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Open Access Publications from the University of California

Characterizing the Interaction of Organic Compounds with Indoor Surfaces and QM/MM Simulation of Proton Transport in the Hv1 Protein

  • Author(s): riahi samani, saleh
  • Advisor(s): Tobias, Douglas J
  • et al.
Abstract

Atomic level understanding of the interactions between the prevalent organic compounds and indoor surfaces is essential to study the potential impacts of these compounds on public health. Computer simulation methods provide an accurate means to explore physiochemiccal processes with atomistic detail. In this study molecular simulation methods are applied to elucidate the type and strength of interactions occurring between the indoor surfaces and organic compounds. Moreover, the energetics and structural information provided by the molecular simulations exhibited in this work are used to justify the experimental observations. Furthermore, hybrid quantum mechanics/molecular mechanics simulation protocol is used to explore the proton transport in the Hv1 protein. Specifically, the role of polar side chains located at the pore region of Hv1 channel in the proton translocation is explored.

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