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Modeling the spontaneous evolution of morphology in natural systems and its preservation by proportionate growth remains a major scientific challenge. Yet, it is conceivable that if the basic mechanisms of growth and the coupled kinetic…
Modern computational chemistry has reached a stage at which massive exploration into chemical reaction space with unprecedented resolution with respect to the number of potentially relevant molecular structures has become possible. Various…
We consider various modeling levels for spatially homogeneous chemical reaction systems, namely the chemical master equation, the chemical Langevin dynamics, and the reaction-rate equation. Throughout we restrict our study to the case where…
Emergence is a pregnant property in various fields. It is the fact for a phenomenon to appear surprisingly and to be such that it seems at first sight that it is not possible to predict its apparition. That is the reason why it has often…
The theory of biochemical processes needs simple but realistic models of phenomena underlying microscopic dynamics of proteins. Many experiments performed in the 1980s have demonstrated that within the protein native state, apart from usual…
This study explores the emergence of life through a simulation model approach. The model "Multi-set chemical lattice model" is a model that allows virtual molecules of multiple types to be placed in each lattice cell on a two-dimensional…
The inverse problem of designing component interactions to target emergent structure is fundamental to numerous applications in biotechnology, materials science, and statistical physics. Equally important is the inverse problem of designing…
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…
Generative molecular design has moved from proof-of-concept to real-world applicability, as marked by the surge in very recent papers reporting experimental validation. Key challenges in explainability and sample efficiency present…
Neo-Darwinian evolutionary theory explains how the appearance of purposive design in the sophisticated adaptations of living organisms can have come about without their intentionally being designed. The explanation relies crucially on the…
Emergent phenomena share the fascinating property of not being obvious consequences of the design of the system in which they appear. This characteristic is no less relevant when attempting to simulate such phenomena, given that the outcome…
Molecular circuits capable of autonomous learning could unlock novel applications in fields such as bioengineering and synthetic biology. To this end, existing chemical implementations of neural computing have mainly relied on emulating…
To build a large library of mathematics, it seems more efficient to take advantage of the inherent structure of mathematical theories. Various theory presentation combinators have been proposed, and some have been implemented, in both…
We propose an artificial life framework aimed at facilitating the emergence of intelligent organisms. In this framework there is no explicit notion of an agent: instead there is an environment made of atomic elements. These elements contain…
Hash Chemistry, a minimalistic artificial chemistry model of open-ended evolution, has recently been extended to non-spatial and cellular versions. The non-spatial version successfully demonstrated continuous adaptation and unbounded growth…
Spatial pattern formation is a key feature of many natural systems in physics, chemistry and biology. The essential theoretical issue in understanding pattern formation is to explain how a spatially homogeneous initial state can undergo…
Photomosaic images are a type of images consisting of various tiny images. A complete form can be seen clearly by viewing it from a long distance. Small tiny images which replace blocks of the original image can be seen clearly by viewing…
A continuous route from a disordered soup of simple chemical feedstocks to a functional protocell -- a compartment that metabolizes, grows, and propagates -- remains elusive. Here, we show that a homogeneous aqueous chemical mixture…
Biomolecules composed of a limited set of chemical building blocks can co-localize into distinct, spatially segregated compartments known as biomolecular condensates. While many condensates are known to form spontaneously via phase…
We describe a new class of models of quantum space-time based on energetic causal sets and show that under natural conditions space-time emerges from them. These are causal sets whose causal links are labelled by energy and momentum and…