Biological time scales

Thode, H.G., Macnamara, J. and Fleming, W.H., 1953. Sulfur isotope fractionation and geological and biological time scales. Geochim. Cosmochim. Acta, 3 235—243. 

One of the main attractions of normal mode analysis is that the results are easily visualized. One can sort the modes in tenns of their contributions to the total MSF and concentrate on only those with the largest contributions. Each individual mode can be visualized as a collective motion that is certainly easier to interpret than the welter of information generated by a molecular dynamics trajectory. Figure 4 shows the first two normal modes of human lysozyme analyzed for their dynamic domains and hinge axes, showing how clean the results can sometimes be. However, recent analytical tools for molecular dynamics trajectories, such as the principal component analysis or essential dynamics method [25,62-64], promise also to provide equally clean, and perhaps more realistic, visualizations. That said, molecular dynamics is also limited in that many of the functional motions in biological molecules occur in time scales well beyond what is currently possible to simulate. 

For 25 years, molecular dynamics simulations of proteins have provided detailed insights into the role of dynamics in biological activity and function [1-3]. The earliest simulations of proteins probed fast vibrational dynamics on a picosecond time scale. Fifteen years later, it proved possible to simulate protein dynamics on a nanosecond time scale. At present it is possible to simulate the dynamics of a solvated protein on the microsecond time scale [4]. These gains have been made through a combination of improved computer processing (Moore s law) and clever computational algorithms [5]. 

W Pfeiffer, T Henkel, E Sackmann, W Knoll, D Richter. Europhys Lett 8 201-206, 1989. RW Pastor, SE Eeller. Time scales of lipid dynamics and molecular dynamics. In KM Merz Jr, B Roux, eds. Biological Membranes A Molecular Perspective from Computation and Experiment. Boston Birkhauser, 1996, pp 3-30. 

The sediment reservoir (1) represents all phosphorus in particulate form on the Earth s crust that is (1) not in the upper 60 cm of the soil and (2) not mineable. This includes unconsolidated marine and fresh water sediments and all sedimentary, metamorphic and volcanic rocks. The reason for this choice of compartmentalization has already been discussed. In particulate form, P is not readily available for utilization by plants. The upper 60 cm of the soil system represents the portion of the particulate P that can be transported relatively quickly to other reservoirs or solubilized by biological uptake. The sediment reservoir, on the other hand, represents the particulate P that is transported primarily on geologic time scales. 

While these calculations provide information about the ultimate equilibrium conditions, redox reactions are often slow on human time scales, and sometimes even on geological time scales. Furthermore, the reactions in natural systems are complex and may be catalyzed or inhibited by the solids or trace constituents present. There is a dearth of information on the kinetics of redox reactions in such systems, but it is clear that many chemical species commonly found in environmental samples would not be present if equilibrium were attained. Furthermore, the conditions at equilibrium depend on the concentration of other species in the system, many of which are difficult or impossible to determine analytically. Morgan and Stone (1985) reviewed the kinetics of many environmentally important reactions and pointed out that determination of whether an equilibrium model is appropriate in a given situation depends on the relative time constants of the chemical reactions of interest and the physical processes governing the movement of material through the system. This point is discussed in some detail in Section 15.3.8. In the absence of detailed information with which to evaluate these time constants, chemical analysis for metals in each of their oxidation states, rather than equilibrium calculations, must be conducted to evaluate the current state of a system and the biological or geochemical importance of the metals it contains. 

The selection of biological indicators shoirld be guided by criteria to ensure that the indicators are relevant, useful, and sufficiently diagnostic to detect a change in the concentration of mercury in whole organisms or specific tissue(s) over multi-year or decadal time scales. We identified 9 criteria for the selection of biological indicators ... 

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