Biochemical dynamics

Love, R.M. (1997). Biochemical dynamics and the quality of fresh and frozen fish. In Fish Processing Technology , 2nd edn (G.M. Hall, ed.), pp.1-31. Blackie Academic and Professional, London. 

It is possible to understand the biochemical dynamics of life processes by detecting and tracking individual macromolecules in living cell membranes and tissues. 

Semiconducting nanocrystals, usually CdSe-ZnS crystals a few nanometers in diameter, called quantum dots, can be useful for in vivo imaging of biochemical dynamics but still suffer from three limitations.51 The most severe problem is that quantum dots blink at probability distributions that lead to loss of continuity in keeping track of individual molecules, limiting the ability to measure the dynamics and mechanisms of biophysical chemistry in vivo and ex vivo. Some significant fraction of fabricated quantum dots appear to be totally dark, reducing... 

R2) 1972 Gurel, O. Bifurcation Theory in Biochemical Dynamics, In Analysis and Simulation... 

The steroids constitute a group of structurally related compounds that are widely distributed both in the plant and the animal kingdom. The basic nucleus of these physiologically potent and biochemically dynamic medicinal compounds do possess a more or less similar stereochemical relationship. The steroids, in gemeal, have been found to contain either the partly or completely hydrogenated 17H-cyclopenta-phenanthrene nucleus. 

Note Abbreviations used BD, biochemical dynamics DB, database PDF, portable document format PS, postscript SS, spread sheets, WP, word processing. 

Kincaid J R 1995 Structure and dynamics of transient species using time-resolved resonance Raman-spectroscopy Biochemical Spectroscopy Methods Enzymol. vol 246, ed K Sauer (San Diego, CA Academic) pp 460-501... 

Interpretable high-resolution structural infomiation (e.g. preservation of dimensions, or correlation of the stmctiiral detail with a physiologically or biochemically controlled state) is therefore obtained exclusively from samples in which life has been stopped very quickly and with a sufficiently high time resolution for the cellular dynamics [19]. Modem concepts for specimen preparation therefore try to avoid traditional, chemical... 

Knoll G and Plattner H 1989 Ultrastructural analysis of biological membrane fusion and a tentative correlation with biochemical and biophysical aspects Electron Microscopy of Subcellular Dynamics ed H Plattner (London CRC) pp 95-117... 

Most chemically reacting systems tliat we encounter are not tliennodynamically controlled since reactions are often carried out under non-equilibrium conditions where flows of matter or energy prevent tire system from relaxing to equilibrium. Almost all biochemical reactions in living systems are of tliis type as are industrial processes carried out in open chemical reactors. In addition, tire transient dynamics of closed systems may occur on long time scales and resemble tire sustained behaviour of systems in non-equilibrium conditions. A reacting system may behave in unusual ways tliere may be more tlian one stable steady state, tire system may oscillate, sometimes witli a complicated pattern of oscillations, or even show chaotic variations of chemical concentrations. 

The existence of chaotic oscillations has been documented in a variety of chemical systems. Some of tire earliest observations of chemical chaos have been on biochemical systems like tire peroxidase-oxidase reaction [12] and on tire well known Belousov-Zhabotinskii (BZ) [13] reaction. The BZ reaction is tire Ce-ion-catalyzed oxidation of citric or malonic acid by bromate ion. Early investigations of the BZ reaction used tire teclmiques of dynamical systems tlieory outlined above to document tire existence of chaos in tliis reaction. Apparent chaos in tire BZ reaction was found by Hudson et a] [14] aiid tire data were analysed by Tomita and Tsuda [15] using a return-map metliod. Chaos was confinned in tire BZ reaction carried out in a CSTR by Roux et a] [16, E7] and by Hudson and... 

Schreiber, H., Steinhauser, O. Cutoff size does strongly influence molecular dynamics results on solvated polypeptides. Biochem. 31 (1992) 5856-5860. 

Many of the species involved in the endogenous metabolism can undergo a multitude of transformations, have many reaction channels open, and by the same token, can be produced in many reactions. In other words, biochemical pathways represent a multi-dimensional space that has to be explored with novel techniques to appreciate and elucidate the full scope of this dynamic reaction system. 

A numerical study of the effect of area ratio on the flow distribution in parallel flow manifolds used in a Hquid cooling module for electronic packaging demonstrate the useflilness of such a computational fluid dynamic code. The manifolds have rectangular headers and channels divided with thin baffles, as shown in Figure 12. Because the flow is laminar in small heat exchangers designed for electronic packaging or biochemical process, the inlet Reynolds numbers of 5, 50, and 250 were used for three different area ratio cases, ie, AR = 4, 8, and 16. 

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]. 

Walmsley, A. R., 1988. The dynamics of die glucose transporter. Trends in Biochemical Sciences 13 226—231. 

Mackintosh C (2004) Dynamic interactions between 14-3-3 proteins and phosphoproteins regulate diverse cellular processes. Biochem J 381 329-342... 

Ovadi, J. (1988). Old pathway—new concept Control of glycolysis by metabolite-modulated dynamic enzyme associations. Trends Biochem. Sci. 13,486-490. 

---