Related papers: An All-Encompassing Global Convergence Result for …
A family of results, referred to as inheritance results, tell us which enlargements of a chemical reaction network (CRN) preserve its capacity for nontrivial behaviours such as multistationarity and oscillation. In this paper, the following…
Polydispersity is a universal feature of synthetic polymers and biological molecules in the cytoplasm. However, its quantitative impact on collective behavior remains poorly understood because conventional metrics, such as the…
The global existence of bounded solutions to reaction-diffusion systems with fractional diffusion in the whole space $\mathbb R^N$ is investigated. The systems are assumed to preserve the non-negativity of initial data and to dissipate…
Systems that evolve towards a state from which they cannot depart are common in nature. But the fluctuation-dissipation theorem, a fundamental result in statistical mechanics, is mainly restricted to systems near-stationarity. In processes…
Modeling molecules as undirected graphs and chemical reactions as graph rewriting operations is a natural and convenient approach tom odeling chemistry. Graph grammar rules are most naturally employed to model elementary reactions like…
Biochemical covalent modification networks exhibit a remarkable suite of steady state and dynamical properties such as multistationarity, oscillations, ultrasensitivity and absolute concentration robustness. This paper focuses on conditions…
Under mass-action kinetics, biochemical reaction networks give rise to polynomial autonomous dynamical systems whose parameters are often difficult to estimate. We deal in this paper with the problem of identifying the kinetic parameters of…
This paper introduces a reformulation of the classical convergence theorem for spectral sequences of filtered complexes which provides an algorithm to effectively compute the induced filtration on the total (co)homology, as soon as the…
A protocell model consisting of mutually catalyzing molecules is studied in order to investigate how chemical compositions are transferred recursively through cell divisions under replication errors. Depending on the path rate, the numbers…
Molecule inverse folding has been a long-standing challenge in chemistry and biology, with the potential to revolutionize drug discovery and material science. Despite specified models have been proposed for different small- or…
We report the first study of a network of connected enzyme-catalyzed reactions, with added chemical and enzymatic processes that incorporate the recently developed biochemical filtering steps into the functioning of this biocatalytic…
In this paper we are interested in a degenerate parabolic system of reaction-diffusion equations arising in biology when studying cell adhesion at the protein level. In this modeling the unknown is the couple of the distribution laws of the…
The trend to equilibrium for reaction-diffusion systems modelling chemical reaction networks is investigated, in the case when reaction processes happen on subsets of the domain. We prove the convergence to equilibrium by directly showing…
Background: Autocatalytic sets are often considered a necessary (but not sufficient) condition for the origin and early evolution of life. Although the idea of autocatalytic sets was already conceived of many years ago, only recently have…
From the vasculature of animals to the porous media making up batteries, the core task of flow networks is to transport solutes and perfuse all cells or media equally with resources. Yet, living flow networks have a key advantage over…
The idea of using fragment embedding to circumvent the high computational scaling of accurate electronic structure methods while retaining high accuracy has been a long-standing goal for quantum chemists. Traditional fragment embedding…
Motivated by partition regularity problems of homogeneous quadratic equations, we prove multiple recurrence and convergence results for multiplicative measure preserving actions with iterates given by rational sequences involving…
This paper presents the foundation for a decomposition theory for Boolean networks, a type of discrete dynamical system that has found a wide range of applications in the life sciences, engineering, and physics. Given a Boolean network…
Proteins with multiple binding sites play important roles in cell signaling systems by nucleating protein complexes in which, for example, enzymes and substrates are co-localized. Proteins that specialize in this function are called by a…
In transitions between different environmental settings, a molecular system inevitably undergoes a range of detectable changes, and the ability to accurately simulate such responses, e.g., in the form of shifts to molecular energies,…