Biological systems mechanisms

Interactions between macromolecules (protems, lipids, DNA,.. . ) or biological structures (e.g. membranes) are considerably more complex than the interactions described m the two preceding paragraphs. The sum of all biological mteractions at the molecular level is the basis of the complex mechanisms of life. In addition to computer simulations, direct force measurements [98], especially the surface forces apparatus, represent an invaluable tool to help understand the molecular interactions in biological systems. 

Handy, N.C. Density functional theory. In Quantum mechanical simulation methods for studying biological systems, D. Bicout and M. Field, eds. Springer, Berlin (1996) 1-35. 

Devault, D. Quantum mechanical tunnelling in biological systems. Quart. Rev. Biophys. 13 (1980) 387-564. 

P. Bala, P. Grochowski, B. Lesyng, and J. A. McCammon Quantum-classical molecular dynamics. Models and applications. In Quantum Mechanical Simulation Methods for Studying Biological Systems (M. Fields, ed.). Les Houches, France (1995)... 

The mechanisms of formation of oxiranes by biological systems (which are relevant to carcinogenesis — see the penultimate paragraph) are the subject of continuing interest <81JA6744. 81JA7371). 

Peroxide oxidation processes in human organism are one of based phenomena that is responsible for homeostasis. For this reason development and investigation of interaction mechanism between different biomacromolecules and lipids peroxide are important for forming complete picture of functioning of human being as biological system. 

Mechanism of action of nanosized (0.005 - 0.02 p.m) powders of ferromagnetics on biological systems is based on effect of magnetic fields created by ferromagnetic microcrystal assemblies and on specific action of every metal added which determined the field of practical application. 

Empirical energy functions can fulfill the demands required by computational studies of biochemical and biophysical systems. The mathematical equations in empirical energy functions include relatively simple terms to describe the physical interactions that dictate the structure and dynamic properties of biological molecules. In addition, empirical force fields use atomistic models, in which atoms are the smallest particles in the system rather than the electrons and nuclei used in quantum mechanics. These two simplifications allow for the computational speed required to perform the required number of energy calculations on biomolecules in their environments to be attained, and, more important, via the use of properly optimized parameters in the mathematical models the required chemical accuracy can be achieved. The use of empirical energy functions was initially applied to small organic molecules, where it was referred to as molecular mechanics [4], and more recently to biological systems [2,3]. 

The treatment of electrostatics and dielectric effects in molecular mechanics calculations necessary for redox property calculations can be divided into two issues electronic polarization contributions to the dielectric response and reorientational polarization contributions to the dielectric response. Without reorientation, the electronic polarization contribution to e is 2 for the types of atoms found in biological systems. The reorientational contribution is due to the reorientation of polar groups by charges. In the protein, the reorientation is restricted by the bonding between the polar groups, whereas in water the reorientation is enhanced owing to cooperative effects of the freely rotating solvent molecules. 

DeVault, D., 1984, Quantum-Mechanical Tunneling in Biological Systems (Cambridge Univ. Press, Cambridge). 

The molecular structure and dynamics of the ice/water interface are of interest, for example, in understanding phenomena like frost heaving, freezing (and the inhibition of freezing) in biological systems, and the growth mechanisms of ice crystals. In a series of simulations, Haymet and coworkers (see Refs. 193-196) studied the density variation, the orientational order and the layer-dependence of the mobilitity of water molecules. The ice/water basal interface is found to be a relatively broad interface of about... 

Further work on these systems would obviously be very welcome, considering the implications of such stereoregulated mechanisms to biological systems, and in view of the rather unexpected findings reported lately66,67 which add new interest to this field. 

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