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We present a new type of feedback linearization that is tailored for mechanical control systems. We call it a mechanical feedback linearization. Its basic feature is preservation of the mechanical structure of the system. For mechanical…

Despite widespread calls for the incorporation of mathematical modeling into the undergraduate biology curriculum, there is lack of a common understanding around the definition of modeling, which inhibits progress. In this paper, we extend…

We have developed a coarse-grained formulation for modeling the dynamic behavior of cells quantitatively, based on stochasticity and heterogeneity, rather than on biochemical reactions. We treat each reaction as a continuous-time stochastic…

The integral control of positive systems using nonnegative control input is an important problem arising, among others, in biochemistry, epidemiology and ecology. An immediate solution is to use an ON-OFF nonlinearity between the controller…

We advocates here the use of (mathematical) logic for systems biology, as a unified framework well suited for both modeling the dynamic behaviour of biological systems, expressing properties of them, and verifying these properties. The…

Antifragility characterizes the benefit of a dynamical system derived from the variability in environmental perturbations. Antifragility carries a precise definition that quantifies a system's output response to input variability. Systems…

For the first time in history, humankind might conceivably begin to imagine itself as a multi-planetary species. This goal will entail technical innovation in a number of contexts, including that of healthcare. All life on Earth shares an…

A (closed) dynamical system is a notion of how things can be, together with a notion of how they may change given how they are. The idea and mathematics of closed dynamical systems has proven incredibly useful in those sciences that can…

Using bioimaging technology, biologists have attempted to identify and document analytical interpretations that underlie biological phenomena in biological cells. Theoretical biology aims at distilling those interpretations into knowledge…

There has been on-going philosophical debate on whether artificial life models, also known as digital organisms, are truly alive. The main difficulty appears to be finding an encompassing and definite definition of life. By examining…

The calculus of looping sequences is a formalism for describing the evolution of biological systems by means of term rewriting rules. We enrich this calculus with a type discipline to guarantee the soundness of reduction rules with respect…

Reaction systems are discrete dynamical systems inspired by bio-chemical processes, whose dynamical behaviour is expressed by set-theoretic operations on finite sets. Reaction systems thus provide a description of bio-chemical phenomena…

Equations of motion that recognize biochemical patterns are described. The equations are partial differential equations in a continuous multiple component system in which adequate initial and boundary conditions are given. The biochemical…

The goal of Science is to understand phenomena and systems in order to predict their development and gain control over them. In the scientific process of knowledge elaboration, a crucial role is played by models which, in the language of…

Biological signaling is imagined as a combination of activation and transport. The former is triggered by local molecular interactions and the latter is the result of molecular diffusion. However, other fundamental physical principles of…

The organism is a fundamental concept in biology. However there is no universally accepted, formal, and yet broadly applicable definition of what an organism is. Here we introduce a candidate definition. We adopt the view that the…

Living systems are made of active materials with microscopic components that work together to perform macroscopic biological tasks. The breakdown of these collective functionalities leads to diseases, which, conversely, could be treated by…

The Stochastic Calculus of Looping Sequences is suitable to describe the evolution of microbiological systems, taking into account the speed of the described activities. We propose a type system for this calculus that models how the…

We consider systems whose lifetime is measured by the time of physical degradation of components, as well as the degree of power each component contributes to the system. The lifetimes of the components of the system are random variables.…

In classical physics, a single measurement can in principle reveal the state of a system. However, quantum theory permits numerous non-equivalent measurements on a physical system, each providing only limited information about the state.…