Transforming energy, biological models

In order to address the characteristics of biological models, we have to first define the basic principles of biological systems that a supramolecular model may mimic. Among the most important are selective molecular recognition of a molecular entity selective and highly accelerated modification of a substrate (typieal role of enzymes) compartmentalization and selective translocation of chemical species across boundaries (typieal role of biomembranes) harvesting and transformation of energy and self-replication. 

Two hundred years were required before the molecular structure of the double layer could be included in electrochemical models. The time spent to include the surface structure or the structure of three-dimensional electrodes at a molecular level should be shortened in order to transform electrochemistry into a more predictive science that is able to solve the important technological or biological problems we have, such as the storage and transformation of energy and the operation of the nervous system, that in a large part can be addressed by our work as electrochemists. 

Mathematical modeling is the science or art of transforming any macro-scale or microscale problem to mathematical equations. Mathematical modeling of chemical and biological systems and processes is based on chemistry, biochemistry, microbiology, mass diffusion, heat transfer, chemical, biochemical and biomedical catalytic or biocatalytic reactions, as well as noncatalytic reactions, material and energy balances, etc. 

This paper presents a phytoplankton population model in natural waters, constructed on the basis of the principle of conservation of mass. This is an elementary physical law which is satisfied by macroscopic natural systems. The use of this principle is dictated primarily by the lack of any more specific physical laws which can be applied to these biological systems. An alternate conservation law, that of conservation of energy, can also be used. However, the details of how mass is transferred from species to species are better understood than the corresponding energy transformations. The mass interactions are related, among other factors, to the kinetics of the populations, and it is this that the bulk of the paper is devoted to exploring. 

Further developments of these ideas took place in computational structural biology, where nonphysical local transformations were implemented within the framework of thermodynamic cycles. These nonphysical transformations were introduced in 1981 by Warshel, who studied ionization in acidic residues in proteins pK calculations). Although the cycle included nonphysical transformations, they were not carried out by the perturbation technique. A year later Warshel used the perturbation method together with umbrella sampling to study the solvation free energy contribution to an electron transfer reaction coordinate, using two spheres for donor and acceptor in water the perturbation, however, was performed along a physical path. Warshel also modeled some enzymatic reactions that involve nonphysical processes. ... 

A common model used in behavioural science, and in the biological and engineering sciences, is the systems model. Systems are defined as organised entities which are separated by distinct boundaries from the environment in which they operate. They import things across those boundaries, such as energy and information they transform those inputs inside the system, and export some form of output back across the... 

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