Model nucleation-condensation

The nucleation condensation model of protein folding (Chapter 2)... 

The kinetic mechanism described above bears some resemblance to the framework and to the nucleation-condensation models." " In fact, the compact structure formed immediately after the early process of condensation is very similar to the molten globule concept proposed by Ptitsyn " in the case of all a and mainly a proteins, the molten globule does not suffer any other drastic changes, thus essentially following the two-state kinetics of many small proteins, " but in the case of a/jS and mainly jS proteins, the molten globule continues to evolve into a different shape as proposed in the... 

A key feature of the framework and nucleation-condensation models is the formation of secondary structure—which might or might not be coupled to the formation of tertiary structure—early in the folding process. It follows that a full description of the mechanism of protein folding also requires an understanding of the rules that stabilize molecular interactions in polypeptides. We consider these rules in Chapter 11. 

The nucleation-condensation mechanism can be accommodated in modified framework and hydrophobic-collapse models the framework model must be modified so that formation of secondary structure is linked to the formation of tertiary interactions and the hydrophobic collapse model must have the formation of tertiary interactions linked to the formation of secondary structure. Another variation of concerted structure formation is the hydrophobic zipper. 68 Whatever the distinctions of names, stable tertiary and secondary structural interactions must form concurrently. 

Although the fly ash particle size distribution in the submicron regime is explained qualitatively by a vaporization/homogeneous nucleation mechanism, almost all of the available data indicate particles fewer in number and larger in size than predicted theoretically. Also, data on elemental size distributions in the submicron size mode are not consistent with the vapor-ization/condensation model. More nonvolatile refractory matrix elements such as A1 and Si are found in the submicron ash mode than predicted from a homogeneous nucleation mechanism. Additional research is needed to elucidate coal combustion aerosol formation mechanisms. 

Acknowledgments The work is supported by the Russian Science Foundation grant 14-50-00124. The authors are thankful to prof. V.M. Zaichenko, who paid our attention to connection of our nucleation study with natural gas condensates modeling and to Drs V.V. Kachalov and V.M. Torchinskii for their interest to the work and valuable discussions. 

Li, Y., Roberts, C.J. (2009) Lumry-Eyring nucleated-polymeiization model of protein aggregation kinetics. 2. Competing growth via condensation and chain polymerization. J Phys Chem S, 113 (19), 7020-7032. 

The thermodynamic state in the Wilson point and the progress of cbndensation in the flow were calculated with a model of the condensation process based on the classical nucleation model and a formulation of droplet growth proposed by Gyarmathy. It is remarkable that the results of the calculation, obtained with a uniform choice of the free parameters of this condensation model, agree well with the experimental results, both for pure COp and for COp/air-mixtures. ... 

The variant of the cylindrical model which has played a prominent part in the development of the subject is the ink-bottle , composed of a cylindrical pore closed one end and with a narrow neck at the other (Fig. 3.12(a)). The course of events is different according as the core radius r of the body is greater or less than twice the core radius r of the neck. Nucleation to give a hemispherical meniscus, can occur at the base B at the relative pressure p/p°)i = exp( —2K/r ) but a meniscus originating in the neck is necessarily cylindrical so that its formation would need the pressure (P/P°)n = exp(-K/r ). If now r /r, < 2, (p/p ), is lower than p/p°)n, so that condensation will commence at the base B and will All the whole pore, neck as well as body, at the relative pressure exp( —2K/r ). Evaporation from the full pore will commence from the hemispherical meniscus in the neck at the relative pressure p/p°) = cxp(-2K/r ) and will continue till the core of the body is also empty, since the pressure is already lower than the equilibrium value (p/p°)i) for evaporation from the body. Thus the adsorption branch of the loop leads to values of the core radius of the body, and the desorption branch to values of the core radius of the neck. 

Aerosol Dynamics. Inclusion of a description of aerosol dynamics within air quaUty models is of primary importance because of the health effects associated with fine particles in the atmosphere, visibiUty deterioration, and the acid deposition problem. Aerosol dynamics differ markedly from gaseous pollutant dynamics in that particles come in a continuous distribution of sizes and can coagulate, evaporate, grow in size by condensation, be formed by nucleation, or be deposited by sedimentation. Furthermore, the species mass concentration alone does not fliUy characterize the aerosol. The particle size distribution, which changes as a function of time, and size-dependent composition determine the fate of particulate air pollutants and their... 

By using the classical theory of ion induced nucleation to describe the growth of radon daughters from the free activity mode to the nucleation mode, we loose information about the size of the subcritical clusters. These clusters are all lumped together between the size of a pure H2O ion cluster at 75% r.h. and the size of the critical H2O-H2SO4 cluster. The model only does keep track of the growth by condensation of the radon daughters once they arrived in the nucleation mode. 

The prediction made by the model calculations should be taken with some care for two reasons 1) H2O and H2SO4 are considered to be the condensing species, whereas other species may be active in experimental or domestic environments 2) the model uses classical nucleation theory, which is the only workable theory, but which is also to be criticized because it applies macroscopic entities to clusters that contain only a few molecules (3). 

Experimental determination of Ay for a reaction requires the rate constant k to be determined at different pressures, k is obtained as a fit parameter by the reproduction of the experimental kinetic data with a suitable model. The data are the concentration of the reactants or of the products, or any other coordinate representing their concentration, as a function of time. The choice of a kinetic model for a solid-state chemical reaction is not trivial because many steps, having comparable rates, may be involved in making the kinetic law the superposition of the kinetics of all the different, and often unknown, processes. The evolution of the reaction should be analyzed considering all the fundamental aspects of condensed phase reactions and, in particular, beside the strictly chemical transformations, also the diffusion (transport of matter to and from the reaction center) and the nucleation processes. 

The threshold concentration of monomer that must be exceeded for any observable polymer formation in a self-assembling system. In the context of Oosawa s condensation-equilibrium model for protein polymerization, the cooperativity of nucleation and the intrinsic thermodynamic instability of nuclei contribute to the sudden onset of polymer formation as the monomer concentration reaches and exceeds the critical concentration. Condensation-equilibrium processes that exhibit critical concentration behavior in vitro include F-actin formation from G-actin, microtubule self-assembly from tubulin, and fibril formation from amyloid P protein. Critical concentration behavior will also occur in indefinite isodesmic polymerization reactions that involve a stable template. One example is the elongation of microtubules from centrosomes, basal bodies, or axonemes. 

At the most fundamental level, monolayers of surfactants at an air-liquid interface serve as model systems to examine condensed matter phenomena. As we see briefly in Section 7.4, a rich variety of phases and structures occurs in such films, and phenomena such as nucleation, dendritic growth, and crystallization can be studied by a number of methods. Moreover, monolayers and bilayers of lipids can be used to model biological membranes and to produce vesicles and liposomes for potential applications in artificial blood substitutes and drug delivery systems (see, for example, Vignette 1.3 on liposomes in Chapter 1). 

The droplet current / calculated by nucleation models represents a limit of initial new phase production. The initiation of condensed phase takes place rapidly once a critical supersaturation is achieved in a vapor. The phase change occurs in seconds or less, normally limited only by vapor diffusion to the surface. In many circumstances, we are concerned with the evolution of the particle size distribution well after the formation of new particles or the addition of new condensate to nuclei. When the growth or evaporation of particles is limited by vapor diffusion or molecular transport, the growth law is expressed in terms of vapor flux equation, given by Maxwell s theory, or... 

The notion that folding proceeds from a condensed state rather than from a random coil state is somewhat heretical in an age dominated by the secondary structure nucleation point of view. However, the question has not been addressed experimentally, and the Dill model is in accord with the thermodynamics of unfolding for many globular proteins. 

The first hypothesis, proposed by Breck and Flanigen [52,55], to account for the crystallization of aluminosilicate zeolites affirms that it proceeds through the formation of the aluminosilicate gel or reaction mixture, and the nucleation and growth of zeolite crystals from the reaction mixture. This initial model has been almost abandoned, and replaced by the hypothesis of Barrer and others [53,55], In the framework of this hypothesis, it is assumed that the formation of zeolite crystals occurs in solution. Accordingly, in this model, the nucleation and growth of crystalline nuclei are a consequence of condensation reactions between soluble species, where the gel plays a limited role as a reservoir of matter. 

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