Limits of modeling

In discussing the benefits and limitations of modeling we distinguish between three types ... 

Currie LA (1985) The limitations of models and measurements as revealed through chemo-metric intercomparisons. J Res NBS 90 409... 

A generic problem with profile methods that iterate is the possibility of profile wander (also called matrix migration). This occurs when sequences found in early rounds of the iterative search are not found in later rounds of the search. This problem affects both PSI-BLAST and HMMER. This means that one should record all the intermediate steps so that these lost members of the family can be recovered. Profile wander only becomes a problem for large protein families, and therefore the cause of the profile wander may be related to the limits of modeling using profiles. 

The spectrum of B is fairly well defined while the spectrum of A is not, there is a long extrapolation required until the its spectrum turns negative at 400nm. This exemplifies the limitation of model-free methods they rely on very simple constraints but in certain cases the range of feasible answers can be very wide, sometimes too wide to be useful. This will be discussed later in Chapter 5.4.3, Rotational Ambiguity. 

DilP recently discussed the merits and limitations of models that assume thermodynamic additivity and independence (of energy types, of neighbor interactions, of conformational freedom, of monomer contact pairing frequencies, etc.). He states that biological molecules may achieve stability in the face of thermal uncertainty, as polymers do, by compounding many small interactions this summing can stump modelers because application of the additivity principle leads to accumulated error. Entropies and free energy may not be additive to describe weak interactions that are ensembles of states. He concludes that additivity principles appear to be few and limited in scope in biochemistry. 

Gottschalk, F., Sonderer, T., Scholz, R.W. and Nowack, B. (2010) Possibilities and limitations of modeling environmental exposure to engineered nanomaterials by probabilistic material flow analysis. Environ. Toxicol. Chem., 29, 1036-1048. 

The possible results and limitations of model experiments for semiconductor/electrolyte interfaces are discussed for non-reactive and reactive interfaces and related to the use of UHV techniques for obtaining microscopic information of interfacial processes in photoelectrochemical processes. 

In general, performance data published in the literature are usually obtained from small laboratory equipment. As a result, efficiency and flooding correlations should be used with caution. The limits of models should be checked. For example, since most published packed extractor data are based on small diameter columns, the packings studied are usually small with a high specific surface area. The extrapolation of models primarily based on such high specific surface areas to larger packings with much lower areas... 

The explicit solution can be realized quite reasonably with an Excel worksheet in the sense of the, Press-F9-Method (Section 15.3.1). However, in most cases a program written in a higher programming language will be applied, since this type of modeling is made because one desires to include more complex (bio)geochemical reactions. And sooner or later the limits of modeling are reached when an Excel worksheet is used. 

The teachers noted as important the need for a flexibility of approach in the presentation of a given model to diverse audiences. However, they did not emphasise either the need for a consideration of the scope and limitations of models during the process of modelling or the importance of the discussion of such matters during the presentation of any model to students. 

MuUer-Feuga A, Le Guedes R, Pruvost J Benefits and limitations of modeling for optimization of Porphyridium cruentum cultures in an annular photobioreactor, J Biotechnol 103(2) 153-163, 2003a. 

Surface solution theories should be consistent with the Gibbs adsorption equation (Equation 1.24), just as the bulk solution theories should be consistent with the Gibbs-Duhem equation. It is readily shown that ideal surface solution theory, as discussed above, satisfies this criterion (see Problem 1.15). However, regular surface solution theory does not, owing to the limitations of modeling the interfacial region by a single composition. This matter is discussed in some detail by Defay et al. (1966). 

The detection limit of model substances should be low enough to meet the established requirements. 

Ciborra, C.U. (1998) Crisis and Foundations an Inquiry into the Nature and Limits of Models and Methods in the Information Systems Discipline.of Strategic Information Systems, 7, 5-16. 

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