Models/modeling biological interactions

The bilinear model has been used to model biological interactions in isolated receptor systems and in adsorption, metabolism, elimina- tion, and toxicity studies, although it has a few limitations. These include the need for at least 15 data points (because of the presence of the additional disposable parameter jS and data points beyond optimum LogP. If the range in values for the dependent variable is limited, unreasonable slopes are obtained. 

Developing chemical engineering models for fundamental biological interactions. 

L Herbette, AM Katz, JM Sturtevant. Comparisons of the interaction of propranolol and timolol with model biological membrane systems. Molec Pharmacol 24 259-269, 1983. 

An evaluation of the fate of trace metals in surface and sub-surface waters requires more detailed consideration of complexation, adsorption, coagulation, oxidation-reduction, and biological interactions. These processes can affect metals, solubility, toxicity, availability, physical transport, and corrosion potential. As a result of a need to describe the complex interactions involved in these situations, various models have been developed to address a number of specific situations. These are called equilibrium or speciation models because the user is provided (model output) with the distribution of various species. 

Luoma, S.N. and G.W. Bryan. 1979. Trace metal bioavailability modehng chemical and biological interactions of sediment-bound zinc. Pages 577-609 in E.A. Jenne (ed.). Chemical Modeling in Aqueous Systems. Amer. Chem. Soc., Sympos. Ser. 93, Washington, D.C. 

The processes controlling transfer and/or removal of pollutants at the aqueous-solid phase interface occur as a result of interactions between chemically reactive groups present in the principal pollutant constituents and other chemical, physical and biological interaction sites on solid surfaces [1]. Studies of these processes have been investigated by various groups (e.g., [6-14]). Several workers indicate that the interactions between the organic pollutants/ SWM leachates at the aqueous-solid phase surfaces involve chemical, electrochemical, and physico-chemical forces, and that these can be studied in detail using both chemical reaction kinetics and electrochemical models [15-28]. 

Biochemistry and chemistry takes place mostly in solution or in the presence of large quantities of solvent, as in enzymes. As the necessary super-computing becomes available, molecular dynamics must surely be the method of choice for modeling structure and for interpreting biological interactions. Several attempts have been made to test the capability of molecular dynamics to predict the known water structure in crystalline hydrates. In one of these, three amino acid hydrates were used serine monohydrate, arginine dihydrate and homoproline monohydrate. The first two analyses were by neutron diffraction, and in the latter X-ray analysis was chosen because there were four molecules and four waters in the asymmetric unit. The results were partially successful, but the final comments of the authors were "this may imply that methods used currently to extract potential function parameters are insufficient to allow us to handle the molecular-level subtleties that are found in aqueous solutions" (39). 

The spread mixed lipid monolayer studies provide information about the packing and orientation of such molecules at the water interface. These interfacial characteristics affect many other systems. For instance, mixed surfactants are used in froth flotation. The monolayer surface pressure of a pure surfactant is measured after the injection of the second surfactant. From the change in n, the interaction mechanism can be measured. The monolayer method has also been used as a model biological membrane system. In the latter BLM, lipids are found to be mixed with other lipidlike molecules (such as cholesterol). Hence, mixed monolayers of lipids + cholesterol have been found to provide much useful information on BLM. The most important BLM and temperature melting phenomena is the human body temperature regulation. Normal body temperature is 37°C (98°F), at which all BLM function efficiently. 

Determination of the binding site or possible biological interactions to use as a template for the modelling,... 

Grant, G.T., Morris, E.R., Rees, D.A., Smith, P.J.C., Thom, D. (1973). Biological interactions between polysaccharides and divalent cations the egg-box model. FEES Letters, 32, 195-198. 

Many publications are devoted to the synthesis of nitrile complexes, carried out by the immediate (direct) interaction of RCN and MX , mostly in the absence of a solvent [10, p. 95]. A series of N-donors, N-containing heterocyclic donors, whose complexes frequently model biologically important objects (Sec. 2.2.42), should be mentioned apart. The following compounds belong to this type azoles 188, azines 189, and their amino derivatives 572. Their interaction with metal salts takes place usually without a solvent with the use of liquid heterocyclic ligands, for example pyridine [10, ch. 4, p. 107 11], in alcohol or alcohol-aqueous mediums in cases of crystalline ligands (3.10)—(3.12). The specific conditions are presented in the literature, cited in Sec. 2.2.4.2. 

In the first model, we sought to reveal subgraphs of a biological interaction network that show substantial adaptations when cells transcriptionally respond to a changing environment or treatment. As a case study, we investigated the response of the malaria parasite Plasmodium falciparum to chloroquine and tetracycline treatments. 

Thin liquid films (especially foam films) stabilised with phospholipids, proteins, etc., prove to be very suitable in the study of surface forces, since they could model the interacting biological membranes in aqueous medium. 

Michael E. Paulaitis is Professor of Chemical and Biomolecular Engineering and Ohio Eminent Scholar at Ohio State University. He is also Director of the Institute of Multiscale Modeling of Biological Interactions at Johns Hopkins University. His research focuses on molecular thermodynamics of hydration, protein solution thermodynamics, and molecular simulations of biological macromolecules. 

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