Fast-Time Structure

Because the electrons in a storage ring circulate precisely in the form of a bunch, the synchrotron light produced is very stable, with subnanosecond pulses repeated on a microsecond time scale. 

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As an example for an efficient yet quite accurate approximation, in the first part of our contribution we describe a combination of a structure adapted multipole method with a multiple time step scheme (FAMUSAMM — fast multistep structure adapted multipole method) and evaluate its performance. In the second part we present, as a recent application of this method, an MD study of a ligand-receptor unbinding process enforced by single molecule atomic force microscopy. Through comparison of computed unbinding forces with experimental data we evaluate the quality of the simulations. The third part sketches, as a perspective, one way to drastically extend accessible time scales if one restricts oneself to the study of conformational transitions, which arc ubiquitous in proteins and are the elementary steps of many functional conformational motions. 

For comparison, the calculated linear and 2D spectra using ft = 12.3 cm-1 and 6 = 52°, which correspond to an a-helical structure (see the contour plot Fig. 19) for the isotopomer Ala -Ala-Ala are shown in Figure 21. The observed spectra for Ala -Ala-Ala are strikingly different from the calculated spectra for a molecule in an a-helical conformation. We emphasize here an important point In contrast to the NMR results on oligo(Ala), in which averaging of different backbone conformations might be present because measurements are made on a time scale that is slow compared to that of conformational motions, these vibrational spectroscopy results are detected on a very fast time scale (Hamm et al, 1999 Woutersen and Hamm, 2000, 2001). This rules out conformational averaging. 

Although in principle the time structure of the SR beam may be exploited in time resolved studies the major limiting factor is the rate at which three dimensional data may be accumulated. In this respect time resolved methods are bound to develop in tandem with the development of high count rate/fast refresh rate electronic area detectors. This applies to both monochromatic and white beam methods. For the latter the use of an integrating detector such as a CCD or image plate are the main expected improvements over film. 

The value of ( used here corresponds to 10 3 of its value in room temperature aqueous solutions. [80] On the one hand, using such weak friction improves the sampling efficiency in the simulations and does not affect equilibrium structural properties. On the other hand, the dynamical properties that we observe may be different from those probed by SM-FRET techniques, which would not be able to resolve conformational dynamics on such fast time scales. Thus, the relevance of the following analysis of dynamical properties relies on the assumption that increasing the friction will not significantly alter our main conclusions. It is interesting to note in this context that the folding mechanism in similar models has been observed to be relatively insensitive to the value of the friction coefficient. [81]... 

Remark 3.2. We can regard the developments above from a converse perspective. Namely, if we consider the model of each individual unit (preserving the input and output flow structure of the process) in the fast time scale t, we can write a simplified model for unit i in the form... 

Unlike a glass, a liquid does not have essentially static structures that give rise to inhomogeneous broadening. Nonetheless, liquids can have fast time scale fluctuations that give rise to homogeneous broadening and much... 

Additional evidence for structural flexibility of small peptides on very fast time scales can be obtained from dynamical hole-burning experiments. An example is shown in Fig. 23, (30) which reflects a cut through the 2D... 

It is possible that the absence of some of the most stable structures of base pairs in the gas phase is due to short excited state dynamics. Direct experimental proof of this explanation requires fast time resolved measurements. For an indirect measure one can consider the linewidths in UV spectra. Of the 27 base pairs analyzed in the gas phase so far, 24 structures do not form WC type pairs and all of those exhibit sharp structured REMPI spectra, as shown in Figure 12.9(a). Only three... 

A new technique of investigating short-lived species is fast time-resolved TR spectroscopy. With the help of this method the first gas phase spectrum of naked Cr(CO)5, generated by photolysis of Cr(CO)6, was obtained (Seder et al., 1985). The structure is similar to that shown by matrix experiments C4,. 

These findings indicate general difficnlties in interpreting the results of flash photolysis experiments with UV visible detection. First, no detailed structural information can be obtained. Second, minnte traces of imparity in the solvent interfere strongly with the spectral behavior. It has now become clear that Cr(CO)s (and other unsaturated carbonyls) are almost always complexed by solvent or matrix molecnles or atoms. Even in a neon matrix there is some interaction to produce the species Ne- Cr(CO)5. Naked Cr(CO)s can be made in the gas phase, and by some rather cunning time-resolved solution experiments. Here, solvated Cr(CO)s is formed by UV photolysis of Cr(CO)6, then the solvating molecule is removed by visible photolysis. Fast time-resolved spectroscopy allows the decay of the naked Cr(CO)s, as it resolvates, to be moiutored. It is clear that this decay is extremely rapid. 

The computation times are much higher than in the database approach the recalculations in the modeling process must be performed on each relevant initial model found in the database. Depending on the number of operations, this leads to between approximately 500 and 5000 recalculations of new 3D models and RDF descriptors for each initial model. With respect to about 100,000 compounds in the binary database for the initial models, this can result in several million calculations per prediction if several initial models should be regarded. The method can be improved by implementation of a fast 3D structure generator into the prediction software. In this case, a reliable 3D structure is calculated after each modeling operation directly. 

The approach is capable of achieving a resolution of about 10 ps [43]. Optical/ vibrational spectroscopies can follow events and structural changes on such fast time scales since their characteristic time scales are sub-picosecond, even femtosecond. The methodology is therefore suitable to study the dynamics of en2ymatic catalysis over multiple time scales from picoseconds to minutes [44],... 

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