Rotation projects category listing 1 | Beckstein Lab

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Project: Transport of divalent cations

Project: Transport of divalent cations

Divalent cations such as zinc or magnesium are essential for living organisms but the mechanisms by which they are transported into and out of the cell are not well understood at the molecular level. Classical molecular dynamics simulations of divalent ions are challenging because the high electric field strength near the ion leads to polarization effects that are not accurately accounted for in standard MD force fields. In this project you will explore alternative models for simulating divalent ions in order to find models that combine computational speed with sufficient accuracy to study transport of divalent ions with transporter proteins.

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Project: Predicting protonation states in proteins

Project: Predicting protonation states in proteins

In this rotation project you will predict known and unknown pKa values of key residues in proteins with a new method that combines molecular dynamics simulations with fast heuristic predictions. You will learn to write programs in the Python language and contribute to the open source MDAnalysis library.

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