Funnel picture

Fig. 5. Free energy landscape of a lattice model protein (see Sect. 2.2), as a function of two order parameters, the number of contacts C and the number of native contacts Qo (see Sect. 2.3). Unlike the energy landscape funnel picture, the free energy shows two stable states separated by a barrier (the transition state). Extended unfolded conformers quickly collapse to the molten globule, and have to overcome a barrier to folding to the native state. The funnel picture is thus reconciled with the two-state concept of a free energy barrier. Reprinted from Dinner et ah. Trends Biochem. Sci. 25, 331, (2000) with permission from Elsevier...

The tube models a concrete folding mechanism by following the center of the tube and the fluctuations near that center. This concrete mechanism can be examined with respect to the overall funnel picture. For example, if the rate in the tube is exceptionally slow compared to the experimental rate, it is unlikely that the sampled tube is important. Computationally and conceptually, we should partition the funnel to tubes and analyze them one by one. We note that all the tubes meet at the folded state. Therefore the weight of each tube can be measured by overlapping the equilibrium flux into the reactant with the flux from a tube. The calculation of weights of tubes is a topic for future research. 

Pig. 5. Comparison of the qi expectation value of the uncoupled QCMD bundle ([g]e o) and full QD ( q)qd) for the test system for e = 1/100 (pictures on top) and e = 1/500 (below). Initial data as in Fig. 3. The shaded domain indicates the funnel between the two curves Qbo and geo (cf. Thm. 5). The light dashed line shows Hagedorn s limit solution qna and the dense lines (q )Qo (left hand pictures) and [ ]e s (right hand pictures). 

In the 1993 AATCC standard method (re-affirmed in 1988) a standard weight of dye (10 g) is dropped down a funnel into a cylinder of defined si2e. A wet filter paper is placed as a coUar to the funnel 200 mm above the bottom of the cylinder. After 3 min the stain on the filter paper, obtained by the dust created in the funnel dissolving on the paper, is assessed by comparing the standard photographs and the dye given the number of the picture it resembles the most (1 poor, 5 excellent). 

The solution is cooled to room temperature and is washed with a few milliliters of benzene into a single-necked flask. The solvent is removed with a rotary evaporator connected to a water aspirator vacuum gentle heat is supplied from a steam bath. The residue is cooled to room temperature before air is admitted. About 200 ml. of hexane is added and stirred with the residue to extract most of the carborane. The brownish tar which remains undissolved is allowed to settle and the solution is decanted. A second extraction of the tar with 40 ml. of hexane converts the residue to a solid which is removed by filtration. The solid is washed on the filter with an additional 40 ml. of hexane. The combined hexane extracts are filtered and then washed in a separatory funnel with four 100-ml. portions of a chilled aqueous 10% sodium hydroxide solution, followed by four 100-ml. portions of water. After the yellow hexane solution has been dried over anhydrous magnesium sulfate and filtered, the solvent is removed by use of a rotary evaporator connected to a water aspirator. The carborane is washed with a small amount of pentane into a 300-ml. single-necked flask which is attached to an alembic column as pictured in Fig. 13. 

The reaction is carried out in a 500-ml. three-necked flask equipped with a reflux condenser, mechanical stirrer, heating mantle, and nitrogen inlet. The equipment is similar to that pictured in Fig. 11, except that an addition funnel is not required. In the reaction flask 20 g. (0.36 mol, 100% excess) of potassium hydroxide is dissolved in 300 ml. of absolute ethanol. The spare neck is closed with a ground-glass stopper, and the solution is stirred until it reaches room temperature. Addition of the carborane to the warm basic solution may result in an initial vigorous reaction. To this solution is added 30.0 g. (0.175 mol) of solid dimethylcarborane. The solution is stirred for one hour at room temperature and is then heated at the reflux temperature for 14 hours or until hydrogen evolution has stopped. 

Commonly, it is asserted that upward transitions from the lower adiabat to the upper one should be less likely than downward transitions because of the funneling property of the intersection [144,145]. This is clearly seen in the usual model conical intersection—as seen, for example, in Fig. 1 of Ref. 146, where there is (a) a well, or funnel, in the upper adiabat which guides the wavepacket to the intersection and (b) a peak on the lower adiabat which tends to guide the wavepacket away from the intersection. The potential energy surfaces shown in Fig. 7 differ from this canonical picture, and in particular it is not at all clear that the wavepacket on the lower adiabatic state will be funneled away from the intersection. For the conditions chosen in our calculations, we... 

The current picture of protein folding is nicely summarized in Figure 17.1. There are a multitude of pathways from the state of unfolded protein at the top of the figure to the native protein at the bottom. Without folding intermediates, the walls of the funnel to the bottom would be smooth. If the energy trough around a nonnative protein is too deep, the misfolded protein cannot exit this local minimum. 

Following ingestion of mescaline, one first sees spirals, tunnels, funnels, and alleys. Then scenes picturing episodes become connected much as they do in dreams. One sees this very same progression, from geometric forms, through synesthesia, to architectural visions, at sleep onset when... 

Localized transformation processes such as those observed in scarred liver (s. p. 405) are not considered to be cirrhosis. The loss of parenchyma in scarred liver is generally the result of reduced blood supply in the respective area. Deep-set scars create the picture of a funnel-shaped liver (s. p. 406). Similarly, pronounced liver fibrosis (s. p. 405) does not fulfil the criteria of cirrhosis, since the lobular architecture as well as the intrahepatic and intra-acinar vascular supply are uncompromised. While fibrosis constitutes a precirrhotic stage, it does not necessarily progress to cirrhosis itself Fibrosis can regress Thus, liver cirrhosis is characterized by the following five criteria ... 

There is a way around the hasslesome purification procedure that will allow the underground chemist to use the ethyl nitrite he has made quickly and easily. The way to do this is to bubble the vapors of the ethyl nitrite into the reaction mixture. This method avoids the unpleasant and possibly dangerous procedure with the sep funnel and subsequent distillation. See Figure 8 back in Chapter 4 on N-methyl formamide. If in that figure, the methylamine containing flask instead contained the ethyl nitrite reaction mixture, and the formic acid containing flask instead had the allylbenzene and palladium chloride in alcohol needed for phenylacetone production, then one could easily picture how to get the ethyl nitrite vapors to directly bubble into the phenylacetone production mix without any need to manipulate the nitrite directly. 

Figure 3. A schematic picture of the light-harvesting funnel in purple bacteria (left) and an illustration of how this corresponds to the layout of pigment-protein complexes (right). The approximate time scales of the various energy transfer processes are indicated.

The Mount Vernon iex-Kronprinzessin Cecilie), seen postwar but still sporting deliberately contrasted funnel colours. Compare this with the picture on page 69. 

Intercepted by IIMS Hyperion on 19 December 1939, the Columbus s crew scuttled their ship.. As special squads opened her sea cocks and lit fires aboard her, the remainder of her complement took to the boats. The black tops added to ber normal funnel colours are clearly seen in this picture. 

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