Related papers: Computational Theory of Biological Function I
We need much better understanding of information processing and computation as its primary form. Future progress of new computational devices capable of dealing with problems of big data, internet of things, semantic web, cognitive robotics…
One of the greatest research challenges of this century is to understand the neural basis for how behavior emerges in brain-body-environment systems. To this end, research has flourished along several directions but have predominantly…
In the fields of computation and neuroscience, much is still unknown about the underlying computations that enable key cognitive functions including learning, memory, abstraction and behavior. This paper proposes a mathematical and…
Integrative biological simulations have a varied and controversial history in the biological sciences. From computational models of organelles, cells, and simple organisms, to physiological models of tissues, organ systems, and ecosystems,…
Axiomatic approach has demonstrated its power in mathematics. The main goal of this preprint is to show that axiomatic methods are also very efficient for computer science. It is possible to apply these methods to many problems in computer…
Bacteria are easily characterizable model organisms with an impressively complicated set of capabilities. Among their capabilities is quorum sensing, a detailed cell-cell signaling system that may have a common origin with eukaryotic…
In this article we highlight chemotaxis (cellular movement) as a rich source of potential engineering applications and computational models, highlighting current research and possible future work. We first give a brief description of the…
Single-cell analysis is currently one of the most high-resolution techniques to study biology. The large complex datasets that have been generated have spurred numerous developments in computational biology, in particular the use of…
It is a fascinating subject to explore how well we can understand the processes of life on the basis of fundamental laws of physics. It is emphasised that viewing biological processes as manipulation of information extracts their essential…
We formally characterize a set of causality-based properties of metabolic networks. This set of properties aims at making precise several notions on the production of metabolites, which are familiar in the biologists' terminology. From a…
Theoretical computer science discusses foundational issues about computations. It asks and answers questions such as "What is a computation?", "What is computable?", "What is efficiently computable?","What is information?", "What is…
This study presents a theoretical model for a self-replicating mechanical system inspired by biological processes within living cells and supported by computer simulations. The model decomposes self-replication into core components, each of…
This article reformulates the theory of computable physical models, previously introduced by the author, as a branch of applied model theory in first-order logic. It provides a semantic approach to the philosophy of science that…
Characterizing structural and dynamic properties of proteins and large macromolecular assemblies is crucial to understand the molecular mechanisms underlying biological functions. In the field of Structural Biology, no single method…
When can a model of a physical system be regarded as computable? We provide the definition of a computable physical model to answer this question. The connection between our definition and Kreisel's notion of a mechanistic theory is…
We investigate the computational power of particle methods, a well-established class of algorit hms with applications in scientific computing and computer simulation. The computational power of a compute model determines the class of…
The chapter presents some new approaches to describing the collective behavior of complex systems of mathematical biology based on the evolution equations of observables such as open systems. This representation of kinetic evolution has…
An astonishingly diverse biomolecular circuitry orchestrates the functioning machinery underlying every living cell. These biomolecules and their circuits have been engineered not only for various industrial applications but also to perform…
Molecular communication is a biologically-inspired method of communication with attractive properties for microscale and nanoscale devices. In molecular communication, messages are transmitted by releasing a pattern of molecules at a…
We consider a new approach to the description of the collective behavior of complex systems of mathematical biology based on the evolution equations for observables of such systems. This representation of the kinetic evolution seems, in…