Project: Transport of divalent cations | Positions | 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.

In this project you will

  • carry out molecular dynamics simulations, including advanced simulation techniques to calculate free energies
  • implement different models to represent divalent ions
  • write code to quantitatively analyze your simulations (and learn the Python programming language to do so)
  • simulate membrane transport proteins with divalent ions in order to determine where and how the ions are transported.

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