Publication Details (including relevant citation information):
Published at World Scientific and Engineering Academy and Society,
cited journals include: nature, Origin of Life, Jurnal of American Chemical Society, European Journal of Biochemistry, The Journal of Biological Chemistry, Clinical Chemistry, Journal of American Physiology, Bioorganic chemistry, Science, Journal of Molecular Biology, Endocrinology and Metabolism, American Journal of Cell Physiology, Bioinformatics, Protein Science, Biophisica and Biochemica acta,
How can we model the causative force of reversible covalent modifications? DNA provides information for synthesizing proteins which in term drive metabolic processes. Understanding basic metabolic processes currently do not help explain regulative forces controlling gene expression. Rather it is claimed that the chromatin state determined by DNA and histone modifications regulate gene expression. We now know that chemistry underlines and explains biological phenomena. However, understanding dynamic chemistry in large space such as a cell has been difficult through conventional models capturing structural changes of metabolites in spatially defined motifs where active sites determine change of mass. How do we expand in space? We certainly need to implement defined physical concepts and to elaborate on set of principles in order to construct emergent principles. The results from sequencing technology have posed new questions that require alternative approaches of system analysis. The functions of non-coding RNA’s have linked gene expression with the smallest covalent modifications, methylation and acetylation. The smallest and the largest molecules such as protein complexes are the most difficult to study in biological systems because of their transient characteristics. Hierarchical time scale differences additionally complicate computational models as open systems tend to be difficult to analyze due to environmental, transport, irreversible, or regulatory constrains. Building a dynamic model of multiple dimensional composite functions at each moment by approximating negativity as a function of mass change is what may be necessary for discovering the causative force underlying oscillations in concentrations and states of small molecules and therefore populations. Is there a mechanism to define species’ variability through the physics of small molecules relative to the origin of carbon signaling?