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Simul 6.1

...the generation of the Simul software


#simulator #electrophoresis #electromigration

About Simul

Simul is a series of simulation software for electrophoresis which has been continuously developing.

It simulates the movement of ions in liquid solutions in an electric field. It solves numerically a set of nonlinear partial differential equations and nonlinear algebraic equations describing the continuity of ionic movement and acid-base equilibria.

Simul 6.1 is a continuation of the previous version 5. Its code was rewritten using the Qt toolkit so it has become cross-platform software. The computation engine has been completely redesigned in order to take full advantage of parallelization and multithreading computation. It is 5 – 15 times faster than Simul 5.

Simul 6.1 is described in more details in a paper in ELECTROPHORESIS.

The typical use of Simul 6.1:

  • to simulate experimental runs and optimize separation conditions (buffers, injection),
  • to inspect or explain unusual phenomena observed in experiments: system peaks (zones), overshoots, peak distortion,
  • to inspect stacking and preconcentrating analytes, electromigration dispersion,
  • to show beginners how electrophoresis works.

Features of Simul 6.1:

  • A mathematical model of electromigration which accounts for any number of multivalent electrolytes or ampholytes, even in the hundreds.
  • Simul 6.1 includes a database of electrophoretic mobilities and pKa constants based on Takeshi Hirokawa's tables with the data of many ions.

Download

No installer needed. The program itself is packed in the file Simul61Run.zip. After downloading and unpacking it, you can copy the directory Simul61Run to the desired folder on your hard drive. The package contains the application itself, sample data and the user manual. Double click simul6.exe to run it.


Download the AppImage file. The downloaded file is not executable by default, so the executable flag must be set manually. Open the command line console (for example Xterm, Terminal or Console) and find your downloaded file. Then, write on the command line:
chmod +x Simul6-6.1.4-x86_64.AppImage
After that the file can be run by clicking on it in a file manager. These are sample data as examples of configurations.


Installation instructions: After downloading, open the Simul 6.dmg file and drag-and-drop Simul 6 to the Applications folder. Depending on your Gatekeeper configuration, on the first launch of Simul 6 you may need to open the Applications folder with the Finder, so right-click on Simul 6 and choose Open from the context menu. The Simul 6.dmg package also contains sample data and a copy of the user manual. macOS 11 or later is required.


The user manual is also included in the Simul 6 packages

A word from the authors

Bohuslav Gaš: A really fast engine optimized for a multithreaded environment. And, well, it runs like lightning!

Petr Bravenec: It’s fun to hear the fans switching on for the processor!

Pablo A. Kler: A lot of effort was put into making the new engine extra efficient. And it shows!

Gabriel Gerlero: Simul is now open-source and cross-platform. From an overpowered Linux workstation to a MacBook, it runs the same everywhere!