Related papers: An enzymatic hormesis box
Inside every living cell is the cytoplasm: a fluid mixture of thousands of different macromolecules, predominantly proteins. This mixture is where most of the biochemistry occurs that enables living cells to function, and it is perhaps the…
In this note we introduce a notion of a morphism between two hyperbolic iterated function systems. We prove that the graph of a morphism is the attractor of an iterated function system, giving a Closed Graph Theorem, and show how it can be…
We introduce a mathematically rigorous framework for an artificial intelligence system composed of probabilistic agents evolving through structured competition and belief revision. The architecture, grounded in Bayesian inference, measure…
Entanglement monotones, such as the concurrence, are useful tools to characterize quantum correlations in various physical systems. The computation of the concurrence involves, however, difficult optimizations and only for the simplest case…
Understanding and modelling the complexity of the immune system is a challenge that is shared by the ImmunoComplexiT$^1$ thematic network from the RNSC. The immune system is a complex biological, adaptive, highly diversified, self-organized…
Port-Hamiltonian systems theory provides a structured approach to modelling, optimization and control of multiphysical systems. Yet, its relationship to thermodynamics seems to be unclear. The Hamiltonian is traditionally thought of as…
Reaction systems, introduced by Ehrenfeucht and Rozenberg, are elementary computational models based on biochemical reactions transpiring within the living cells. Numerous studies focus on mathematical aspects of minimal reaction systems…
Bayesian mechanics provides a framework that addresses dynamical systems that can be conceptualised as Bayesian inference. However, elucidating the requisite generative models is essential for empirical applications to realistic…
Patterns in reaction-diffusion systems near primary bifurcations can be studied locally and classified by means of amplitude equations. This is not possible for excitable reaction-diffusion systems. In this Letter we propose a global…
In this paper we outline a Matrix Ansatz approach to some problems of combinatorial enumeration. The idea is that many interesting quantities can be expressed in terms of products of matrices, where the matrices obey certain relations. We…
The quasi-steady state assumption (QSSA) forms the basis for rigorous mathematical justification of the Michaelis-Menten formalism commonly used in modeling a broad range of intracellular phenomena. A critical supposition of QSSA-based…
The simplest non-trivial model of chaotic Bohmian dynamics is identified. We argue that its most important features can be observed in more complex models, above all, the presumable mechanism of the appearance of chaos in the Bohmian-type…
We propose a categorical framework for processes which interact bidirectionally with both an environment and a 'controller'. Examples include open learners, in which the controller is an optimiser such as gradient descent, and an approach…
We consider the problem of designing synthetic cells to achieve a complex goal (e.g., mimicking the immune system by seeking invaders) in a complex environment (e.g., the circulatory system), where they might have to change their control…
In this work we study, at the single molecular level, the thermodynamic and dynamic characteristics of an enzymatic reaction comprising a rate limiting step. We investigate how the stability of the enzyme-state stationary probability…
We present a new approach, called a lazy matching, to the problem of on-line matching on bipartite graphs. Imagine that one side of a graph is given and the vertices of the other side are arriving on-line. Originally, incoming vertex is…
Motivated by the recent proposed models of the information engine [D. Mandal and C. Jarzynski, Proc. Natl. Acad. Sci. 109, 11641 (2012)] and the information refrigerator [D. Mandal, H. T. Quan, and C. Jarzynski, Phys. Rev. Lett. 111, 030602…
Advances in experimental techniques and in theoretical models have improved our understanding of protein crystallization. But they have also left open questions regarding the protein phase behavior and self-assembly kinetics, such as why…
We propose a natural strategy to deal with compatible and incompatible binary questions, and with their time evolution. The strategy is based on the simplest, non-commutative, Hilbert space $\mathcal{H}=\mathbb{C}^2$, and on the (commuting…
In this paper we investigate a class of natural Hamiltonian systems with two degrees of freedom. The kinetic energy depends on coordinates but the system is homogeneous. Thanks to this property it admits, in a general case, a particular…