Related papers: Biological Organization and Negative Entropy: Base…
We present a novel approach to represent ecological systems using reaction networks, and show how a particular framework called Chemical Organization Theory (COT) sheds new light on the longstanding complexity-stability debate. Namely, COT…
Over the last decade, significant progress has been made in understanding complex biological systems, however there have been few attempts at incorporating this knowledge into nature inspired optimization algorithms. In this paper, we…
We review the physical foundations of Landauer's Principle, which relates the loss of information from a computational process to an increase in thermodynamic entropy. Despite the long history of the Principle, its fundamental rationale and…
The possible distinction between inanimate and living matter has been of interest to humanity since thousands of years. Clearly, such a rich question can not be answered in a single manner, and a plethora of approaches naturally do exist.…
Following arXiv:2210.12963 [hep-th], we investigate aspects of the time evolution operator regarded as a density operator and associated entanglement-like structures in various quantum systems. These involve timelike separations and…
Many entropy-conservative and entropy-stable (summarized as entropy-preserving) methods for hyperbolic conservation laws rely on Tadmor's theory for two-point entropy-preserving numerical fluxes and its higher-order extension via flux…
This paper proposes a variational approach to describe the evolution of organization of complex systems from first principles, as increased efficiency of physical action. Most simply stated, physical action is the product of the energy and…
Our planet is roughly closed to matter, but open to energy input from the sun. However, to harness this energy, organisms must transform matter from one chemical (redox) state to another. For example, photosynthetic organisms can capture…
Life is a complex biological phenomenon represented by numerous chemical, physical and biological processes performed by a biothermodynamic system/cell/organism. Both living organisms and inanimate objects are subject to aging, a biological…
The thermodynamic entropy of coarse-grained (CG) models stands as one of the most important properties for quantifying the missing information during the CG process and for establishing transferable (or extendible) CG interactions. However,…
Living systems maintain or increase local order by working against the Second Law of Thermodynamics. Thermodynamic consistency is restored as they dissipate heat, thereby increasing the net entropy of their environment. Recently introduced…
We study open-ended evolution by focusing on computational and information-processing dynamics underlying major evolutionary transitions. In doing so, we consider biological organisms as hierarchical dynamical systems that generate…
Current mathematical frameworks for predicting the flux state and macromolecular composition of the cell do not rely on thermodynamic constraints to determine the spontaneous direction of reactions. These predictions may be biologically…
Organisms are nonequilibrium, stationary systems self-organized via spontaneous symmetry breaking and undergoing metabolic cycles with broken detailed balance in the environment. The thermodynamic free-energy principle describes an…
Thermodynamic extensivity is commonly introduced as a postulate -- the homogeneity of degree one in thermodynamic potentials. We provide a constructive derivation of this property from microscopic conditions on the pair potential, without…
In a genetic algorithm, fluctuations of the entropy of a genome over time are interpreted as fluctuations of the information that the genome's organism is storing about its environment, being this reflected in more complex organisms. The…
The possibility that evolutionary forces -- together with a few fundamental factors such as thermodynamic constraints, specific computational features enabling information processing, and ecological processes -- might constrain the logic of…
Combining a spatiotemporal, multi-agent based model of a foraging ecosystem with linear, genetically programmed rules for the agents' behaviors results in implicit, endogenous, objective functions and selection algorithms based on "natural…
One of the major challenges in biology concerns the integration of data across length and time scales into a consistent framework: how do macroscopic properties and functionalities arise from the molecular regulatory networks - and how can…
The managed-metabolism hypothesis suggests that a cooperation barrier must be overcome if self-producing chemical organizations are to transition from non-life to life. This barrier prevents un-managed, self-organizing, autocatalytic…