Related papers: A tropical geometry for bounded biochemical state …
We study the behavior of phylogenetic tree shapes in the tropical geometric interpretation of tree space. Tree shapes are formally referred to as tree topologies; a tree topology can also be thought of as a tree combinatorial type, which is…
Malignant membranes cluster nutrient transporters within glycan-rich domains, sustaining metabolism through redundant intake routes. A theoretical framework links interfacial chemistry to transport suppression and energetic or redox…
Complex systems of intracellular biochemical reactions have a central role in regulating cell identities and functions. Biochemical reaction systems are typically studied using the language and tools of graph theory. However, graph…
The study of the laws of nature has traditionally been pursued in the limit of isolated systems, where energy is conserved. This is not always a valid approximation, however, as the inclusion of features like gain and loss, or periodic…
We discuss a method of approximate model reduction for networks of biochemical reactions. This method can be applied to networks with polynomial or rational reaction rates and whose parameters are given by their orders of magnitude. In…
Biochemical networks are used in computational biology, to model the static and dynamical details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as…
We introduce and investigate the concept of Stratified Algebra, a new algebraic framework equipped with a layer-based structure on a vector space. We formalize a set of axioms governing intra-layer and inter-layer interactions, study their…
Statistical mechanics has grown without bounds in space. Statistical mechanics of point particles in an unbounded perfect gas is commonly accepted as a foundation for understanding many systems, including liquids like the concentrated salt…
This paper uses linear magnetohydrodynamics to model resonant absorption in coronal plasma with a Cartesian coordinate system. We impose line-tied boundary conditions and tilt the background magnetic field to be oblique to the transition…
The chain of algebraic geometry constructions permits to transfer from the minimal surface with zero instability index, and from the lattice over the ring of cyclotomic integers to the tetra-block helix. The tetra-block is the 7-vertex…
Predictive dynamical models for marine ecosystems are used for a variety of needs. Due to sparse measurements and limited understanding of the myriad of ocean processes, there is however significant uncertainty. There is model uncertainty…
Topology transcends boundaries that conventionally delineate physical, biological and engineering sciences. Our ability to mathematically describe topology, combined with our access to precision tracking and manipulation approaches, has…
The interaction between a turbulent convective boundary layer (CBL) and the underlying land surface is an important research problem in the geosciences. In order to model this interaction adequately, it is necessary to develop tools which…
In this paper we present with algebraic trees a novel notion of (continuum) trees which generalizes countable graph-theoretic trees to (potentially) uncountable structures. For that purpose we focus on the tree structure given by the branch…
Coarse-grained models are a core computational tool in theoretical chemistry and biophysics. A judicious choice of a coarse-grained model can yield physical insight by isolating the essential degrees of freedom that dictate the…
Mixed states are introduced in physics in order to express our ignorance about the actual state of a physical system and are represented in standard quantum mechanics (QM) by density operators. Such operators also appear if one considers a…
Chemical space which encompasses all stable compounds is unfathomably large and its dimension scales linearly with the number of atoms considered. The success of machine learning methods suggests that many physical quantities exhibit…
We study the boundary symmetries of models of nonequilibrium physics where the steady state behaviour strongly depends on the boundary rates. Within the matrix product state approach to many-body systems the physics is described in terms of…
Reduced density matrices are a powerful tool in the analysis of entanglement structure, approximate or coarse-grained dynamics, decoherence, and the emergence of classicality. It is straightforward to produce a reduced density matrix with…
In this article, it is experimentally verified that nonreciprocal photonic systems with a continuous translation symmetry may have an ill-defined topology. The topological classification of such systems is only feasible when the material…