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Highly nonlinear behavior of a system of discrete sites on a lattice is observed when a specific feedback loop is introduced into models employing coupled map lattices, quantum cellular automata, or the real-valued analogues of the latter.…
Living systems self-organize in ways that conventional physical frameworks-based on forces, energies, and continuous fields-cannot fully capture. Processes like gene regulation and cellular decision-making involve rule-based logic and…
Control systems are sets of interconnected hardware and software components which regulate the behaviour of processes. The software of modern control systems rises for some years by requirements regarding the flexibility and functionality.…
The loop quantum theory, which constitutes a very small discontinuous space, as new method is applied to biology. The model of protein folding and lungs is proposed. In the model, some known results are used, and four approximate…
Quantum physics is a linear theory, so it is somewhat puzzling that it can underlie very complex systems such as digital computers and life. This paper investigates how this is possible. Physically, such complex systems are necessarily…
Biology is data-rich, and it is equally rich in concepts and hypotheses. Part of trying to understand biological processes and systems is therefore to confront our ideas and hypotheses with data using statistical methods to determine the…
Large-scale manufacturing of induced pluripotent stem cells (iPSCs) is essential for cell therapies and regenerative medicines. Yet, iPSCs form large cell aggregates in suspension bioreactors, resulting in insufficient nutrient supply and…
The biological immune system is a robust, complex, adaptive system that defends the body from foreign pathogens. It is able to categorize all cells (or molecules) within the body as self or non-self substances. It does this with the help of…
Multiset rewriting systems provide a formalism particularly suitable for the description of biological systems. We present an extension of this formalism with additional controls on the derivations as a tool for reducing possible…
The brain is an intricately structured organ responsible for the rich emergent dynamics that support the complex cognitive functions we enjoy as humans. With around $10^{11}$ neurons and $10^{15}$ synapses, understanding how the human brain…
This paper addresses the decomposition of biochemical networks into functional modules that preserve their dynamic properties upon interconnection with other modules, which permits the inference of network behavior from the properties of…
Many biological phenomena such as locomotion, circadian cycles, and breathing are rhythmic in nature and can be modeled as rhythmic dynamical systems. Dynamical systems modeling often involves neglecting certain characteristics of a…
Multiple organs in a living system respond to environmental changes, and the signals from the organs regulate the physiological environment. Inspired by this biological feedback, we propose a simple autonomous system of active rotators to…
Understanding how biomechanical reorganization governs key biological processes, such as morphogenesis and development, requires predictive insights into stress distributions and cellular behavior. While traditional approaches focused on…
This paper is a first step to chase the ambitious objective of developing a mathmatical theory of living systems. The contents refer modeling large systems of interacting living entities with the aim of describing their collective behaviors…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
Life depends as much on the flow of information as on the flow of energy. Here we review the many efforts to make this intuition precise. Starting with the building blocks of information theory, we explore examples where it has been…
The long-time dynamics of somatic adaptability in immune system is simulated by a simple physical model. The immune system described by the model exhibits a scale free behavior as is observed in living systems. The balance between the…
Feedback is an essential composition operator in many classes of reactive and other systems. This paper studies feedback in the context of compositional theories with refinement. Such theories allow to reason about systems on a…
The metabolic processes complexity is at the heart of energy conversion in living organisms and forms a huge obstacle to develop tractable thermodynamic metabolism models. By raising our analysis to a higher level of abstraction, we develop…