Software Citation in Theory and Practice

In most fields, computational models and data analysis have become a significant part of how research is performed, in addition to the more traditional theory and experiment. Mathematics is no exception to this trend. While the system of publication and credit for theory and experiment (journals and books, often monographs) has developed and has become an expected part of the culture, how research is shared and how candidates for hiring, promotion are evaluated, software (and data) do not have the same history. A group working as part of the FORCE11 community developed a set of principles for software citation that fit software into the journal citation system, allow software to be published and then cited, and there are now over 50,000 DOIs that have been issued for software. However, some challenges remain, including: promoting the idea of software citation to developers and users; collaborating with publishers to ensure that systems collect and retain required metadata; ensuring that the rest of the scholarly infrastructure, particularly indexing sites, include software; working with communities so that software efforts "count" and understanding how best to cite software that has not been published

T=1 T=1 Pairing Along the N=Z N=Z Line

Pairing energies for the addition of two neutrons on even-even nuclei with $N=Z$ are studied. The $Z$ dependence is attributed to the number and type of orbitals that are occupied in the valence shell-model space. Properties in the region from $Z=60-100$ depend on the location of the $0g_{9/2}$ orbital.Comment: 3 pages and 2 figure

StocHy: automated verification and synthesis of stochastic processes

StocHy is a software tool for the quantitative analysis of discrete-time stochastic hybrid systems (SHS). StocHy accepts a high-level description of stochastic models and constructs an equivalent SHS model. The tool allows to (i) simulate the SHS evolution over a given time horizon; and to automatically construct formal abstractions of the SHS. Abstractions are then employed for (ii) formal verification or (iii) control (policy, strategy) synthesis. StocHy allows for modular modelling, and has separate simulation, verification and synthesis engines, which are implemented as independent libraries. This allows for libraries to be easily used and for extensions to be easily built. The tool is implemented in C++ and employs manipulations based on vector calculus, the use of sparse matrices, the symbolic construction of probabilistic kernels, and multi-threading. Experiments show StocHy's markedly improved performance when compared to existing abstraction-based approaches: in particular, StocHy beats state-of-the-art tools in terms of precision (abstraction error) and computational effort, and finally attains scalability to large-sized models (12 continuous dimensions). StocHy is available at www.gitlab.com/natchi92/StocHy

Homotopy continuation methods for coupled-cluster theory in quantum chemistry

Homotopy methods have proven to be a powerful tool for understanding the multitude of solutions provided by the coupled-cluster polynomial equations. This endeavor has been pioneered by quantum chemists that have undertaken both elaborate numerical as well as mathematical investigations. Recently, from the perspective of applied mathematics, new interest in these approaches has emerged using both topological degree theory and algebraically oriented tools. This article provides an overview of describing the latter development

Recent mathematical advances in coupled cluster theory

This article presents an in-depth educational overview of the latest mathematical developments in coupled cluster (CC) theory, beginning with Schneider's seminal work from 2009 that introduced the first local analysis of CC theory. We offer a tutorial review of second quantization and the CC ansatz, laying the groundwork for understanding the mathematical basis of the theory. This is followed by a detailed exploration of the most recent mathematical advancements in CC theory.Our review starts with an in-depth look at the local analysis pioneered by Schneider which has since been applied to analyze various CC methods. We then move on to discuss the graph-based framework for CC methods developed by Csirik and Laestadius. This framework provides a comprehensive platform for comparing different CC methods, including multireference approaches. Next, we delve into the latest numerical analysis results analyzing the single reference CC method developed by Hassan, Maday, and Wang. This very general approach is based on the invertibility of the CC function's Fr\'echet derivative. We conclude the article with a discussion on the recent incorporation of algebraic geometry into CC theory, highlighting how this novel and fundamentally different mathematical perspective has furthered our understanding and provides exciting pathways to new computational approaches

On the Connectivity of the Disguised Toric Locus of a Reaction Network

Complex-balanced mass-action systems are some of the most important types of mathematical models of reaction networks, due to their widespread use in applications, as well as their remarkable stability properties. We study the set of positive parameter values (i.e., reaction rate constants) of a reaction network $G$ that, according to mass-action kinetics, generate dynamical systems that can be realized as complex-balanced systems, possibly by using a different graph $G'$. This set of parameter values is called the disguised toric locus of $G$. The $\mathbb{R}$-disguised toric locus of $G$ is defined analogously, except that the parameter values are allowed to take on any real values. We prove that the disguised toric locus of $G$ is path-connected, and the $\mathbb{R}$-disguised toric locus of $G$ is also path-connected. We also show that the closure of the disguised toric locus of a reaction network contains the union of the disguised toric loci of all its subnetworks.Comment: 18 pages, 2 figure

Characteristic polynomials and eigenvalues of tensors

We lay the geometric foundations for the study of the characteristic polynomial of tensors. For symmetric tensors of order $d \geq 3$ and dimension $2$ and symmetric tensors of order $3$ and dimension $3$, we prove that only finitely many tensors share any given characteristic polynomial, unlike the case of symmetric matrices and the case of non-symmetric tensors. We propose precise conjectures for the dimension of the variety of tensors sharing the same characteristic polynomial, in the symmetric and in the non-symmetric setting.Comment: 25 pages, comments are welcom