Cutting the Gordian knot of excited-state modeling in complex environments

C. Daday

Research output: ThesisPhD Thesis - Research UT, graduation UT

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Abstract

Autofluorescent proteins are a class of photoactive proteins widely used in biological experiments, being compatible with noninvasive imaging in living cells. The focus of this thesis is to develop a reliable and accurate modeling framework for the photophysical properties of these and other photosensitive biosystems. To this end, a multiscale approach is necessary given the size of the systems: A protein contains thousands of atoms and a quantum mechanical treatment thereof is clearly impossible. The light absorption and electronic excitation of these proteins is however typically localized on the so-called chromophore (or antenna) and a quantum description of this limited area combined with a less accurate but faster treatment of the rest of the protein is a possible solution. In this thesis, we propose a new multiscale scheme where the environment is still treated quantum mechanically but through the computationally cheaper density functional theory (DFT), and allowed to respond to the excitation of the embedded chromophore. This scheme is demonstrated on several small molecules and shown to improve on the use of a unresponsive environment. We also present its application to a prototypical autofluorescent protein and pinpoint the important ingredients for a successful modeling of the photoexcitation in this coupled chromophore-protein complex.
Original languageEnglish
Awarding Institution
  • University of Twente
Supervisors/Advisors
  • Filippi, C., Supervisor
Award date18 Sep 2015
Place of PublicationEnschede
Publisher
Print ISBNs978-90-365-3933-3
DOIs
Publication statusPublished - 18 Sep 2015

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Excited states
Chromophores
Proteins
Photoexcitation
Light absorption
Density functional theory
Cells
Antennas
Imaging techniques
Atoms
Molecules
Experiments

Keywords

  • METIS-311527
  • IR-97065

Cite this

Daday, C.. / Cutting the Gordian knot of excited-state modeling in complex environments. Enschede : Universiteit Twente, 2015. 193 p.
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Cutting the Gordian knot of excited-state modeling in complex environments. / Daday, C.

Enschede : Universiteit Twente, 2015. 193 p.

Research output: ThesisPhD Thesis - Research UT, graduation UT

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N2 - Autofluorescent proteins are a class of photoactive proteins widely used in biological experiments, being compatible with noninvasive imaging in living cells. The focus of this thesis is to develop a reliable and accurate modeling framework for the photophysical properties of these and other photosensitive biosystems. To this end, a multiscale approach is necessary given the size of the systems: A protein contains thousands of atoms and a quantum mechanical treatment thereof is clearly impossible. The light absorption and electronic excitation of these proteins is however typically localized on the so-called chromophore (or antenna) and a quantum description of this limited area combined with a less accurate but faster treatment of the rest of the protein is a possible solution. In this thesis, we propose a new multiscale scheme where the environment is still treated quantum mechanically but through the computationally cheaper density functional theory (DFT), and allowed to respond to the excitation of the embedded chromophore. This scheme is demonstrated on several small molecules and shown to improve on the use of a unresponsive environment. We also present its application to a prototypical autofluorescent protein and pinpoint the important ingredients for a successful modeling of the photoexcitation in this coupled chromophore-protein complex.

AB - Autofluorescent proteins are a class of photoactive proteins widely used in biological experiments, being compatible with noninvasive imaging in living cells. The focus of this thesis is to develop a reliable and accurate modeling framework for the photophysical properties of these and other photosensitive biosystems. To this end, a multiscale approach is necessary given the size of the systems: A protein contains thousands of atoms and a quantum mechanical treatment thereof is clearly impossible. The light absorption and electronic excitation of these proteins is however typically localized on the so-called chromophore (or antenna) and a quantum description of this limited area combined with a less accurate but faster treatment of the rest of the protein is a possible solution. In this thesis, we propose a new multiscale scheme where the environment is still treated quantum mechanically but through the computationally cheaper density functional theory (DFT), and allowed to respond to the excitation of the embedded chromophore. This scheme is demonstrated on several small molecules and shown to improve on the use of a unresponsive environment. We also present its application to a prototypical autofluorescent protein and pinpoint the important ingredients for a successful modeling of the photoexcitation in this coupled chromophore-protein complex.

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