Related papers: Homeostatic Mechanisms in Biological Systems
A new class of control problems is discussed - homeostasis control. Homeostasis control problems can be considered as control problems with a given target set, in particular, as a problem of stabilizing the values of some target function,…
This paper analyzes stochastic networks consisting of a set of finite capacity sites where different classes of individuals move according to some routing policy. The associated Markov jump processes are analyzed under a thermodynamic limit…
The study of network structure has uncovered signatures of the organization of complex systems. However, there is also a need to understand how to control them; for example, identifying strategies to revert a diseased cell to a healthy…
How could primordial life, before the evolution of genetic systems, adapt to fluctuating environments and achieve homeostasis? This study proposes a minimal, chemically plausible model where homeostasis emerges from a simple chemical…
We analyze the two-field formulation of the quasi-static Biot's equations in bounded domains by means of the inf-sup theory. For this purpose, we exploit an equivalent four-field formulation of the equations, introducing the so-called total…
The strategic induction of cell death serves as a crucial immune defense mechanism for the eradication of pathogenic infections within host cells. Investigating the molecular mechanisms underlying immunogenic cell pathways has significantly…
Electrostatic forces play many important roles in molecular biology, but are hard to model due to the complicated interactions between biomolecules and the surrounding solvent, a fluid composed of water and dissolved ions. Continuum model…
Autocatalytic systems are very often incorporated in the "origin of life" models, a connection that has been analyzed in the context of the classical hypercycles introduced by Manfred Eigen. We investigate the dynamics of certain networks…
The differing ability of polypeptide conformations to act as the native state of proteins has long been rationalized in terms of differing kinetic accessibility or thermodynamic stability. Building on the successful applications of physical…
In this brief and speculative commentary, we explore ideas inspired by neural networks in machine learning, proposing that a simple neural XOR motif, involving both excitatory and inhibitory connections, may provide the basis for a relevant…
We investigate dynamics of a kinetic model of inhibitory autoregulation as exemplified when a protein inhibits its own production by interfering with its messenger RNA, known in molecular biology as translational autoregulation. We first…
For a single enzyme or molecular motor operating in an aqueous solution of non-equilibrated solute concentrations, a thermodynamic description is developed on the level of an individual trajectory of transitions between states. The concept…
Feedback is ubiquitous in both biological and engineered control systems. In biology, in addition to typical feedback between plant and controller, we observe feedback pathways within control systems, which we call internal feedback…
We propose a theoretical formalism, molecular finite automata (MFA), to describe individual proteins as rule-based computing machines. The MFA formalism provides a framework for modeling individual protein behaviors and systems-level…
This paper gives an overview of the use of control systems engineering in synthetic biology, motivated by applications such as cell therapy and cell fate reprogramming for regenerative medicine. A ubiquitous problem in these and other…
In this review, we discuss modularity and hierarchy in biological systems. We review examples from protein structure, genetics, and biological networks of modular partitioning of the geometry of biological space. We review theories to…
This article presents a biological neural network model driven by inhomogeneous Poisson processes accounting for the intrinsic randomness of synapses. The main novelty is the introduction of local interactions: each firing neuron triggers…
Recently Prosen and Mej\'ia-Monasterio (J. Phys. A: Math. Theor. 49 (2016) 185003) obtained exact nonequilibrium steady states of an integrable and reversible cellular automaton driven by some stochastic boundary conditions. In this paper,…
A single gene, regulating its own expression via a positive feedback loop, constitutes a common motif in gene regulatory networks and signalling cascades. Recent experiments on the development of competence in the bacterial population…
One of the main trend in to date research and development is the miniaturization of electronic devices. In this perspective, integrated nanodevices based on proteins or biomolecules are attracting a major interest. In fact, it has been…