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%%% Primary Title: complex systems biophysics
%%% Primary Category Code: 82.39.Rt
%%% Filename: ComplexSystemsBiophysics.tex
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\begin{document}
\section{Complex Systems Biophysics}
\subsection{Introduction}
{\em Complex Systems Biophysics ($CSB$)} or
{\em Complex systems biology ($CSB$)} is generally described as a non-reductionist, mathematical theory of emergent living organisms or biosystems in terms of a network, \htmladdnormallink{graph}{http://planetphysics.us/encyclopedia/Bijective.html} or \htmladdnormallink{category}{http://planetphysics.us/encyclopedia/Cod.html} of integrated interactions between their structural and functional components or \htmladdnormallink{subsystems}{http://planetphysics.us/encyclopedia/GenericityInOpenSystems.html}. This is often abbreviated to
\htmladdnormallink{systems biology}{http://planetphysics.org/?op=getobj&from=books&id=248} in entries that should be described in fact as {\em complex systems biology}.
\subsection{Categorical ontology: theories of existence levels}
\begin{definition}
A {\em \htmladdnormallink{categorical ontology}{http://planetphysics.us/encyclopedia/CategoricalOntology.html} theory of levels} is often defined as the \htmladdnormallink{classification}{http://planetphysics.us/encyclopedia/TrivialGroupoid.html} of ontology, or theory of existence of items (objects--in the mathematical sense) by means of the mathematical theory of categories into three levels of \htmladdnormallink{dynamic systems}{http://planetphysics.us/encyclopedia/GenericityInOpenSystems.html} pertaining to: the physical/chemical level, the biological level, and the psychological level (or human mind). Connections between the three levels of reality and their transformations are represented, respectively, by \htmladdnormallink{morphisms/}{http://planetphysics.us/encyclopedia/TrivialGroupoid.html} and \htmladdnormallink{natural transformations}{http://planetphysics.us/encyclopedia/VariableCategory2.html} defined for \htmladdnormallink{categories of molecular sets}{http://planetphysics.us/encyclopedia/CategoryOfMolecularSets.html},
categories of $(M,R)$-systems and \htmladdnormallink{organismic supercategories}{http://planetphysics.us/encyclopedia/SuperCategory6.html}.
\end{definition}
From a categorical ontology theory of levels viewpoint, however, the term complex is misplaced because {\em \htmladdnormallink{systems}{http://planetphysics.us/encyclopedia/SimilarityAndAnalogousSystemsDynamicAdjointnessAndTopologicalEquivalence.html} with chaos}, or chaotic \htmladdnormallink{dynamics}{http://planetphysics.us/encyclopedia/MathematicalFoundationsOfQuantumTheories.html}, are currently defined by physicists as {\em `complex systems'}, which may have placed a role in the emergence of living systems that are, in fact, {\em super-complex}. Therefore, the more appropriate classification of this relatively new area in mathematical or theoretical biology and Biophysics is super-complex systems biology, $s$-complex systems biology, or simply ``systems biology''--as a more general approach where the focus may be not on the super-complexity aspects of living systems but on \htmladdnormallink{computer}{http://planetphysics.us/encyclopedia/SupercomputerArchitercture.html} modeling of physiological, or functional genomics, integration of physiological flows, signaling pathways or interactomics. However, unlike the case of purely functional $(M,R)$-systems theory in abstract relational biology (\htmladdnormallink{ARB}{http://planetphysics.us/encyclopedia/RSystemsCategory.html}), complex systems biology (or systems biology) proponents are primarily concerned with the integration of data from a multitude of bioinformatics and genomic/proteomic/post-genomic (primarily structural) data; $CSB$ scientists also aim to study {\em interactomics} or {\em metabolomics} primarily through computer-based data analysis, and often Bayesian-based attempts at integration. branches of mathematics that find applications in $CSB$ are, for example: computer modeling, colored graphs, graph-theoretical based approaches, biotopology, genetic, metabolic and signaling network theories, \htmladdnormallink{Bayesian models}{http://planetphysics.us/encyclopedia/GeneNetDigraph.html}, biostatistics, correlation techniques, and less frequently: \htmladdnormallink{abstract algebra}{http://planetphysics.us/encyclopedia/PAdicMeasure.html}, \htmladdnormallink{group}{http://planetphysics.us/encyclopedia/TrivialGroupoid.html} theory, \htmladdnormallink{groupoid}{http://planetphysics.us/encyclopedia/QuantumOperatorAlgebra5.html} and \htmladdnormallink{category theory}{http://planetphysics.us/encyclopedia/TrivialGroupoid.html} modeling of cell-cell interactions and biodynamics.
\end{document}
