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Thermodynamics is commonly presented as a theory of macroscopic systems in stable equilibrium, built upon assumptions of extensivity and scaling with system size. In this paper, we present a universal formulation of the elementary…
In multicellular organisms, relations among parts and between parts and the whole are contextual and interdependent. These organisms and their cells are ontogenetically linked: an organism starts as a cell that divides producing…
Recent decades, the emergence of numerous novel algorithms makes it a gimmick to propose an intelligent optimization system based on metaphor, and hinders researchers from exploring the essence of search behavior in algorithms. However, it…
In this paper we show that the existence of a primarily discrete space-time may be a fruitful assumption from which we may develop a new approach of statistical thermodynamics in pre-relativistic conditions. The discreetness of space-time…
We review the derivation of quantum theory as an application of entropic methods of inference. The new contribution in this paper is a streamlined derivation of the Schr\"odinger equation based on a different choice of microstates and…
Entropy production along a single stochastic trajectory of a biomolecule is discussed for two different sources of non-equilibrium. For a molecule manipulated mechanically by an AFM or an optical tweezer, entropy production (or…
A key challenge in systems biology is the elucidation of the underlying principles, or fundamental laws, which determine the cellular phenotype. Understanding how these fundamental principles are altered in diseases like cancer is important…
Configurational entropy is an important factor in the free energy change of many macromolecular recognition and binding processes, and has been intensively studied. Despite great progresses that have been made, the global sampling remains…
Biological systems reach organizational complexity that far exceeds the complexity of any known inanimate objects. Biological entities undoubtedly obey the laws of quantum physics and statistical mechanics. However, is modern physics…
During a spontaneous change, a macroscopic physical system will evolve towards a macro-state with more realizations. This observation is at the basis of the Statistical Mechanical version of the Second Law of Thermodynamics, and it provides…
How do complex adaptive systems, such as life, emerge from simple constituent parts? In the 1990s Walter Fontana and Leo Buss proposed a novel modeling approach to this question, based on a formal model of computation known as $\lambda$…
The concept of evolutionary development of structures constituted a \emph{real} revolution in biology: it was possible to understand how the very complex structures of life can arise in an out-of-equilibrium system. The investigation of…
Assessing quantitatively the state and dynamics of a social system is a very difficult problem. It is of great importance for both practical and theoretical reasons such as establishing the efficiency of social action programs, detecting…
We introduce a methodology to study the possible matter flows of an ecosystem defined by observational biomass data and realistic biological constraints. The flows belong to a polyhedron in a multi dimensional space making statistical…
Extremal principles are fundamental in our interpretation of phenomena in nature. One of the best known examples is the second law of thermodynamics, governing most physical and chemical systems and stating the continuous increase of…
Why can the world resist the law of entropy increase and produce self-organizing structure? Does the entropy of an isolated system always only increase and never decrease? Can be thermodymamic degradation and self-organizing evolution…
Quantum mechanics is derived as an application of the method of maximum entropy. No appeal is made to any underlying classical action principle whether deterministic or stochastic. Instead, the basic assumption is that in addition to the…
In this paper we review various information-theoretic characterizations of the approach to equilibrium in biological systems. The replicator equation, evolutionary game theory, Markov processes and chemical reaction networks all describe…
Several results of black holes thermodynamics can be considered as firmly founded and formulated in a very general manner. From this starting point we analyse in which way these results may give us the opportunity to gain a better…
We analyze the Schr\"odingerization method for quantum simulation of a general class of non-unitary dynamics with inhomogeneous source terms. The Schr\"odingerization technique, introduced in [31], transforms any linear ordinary and partial…