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A possible mechanism of time is formulated by developing an idea of time replaced by quantum correlations, with the aid of modern quantum information theory. We invent a microscopic model, where correlations of a closed system are steadily…
Living organisms exhibit remarkable adaptations across all scales, from molecules to ecosystems. We believe that many of these adaptations correspond to optimal solutions driven by evolution, training, and underlying physical and chemical…
Mechanical systems are often characterized only by their response to certain loads known from experiments or simulations. The obtained data can be used for various purposes: system analysis, design of mathematical models, or construction of…
We propose a housekeeping/excess decomposition of entropy production for general nonlinear dynamics in a discrete space, including chemical reaction networks and discrete stochastic systems. We exploit the geometric structure of…
Traditional form of the second law of thermodynamics is strongly restricted by three conditions: One is the initial joint state of the system and surroundings should be a product state, so that there exists no initial correlations. The…
We investigate the possible origin of hierarchical structures in complex systems describable in terms of a finite and small number of parameters which control the behavioral pattern at each level of organization. We argue that the…
In this review, we discuss the applications of the theory of birth-and-death processes to problems in biology, primarily, those of evolutionary genomics. The mathematical principles of the theory of these processes are briefly described.…
Entropy is a fundamental concept from Thermodynamics and it can be used to study models on context of Creation Cold Dark Matter (CCDM). From conditions on the first ($\dot{S}\geq0$)\footnote{Throughout the present work we will use dots to…
The laws of thermodynamics apply to biophysical systems on the nanoscale as described by the framework of stochastic thermodynamics. This theory provides universal, exact relations for quantities like work, which have been verified in…
The second law of thermodynamics states that the entropy of an isolated system can only increase over time. This appears to conflict with the reversible evolution of isolated quantum systems under the Schr\"odinger equation, which preserves…
Natural selection has shaped the evolution of cells and multi-cellular organisms such that social cooperation can often be preferred over an individualistic approach to metabolic regulation. This paper extends a framework for dynamic…
Identifying the physical basis of heterosis (or hybrid vigor) has remained elusive despite over a hundred years of research on the subject. The three main theories of heterosis are dominance theory, overdominance theory, and epistasis…
Research on the birth and evolution of life are reviewed with reference to the maximum entropy production principle (MEPP). It has been shown that this principle is essential for consistent understanding of the birth and evolution of life.…
Thermodynamics makes definite predictions about the thermal behavior of macroscopic systems in and out of equilibrium. Statistical mechanics aims to derive this behavior from the dynamics and statistics of the atoms and molecules making up…
Turing patterns play a fundamental role in morphogenesis and population dynamics, encoding key information about the underlying biological mechanisms. Yet, traditional inverse problems have largely relied on non-biological data such as…
The past few decades have seen great leaps in technologies to analyze cells and tissues. Omics methods in particular now allow us unprecedented access to their the molecular composition where the base-level resolution of transcripts and…
Here we develop an approach to bio-structural robustness integrated with structure-function relationship in a unified conceptual and methodological framework, and envision its study using adequate computational and experimental methods. To…
Firstly, we calculate quantitatively decrease of entropy by the known formulas in the ordering phenomena and nucleation of thermodynamics of microstructure. They show again that a necessary condition of decrease of entropy in isolated…
Imaging systems are commonly described using resolution, contrast, and signal-to-noise ratio, but these quantities do not provide a general account of how physical transformations affect the flow of information. This paper introduces an…
The physical foundations of a variety of emerging technologies --- ranging from the applications of quantum entanglement in quantum information to the applications of nonequilibrium bulk and interface phenomena in microfluidics, biology,…