Refinement of models

The greatest value of molecular dynamic simulations is that they complement and help to explain existing data for designing new experiments. The simulations are increasingly useful for structural refinement of models generated from NMR, distance geometry, and X-ray data. 

Refinement of models of radionuclide transfer in food chains to aid in the assessment of radioactive releases from nuclear reactors and other point sources, including possible biomagnification by trophic components and turnover rates by receptor organisms (Kitchings et al. 1976)... 

An Emphasis on Models Chemistry proceeds by the construction and refinement of models. Models are proposed on the basis of insight, developed with mathematics, and refined in the light of experiment. In each chapter, we therefore take care to assemble experimental information, then devise or adapt a simple model to account for the observation. When possible, we express that model mathematically. Then we explore how the model may be refined to match experimental facts. 

Each refined orientation of the probe received a correlation coefficient that shows how well it fits the Patterson map of ALBP. The orientation receiving the highest correlation coefficient was taken as the best orientation of the probe, and then used to refine the position of the probe in the ALBP unit cell. The orientation and position of the model obtained from the molecular replacement search was so good that refinement of the model as a rigid body produced only slight improvement in R. The authors attribute this to the effectiveness of the Patterson correlation refinement of model orientation, stage two of the search. 

Refinement of modeling techniques Compare predicted spray patterns with measurements... 

Summary. Most of the automatic burets which have been discussed have been primarily refinements of models that were introduced many years ago. In the adaptations of automatic burets to microchemistry, some burets have eliminated major drainage errors and contact of titrant with mercury and have provided readily readable volumes on dials or mechanical counters. These improvements are reflected in increased... 

In summary the refinement of model B gives a much better agreement between theory and experiment and should therefore represent a more reliable molecular geometry than that of model A. For model A we achieved an R value of0.0424 with 163 parameters refined based on 1799 intensities for model B these values are R = 0.0420, 172 parameters. Based on the ab initio data in Table 2, we suggest 1.39 A as a reference value for the B-O bond distance in oxadiboriranes. 

These types of partially independent validation are of course tempting, and they do allow refinement of models and scores (Verweij and van HouweUngen 1993 Schumacher et al. 1997 Babyak 2004), but they are not a sufficient validation. Clearly, with each of the approaches listed above, there will be many similarities between the derivation and validation sets of patients, and between the clinical and laboratory techniques used in evaluating them. Indeed, this lack of true independence of the validation group of patients probably explains, in part, the fact that researchers tend to confirm the validity of their own models more often than do independent researchers (Altman and Royston 2000 Altman and Royston 2007). The likely generalizability and so usefulness of a model can usually only be shown convincingly in a completely independent group of patients. 

As writing was completed for this Special Issue in 2007, the articles testify to the growth and vitality of the field due to refinements of modeling and theories, advancements in computational science, and collaboration across scientific disciplines. 

Unfortunately, a straightforward Rietveld refinement of model A fails because it is far from reality, in addition to the low resolution of powder diffraction data. Therefore, the initial model A must be improved before attempting the Rietveld refinement. The improvement was achieved using the following two approaches to geometry optimization ... 

Although activation of the AHR by DLCs is a key event, mechanistic data indicate that AHR-mediated responses are not well conserved across species, with lower sensitivity in humans. A TEF value for a DLC based on rodent data may overestimate the potency of a DLC in humans, and this has not been considered in the current risk assessment of DLCs. Thus, the current TEF-Toxic Equivalency Quotient scheme tends to compound the conservative estimates of risk that exist within standard risk assessment approaches. Moreover mechanistic differences will now be considered by US EPA in the risk assessment of chemical carcinogens. The mechanistic data currently available for receptor-mediated DLCs and PPs clearly indicate that humans respond differently to these two classes of rodent carcinogens, and these data will need to be incorporated into cancer risk assessments for these chemicals. Full appreciation of the species differences in these receptor mechanisms will require continued development and refinement of models such as primary... 

Estimation or refinement of model parameters, sometimes described as the inverse problem, is complex because such problems usually do not have a unique... 

An entirely new level of sophistication—not only in experiments but also in modeling—will be required for particles, aerosols, and the associated radiation field sets. New mid-IR laser-based instrumentation and use of long-duration balloons have helped make major advances in observations. The balloons can sit in the upper stratosphere and then be lowered to the lower stratosphere with power from fuel cells and solar panels. The modeling elements are equally important it is necessary to test the model and its validity, and the model must link the measurements. The observations must be linked to trajectories, the trajectories must be initialized, and sources of specific chemicals must be identified along with the positions of those sources. Considerable progress has been made on observations and refinement of models to help explain low ozone loss at the mid-altitudes, the increase in UV dosage, the appearance of water vapor in the stratosphere, and possibly, of climate changes 50 million years ago. 

The question becomes, then, whether further refinements of models and of the methods used to formulate them are likely to provide the predictive configurations that a systematic rank-dependent molecular chemistry implies, or whether coals of similar rank and petrographic compositions can be so differentiated by their source materials and formative histories so as to make them chemically quite disparate solids. 

At atomic resolution, the number of observables is much higher than at medium or low resolution (see Table 10.1) allowing for the refinement of models with more parameters representing a more detailed description of the structure and the flexibility of the molecule in the crystal, for example by using anisotropic displacements parameters (17, U, 17, instead of isotropic 5-values that are... 

Refinement of model in the light of the quantum theory of atoms... 

The RNA pseudoatom method has also been applied to the building and refinement of models for the catalytic RNA of RNase P (9). 

The extensive data requirements for a CGE model present a significant limitation to the more widespread application in earthquake economic impact assessment. In addition to all of the data requirements of a typical lO model, a CGE model requires the input of numerous behavioral functions and substitution parameters. Parameter estimation is also often based on data from historic behavior under business-as-usual conditions, and such behavior may be ill suited to describing behavior following a seismic event. Although some advancements have been made toward refinement of model parameters to better suit disaster analysis (Rose and Liao 2005), the examples of such work are still relatively few. 

This rather simplistic model leads to a predicted behavior which is at least in qualitative agreement with the experimental results depicted in Fig. 3.22. The refinement of models of this type must await the development of a better understanding of sintering kinetics. 

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