Models of Biological Systems

Kohl, R, Noble, D., Winslow, R. L. fit Hunter, P. J. 2000 Computational modelling of biological systems tools and visions. Phil. Trans. R. Soc. Land. A 358, 579-610. 

Pyrazolate as a ligand can exhibit various coordination modes, inter alia, monodentate, exo-bidentate, and endo-bidentate. Several review articles have been published in the field.556-559 The use of pyrazole in the modeling of biological systems was also reviewed.560,561 The most common application of pyrazole ligands is to use its exo-bidentate coordination mode linking two metal centers that may be identical or different (compare Section 6.3.4.12.6). Polypyrazolylborates and related ligands are covered in the subsequent section. 

Modeling of biological systems frequently requires that the accuracy of calculated energy differences are at the kT level (which amounts to less than 1.0 kcal/mol in room temperature). In conventional ab initio methods, such accuracy has been achieved because of effective error cancelation, which is not always the case for the Kohn-Sham calculations. 

Gold, H.J. (1977). Mathematical Modeling of Biological System—An Introductory Guidebook. Wiley, New York. 

Yates FE (1975) On the mathematical modeling of biological systems a qualified pro . In Vemberg FJ (ed) Physiological Adaptation to the Environment. Intext Educational Publishers, New York... 

Iron and Ru porphyrins and phthalocyanines , which are models of biological systems, react with CO at an axial position. Solvent molecules can be involved in the exchange see also ref. 23. Other macrocyclic ligands, e.g., tetradyidines, behave similarly. 

Dr Adrian Mulholland Multiscale modelling of biological systems... 

This review is organized ais follows. In Section 2, we describe the foundations of the method in its most wide-spread implementation, the one based on DPT, plane wave basis sets and pseudopotentials. In Section 3, we outline the different approaches to AIMD modeling of biological systems. This is followed by a summary of the applications that appeared so far (Section 4), with particular emphasis on enzymes (Section 5). Finally, in Section 6, we give an outlook on possible future directions for the investigation of enzymes and other fundamental claisses of biomolecules. 

Kinetic models of biological systems show great potential in guiding the manipulation biological... 

Hall, K., R. Baillie, and S. Michelson. 2002. Biosimulation Dynamic modeling of biological systems. Annu Rep Medicinal Chem 37 279-88. 

Most of the interest in the hydrogen-bond-transmitted spin-spin coupling constants lies in their potential application for determination of the higher order structures of biomolecules proteins and nucleic acids. Consequently, the theoretical papers reporting calculations of the hydrogen-bond-transmitted spin-spin coupling constants in models of biological systems are abundant. 

Computational modeling of biological systems involves the development and use of databases on cellular processes and functions of molecular species. The Pathguide... 

In the previous sections, we have focused on the representation, visualization, and analysis of static graphs and networks. Life, in contrast, is never static, so many models of biological systems are dynamic. A common way to analyze the dynamics of such models is simulation. 

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