Computational methods biochemical systems theory

The relevant calculations are commonly handled poorly, because the equilibrium equations involved are difficult to solve manually (but not with computers). The few calculations that are actually reported in the biochemical literature use simplified methods of limited and frequently unknown validity. Large excesses of magnesium ion are frequently used in experiments, perhaps in an attempt to avoid such calculations. The relevant theory is well worked out and there are excellent reviews. The limitation appears to involve diffusion to the (mathematically) inexpert user, which is one of the motivations of building expert systems. 

As most chemical and virtually all biochemical processes occur in liquid state, solvation of the reaction partners is one of the most prominent topics for the determination of chemical reactivity and reaction mechanisms and for the control of reaction conditions and resulting materials. Besides an exhaustive investigation by various experimental methods [1,2,3], theoretical approaches have gained an increasing importance in the treatment of solvation effects [4,5,6,7,8], The reason for this is not only the need for sufficiently accurate models for a physically correct interpretation of the experimental data (Theory determines, what we observe ), but also the limitation of experimental methods in dealing with ultrafast reaction dynamics in the pico- or even subpicosecond regime. These processes have become more and more the domain of computational simulations and a critical evaluation of the accuracy of simulation methods covering experimentally inaccessible systems is of utmost importance, therefore. 

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