Related papers: An enzymatic hormesis box
Competitive inhibitors can, paradoxically, stimulate an enzymatic reaction at low to moderate doses. Competitive inhibition of an enzyme occurs when an inhibitor binds to the enzyme's binding site and blocks the enzyme's target molecule…
An inverse problem framework for constructing reaction systems with prescribed properties is presented. Kinetic transformations are defined and analysed as a part of the framework, allowing an arbitrary polynomial ordinary differential…
The classical theory of enzymatic inhibition aims to quantitatively describe the effect of certain molecules -- called inhibitors -- on the progression of enzymatic reactions, but growing signs indicate that it must be revised to keep pace…
We analyze some features of alternative Hermitian and quasi-Hermitian quantum descriptions of simple and bipartite compound systems. We show that alternative descriptions of two interacting subsystems are possible if and only if the metric…
We classify general systems of polynomial equations with a single solution, or, equivalently, collections of lattice polytopes of minimal positive mixed volume. As a byproduct, this classification provides an algorithm to evaluate the…
Enzyme catalysis in reactors for industrial applications usually require an external intervention of the species involved in the chemical reactions. We analyze the most elementary open enzyme catalysis with competitive inhibition where a…
We describe modeling approaches to a "network" of connected enzyme-catalyzed reactions, with added (bio)chemical processes that introduce biochemical filtering steps into the functioning of such a biocatalytic cascade. Theoretical…
The theory of biochemical processes needs simple but realistic models of phenomena underlying microscopic dynamics of proteins. Many experiments performed in the 1980s have demonstrated that within the protein native state, apart from usual…
We present a simple mechanism for intra-molecular refrigeration, where parts of a molecule are actively cooled below the environmental temperature. We discuss the potential role and applications of such a mechanism in biology, in particular…
Developing robust representations of chemical structures that enable models to learn topological inductive biases is challenging. In this manuscript, we present a representation of atomistic systems. We begin by proving that our…
The one-dimensional harmonic oscillator in a box problem is possibly the simplest example of a two-mode system. This system has two exactly solvable limits, the harmonic oscillator and a particle in a (one-dimensional) box. Each of the two…
Live cells have ambiguous mechanical properties. They were often described as either elastic solids or viscoelastic fluids and have recently been classified as soft glassy materials characterized by weak power-law rheology. Nonlinear…
A biomolecular system representing the first realization of associative memory based on enzymatic reactions in vitro has been designed. The system demonstrated "training" and "forgetting" features characteristic of memory in biological…
A feedback stabilization scheme to stabilize a classical reacting Hamiltonian system is proposed. It is based on transforming a saddle-type equilibrium to an asymptotically stable one, and is given in a simple and algorithmic way. The…
The concept of allostery in which macromolecules switch between two different conformations is a central theme in biological processes ranging from gene regulation to cell signaling to enzymology. Allosteric enzymes pervade metabolic…
The particle in a box is a simple model that has a classical Hamiltonian $H=p^2$ (using $2m=1$), with a limited coordinate space, $-b<q<b$, where $0<b<\infty$. Using canonical quantization, this example has been fully studied thanks to its…
A balance is described with Langmuir binding of weights to each side. This simple physical system, when coupled with a previously derived equation for the equivalent displacement of weight that perturbs the equilibrium of a balance, models…
I show how transition systems can be applied to the naturally concurrent behaviour of excitable media. I consider structured excitable media, in which excitations are constrained to propagate only in defined narrow channels, and cannot…
We introduce two numerical conjugacy invariants for dynamical systems -- the complexity and weak complexity indices -- which are well-suited for the study of "completely integrable" Hamiltonian systems. These invariants can be seen as "slow…
Our aim is to introduce a category-theoretic framework sufficiently general to describe a wide variety of open kinematic systems in classical mechanics while uniquely characterizing systems with specified simplest components. The framework…