ADmoND: MathWorks Matlab Package for simulation of monolayer adsorption processes in nano devices

Published: 21-02-2019| Version 4 | DOI: 10.17632/r9yt6tjznj.4
Contributor:
Olga Jakšić

Description

ADmoNDv2 can be used as a MATLAB toolbox or a MATLAB application. Both versions allow for flexible investigations of adsorption-desorption processes in time domain and in frequency domain, whereby the process itself may be treated as a deterministic or a stochastic one. Some system parameters are stored in an Microsoft Office Excel file and some can be accessed or modified through dialogues. Graphical user interface (GUI) for ADmoND is based on MATLAB GUI for figure handling. Original task ribbon is extended with three new tabs: System, Evolutions and Equilibrium. System tab is equipped with buttons that activate dialogues for setting the environmental parameters like temperature, effective sensing (adsorbent) area and reaction chamber volume and composition of an adsorbate mixture. These dialogues are for communicating with Microsoft Office Excel file where parameters are stored. Button Visual aims to give stills and animations. It produces figures that show system of adsorbate species with different molecular projection areas (some calculations are coded for adsorbate particles that occupy more than 1 adsorption center). Evolutions tab is equipped with buttons that activate calculations of time evolutions of adsorbed particles on the surface for system defined by the use of System tab. One can choose calculations applicable to nonlinear model of adsorption based on nonlinear Riccati equations or calculations applicable to linear Lagergren pseudo first order kinetic model. Button Hold Toggle aims for keeping or discarding obtained diagrams which makes ADmoND a versatile tool which allows quick and convenient quantitative and qualitative analysis of various adsorption-based systems with ease. Equilibrium tab is equipped with buttons that activate calculations of equilibrium coverage and power spectral densities of stochastic variables in the system. Genuinely, the number of adsorbed particles on the surface is a stochastic variable, thus every other variable related to this number is also stochastic. In resonant micro structures fluctuations in number of adsorbate particles cause fluctuations in resonating frequency and in refractometric adsorption based sensors we have fluctuations in refractive index change caused by the same mechanism. Since these fluctuations are pressure or temperature dependent, buttons for 3D profiling of adsorption induced fluctuations are also added. Here also, one can use Hold Toggle button in order to change temperature for instance and then observe the impact of temperature rise on the position of knees and low frequency noise magnitudes in typical Lorentzian spectra in the same diagram. This is beta version, some functions may happen untested, but all are available upon request from olga@nanosys.ihtm.bg.ac.rs .

Files

Steps to reproduce

If you use ADmoND package as MATLAB toolbox, double click and run from Matlab editor or type ADmoNDv2 in command window. It is main function that generates figure with additional tabs with drop down menus. Using options in menus is intuitive, some parameters are imported interactively via dialogue boxes and some are imported from Microsoft Excel file gasovi.xls where gas parameters and constants are stored alongside with pressures and comments. In case of problems with graphics, one should check renderer and system preferences.