Thermal structural fluctuations

Like any other protein, the molecular structure of the prion is subject to conformational flexibility and to various thermal-induced fluctuations between varying conformational states. However, if these fluctuations permit the PrP conformation to be attained, then this abnormal conformer promotes the widespread conversion of PrP to PrP , leading to the precipitous deposition of the abnormal protein throughout the brain (mirrored by the rapid and relentlessly downhill clinical course). This pathological self-propagating shape conversion of a-helical PrP to P-sheet PrP may in principle be initiated by a seed PrP molecule in the neurotoxic conformation. This explains the transmissibility of prion diseases and accounts for how susceptible humans exposed to beef from an animal with mad cow disease develop variant Creutzfeldt-Jakob disease. 

The structure, however, is not static but is subject to thermally driven fluctuations. The local structure changes continuously as a function of time due to orientational and translational molecular motions. The time scale of these motions may range from nanoseconds up to several hundred years. The structure of the amorphous state as well as its time-dependent fluctuations can be analysed by various scattering techniques, such as X-ray, neutron, electron and light scattering. 

MCT considers interacting Brownian particles, predicts a purely kinetic glass transition, and describes it using only equilibrium structural input, namely the equilibrium structure factor Sq [3,46] measuring thermal density fluctuations. MCT-ITT extends this statistical mechanics, particle based many-body approach to dispersions in steady flow assuming a linear solvent velocity profile, but neglecting the solvent otlrerwlse. 

If one traces a longer stretch of a DNA molecule in solution, a clear divergence from linearity becomes evident. Thermally induced structural fluctuations allow a bending of DNA, which is why long DNA molecules are described as a random coil. This bending of the DNA occurs in molecules with a length of more than ca. 200 bp. 

When water is finely dispersed as an aerosol, an emulsion, or as small clusters in polymeric host media, its thermal behavior can deviate significantly from that exhibited by bulk water. The reasons for these deviations are examined, and a statistical-mechanical approach for their study is proposed. A rough estimate is obtained for the depression of the temperature of maximum mean density for small spherical droplets. An explanation is advanced (in terms of specific structural fluctuations) for the singular behavior of strongly supercooled water that has been observed in emulsions near -40 by Angell and collaborators. 

Figure 10.5 illustrates the chemical structure of a plane parallel PDR by giving the relative abundances of C+, C and CO as a function of the penetration depth into the model cloud [11]. We assumed a kinetic equilibrium and determined the relative abundances from a chemical network consisting of 38 different species formed and destroyed in 434 reactions. The PDR is illuminated from the left by the mean interstellar radiation field and extends from the predominantly atomic surface region to the point where almost all carbon is bound into CO. One of the difficulties in calculating the chemical and thermal structure of a PDR arises from the effect of self-shielding. Molecules already formed absorb UV photons which are able to dissociate the respective molecule. In other words they cast a shadow into the cloud which enhances the further formation of the respective molecule. This effects becomes especially important for the formation of key molecules like O2, H2 and CO. Our current research addresses the question under which physical conditions an instability due to shadowing effects could occur. Another difficulty concerns the effects of small-scale fluctuations of the UV radiation field on the chemical network. 

The emergence of a new phase due to local structural fluctuations in a lattice of the original solid phase Ag occurs most often at the boundaries and defect sites of the crystals. Thermodynamically stable nucleus of new phase has often a critical size close to unit cell volume, which differs from the normal one. This gives rise to mechanical stresses in the transformation zone, and even the destruction of the original crystal. Such effect leads to smaller quantity of a desired product. Thermal decomposition reaction, like all topochemical reactions, proceeds more rapidly... 

In order to describe the static structure of the amorphous state as well as its temporal fluctuations, correlation functions are introdnced, which specify the manner in which atoms are distributed or the manner in which fluctuations in physical properties are correlated. The correlation fimctions are related to various macroscopic mechanical and thermodynamic properties. The pair correlation function g r) contains information on the thermal density fluctuations, which in turn are governed by the isothermal compressibility k T) and the absolute temperature for an amorphous system in thermodynamic equilibrium. Thus the correlation function g r) relates to the static properties of the density fluctuations. The fluctuations can be separated into an isobaric and an adiabatic component, with respect to a thermodynamic as well as a dynamic point of view. The adiabatic part is due to propagating fluctuations (hypersonic soimd waves) and the isobaric part consists of nonpropagating fluctuations (entropy fluctuations). By using inelastic light scattering it is possible to separate the total fluctuations into these components. 

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