Biological systems, modeling

Stokes CL. Biological systems modeling powerful medicine for biomedical eR D. Am Inst Chem g/2000 46 430. 

Bensasson R V, Bienvenue E, Dellinger M, Leach S and Seta P 1994 Cgg in model biological systems. A visible-UV absorption study of solvent-dependent parameters and solute aggregation J. Phys. Chem. 98 3492-5000... 

Bala, P., Grochowsky, R, Lesyng, B., McCammon, J.A. Quantum-classical molecular dynamics. Models and applications. In Quantum mechanical simulation methods for studying biological systems, D. Bicout and M. Field, eds. Springer, Berlin (1996) 119-156. 

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)... 

Biological Antioxidant Models. Tea extracts, tea polyphenol fractions, and purified catechins have all been shown to be effective antioxidants in biologically-based model systems. A balance between oxidants and antioxidants is critical for maintenance of homeostasis. Imbalances between free radicals and antioxidants may be caused by an increased production of free radicals or decreased effectiveness of the antioxidants within the reaction system. These imbalances can be caused by the radicals overwhelming the antioxidants within the system, or by an excess of antioxidants leading to a prooxidant functionaHty (105—118). When antioxidant defense systems are consistently overwhelmed by oxidative reactions, significant damage can... 

Since biological systems can reasonably cope with some of these problems, the intuition behind neural nets is that computing systems based on the architecture of the brain can better emulate human cognitive behavior than systems based on symbol manipulation. Unfortunately, the processing characteristics of the brain are as yet incompletely understood. Consequendy, computational systems based on brain architecture are highly simplified models of thek biological analogues. To make this distinction clear, neural nets are often referred to as artificial neural networks. 

The activity of antioxidants in food [ 1 ] emulsions and in some biological systems [2] is depends on a multitude of factors including the localisation of the antioxidant in the different phases of the system. The aim of this study is determining antioxidant distributions in model food emulsions. For the purpose, we measured electrochemically the rate constant of hexadecylbenzenediazonium tetrafluorborate (16-ArN,BF ) with the antioxidant, and applied the pseudophase kinetic model to interpret the results. 

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 potential energy function presented in Eqs. (2) and (3) represents the minimal mathematical model that can be used for computational studies of biological systems. Currently,... 

The concentration of salt in physiological systems is on the order of 150 mM, which corresponds to approximately 350 water molecules for each cation-anion pair. Eor this reason, investigations of salt effects in biological systems using detailed atomic models and molecular dynamic simulations become rapidly prohibitive, and mean-field treatments based on continuum electrostatics are advantageous. Such approximations, which were pioneered by Debye and Huckel [11], are valid at moderately low ionic concentration when core-core interactions between the mobile ions can be neglected. Briefly, the spatial density throughout the solvent is assumed to depend only on the local electrostatic poten-... 

One of the major uses of molecular simulation is to provide useful theoretical interpretation of experimental data. Before the advent of simulation this had to be done by directly comparing experiment with analytical (mathematical) models. The analytical approach has the advantage of simplicity, in that the models are derived from first principles with only a few, if any, adjustable parameters. However, the chemical complexity of biological systems often precludes the direct application of meaningful analytical models or leads to the situation where more than one model can be invoked to explain the same experimental data. 

It should be noted that compounds of this type " have been of interest as models for hydride transfer reductions in biological systems. Van Bergen and Kellogg state clearly their hope, if not expectation, that when ions such as H, Zn , Mg, etc. are com-plexed in the vicinity of the donor, beneficial catalytic effects might be forthcoming . ... 

This model was first introduced by Kauffman [kauff69] in a study of cellular differentiation in a biological system (binary sites were interpreted as elements of an ensemble of genes switching on and off according to some set of random rules). Since its original conception, however, related models have found wide application in an... 

Any system whose top-level behavior is a consequence of the aggregate behavior of lower-level entities - biological systems, neural systems, social systems, economic systems, among many others - can, in principle, be simulated by an agent-based model. 

In the biological field, much attention has been directed toward the transport phenomena through membrane. Although the function of some natural ionophores has been known, the investigation of active and selective transport of ions using the artificial ionophores in the simple model systems may be important to simulate the biological systems and clarify the transport behaviour of natural membranes. 

Statistics in general is a discipline dealing with ideas on description of data, implications of data (relation to general pharmacological models), and questions such as what effects are real and what effects are different Biological systems are variable. Moreover, often they are living. What this means is that they are collections of biochemical reactions going on in synchrony. Such systems will have an intrinsic variation in their output due to the variances in the... 

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