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Natural systems are remarkably robust and resilient, maintaining essential functions despite variability, uncertainty, and hostile conditions. Understanding these nonlinear, dynamic behaviours is challenging because such systems involve…
Artificial Chemistries (ACs) are symbolic chemical metaphors for the exploration of Artificial Life, with specific focus on the problem of biogenesis or the origin of life. This paper presents authors thoughts towards defining a unified…
The fundamental tension between availability and consistency shapes the design of distributed storage systems. Classical results capture extreme points of this trade-off: the CAP theorem shows that strong models like linearizability…
The determination of chemical mixture components is vital to a multitude of scientific fields. Oftentimes spectroscopic methods are employed to decipher the composition of these mixtures. However, the sheer density of spectral features…
The simulation of open many-body quantum systems is challenging, requiring methods to both handle exponentially large Hilbert spaces and represent the influence of (infinite) particle and energy reservoirs. These two requirements are at…
Persistent homology is a popular method for computing topological features of (metric) data. Standard approaches based on the \v{C}ech or Rips filtration are stable under small perturbations of the data, but highly sensitive to outliers.…
A chemical reaction network (CRN) is composed of reactions that can be seen as interactions among entities called species, which exist within the system. Endowed with kinetics, CRN has a corresponding set of ordinary differential equations…
Understanding the asymptotic behavior of reaction-diffusion (RD) systems is crucial for modeling processes ranging from species coexistence in ecology to biochemical interactions within cells. In this work, we analyze RD systems in which…
We present a new approach to singularity confinement which makes it an efficient and reliable discrete integrability detector. Our method is based on the full-deautonomisation procedure, which consists in analysing non-autonomous extensions…
Network translation has recently been used to establish steady state properties of mass action systems by corresponding the given system to a generalized one which is either dynamically or steady state equivalent. In this work we further…
Chemical Reaction Networks (CRNs) provide a useful abstraction of molecular interaction networks in which molecular structures as well as mass conservation principles are abstracted away to focus on the main dynamical properties of the…
We present a benchmark study of autonomous, chemical agents exhibiting associative learning of an environmental feature. Associative learning has been widely studied in cognitive science and artificial intelligence, but are most commonly…
Exact sequences are a well known notion in homological algebra. We investigate here the more vague properties of 'homotopical exactness', appearing for instance in the fibre or cofibre sequence of a map. Such notions of exactness can be…
This report proposes a novel framework for a rigorous robustness analysis of stochastic biochemical systems. The technique is based on probabilistic model checking. We adapt the general definition of robustness introduced by Kitano to the…
We analyze a 1-d ring structure composed of many two-level systems, in the limit where only one excitation is present. The two-level systems are coupled to a common environment, where the excitation can be lost, which induces super and…
Dynamical systems in biology are complex, and one often does not have comprehensive knowledge about the interactions involved. Chemical reaction network (CRN) inference aims to identify, from observing species concentrations over time, the…
Computational searches for new materials are naturally turning from binary systems, to ternary and other multicomponent systems, and beyond. Here, we select the industrially-relevant metals titanium and aluminium and report the results of…
Diffraction methods are at the heart of structure determination of solids. While Bragg-like scattering (pure point diffraction) is a characteristic feature of crystals and quasicrystals, it is not straightforward to interpret continuous…
This paper deals with strong structural controllability of linear systems. In contrast to existing work, the structured systems studied in this paper have a so-called zero/nonzero/arbitrary structure, which means that some of the entries…
We perform stability analysis of a kinetic bacterial chemotaxis model of bacterial self-organization, assuming that bacteria respond sharply to chemical signals. The resulting discontinuous tumbling kernel represents the key challenge for…