BioMOCA Suite

By David Papke1, Reza Toghraee1, Umberto Ravaioli1, Ankit Raj1

1. University of Illinois at Urbana-Champaign

Simulates ion flow through a channel.

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Version 2.3.1b - published on 04 Jun 2015

doi:10.4231/D37659G65 cite this

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    4.0 out of 5 stars

    BioMOCA tool is a Monte Carlo simulation for ion transport through lipid membranes in electrolyte solutions.

    The tool consists of four programs: Map Generator, Lipid Wrapper, Boundary Force Generator and BioMOCA simulation.

    Map Generator: In the first program, the tool allows its users to set a spatial grid size and boundaries of the simulation domain. If desired, one can also upload a pre-designed simulation domain file. The grid is a uniform triangular grid.

    Lipid Wrapper: The second program, Lipid Wrapper allows the user to set the lipid layer thickness and the pore through this membrane, based on the domain generated by the Map Generator tool. The settings are lumen lipid edge location, cellular lipid edge location and lipid radius. The lipid radius determines the pore size and the other two locations determine where the lipid layer starts and where it ends.

    Boundary Force Simualtor: The third program is the Boundary Force Simulator. In this program one can set the dielectric constant of the protein, the lipid and the channel. The dielectric constant of the channel is set to be equal to the water. It visualizes the potential across the membrane in a graphical interface along with the option to see the plotted data points.

    BioMOCA Simulation: The fourth program is the BioMOCA simulation where one can set the membrane potential, the electrolyte concentrations cis and trans section of the layer and simulate charge transport. At the end of this simulation one can see how many ions crossed the lipid boundary, allowing to find the current through the pore through the lipid.

    This program is a very nice basis for simulating a lot of interesting phenomena in electrolyte solutions. These kind of simulations can shine light on the unknown characteristics of many of the occurrences that the researchers face in biological and synthetic nanopore projects. I believe this is just a very simplified version of the capabilities of the BioMOCA simulator which can explain very complicated and interesting charge transport mechanisms through this system.

    This simulation can be greatly expanded by the addition of electrolyte semiconductor surfaces which are of great interest, such as nanowires, synthetic nanopores and other solid state based biosensors.

    Sukru Yemenicioglu (UIUC)

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