Modeling flexibility

In this section we compare actual polymer chains with the perfectly flexible model discussed in the last section. There are four respects in which an actual molecule differs from the idealized model ... 

With the results of the preceding section thus salvaged, let us look in more detail at the specific areas of discrepancy between the perfectly flexible model... 

J. G. Powles, M. Pogoda. A flexible model for the simulation of fluids in infinite porous systems. Mol Phys 75 757, 1993. 

Instead of a conjunction of preconditions, as used by the STRIPS and conditional operators, the functional operator has a set of conjunctions of preconditions (Fig. 2c). Each element in the set describes some possible situation that might exist before the operator is applied. For each element of the set of preconditions, there is a corresponding element in the set of postconditions. The functional operator is a more flexible model than the STRIPS or conditional operators. It comes closer to the modeling needs for the synthesis of operating procedures for chemical processes, but as we will see in the next section, we need to introduce additional aspects in order to capture the network-like structure of chemical processes. 

Not specified University of Cincinnati and Gradient Corporation Develop a sophisticated, flexible model to be used in a site- and application-specific way to predict impact of lead in various media on general population blood lead levels ILZRO... 

Of all of the methods reviewed thus far in this book, only DNS and the linear-eddy model require no closure for the molecular-diffusion term or the chemical source term in the scalar transport equation. However, we have seen that both methods are computationally expensive for three-dimensional inhomogeneous flows of practical interest. For all of the other methods, closures are needed for either scalar mixing or the chemical source term. For example, classical micromixing models treat chemical reactions exactly, but the fluid dynamics are overly simplified. The extension to multi-scalar presumed PDFs comes the closest to providing a flexible model for inhomogeneous turbulent reacting flows. Nevertheless, the presumed form of the joint scalar PDF in terms of a finite collection of delta functions may be inadequate for complex chemistry. The next step - computing the shape of the joint scalar PDF from its transport equation - comprises transported PDF methods and is discussed in detail in the next chapter. Some of the properties of transported PDF methods are listed here. 

Another dilemma may be posed when some, usually more symmetrical form with large-amplitude motion on one hand, and a mbcture of two or more less flexible models equally well reproduce the experimental data. This problem is dealt with by papers on large-amplitude motion. 

Chem. Soc. Faraday Trans. I. 71 1623-1630 Rustad, J.R. Felmy A.R. Hay, B.P. (1996) Molecular statics calculations for iron oxide and oxyhydroxide minerals Toward a flexible model of the reactive mineral-water interface. Geochim. Cosmochim. Acta 60 1553—1562 Ryan, J.N. Gschwend, P.M. (1991) Extraction of iron oxides from sediments using reductive dissolution by titanium(III). Clays Clay Min. 39 509-518... 

In rigid models each macromolecule has the same set of 4> so <4> = 4 and For flexible models the averages are calculated from the... 

Saturated heterocycles are important ligands. They are flexible models for the problem of competitive coordination of the hard and soft acids with the nonconjugated donor sites. Analysis of these problems is of interest for the chemistry of complex and heteroaromatic compounds. The number of publications in the 1990 s shows that the interest to the problems analyzed in the present review is still enormous. 

Other investigations with flexible models led to the conclusion that in confor-mationally unrestricted systems, there is no significant p-oxygen effect168 in the... 

The need for a more flexible model was met by developing the formalism for diffuse interfaces [15,17,18]. First, the electrostatic solvation for a diffuse interface has been... 

In the case of the fixed models, the optimization and check of the quality criteria are done. Flexible models have to provide a solid support of the appropriateness for the procedure adopted for the model development. 

Sewell and co workers [145-148] have performed molecular dynamics simulations using the HMX model developed by Smith and Bharadwaj [142] to predict thermophysical and mechanical properties of HMX for use in mesoscale simulations of HMX-containing plastic-bonded explosives. Since much of the information needed for the mesoscale models cannot readily be obtained through experimental measurement, Menikoff and Sewell [145] demonstrate how information on HMX generated through molecular dynamics simulation supplement the available experimental information to provide the necessary data for the mesoscale models. The information generated from molecular dynamics simulations of HMX using the Smith and Bharadwaj model [142] includes shear viscosity, self-diffusion [146] and thermal conductivity [147] of liquid HMX. Sewell et al. have also assessed the validity of the HMX flexible model proposed by Smith and Bharadwaj in molecular dynamics studies of HMX crystalline polymorphs. 

Teppen et al. [89] have used a flexible model for clay minerals that allows full movement of the M-O-M bonds in the clay structure, where M represents Si, Al, or other cations in the octahedral sheet. This model was used in MD simulations of interactions of hydrated clay minerals with trichloroethene [90, 91]. The simulations suggest that at least three distinct mechanisms coexist for trichloroethene sorption on clay minerals [90], The most stable interactions of trichloroethene with clay surfaces are by full molecular contact, coplanar with the basal surface. The second type more reversible, less stable is adsorption through single-atom contact between one chlorine atom and the surface. In a third mechanism, trichloroethene interacts with the first water layer and does not interact with clay surface directly. Using MC and MD simulation the structure and dynamics of methane in hydrated Na-smectite were studied [92], Methane particles are solvated by approximately 12-13 water molecules, with six oxygen atoms from the clay surface completing the coordination shell. 

Teodoro ML, Kavraki LE (2003) Conformational flexibility models for the receptor in structure based drug design. Curr Pharm Des 9(20) 1635-1648... 

More work needs to be done to develop increasingly accurate representations of the electronic states of peptides and various side chain chromophores. Once this is completed, the models are in place to examine interactions between these states for a given protein conformation. An accurate and flexible model which can calculate CD spectra of a variety of protein structures would be invaluable in the study of protein folding, stability, and structure. 

Franke H, Galla H, Beuckmann CT (2000) Primary cultures of brain microvessel endothelial cells a valid and flexible model to study drug transport through the blood-brain barrier in vitro. Brain Res Brain Res Protoc 5 248-256... 

The options of using available general purpose process flowsheet simulators, or formulating special purpose models were considered. The latter was chosen to satisfy the need for detailed, accurate, and flexible models, which are suitable for routine use. 

A simple and flexible modeling scheme to quantitatively characterize complete viscoelastic properties of pol3nmers is readily useable with FTMA data. It contains the essential features of the frequency-temperature equivalence of the viscoelastic behaviors of pol3nmers and is easily adapted to modern computer systems. 

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