Related papers: Conception of Biologic System: Basis Functional El…
"Epigenetic Tracking" is a model of systems of biological cells, able to generate arbitrary 2 or 3-dimensional cellular shapes of any kind and complexity (in terms of number of cells, number of colours, etc.) starting from a single cell. If…
A new model is suggested and used to mimic various spatial or temporal designs in biological or non biological formations where the focus is on the normal or irregular electrical signals coming from human heart (ECG) or brain (EEG). The…
The mathematical models used to capture features of complex, biological systems are typically non-linear, meaning that there are no generally valid simple relationships between their outputs and the data that might be used to validate them.…
Living systems continuously transform matter and energy through the chemical processes that constitute their metabolism. The overall metabolic rate of an organism correlates positively with its body mass, however both the exact scaling…
This series presents an approach to mathematical biology which makes precise the function of biological molecules. Because biological systems compute, the theory is a general purpose computer language. I build a language for efficiently…
Physical systems with symmetry arise abundantly in applications, and are endowed with interesting mathematical structures. The present paper focusses on linear reciprocal and input-output Hamiltonian systems. Their characterization is…
Understanding the mechanisms of interactions within cells, tissues, and organisms is crucial to driving developments across biology and medicine. Mathematical modeling is an essential tool for simulating biological systems and revealing…
The physiological tradition of biological research analyzes biological systems using reduced descriptions much as an engineer uses a 'black box' description of an amplifier. Simple models have been used by physiologists for a very long…
Understanding the behaviour of biological systems requires a complex setting of in vitro and in vivo experiments, which attracts high costs in terms of time and resources. The use of mathematical models allows researchers to perform…
Biological systems are generally complicated and/or complex. In the former approach, one sets up a model with a large number of parameters to describe the system in detail. The latter approach focuses on understanding the universal aspects…
The mathematical formalisms used to model biological systems induce both latent and ambiguous assumptions that can limit or distort their representational capabilities. Developing formalisms that can represent systems more precisely is…
Metabolism displays striking and robust regularities in the forms of modularity and hierarchy, whose composition may be compactly described. This renders metabolic architecture comprehensible as a system, and suggests the order in which…
Component systems - ensembles of realizations built from a shared repertoire of modular parts - are ubiquitous in biological, ecological, technological, and socio-cultural domains. From genomes to texts, cities, and software, these systems…
We propose a general approach to the question of how biological rhythms spontaneously self-regulate, based on the concept of ``stochastic feedback''. We illustrate this approach by considering the neuroautonomic regulation of the heart…
Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical…
Living systems, particularly multicellular systems, often seem hopelessly complex. But recent studies have suggested that beneath this complexity, there may be unifying quantitative principles that we are only now starting to unravel. All…
A clear definition of system dynamics modeling can provide shared understanding and clarify the impact of the field. We introduce a set of characteristics that define quantitative system dynamics, selected to capture core philosophy,…
Physics relies on mathematical spaces carefully matched to the phenomena under study. Phase space in classical mechanics, Hilbert space in quantum theory, configuration spaces in field theory all provide representations in which physical…
Life occurs in concentrated `Ringer Solutions' derived from seawater that Lesser Blum studied for most of his life. As we worked together, Lesser and I realized that the questions asked of those solutions were quite different in biology…
Biological systems, unlike physical or chemical systems, are characterized by the very inhomogeneous distribution of their components. The immune system, in particular, is notable for self-organizing its structure. Classically, the dynamics…