Related papers: The Computational Universality of Metabolic Comput…
Infinite time Turing machines extend the operation of ordinary Turing machines into transfinite ordinal time. By doing so, they provide a natural model of infinitary computability, a theoretical setting for the analysis of the power and…
Topological mapping of a large physical system on a graph, and its decomposition using universal measures is proposed. We find inherent limits to the potential for optimization of a given system and its approximate representations by…
Due to common misconceptions about the Church-Turing thesis, it has been widely assumed that the Turing machine provides an upper bound on what is computable. This is not so. The new field of hypercomputation studies models of computation…
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…
This is the first report, to our knowledge, on a systematic method for constructing a large scale kinetic metabolic model with incomplete information on kinetic parametersr, and its initial application to the modeling of central metabolism…
On the basis of introspective analysis, we establish a crucial requirement for the physical computation basis of consciousness: it should allow processing a significant amount of information together at the same time. Classical computation…
Quantitative studies of cell metabolism are often based on large chemical reaction network models. A steady state approach is suited to analyze phenomena on the timescale of cell growth and circumvents the problem of incomplete experimental…
A major goal of modern computational biology is to simulate the collective behaviour of large cell populations starting from the intricate web of molecular interactions occurring at the microscopic level. In this paper we describe a…
A key challenge in modern computing is to develop systems that address complex, dynamic problems in a scalable and efficient way, because the increasing complexity of software makes designing and maintaining efficient and flexible systems…
In prokaryotic genomes the number of transcriptional regulators is known to quadratically scale with the total number of protein-coding genes. Toolbox model was recently proposed to explain this scaling for metabolic enzymes and their…
Modeling and simulation are recognized as important aspects of the scientific method for more than 70 years but its adoption in biology has been slow. Debates on its representativeness, usefulness, and whether the effort spent on such…
Adaptive control provides techniques for adjusting control parameters in real time to maintain system performance despite unknown or changing process parameters. These methods use real data to tune controllers and adjust plant models or…
Presented with sensory challenges, living cells employ extensive noisy, fluctuating signalling and communication among themselves to compute a physiologically proper response which often results in symmetry breaking. We propose, based on…
Applying the lens of computation and information has been instrumental in driving the technological progress of our civilization as well as in empowering our understanding of the world around us. The digital computer was and for many still…
Measurement in biological systems became a subject of concern as a consequence of numerous reports on limited reproducibility of experimental results. To reveal origins of this inconsistency, we have examined general features of biological…
A universal Turing machine is a powerful concept - a single device can compute any function that is computable. A universal spin model, similarly, is a class of physical systems whose low energy behavior simulates that of any spin system.…
The basic idea of lifelike computing systems is the transfer of concepts in living systems to technical use that goes even beyond existing concepts of self-adaptation and self-organisation (SASO). As a result, these systems become even more…
In recent years, there has been tremendous progress in the development of quantum computing hardware, algorithms and services leading to the expectation that in the near future quantum computers will be capable of performing simulations for…
The performance, reliability, cost, size and energy usage of computing systems can be improved by one or more orders of magnitude by the systematic use of modern control and optimization methods. Computing systems rely on the use of…
Synthetic biologists have made great progress over the past decade in developing methods for modular assembly of genetic sequences and in engineering biological systems with a wide variety of functions in various contexts and organisms.…