First-principles simulation of photoreactions in biological systems
Open accessAbstract
First-principles simulations start to be applicable to the photochemistry and photophysics in biological systems. In this review the prerequisites for investigating such excited state phenomena in large systems are outlined. Generally, a quantum mechanical description of the electronic structure is combined with molecular dynamics simulations, which allows to describe the motion of the atoms in the field produced by the quantum-mechanical potential. Like this, bonds can be formed and broken, that is, chemical reactions can be simulated. The review focuses on applications of first-principles molecular dynamics to photoactive proteins.
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In bacteria, opsins act as pumps for cations and anions.
“in bacteria they function as cation and anion pumps,217−223”
From Chemistry of the Retinoid (Visual) Cycle (2014) · cites this paper as [221]
Section 4.4, “Bacteriorhodopsin” (page unavailable), describes bacteriorhodopsin as a light-driven pump that transports protons, which are cations, across a cell membrane. It does not describe anion pumping, so it supports only the cation part of the claim. (LLM, conf=0.88)
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- Authors
- Rossle, S.
- Venue
- Frontiers in Bioscience
- Publisher
- IMR Press
- Published
- 2009
- Volume
- 14
- Issue
- 1
- Pages
- 4862
- ISSN
- 1093-4715 (ISSN-L)
- 1093-9946
- DOI
- 10.2741/3574
- OpenAlex
- W2466207538
- Cited by
- 9
- References
- 91
- Citations by year
- 2024: 1 · 2022: 1 · 2017: 1 · 2016: 1 · 2014: 1 · 2013: 1 · 2012: 2
- FWCI
- 0.08
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Frontiers in bioscience (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Deutsche Forschungsgemeinschaft
- Topics
- Physical Sciences › Physics and Astronomy › Atomic and Molecular Physics, and Optics › Advanced Chemical Physics Studies
- Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Photoreceptor and optogenetics research
- Physical Sciences › Physics and Astronomy › Atomic and Molecular Physics, and Optics › Spectroscopy and Quantum Chemical Studies
- Keywords
- ab initio molecular dynamics, photochemical reactions, photochemistry, photophysical properties, excited states, photoactive proteins, electronic structure, quantum mechanical potentials
- MeSH terms
- Bacterial Proteins, Bacteriorhodopsins, Models, Biological, Models, Molecular, Quantum Theory, Rhodopsin, Thermodynamics, Photoreceptors, Microbial, Green Fluorescent Proteins, Phototrophic Processes, Photochemical Processes
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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