Related papers: Computational Theory of Biological Function I

We extend the concept that life is an informational phenomenon, at every level of organisation, from molecules to the global ecological system. According to this thesis: (a) living is information processing, in which memory is maintained by…

Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…

Whole-cell computational models aim to predict cellular phenotypes from genotype by representing the entire genome, the structure and concentration of each molecular species, each molecular interaction, and the extracellular environment.…

We propose a variant of the CCS process algebra with new features aiming at allowing multiscale modelling of biological systems. In the usual semantics of process algebras for modelling biological systems actions are instantaneous. When…

The neural mechanism of memory has a very close relation with the problem of representation in artificial intelligence. In this paper a computational model was proposed to simulate the network of neurons in brain and how they process…

Many cell functions are accomplished thanks to intracellular transport mechanisms of macromolecules along filaments. Molecular motors such as dynein or kinesin are proteins playing a primary role in these processes. The behavior of such…

Living cells use readout molecules to record the state of receptor proteins, similar to measurements or copies in typical computational devices. But is this analogy rigorous? Can cells be optimally efficient, and if not, why? We show that,…

Inspired by the work of Feynman, Deutsch, We formally propose the theory of physical computability and accordingly, the physical complexity theory. To achieve this, a framework that can evaluate almost all forms of computation using various…

In current molecular communication (MC) systems, performing computational operations at the nanoscale remains challenging, restricting their applicability in complex scenarios such as adaptive biochemical control and advanced nanoscale…

Biochemical networks are used in computational biology, to model the static and dynamical details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as…

Mathematical modelling allows us to concisely describe fundamental principles in biology. Analysis of models can help to both explain known phenomena, and predict the existence of new, unseen behaviours. Model analysis is often a complex…

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…

Many real-world dynamic systems, both natural and artificial, are understood to be performing computations. For artificial dynamic systems, explicitly designed to perform computation - such as digital computers - by construction, we can…

Basic principles of mathematical modeling are reviewed in this book, with the focus on physics and its practical applications, and examples of selected mathematical methods are presented. Most of the models have been imported from physics…

Living systems, from single cells to higher vertebrates, receive a continuous stream of non-stationary inputs that they sense, e.g., via cell surface receptors or sensory organs. Integrating these time-varying, multi-sensory, and often…

Cellular automata are a discrete dynamical system which models massively parallel computation. Much attention is devoted to computations with small time complexity for which the parallelism may provide further possibilities. In this paper,…

We present a method for logical specification of the behavior of a system based on the specification of its components and for representing and specifying the effect of a class of communication "signaling pathways" among them. Variations in…

It has been shown that a functional interpretation of proofs in mathematical analysis can be given by the product of selection functions, a mode of recursion that has an intuitive reading in terms of the computation of optimal strategies in…

Typology is a subfield of linguistics that focuses on the study and classification of languages based on their structural features. Unlike genealogical classification, which examines the historical relationships between languages, typology…

Computational molecular design -- the endeavor to design molecules, with various missions, aided by machine learning and molecular dynamics approaches, has been widely applied to create valuable new molecular entities, from small molecule…