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The modelling and analysis of biological systems has deep roots in Mathematics, specifically in the field of ordinary differential equations (ODEs). Alternative approaches based on formal calculi, often derived from process algebras or term…
In the present work we will present and analyze some basic processes at the local and global level in linguistic derivations that seem to go beyond the limits of Markovian or Turing-like computation, and require, in our opinion, a quantum…
The relationship between computational models and dynamics has captivated mathematicians and computer scientists since the earliest conceptualizations of computation. Recently, this connection has gained renewed attention, fueled by T.…
Motivation: There is a growing need to integrate mechanistic models of biological processes with computational methods in healthcare in order to improve prediction. We apply data assimilation in the context of Type 2 diabetes to understand…
We consider the basic features of complex dynamical and control systems. Special attention is paid to the problems of synthesis of dynamical models of complex systems, construction of efficient control models, and to the development of…
Systems biology seeks to create math models of biological systems to reduce inherent biological complexity and provide predictions for applications such as therapeutic development. However, it remains a challenge to determine which math…
A resource-bounded version of the statement "no algorithm recognizes all non-halting Turing machines" is equivalent to an infinitely often (i.o.) superpolynomial speedup for the time required to accept any coNP-complete language and also…
The aim of this review is to highlight the possibility to apply the mathematical formalism and methodology of quantum theory to model behaviour of complex biosystems, from genomes and proteins to animals, humans, ecological and social…
Molecular dynamics (MD) has become a powerful tool for studying biophysical systems, due to increasing computational power and availability of software. Although MD has made many contributions to better understanding these complex…
The scope of this work is to provide a self-contained introduction to a selection of basic theoretical aspects in the modeling and control of quantum mechanical systems, as well as a brief survey on the main approaches to control synthesis.…
Metabolism plays a central role in cell physiology because it provides the molecular machinery for growth. At the genome-scale, metabolism is made up of thousands of reactions interacting with one another. Untangling this complexity is key…
Computational biology is on the verge of a paradigm shift in its research practice - from a data-based (computational) paradigm to an information-based (cognitive) paradigm. As in the other research fields, this transition is impeded by…
The ultimate limits of computation are not just logical, but physical. We investigate the physical resources -- time, energy, entropy, and free energy -- required to perform computational work. We apply the resulting measures of physical…
Computational models are an essential tool for the design, characterization, and discovery of novel materials. Hard computational tasks in materials science stretch the limits of existing high-performance supercomputing centers, consuming…
Machine learning methods can be a valuable aid in the scientific process, but they need to face challenging settings where data come from inhomogeneous experimental conditions. Recent meta-learning methods have made significant progress in…
A method is presented which allows for a tremendous speed-up of computer simulations of statistical systems by orders of magnitude. This speed-up is achieved by means of a new observable, while the algorithm of the simulation remains…
P systems are computing conceptual computing devices that are at least as powerful as Turing machines. However, until recently it was not known how one can encode any recursive function as a P~system. Here we propose a new encoding of…
This book develops the conjecture that all kinds of information processing in computers and in brains may usefully be understood as "information compression by multiple alignment, unification and search". This "SP theory", which has been…
The metabolic wiring of patient cells is altered drastically in many diseases, including cancer. Understanding the nature of such changes may pave the way for new therapeutic opportunities, as well as the development of personalized…
Computing systems are omnipresent; their sustainability has become crucial for our society. A key aspect of this sustainability is the ability of computing systems to cope with the continuous change they face, ranging from dynamic operating…