Dark state

Fig. 16. Twisted nematic LCD showiag the V dark state (right), where D is the threshold voltage of the ceU.

The known structure of the OCP is a snapshot of the presumably dark-state-adapted form of the protein. From the model, it is difficult to imagine how the concealed carotenoid could interact with one of the components of the phycobilisome in order to quench the absorbed energy. However, the surface of the OCP has numerous surface cavities and clefts, as shown in Figure 1.3b, including two... 

Nifosi R, Ferrari A, Arcangeli C, Tozzini V, Pellegrini V, Beltram F (2003) Photoreversible dark state in a tristable green fluorescent protein variant. J Phys Chem B 107 1679-1684... 

Donnert, G., Eggeling, C. and Hell, S. W. (2007). Major signal increase in fluorescence microscopy through dark-state relaxation. Nat. Methods 4, 81-6. 

Jacobsen, R.B., Sale, K.L., Ayson, M.J., Novak, P., Hong, J., Lane, P., Wood, N.L., Kruppa, G.H., Young, M.M., and Schoeniger, J.S. (2006) Structure and dynamics of dark-state bovine rhodopsin revealed by chemical cross-linking and high-resolution mass spectrometry. Protein Sci. 15, 1303-1317. 

The potential of photoprobes is increasingly utilized as a remotely controllable tool in the drug discovery process. The difference between the dark state stability and light sensitivity allows the separation of two actions ... 

The sample is continuously irradiated and the fluctuations in the fluorescence intensity arise due to any event which makes the fluorophore unavailable to be excited to the emissive singlet excited state, such as diffusion of the fluorophore out of the detection volume, formation of a dark state, such as a triplet excited state, or photoreaction. The concentration of fluorophore in the detection volume has to be low (10 13—10 8M) so that the fluctuation in the intensity for one molecule is observable over any background emission. The high concentration limit is a consequence of the fact that the correlated photons from single molecules scale with the number of molecules in the detection volume, while the contribution from uncorrelated photons, arising from the emission from different molecules, scales with the square of the number of molecules. The lowest concentration is determined by the probability of finding a molecule in the detection volume.58... 

The autocorrelation function G(t) corresponds to the correlation of a time-shifted replica of itself at various time-shifts (t) (Equation (7)).58,65 This autocorrelation defines the probability of the detection of a photon from the same molecule at time zero and at time x. Loss of this correlation indicates that this one molecule is not available for excitation, either because it diffused out of the detection volume or it is in a dark state different from its ground state. Two photons originating from uncorrelated background emission, such as Raman scattering, or emission from two different molecules do not have a time correlation and for this reason appear as a time-independent constant offset for G(r).58... 

FIGURE 1.3 Concentration profile from a mechanism employing three intermediates, /j, /j, I, plus the initial (dark) state /q. /[(O) = 1 is assumed. The cyclic reaction is started (initiated) by a laser flash. Molecules relax through the intermediate states back to the initial state. The concentration profile of intermediate /j shows all three relaxation times (arrows). 

The excited vibrational states can be considered as quasi-eigenstates [41]. As can be seen in the simplified scheme of Figure 2.2, these states are a result of the relatively strong coupling between a zero-order bright state (ZOBS), namely i >, with several zero-order dark states (ZODS), l > [48], that are further weakly coupled to the bath states that include a dense manifold of nearly equally coupled levels with a finite decay rate. 

We have shown in Ref. [19] that if the systems in question have three levels, one can completely eliminate decoherence and disentanglement by imposing a special symmetry using the appropriate modulation. Thus, even if drastic reduction of all the decoherence matrix elements is not possible, then by using local modulations, one may equate the intraparticle elements, eliminate the interparficle elements, and code the QI in the ground and antisymmetric dark state of the two excited levels, and consequently completely preserve coherence and entanglement. 

This state can be called the polarization dark state in analogy to the dark state used in STIRAP [1-3] it is a superposition of H and V linear polarization, lacking any circular-polarization component. 

If the molecular tumbling rate is slow enough that larger electron-electron dipolar couplings are not motionally averaged, Fourier deconvolution can be used to analyze dipolar interactions in fluid solution.18 Distances in doubly spin-labelled rhodopsin were measured by Fourier deconvolution of CW line-shape changes in room temperature solution.78 The broadening function was modelled as the sum of Pake patterns from a distribution of distances. As a reference point for the distance measurements one label was attached at the cytoplasmic termination of transmembrane helix 1. The second label was attached near the cytoplasmic termination of transmembrane helix 7 or in the short helix 8. The distances and conformational flexibility in the dark state are... 

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