2, Luca Selmi2

1. DPIA, University of Udine 2. DPIA, University of Udine, Italy

A tool to simulate Electrolyte/Insulator/Semiconductor systems in one dimension

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Version 3.0 - published on 14 Apr 2017

doi:10.4231/D3Z02Z963 cite this

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    Modulus and phase of the EIS system admittance versus frequency Parameter Input and output panels for the EIS system DC potential profile without and with site-binding charges AC Ion concentration in Electrolyte at 1kHz and equilibrium DC Potential in 0.1 mM Electrolyte at 0.5V Cation, anion and net charge concentration Impact of Stern layer on system admittance

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Abstract

ENBIOS-1D Lab is a tool to illustrate and to study simple Electrolyte, Electrolyte/Insulator and /Electrolyte/Insulator/Semiconductor systems in one dimension. It is meant for use as a teaching tool in support of undergraduate or graduate courses on the basic physics of transduction in ion and particle sensors, and to assist early stage researchers getting familiar with some basic concepts in the field.

At the present stage, ENBIOS-1D Lab supports simulation and visualization of impedance/admittance spectra as well as DC and AC potential/ion distributions in simple one-dimensional Electrolyte (E), Electrolyte/Insulator (EI) and Electrolyte/Insulator/Semiconductor (EIS) systems. A 2D version of the tool (ENBIOS-2D Lab) is available on nanoHUB to simulate Ion Sensitive Field Effect Transistors (ISFET). A wider set of case studies may become available with future releases of the tool, possibly including interdigitated structures and nanoelectrode array devices; we appreciate your feedback on the most useful updates and case studies. 

The physical systems are modelled with the Poisson/Boltzmann (DC) and Poisson/Nernst/Planck - Poisson/Drift/Diffusion (AC small signal) equations. Dedicated models are implemented for the build up of site-binding charge at Electrolyte/Insulator interfaces and for the frequency and salinity dependence of the electrolyte electrical permittivity.

ENBIOS-1D Lab is powered by ENBIOS, (Electronic Nano-BIOsensor Simulator), a general purpose three-dimensional Control Volume Finite Element Method (CVFEM) simulator developed in-house at the University of Udine - Italy. ENBIOS simulates in three dimensions (3D) the DC and AC small signal impedance response to ions and micro/nanoparticles of three-dimensional devices made of semiconductor, insulator and electrolyte materials.

More details on ENBIOS can be found in the references below.

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ENBIOS-1D Lab is powered by ENBIOS, a general purpose full three-dimensional CVFEM simulator.

Bio

New in Version 3.0 of ENBIOS-1D Lab with respect to previous versions:

  1. Revised User Guide (this file) and Numerical examples file
  2. Option to add a thin dielectric layer to model the Stern layer between the insulator and the electrolyte (Compact Layer)
  3. Revised default options concerning the activation of DC and AC site-binding charge density
  4. Four pH-determining salts: HCl and HNO3 (strong acids), NaOH and KOH (strong bases)
  5. Space charge density plot in both the semiconductor and electrolyte regions
  6. Restyling of a few menus and bug fixes

 

New in Version 2.0 of ENBIOS-1D Lab with respect to previous versions:

0) This documentation (User Guide) and examples (Numerical examples)
1) New Electrode/Electrolyte/Electrode structure
2) AC small signal site binding charge added to the DC one for admittance simulations
3) Custom electrolyte option
4) Temperature dependent intrinsic concentration in semiconductors
5) Improved plotting algorithm to avoid the generation of spurious zeros in the AC response
6) User defined convergence threshold
7) Restyling of a few menus and bug fixes

Credits

Development team: Paolo Scarbolo, Federico Pittino, Matteo Dalla Longa, Andrea Cossettini, and Luca Selmi.

Sponsored by

European Commission FP7 NANOFUNCTION NoE, grant no. 257375

References

Federico Pittino and Luca Selmi, "Use and comparative assessment of the CVFEM method for Poisson–Boltzmann and Poisson–Nernst–Planck three dimensional simulations of impedimetric nano-biosensors operated in the DC and AC small signal regimes", Comput. Methods Appl. Mech. Engrg., v.278, (2014), pp.902–923.

C. Laborde, F. Pittino, H. A. Verhoeven, S. G. Lemay, L. Selmi, M. A. Jongsma, F. P. Widdershoven, “Real-time imaging of microparticles and living cells with CMOS nanocapacitor arrays”, Nature Nanotechnology, vol. 10, issue 9, Sept. 2015, pp. 791-795, DOI: 10.1038/NNANO.2015.163.

F. Pittino, F. Passerini, L. Selmi, F. Widdershoven, “Numerical simulation of the position and orientation effects on the impendance response of nanoelectrode array biosensors to DNA and PNA strands”, Microelectronics Journal, n. 45, Issue 12, pp. 1695-1700, December 2014.

 

Cite this work

Researchers should cite this work as follows:

  • Federico Pittino and Luca Selmi, "Use and comparative assessment of the CVFEM method for Poisson–Boltzmann and Poisson–Nernst–Planck three dimensional simulations of impedimetric nano-biosensors operated in the DC and AC small signal regimes", Comput. Methods Appl. Mech. Engrg., v.278, (2014), pp.902–923.

     

     

  • Paolo Scarbolo; Federico Pittino; Matteo; Andrea Cossettini; Luca Selmi (2017), "ENBIOS-1D Lab," http://nanohub.org/resources/biolab. (DOI: 10.4231/D3Z02Z963).

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