Encoding energy transfer

Fluorescence or Forster resonance energy transfer (FRET) is widely accepted as being one of the most useful methods to observe biochemical events in vitro and in living cells. Generally, there are two forms of FRET sensors those based on a pair of genetically encoded fluorophores, usually employing fluorescent proteins from jellyfish or corals, or those based on small molecules that make use of small organic fluorophores. 

Fehr, M., Takanaga, H., Ehrhardt, D. W. and Frommer, W. B. (2005b). Evidence for high-capacity bidirectional glucose transport across the endoplasmic reticulum membrane by genetically encoded fluorescence resonance energy transfer nanosensors. Mol. Cell. Biol. 25, 11102-12. 

Our application of time-dependent perturbation theory with density functional theory has led to a detailed picture of mode specific energy transfer for a number of model heme compounds in vacuo. Our calculations allow for the interpretation of previous theoretical and experimental observations at a mode-specific level. Our results support the conjecture that the protein structure encodes a tuning of the energy transfer timescales and mechanisms in a way that facilitates protein function and signaling. 

In the first experiment, in which beam 2 was switched on and off and beam 1 was monitored, the intensity of the latter decreased. Conversely, when beam 1 was switched on and off and beam 2 was monitored, the intensity of the latter increased. The occurrence of such asymmetric energy transfer unambiguously confirms the PR nature of the optical encoding and allows a distinction to be made between a grating based on the PR effect and other types of gratings. 

Imamura, H., Nhat, K.P., Togawa, H., Saito, K. et al. (2009) Visualization of ATP levels inside single living cells with fluorescence resonance energy transfer-based genetically encoded indicators. Proc. Natl. Acad. Sci. U.S.A., 106, 15651-15656. 

The way the present ansatze are defined allows one to deal with the strips locally and the matrix elements can be evaluated by a transfer-matrix technique [22,23,34,35,40-44]. Within this technique one can define transfer and connection matrices that encode the local features and reduce the computation expectation values of any observable accepting a local expression, such as that of Eq. (61) for the energy. The results entails simple products of matrices [22,34],... 

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