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Artificial ecosystems provide an additional experimental tool to support laboratory work, field work, and theoretical development in competitive exclusion research. A novel application of a spatiotemporal agent based model is presented…
Through extensive studies of dynamical system modeling cellular growth and reproduction, we find evidence that complexity arises in multicellular organisms naturally through evolution. Without any elaborate control mechanism, these systems…
A universal framework is proposed, where all laws are regularities of relations between things or agents. Parts of the world at one or all times are modeled as networks called SYSTEMS with a minimum of axiomatic properties. A notion of…
To analyze the evolutionary emergence of structural complexity in physical processes we introduce a general, but tractable, model of objects that interact to produce new objects. Since the objects--\emph{$epsilon$-machines}--have well…
We compare an evolutionary chemical model with simple empirical models of the abundance and with static chemical models. We focus on the prediction of molecular line profiles that are commonly observed in low mass star forming cores. We…
In this paper we will try to provide a formalization of some characteristics of the development of biological systems aiming at the highest level of adequacy: justificative adequacy, that is, not only what we observe (descriptive adequacy)…
Reduction of information entropy along with ever-increasing complexity are among the key signatures of living matter. Understanding the onset of such behavior in early prebiotic world is essential for solving the problem of origins of life.…
The primordial confrontation underlying the existence of our universe can be conceived as the battle between entropy and complexity. The law of ever-increasing entropy (Boltzmann H-theorem) evokes an irreversible, one-directional evolution…
Emergence of various properties is mapped in a two-component system from quantum to mesoscale, using Au-Ag alloys. Experiments are designed so that composition is the primary 'interaction' guiding the evolution of properties across…
Mathematical models are increasingly being used to understand complex biochemical systems, to analyze experimental data and make predictions about unobserved quantities. However, we rarely know how robust our conclusions are with respect to…
An intriguing interpretation of the time-evolution of dynamical systems is to view it as a computation that transforms an initial state to a final one. This paradigm has been explored in discrete systems such as cellular automata models,…
Unlike computation or the numerical analysis of differential equations, simulation does not have a well established conceptual and mathematical foundation. Simulation is an arguable unique union of modeling and computation. However,…
Symmetries impose structure on the Hilbert space of a quantum mechanical model. The mathematical units of this structure are the irreducible representations of symmetry groups and I consider how they function as conceptual units of…
Classical approaches like process algebras or labelled transition systems deal with static composition to model non-trivial concurrent or distributed systems; this is not sufficient for systems with dynamic architecture and with variable…
Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical…
We develop a novel method to analyze the dynamics of stochastic rewriting systems evolving over finitary adhesive, extensive categories. Our formalism is based on the so-called rule algebra framework and exhibits an intimate relationship…
Understanding how simple local interactions give rise to emergent exploration patterns is a fundamental question in statistical physics. We introduce a minimal model of two coupled agents that avoid retracing their own paths while being…
Finding proper collective variables for complex systems and processes is one of the most challenging tasks in simulations, which limits the interpretation of experimental and simulated data and the application of enhanced sampling…
Computational approaches to exploring "chemical universes", i.e., very large sets, potentially infinite sets of compounds that can be constructed by a prescribed collection of reaction mechanisms, in practice suffer from a combinatorial…
Self-organized emergent patterns can be widely seen in particle interactions producing complex structures such as chemical elements and molecules. Inspired by these interactions, this work presents a novel stochastic approach that allows a…