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Biology has taken strong steps towards becoming a computer science aiming at reprogramming nature after the realisation that nature herself has reprogrammed organisms by harnessing the power of natural selection and the digital prescriptive…
A Topological examination of phospholipid dynamics in the Far from Equilibrium state has demonstrated that metabolically active cells use waste heat to generate spatially patterned membrane flows by forced convection and shear. This paper…
Mathematical methods provide useful framework for the analysis and design of complex systems. In newer contexts such as biology, however, there is a need to both adapt existing methods as well as to develop new ones. Using a combination of…
This paper discusses the meaning and scope of biological hypercomputation (BH). The framework here is computational, and from the outset it should be clear that life is not a standard Turing Machine. Living systems hypercompute, but the…
The payload performance of conventional computing systems, from single processors to supercomputers, reached its limits the nature enables. Both the growing demand to cope with "big data" (based on, or assisted by, artificial intelligence)…
While there has been some discussion on how Symbolic Computation could be used for AI there is little literature on applications in the other direction. However, recent results for quantifier elimination suggest that, given enough example…
A vast array of transformative technologies developed over the past decade has enabled measurement and perturbation at ever increasing scale, yet our understanding of many systems remains limited by experimental capacity. Overcoming this…
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…
Quantum computation has emerged as a powerful computational medium of our time, having demonstrated the remarkable efficiency in factoring a positive integer and searching databases faster than any currently known classical computing…
Do quantum computers already exist in Nature? It is proposed that they do. Photosynthesis is one example in which a 'quantum computer' component may play a role in the 'classical' world of complex biological systems. A 'translation' of the…
Systems are growing into more complex ones for developing and maintaining. Existing systems which do not have much in common on the first look are connected, due to the technical progress, even if it was never intended that way. It is an…
The Turing machine is one of the simple abstract computational devices that can be used to investigate the limits of computability. In this paper, they are considered from several points of view that emphasize the importance and the…
At its core, the physics paradigm adopts a reductionist approach, aiming to understand fundamental phenomena by decomposing them into simpler, elementary processes. While this strategy has been tremendously successful in physics, it has…
Quantum Computing is a new paradigm that enables several advances which are impossible using classical technology. With the rise of quantum computers, the software is also invited to change so that it can better fit this new computation…
Cellular automata are arrays of finite state machines that can exist in a finite number of states. These machines update their states simultaneously based on specific local rules that govern their interactions. This framework provides a…
Metabolism is a fascinating cell machinery underlying life and disease and genome-scale reconstructions provide us with a captivating view of its complexity. However, deciphering the relationship between metabolic structure and function…
Approaching limitations of digital computing technologies have spurred research in neuromorphic and other unconventional approaches to computing. Here we argue that if we want to systematically engineer computing systems that are based on…
This work proposes to use evolutionary computation as a pathway to allow a new perspective on the modeling of energy expenditure and recovery of an individual athlete during exercise. We revisit a theoretical concept called the "three…
We show that many important natural science models in their mathematical formulation can be reduced to non-strictly hyperbolic systems of the same kind. This allows the same methods to be applied to them so that some essential results…
Recent studies have shown that the majority of published computational models in systems biology and physiology are not repeatable or reproducible. There are a variety of reasons for this. One of the most likely reasons is that given how…