Exploration of Chemical Space: Formal, chemical and historical aspects

Starting from the observation that substances and reactions are the central entities of chemistry, I have structured chemical knowledge into a formal space called a directed hypergraph, which arises when substances are connected by their reactions. I call this hypernet chemical space. In this thesis, I explore different levels of description of this space: its evolution over time, its curvature, and categorical models of its compositionality. The vast majority of the chemical literature focuses on investigations of particular aspects of some substances or reactions, which have been systematically recorded in comprehensive databases such as Reaxys for the last 200 years. While complexity science has made important advances in physics, biology, economics, and many other fields, it has somewhat neglected chemistry. In this work, I propose to take a global view of chemistry and to combine complexity science tools, modern data analysis techniques, and geometric and compositional theories to explore chemical space. This provides a novel view of chemistry, its history, and its current status. We argue that a large directed hypergraph, that is, a model of directed relations between sets, underlies chemical space and that a systematic study of this structure is a major challenge for chemistry. Using the Reaxys database as a proxy for chemical space, we search for large-scale changes in a directed hypergraph model of chemical knowledge and present a data-driven approach to navigate through its history and evolution. These investigations focus on the mechanistic features by which this space has been expanding: the role of synthesis and extraction in the production of new substances, patterns in the selection of starting materials, and the frequency with which reactions reach new regions of chemical space. Large-scale patterns that emerged in the last two centuries of chemical history are detected, in particular, in the growth of chemical knowledge, the use of reagents, and the synthesis of products, which reveal both conservatism and sharp transitions in the exploration of the space. Furthermore, since chemical similarity of substances arises from affinity patterns in chemical reactions, we quantify the impact of changes in the diversity of the space on the formulation of the system of chemical elements. In addition, we develop formal tools to probe the local geometry of the resulting directed hypergraph and introduce the Forman-Ricci curvature for directed and undirected hypergraphs. This notion of curvature is characterized by applying it to social and chemical networks with higher order interactions, and then used for the investigation of the structure and dynamics of chemical space. The network model of chemistry is strongly motivated by the observation that the compositional nature of chemical reactions must be captured in order to build a model of chemical reasoning. A step forward towards categorical chemistry, that is, a formalization of all the flavors of compositionality in chemistry, is taken by the construction of a categorical model of directed hypergraphs. We lifted the structure from a lineale (a poset version of a symmetric monoidal closed category) to a category of Petri nets, whose wiring is a bipartite directed graph equivalent to a directed hypergraph. The resulting construction, based on the Dialectica categories introduced by Valeria De Paiva, is a symmetric monoidal closed category with finite products and coproducts, which provides a formal way of composing smaller networks into larger in such a way that the algebraic properties of the components are preserved in the resulting network. Several sets of labels, often used in empirical data modeling, can be given the structure of a lineale, including: stoichiometric coefficients in chemical reaction networks, reaction rates, inhibitor arcs, Boolean interactions, unknown or incomplete data, and probabilities. Therefore, a wide range of empirical data types for chemical substances and reactions can be included in our model

Q(sqrt(-3))-Integral Points on a Mordell Curve

We use an extension of quadratic Chabauty to number fields,recently developed by the author with Balakrishnan, Besser and M ̈uller,combined with a sieving technique, to determine the integral points overQ(√−3) on the Mordell curve y2 = x3 − 4

Conceptual Factors and Fuzzy Data

With the growing number of large data sets, the necessity of complexity reduction applies today more than ever before. Moreover, some data may also be vague or uncertain. Thus, whenever we have an instrument for data analysis, the questions of how to apply complexity reduction methods and how to treat fuzzy data arise rather naturally. In this thesis, we discuss these issues for the very successful data analysis tool Formal Concept Analysis. In fact, we propose different methods for complexity reduction based on qualitative analyses, and we elaborate on various methods for handling fuzzy data. These two topics split the thesis into two parts. Data reduction is mainly dealt with in the first part of the thesis, whereas we focus on fuzzy data in the second part. Although each chapter may be read almost on its own, each one builds on and uses results from its predecessors. The main crosslink between the chapters is given by the reduction methods and fuzzy data. In particular, we will also discuss complexity reduction methods for fuzzy data, combining the two issues that motivate this thesis.Komplexitätsreduktion ist eines der wichtigsten Verfahren in der Datenanalyse. Mit ständig wachsenden Datensätzen gilt dies heute mehr denn je. In vielen Gebieten stößt man zudem auf vage und ungewisse Daten. Wann immer man ein Instrument zur Datenanalyse hat, stellen sich daher die folgenden zwei Fragen auf eine natürliche Weise: Wie kann man im Rahmen der Analyse die Variablenanzahl verkleinern, und wie kann man Fuzzy-Daten bearbeiten? In dieser Arbeit versuchen wir die eben genannten Fragen für die Formale Begriffsanalyse zu beantworten. Genauer gesagt, erarbeiten wir verschiedene Methoden zur Komplexitätsreduktion qualitativer Daten und entwickeln diverse Verfahren für die Bearbeitung von Fuzzy-Datensätzen. Basierend auf diesen beiden Themen gliedert sich die Arbeit in zwei Teile. Im ersten Teil liegt der Schwerpunkt auf der Komplexitätsreduktion, während sich der zweite Teil der Verarbeitung von Fuzzy-Daten widmet. Die verschiedenen Kapitel sind dabei durch die beiden Themen verbunden. So werden insbesondere auch Methoden für die Komplexitätsreduktion von Fuzzy-Datensätzen entwickelt

Rendiconti dell'Istituto di Matematica dell'Università di Trieste. An International Journal of Mathematics. Vol. 44 (2012)

Rendiconti dell’Istituto di Matematica dell’Università di Trieste was founded in 1969 by Arno Predonzan, with the aim of publishing original research articles in all fields of mathematics and has been the first Italian mathematical journal to be published also on-line. The access to the electronic version of the journal is free. All published articles are available on-line. The journal can be obtained by subscription, or by reciprocity with other similar journals. Currently more than 100 exchange agreements with mathematics departments and institutes around the world have been entered in

Understanding Quantum Technologies 2022

Understanding Quantum Technologies 2022 is a creative-commons ebook that provides a unique 360 degrees overview of quantum technologies from science and technology to geopolitical and societal issues. It covers quantum physics history, quantum physics 101, gate-based quantum computing, quantum computing engineering (including quantum error corrections and quantum computing energetics), quantum computing hardware (all qubit types, including quantum annealing and quantum simulation paradigms, history, science, research, implementation and vendors), quantum enabling technologies (cryogenics, control electronics, photonics, components fabs, raw materials), quantum computing algorithms, software development tools and use cases, unconventional computing (potential alternatives to quantum and classical computing), quantum telecommunications and cryptography, quantum sensing, quantum technologies around the world, quantum technologies societal impact and even quantum fake sciences. The main audience are computer science engineers, developers and IT specialists as well as quantum scientists and students who want to acquire a global view of how quantum technologies work, and particularly quantum computing. This version is an extensive update to the 2021 edition published in October 2021.Comment: 1132 pages, 920 figures, Letter forma