Graphical modeling

Since the early 20th century, chemists have represented molecular information by molecular models. The human brain comprehends these representations of graphical models with 3D relationships more effectively than numerical data of distances and angles in tabular form. Thus, visualization makes complex information accessible to human understanding easily and directly through the use of images. 

Graphics- model generated results can be viewed as single/multiple bar, pie, line, and XY. 

Jones TA. A graphics model building and refinement system for macromolecules. JAppl Cryst 1918 11 268. 

Figure 1. Graphical model for the generation of size-controlled metal nanoparticles inside metallated resins, (a) Pd is homogeneously dispersed inside the polymer framework (b) Pd is reduced to Pd (c) Pd atoms start to aggregate in subnanoclusters (d) a single 3 nm nanocluster is formed and blocked inside the largest mesh present in that slice of polymer framework (Reprinted from Ref [5], 2004, with permission from Wiley-VCH.)...

Flow-sheeting is a very useful tool at any stage of process development, regardless the strategy taken. A flow-sheet is a graphical representation of the equipment in the commercial plant. It can be considered to be a graphical model of the plant. A flow-sheet contains (1) all... 

Some of the advantages of computer graphics modelling compared with actual scale models are ... 

Mandagere, A. K., T. N. Thompson, and K. K. Hwang. Graphical model for estimating oral bioavailability of drugs in humans and other species from their Caco-2 permeability and in vitro liver enzyme metabolic stability rates, J. Med. Chem. 2002, 45, 304-311... 

MODELMAKER PC Easy to use, graphical model representation, parameter estimation and optimisation. 

Chatteijee, A., Onodera, Y., Ebina, T., and Mizukami, F. 2003. 2,3,7,8-tetrachloro dibenzo-p-dioxin can be successfully decomposed over 2 1 dioctahedral smectite—a reactivity index study. J. Mol. Graphics Model. 22 93-104. 

Chatteijee, A. 2006. A reactivity index study to rationalize the effect of dopants on Bronsted and Lewis acidity occurring in MeAlPOs. J. Mol. Graphics Model. 24 262-270. 

I. and Andricopulo, A.D. (2007) 3D QSAR comparative molecular field analysis on nonsteroidal farnesoid X receptor activators. Journal of Molecular Graphics Modelling, 25, 921-927. 

Fault Tree Analysis (ETA) provides a structured method for determining the causes of an incident.< 25,26,27) fault tree itself is a graphic model that displays the various comhinations of equipment failures and human errors that can result in an incident. 

Hawkins, D. M. and Musser, B. J. (1999) One tree or a forest Alternative dendro-graphic models. Computing Science and Statistics 30, 534-542... 

Mason, J. S. and Beno, B. R. (2000) Library design using BCUT chemistry-space descriptors and multiple four-point pharmacophore fingerprints Simultaneous optimization and structure-based diversity. J. Mol. Graphics Model. 18, 438-451. 

Cazeau S, Bordachar P, Jauvert G, et al. Echocardio-graphic modeling of cardiac dyssynchrony before and during multisite stimulation a prospective study. Pacing Clin. Electrophysiol. 2003 26 137 3. 

Important quantities which come out of molecular mechanics and quantum chemical models are typically related in terms of numbers , e.g., the heat of a chemical reaction, or in terms of simple diagrams, e.g., an equilibrium structure. Other quantities, in particular those arising from quantum chemical models, may not be best expressed in this way, e.g., the distribution of electrons in molecules. Here computer graphics provides a vessel. This is addressed in the concluding chapter in this section. Graphical Models. 

This chapter introduces a number of useful graphical models, including molecular orbitals, electron densities, spin densities, electrostatic potentials and local ionization potentials, and relates these models both to molecular size and shape and molecular charge distributions. The chapter also introduces and illustrates property maps which simultaneously depict molecular size and shape in addition to a molecular property. Properties include the electrostatic potential, the value of the LUMO, the local ionization potential and the spin density. 

Among the quantities which have proven of value as graphical models are the molecular orbitals, the electron density, the spin density (for radicals and other molecules with unpaired electrons), the electrostatic potential and the local ionization potential. These may all be expressed as three-dimensional functions of the coordinates. One way to display them on a two-dimensional video screen (or on a printed page) is to define a surface of constant value, a so-called isovalue surface or, more simply, isosurface. ... 

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