Projects

Some of my projects are linked here, more can be found on Github

Molten is a WebUI for the REST API exposed by Salt. Molten aims to make the API features accessible and to provide an easily deployable alternative to the salt cli interface. No additional service besides salt-api is required.

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Here, I explain how a patched GROMACS allows running of interactive simulations by implementing the interactive molecular dynamics (IMD) protocol. IMD allows monitoring of running simulations from a VMD client. In addition, the user can interact with the simulation by pulling on atoms, residues or fragments with a mouse or force-feedback devices.

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Single molecule fluorescence resonance energy transfer (smFRET) experiments exploit the distance dependency of the measurable transfer efficiency between two dyes to determine distances on the nm scale. The transfer efficiency in addition depends on the instantaneous mutual orientation inaccesible to experiments. In molecular dynamics simulations, the mutual orientation of the dyes is accessible. Therefore, combining simulations with experiments results in more accurate distances as estimated from experiments alone.

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