Electromicrotransport V2107: Open-Source Toolbox For Paper-Based Electromigrative Separations

Paper-based electromigrative separations have recently gained relevance due to the rise of paper based microfluidic devices and their combination with electrophoretic methods, used for many different analytical applications [1]. A new version of the open source toolbox electroMicroTransport for the numerical solution of electromigrative separations is presented, now featuring support for porous substrates, like paper, nitrocellulose and other materials used in paper-based microfluidics. This new version is based on a novel mathematical model for these phenomena recently published by our group. Similar to its previous versions, the toolbox was implemented using OpenFOAM (R), meaning that it features native 3D problem handling, support for parallel computation, and a GNU GPL license. This new version of electroMicroTransport includes full support for electroosmotic flow and the novels mechanical and electrical dispersion effects. It is now integrated with a well-recognized electrolyte database with its own management utility, and also includes a renewed algorithm for computing and controlling the electric current drainage in arbitrary surfaces. Moreover, for the first time electroMicroTransport is available for installation as a Docker image, which means that it is able to correctly run on any operating system. Finally, new tutorial examples and a user manual are provided. This new version of electroMicroTransport will enable efficient and reliable numerical prototypes of paper-based electromigrative separations to boost the continuous growth of paper-based microfluidics.New version program summaryProgram Title: electroMicroTransportCPC Library link to program files:: https://doi.org/10.17632/9wpvypzj9y.2Developer's repository link: https://gitlab.com/santiagomarquezd/electromicrotransportLicensing provisions: GPLv3Programming language: C++, PythonJournal reference of previous version: Computer Physics Communications 237 (2019) 244-252Does the new version supersede the previous version?: YesReasons for the new version: This new version adds several new features, including support for porous substrates, new boundary conditions, a comprehensive electrolyte database, new tutorial cases, a streamlined installation process, and a Docker installation option.Summary of revisions:center dot Electrolyte database- electroMicroTransport now includes an electrolyte database based on the one bundled with Simul 6, itself built from the work of Prof. Hirokawa. [2,3]- The dabatabase includes the properties of 518 components by default.- Simulation cases can directly name database components for easy initialization of electrolyte properties.- A new electrolytes command-line utility provides access the default electrolyte database to search and query for component propertiesas well as to add, update and remove user-defined components.New algorithm for electric constant current- The new boundary condition called uniformCurrentDensity replaces the earlier uniform1DCurrentDensity boundary condition [4] which was valid only for 1D domains. With this new condition, it is possible to prescribe a value for constant electric current drained from an arbitrary 3D shaped electrode.- Drained current I is calculated as the sum of all of the individual currents flowing through every cell adjacent to the electrode surface.- When using a uniformCurrentDensity boundary condition, on each iteration, electroMicroTransport will provide the user with information on the applied electric current and current density values, the target current, and the effective applied electric potential at the electrode.Support for paper substrates- This new version of electroMicroTransport offers full support for paper-based electrophoretic devices with modified transport equations based on a recent model [5].- Users can provide different substrate properties such as porosity, tortuosity, Darcy permeability, bias conductivity, and electrokinetic potential.- Mechanical and electrophoretically driven dispersion terms require setting values for the coefficients and .- When the user cannot provide reliable values for these parameters, default values are used which match the physical characteristics of Whatman #1 paper.- A new body force term in the momentum equation for fluid flow was introduced in order to obtain a proper representation of EOF in porous substrates [6].New tutorial cases showcasing the new functionality- Paper-based zone electrophoresis experiments: paperBasedZE, paperBasedZE1, paperBasedZE2- Paper-based moving-boundary electrophoresis cases: paperBasedMBE1 (constant voltage), paperBasedMBE2 (constant current)- Paper-based free-flow isoelectric focusing case: paperBasedFFIEFAutomated test suite - The electroMicroTransport project now includes an automated test suite used by developers to validate the implementations. Test cases are written using the pytest framework.- Following best practices, the test suite is run automatically as part of the continuous integration/deployment (CI/CD) process.User manual - A user manual of electroMicroTransport is now available, which guides users through the installation and use of the software.- The manual also covers many details of the software that might be of interest to users.Streamlined installation process- This new version of electroMicroTransport drops the requirement of a user-writable OpenFOAM installation. This means that electroMicroTransport can now be set up to use a system-wide installation of OpenFOAM without any privileges.- To allow this, code that previously required modifications to base OpenFOAM has now been packaged into a standalone shared library.- This change will benefit users who get OpenFOAM from their system's package manager, as well as any users of shared computers where they might not be able to modify existing packages (e.g. computer clusters).- This improvement in the architecture of the program implies a significant reduction in compilation time and resources.Docker installation option - electroMicroTransport is now also available as a Docker image for use with the Docker software [7]. This image is based on an official Docker image of OpenFOAM and contains pre-built installation of electroMicroTransport. It does not require an existing OpenFOAM installation.- Official images of the toolbox can be obtained from the microfluidica/electromicrotransport repository on Docker Hub.- All Docker images are built and tested automatically during the CI/CD process. This ensures that Docker users always have access to an up-to-date, validated version of the toolbox.- Docker allows electroMicroTransport to be used on non-Linux systems that do not natively support OpenFOAM.Nature of problem: The electroMicroTransport toolbox is intended to offer a complete suite for performing numerical simulations of electromigrative transport, including electroosmotic flow in both open channels and porous substrates. In order to perform these simulations, three partial differential equations and two non-linear conservation equations are solved. The coupled solution of this set of equations provides the different concentration fields for all electrolyte components of the system, the pH and conductivity fields, the fluid flow velocity and pressure fields (associated to the solvent, usually water), and the electric potential field over the entire calculation domain at any simulation time. Numerical simulations provided by electroMicroTransport can improve design process of microfluidic electrophoretic devices and its operational parameters as well as to contribute in basic research on developing new separation strategies for emerging analytical applications.Solution method: As was previously mentioned, electroMicroTransport numerical solutions are based on the coupled solving of three partial differential equations and two non-linear conservation equations. The solution method for the partial (in both space and time) differential equations is the Finite Volume Method whose basic methods and functions are provided by the OpenFOAM(R) platform. The non-linear equations are solved by using ad hoc implemented NewtonRaphson methods in native C++ language. The different equations are solved sequentially employing weak coupling and temporal sub-looping strategies. These strategies are justified by the fact that the various phenomena (chemical, electrochemical, mechanical and electrical) have different characteristic times for their evolutions. This scheme has been validated and has demonstrated both robustness and computational efficiency.Additional comments including restrictions and unusual features: Except when using the Docker image, installing and running electroMicroTransport requires an active installation of OpenFOAM. Only official OpenFOAM(R) releases distributed by OpenCFD Ltd. are supported by electroMicroTransport. This version of electroMicroTransport has been tested with OpenFOAM versions 1912, 2006 and 2012.References[1] G. I. Salentijn, M. Grajewski, E. Verpoorte, Anal. Chem. 90 (23) (2018) 1381513825.[2] T. Hirokawa, M. Nishino, N. Aoki, Y. Kiso, Y. Sawamoto, T. Yagi, J.-I. Akiyama, J. Chromatogr. A 271 (2) (1983) D1D106.[3] B. Gas, P. Bravenec, Electrophoresis (2021).[4] S. Marquez Damian, F. Schaumburg, P.A. Kler, Comput. Phys. Commun. 237 (2019) 244252.[5] F. Schaumburg, P.A. Kler, C.L.A. Berli, Electrophoresis 41 (78) (2020) 598606.[6] N. Franck, F. Schaumburg, R. Urteaga, P.A. Kler, Electrophoresis 42 (78) (2021) 975982.[7] G.S. Gerlero, S.M. Damian, F. Schaumburg, N. Franck, P.A. Kler, Electrophoresis 42 (16) (2021) 15431551. (C) 2021 Elsevier B.V. All rights reserved.