Related papers: The Computational Universality of Metabolic Comput…
The study of biological systems witnessed a pervasive cross-fertilization between experimental investigation and computational methods. This gave rise to the development of new methodologies, able to tackle the complexity of biological…
One of the defining features of living systems is their adaptability to changing environmental conditions. This requires organisms to extract temporal and spatial features of their environment, and use that information to compute the…
As metabolomics datasets are becoming larger and more complex, there is an increasing need for model-based data integration and analysis to optimally leverage these data. Dynamical models of metabolism allow for the integration of…
We study the computational complexity theory of smooth, finite-dimensional dynamical systems. Building off of previous work, we give definitions for what it means for a smooth dynamical system to simulate a Turing machine. We then show that…
One of the main properties of biological systems is modularity, which manifests itself at all levels of their organization, starting with the level of molecular genetics, ending with the level of whole organisms and their communities. In a…
Metabolomics is becoming a mature part of analytical chemistry as evidenced by the growing number of publications and attendees of international conferences dedicated to this topic. Yet, a systematic treatment of the fundamental structure…
This series presents an approach to mathematical biology which makes precise the function of biological molecules. Because biological systems compute, the theory is a general purpose computer language. I build a language for efficiently…
Biological lifeforms can heal, grow, adapt, and reproduce -- abilities essential for sustained survival and development. In contrast, robots today are primarily monolithic machines with limited ability to self-repair, physically develop, or…
Validation of a presumably universal theory, such as quantum mechanics, requires a quantum mechanical description of systems that carry out theoretical calculations and experiments. The description of quantum computers is under active…
Computational complexity theory contains a corpus of theorems and conjectures regarding the time a Turing machine will need to solve certain types of problems as a function of the input size. Nature {\em need not} be a Turing machine and,…
Our understanding of the physics of biological molecules, such as proteins and DNA, is limited because the approximations we usually apply to model inert materials are not in general applicable to soft, chemically inhomogeneous systems. The…
Symmetry is fundamental in the description and simulation of quantum systems. Leveraging symmetries in classical simulations of many-body quantum systems can results in significant overhead due to the exponentially growing size of some…
The increasing relevance of areas such as real-time and embedded systems, pervasive computing, hybrid systems control, and biological and social systems modeling is bringing a growing attention to the temporal aspects of computing, not only…
Living systems are subject to the arrow of time; from birth, they undergo complex transformations (self-organization) in a constant battle for survival, but inevitably ageing and disease trap them to death. Can ageing be understood and…
In the first of this pair of papers, it was proven that that no physical computer can correctly carry out all computational tasks that can be posed to it. The generality of this result follows from its use of a novel definition of…
We start by an introduction to the basic concepts of computability theory and the introduction of the concept of Turing machine and computation universality. Then se turn to the exploration of trade-offs between different measures of…
Numerical optimization of complex systems benefits from the technological development of computing platforms in the last twenty years. Unfortunately, this is still not enough, and a large computational time is still necessary when…
To develop and investigate detailed mathematical models of cellular metabolic processes is one of the primary challenges in systems biology. However, despite considerable advance in the topological analysis of metabolic networks, explicit…
Innovation in synthetic biology often still depends on large-scale experimental trial-and-error, domain expertise, and ingenuity. The application of rational design engineering methods promise to make this more efficient, faster, cheaper…
In living systems, we often see the emergence of the ingredients necessary for computation -- the capacity for information transmission, storage, and modification -- begging the question of how we may exploit or imitate such biological…