Related papers: A tropical geometry for bounded biochemical state …
While ubiquitous, energy redistribution remains a poorly understood facet of the nonequilibrium thermodynamics of biomolecules. At the molecular level, finite-size effects, pronounced nonlinearities, and ballistic processes produce behavior…
Strand displacement and tile assembly systems are designed to follow prescribed kinetic rules (i.e., exhibit a specific time-evolution). However, the expected behavior in the limit of infinite time--known as thermodynamic equilibrium--is…
Complex algebraic varieties become easy piecewise-linear objects after passing to the so-called tropical limit. Geometry of these limiting objects is known as tropical geometry. In this short survey we take a look at motivation and…
There is a decomposition of a Lie algebra for open matrix chains akin to the triangular decomposition. We use this decomposition to construct unitary irreducible representations. All multiple meson states can be retrieved this way.…
Analyzing qualitative behaviors of biochemical reactions using its associated network structure has proven useful in diverse branches of biology. As an extension of our previous work, we introduce a graph-based framework to calculate steady…
This PHD thesis is concerned with uncertainty relations in quantum probability theory, state estimation in quantum stochastics, and natural bundles in differential geometry. After some comments on the nature and necessity of decoherence in…
Weighted Finite State Transducers (WFSTs) are versatile data structures that can model a great number of problems, ranging from Automatic Speech Recognition to DNA sequencing. Traditional computer science algorithms are employed when…
Biological systems exhibit processes on a wide range of time and length scales. This work demonstrates that models, wherein the interaction between system constituents is captured by algebraic operations, inherently allow for successive…
In classical geometry, a linear space is a space that is closed under linear combinations. In tropical geometry, it has long been a consensus that tropical varieties defined by valuated matroids are the tropical analogue of linear spaces.…
Bulk-edge correspondence is a wide-ranging principle that applies to topological matter, as well as a precise result established in a large and growing number of cases. According to the principle, the distinctive topological properties of…
The structural and thermodynamic properties of mixtures of colloidal spheres and non-adsorbing polymer chains are studied within a novel general two-component macromolecular liquid state approach applicable for all size asymmetry ratios.…
Matrix configurations coming from matrix models comprise many important aspects of modern physics. They represent special quantum spaces and are thus strongly related to noncommutative geometry. In order to establish a semiclassical limit…
In recent years, bound states in continuum (BICs) have gained significant value for practitioners in both theoretical and applied photonics. This paper focuses on devices that utilize non-homogeneous thin patterned laminae. The properties,…
A general theory of thermodynamically consistent biomechanical--biochemical growth in a body, considering mass addition in the bulk and at an incoherent interface, is developed. The incoherency arises due to incompatibility of growth and…
We study tropical geometry in the global setting using Berkovich's deformation retraction. We state and prove the generalized balancing conditions in this setting. Starting with a strictly semi-stable formal scheme, we calculate certain…
We study improper mixtures from a quantum logical and geometrical point of view. Taking into account the fact that improper mixtures do not admit an ignorance interpretation and must be considered as states in their own right, we do not…
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…
A quantum system's state is identified with a density matrix. Though their probabilistic interpretation is rooted in ensemble theory, density matrices embody a known shortcoming. They do not completely express an ensemble's physical…
The massless bosonic field compactified on the circle of rational $R^2$ is reexamined in the presense of boundaries. A particular class of models corresponding to $R^2=\frac{1}{2k}$ is distinguished by demanding the existence of a…
This work uncovers the tropical analogue for measured laminations of the convex hull construction of decorated Teichmueller theory, namely, it is a study in coordinates of geometric degeneration to a point of Thurston's boundary for…