Related papers: Computer algebra in systems biology
The applicability of computational models to the biological world is an active topic of debate. We argue that a useful path forward results from abandoning hard boundaries between categories and adopting an observer-dependent, pragmatic…
Graph Theoretic Process Network Synthesis is described as an introduction to biological networks. Genetic, protein and metabolic systems are considered. The theoretical work of Kauffman is discussed and amplified by critical property…
Computation biology helps to understand all processes in organisms from interaction of molecules to complex functions of whole organs. Therefore, there is a need for mathematical methods and models that deliver logical explanations in a…
Biology stores information and computes at the molecular scale, yet the ways in which it does so are often distinct from human-engineered computers. Mapping biological computation onto architectures familiar to computer science remains an…
Bacteria have been a source of inspiration for the design of evolutionary algorithms. At the beginning of the 20th century synthetic biology was born, a discipline whose goal is the design of biological systems that do not exist in nature,…
This paper focuses on the need for a rigorous theory of layered control architectures (LCAs) for complex engineered and natural systems, such as power systems, communication networks, autonomous robotics, bacteria, and human sensorimotor…
We advocate the use of qualitative models in the analysis of large biological systems. We show how qualitative models are linked to theoretical differential models and practical graphical models of biological networks. A new technique for…
We review the key role played by mathematical modelling in elucidating two centre-finding patterning systems in E. coli: midcell division positioning by the MinCDE system and DNA partitioning by the ParABS system. We focus particularly on…
Heterologous gene expression draws resources from host cells. These resources include vital components to sustain growth and replication, and the resulting cellular burden is a widely recognised bottleneck in the design of robust circuits.…
In this note for the joint meeting of DMV and GDM we illustrate with examples the role of computer algebra in university mathematics education. We discuss its potential in teaching algebra, but also computer algebra as a subject in its own…
Cellular metabolism, the integrated interconversion of thousands of metabolic substrates through enzyme-catalyzed biochemical reactions, is the most investigated complex intercellular web of molecular interactions. While the topological…
Many cellular processes involve information processing and decision making. We can probe these processes at increasing molecular detail. The analysis of heterogeneous data remains a challenge that requires new ways of thinking about cells…
A system level view of cellular processes for human and several organisms can be cap- tured by analyzing molecular interaction networks. A molecular interaction network formed of differentially expressed genes and their interactions helps…
The observation of neuron-like behaviour in bacteria, such as the occurrence of electric spiking and extended bioelectric signalling, points to the role of membrane dynamics in prokaryotes. Electrophysiology of bacteria, however, has been…
Flocks of birds and schools of fish are familiar examples of spatial patterns formed by living organisms. In contrast to the patterns on the skins of, say, zebra and giraffe, the patterns of our interest are {\it transient} although…
Biological organisms must perform computation as they grow, reproduce, and evolve. Moreover, ever since Landauer's bound was proposed it has been known that all computation has some thermodynamic cost -- and that the same computation can be…
The aim of this paper is to give an overview of brain organoid computing, its characteristics, challenges, as well as possible advantages for future applications in the field of artificial intelligence. An important part is the extensive…
Artificial Intelligence (AI) and Machine Learning (ML) are weaving their way into the fabric of society, where they are playing a crucial role in numerous facets of our lives. As we witness the increased deployment of AI and ML in various…
We discuss the application of computer algebra to problems commonly arising in numerical relativity, such as the derivation of 3+1-splits, manipulation of evolution equations and automatic code generation. Particular emphasis is put on…
In biological research machine learning algorithms are part of nearly every analytical process. They are used to identify new insights into biological phenomena, interpret data, provide molecular diagnosis for diseases and develop…