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The explosion of data available in life sciences is fueling an increasing demand for expressive models and computational methods. Graph transformation is a model for dynamic systems with a large variety of applications. We introduce a novel method of the graph transformation model construction, combining generative and dynamical viewpoints to give a fully automated data-driven model inference method. The method takes the input dynamical properties, given as a "snapshot" of the dynamics encoded by explicit transitions, and constructs a compatible model. The obtained model is guaranteed to be minimal, thus framing the approach as model compression (from a set of transitions into a set of rules). The compression is permissive to a lossy case, where the constructed model is allowed to exhibit behavior outside of the input transitions, thus suggesting a completion of the input dynamics. The task of graph transformation model inference is naturally highly challenging due to the combinatorics involved. We tackle the exponential explosion by proposing a heuristically minimal translation of the task into a well-established problem, set cover, for which highly optimized solutions exist. We further showcase how our results relate to Kolmogorov complexity expressed in terms of graph transformation., Comment: Preprint

We present an overview on the development and characterization of multiscale laser processing optics for versatile material modifications across more than six orders of magnitude. Starting with solutions for micromachining we present high-NA microscope objectives creating sub-wavelength material modifications on macroscopic scales with highest peak intensities. Moving on to the millimeter range, the adaptability and scalability of scanning optics is examined for large-area machining. Finally, we explore line beam optics in the meter range, evaluating their use in uniform material processing using average powers above 100kW. This study provides an insight into the design and performance characteristics of such optics and demonstrates their potential in advanced laser processing., Comment: Review article with 12 pages, 15 figures and 74 references

Simulations and measurements on selective laser etching of display glasses are reported. By means of a holographic 3D beam splitter, ultrashort laser pulses are focused inside the volume of a glass sample creating type III modifications along a specific trajectory like pearls on a string. Superimposed by a feed of the glass sample a full 3D area of modifications is achieved building the cornerstone for subsequent etch processes. Based on KOH the modifications are selectively etched at a much higher rate compared to unmodified regions resulting in a separation of the glass along the trajectory of modifications. For gaining further insight into the etch process, we perform simulations on this wet chemical process and compare it to our experimental results.

A standardized phase retrieval algorithm is presented and applied to an industry-grade high-energy ultrashort pulsed laser to uncover its spatial phase distribution. We describe in detail how to modify the well-known algorithm in order to characterize particularly strong light sources from intensity measurements only. With complete information about the optical field of the unknown light source at hand, virtual back propagation can reveal weak points in the light path such as apertures or damaged components., Comment: Published Applied Optics manuscript, 12 pages, 10 figures

Chemical reactions can be understood as transformations of multigraphs (molecules) that preserve vertex labels (atoms) and degrees (sums of bonding and non-bonding electrons), thereby implying the atom-atom map of a reaction. The corresponding reaction mechanism is often described by an electron pushing diagram that explains the transformation by consecutive local relocations of invidudal edges (electron pairs). Here, we show that every degree-preserving map between multigraphs, and thus every atom-atom map, can be generated by cyclic electron pushing. Moreover, it is always possible to decompose such an explanation into electron pushing diagrams involving only four electron pairs. This in turn implies that every reaction can be decomposed into a sequence of elementary reactions that involve at most two educt molecules and two product molecules. Hence, the requirement of a mechanistic explantion in terms of electron pushing and small imaginary transition states does not impose a combinatorial constraint on the feasibility of hypothetical chemical reactions.

The exploration of pathways and alternative pathways that have a specific function is of interest in numerous chemical contexts. A framework for specifying and searching for pathways has previously been developed, but a focus on which of the many pathway solutions are realisable, or can be made realisable, is missing. Realisable here means that there actually exists some sequencing of the reactions of the pathway that will execute the pathway. We present a method for analysing the realisability of pathways based on the reachability question in Petri nets. For realisable pathways, our method also provides a certificate encoding an order of the reactions which realises the pathway. We present two extended notions of realisability of pathways, one of which is related to the concept of network catalysts. We exemplify our findings on the pentose phosphate pathway. Lastly, we discuss the relevance of our concepts for elucidating the choices often implicitly made when depicting pathways., Comment: Accepted in LNBI proceedings

Let $\mathbb{F}$ be the field of real Puiseux series and $\mathcal{T}_\mathbb{F}$ the $\mathbb{Q}$-tree defined by Brumfiel. We show that completing all the segments of $\mathcal{T}_\mathbb{F}$ does not result in a complete metric space., Comment: 9 pages, 4 figures, comments are welcome!

These notes transcribe a workshop about the notion of total positivity and $\Theta$-positivity and its relation to Higher Teichm\"uller Theory. $\Theta$-positivity is a notion of positivity in semisimple Lie groups and was recently introduced by Guichard and Wienhard as a generalization of Lusztig's total positivity. It is believed to be the cathartic notion to classify higher Teichm\"uller spaces. Without doubt, substantial progress will be achieved in the near future on the study of $\Theta$-positive structures. These notes provide an account of the state of the art as of 2021., Comment: Proceedings edited by Xenia Flamm and Arnaud Maret

The goal of this article is to show that Hitchin representations over real closed field extensions $\mathbb{F}$ of $\mathbb{R}$ are exactly those representations from the fundamental group of a closed surface into $\textrm{PSL}(n,\mathbb{F})$ that are conjugate to $\mathbb{F}$-positive representations, i.e. representations that admit an equivariant limit map from the set of fixed points in the boundary of the universal cover of the surface into the set of full flags in $\mathbb{F}^n$ satisfying specific positivity properties. They form semi-algebraically connected components of the space of all representations that consist entirely of injective representations with discrete image., Comment: 34 pages, 6 figures, comments welcome! Second version: Minor correction of the statement of Theorem 1.1 (former Theorem 1.2) and its proof, which is now simplified (the appendix was removed); Section 9 was added

Physical mechanisms of phase separation in living systems can play key physiological roles and have recently been the focus of intensive studies. The strongly heterogeneous and disordered nature of such phenomena in the biological domain poses difficult modeling challenges that require going beyond mean field approaches based on postulating a free energy landscape. The alternative pathway we take in this work is to tackle the full statistical mechanics problem of calculating the partition function in these systems, starting from microscopic interactions, by means of cavity methods. We illustrate the procedure first on the simple binary case, and we then apply it successfully to ternary systems, in which the naive mean field approximations are proved inadequate. We then demonstrate the agreement with lattice model simulations, to finally contrast our theory also with experiments of coacervate formation by associative de-mixing of nucleotides and poly-lysine in aqueous solution. In this way, different types of evidence are provided to support cavity methods as ideal tools for quantitative modeling of biomolecular condensation, giving an optimal balance between the accurate consideration of spatial aspects of the microscopic dynamics and the fast computational results rooted in their analytical tractability., Comment: 8 pages, 5 figures

Reaction mechanisms are often presented as sequences of elementary steps, such as codified by arrow pushing. We propose an approach for representing such mechanisms using graph transformation. In this framework, each elementary step is a rule for modifying a molecular graph and a mechanism is a sequence of such rules. To generate a compact representation of a multi-step reaction, we compose the rules of individual steps into a composite rule, providing a rigorous and fully automated approach to coarse-graining. While the composite rule retains the graphical conditions necessary for the execution of a mechanism, it also records information about transient changes not visible by comparing educts and products. By projecting the rule onto a single "overlay graph", we generalize Fujita's idea of an Imaginary Transition Structure from elementary reactions to composite reactions. The utility of the overlay graph construct is exemplified in the context of enzyme-catalyzed reactions. In a first application, we exploit mechanistic information in the Mechanism and Catalytic Site Atlas to construct overlay graphs of hydrolase reactions listed in the database. These graphs point at a spectrum of catalytic entanglement of enzyme and substrate, de-emphasizing the notion of a singular catalyst in favor of a collection of catalytic sites that can be distributed across enzyme and substrate. In a second application, we deploy composite rules to search the Rhea database for reactions of known or unknown mechanism that are, in principle, compatible with the mechanisms implied by the composite rules. We believe this work adds to the utility of graph-transformation formalisms in representing and reasoning about chemistry in an automated yet insightful fashion., Comment: Preprint

Reaction networks (RNs) comprise a set $X$ of species and a set $\mathscr{R}$ of reactions $Y\to Y'$, each converting a multiset of educts $Y\subseteq X$ into a multiset $Y'\subseteq X$ of products. RNs are equivalent to directed hypergraphs. However, not all RNs necessarily admit a chemical interpretation. Instead, they might contradict fundamental principles of physics such as the conservation of energy and mass or the reversibility of chemical reactions. The consequences of these necessary conditions for the stoichiometric matrix $\mathbf{S} \in \mathbb{R}^{X\times\mathscr{R}}$ have been discussed extensively in the literature. Here, we provide sufficient conditions for $\mathbf{S}$ that guarantee the interpretation of RNs in terms of balanced sum formulas and structural formulas, respectively. Chemically plausible RNs allow neither a perpetuum mobile, i.e., a "futile cycle" of reactions with non-vanishing energy production, nor the creation or annihilation of mass. Such RNs are said to be thermodynamically sound and conservative. For finite RNs, both conditions can be expressed equivalently as properties of $\mathbf{S}$. The first condition is vacuous for reversible networks, but it excludes irreversible futile cycles and - in a stricter sense - futile cycles that even contain an irreversible reaction. The second condition is equivalent to the existence of a strictly positive reaction invariant. Furthermore, it is sufficient for the existence of a realization in terms of sum formulas, obeying conservation of "atoms". In particular, these realizations can be chosen such that any two species have distinct sum formulas, unless $\mathbf{S}$ implies that they are "obligatory isomers". In terms of structural formulas, every compound is a labeled multigraph, in essence a Lewis formula, and reactions comprise only a rearrangement of bonds such that the total bond order is preserved.

A procedure and optical concept is introduced for ultrashort pulsed laser cleaving of transparent materials with tailored edges in a single pass. The procedure is based on holographically splitting a number of foci along the desired edge geometry including C-shaped edges with local 45{\deg} tangential angles to the surface. Single-pass, full thickness laser modifications are achieved requiring single-side access to the workpiece only without inclining the optical head. After having induced laser modifications with feed rates of 1 m/s actual separation is performed using a selective etching strategy., Comment: Accepted revised article, 8 pages, 9 figures

Let $p \colon Y \to X$ be a finite, regular cover of finite graphs with associated deck group $G$, and consider the first homology $H_1(Y;\mathbb{C})$ of the cover as a $G$-representation. The main contribution of this article is to broaden the correspondence and dictionary between the representation theory of the deck group $G$ on the one hand, and topological properties of homology classes in $H_1(Y;\mathbb{C})$ on the other hand. We do so by studying certain subrepresentations in the $G$-representation $H_1(Y;\mathbb{C})$. The homology class of a lift of a primitive element in $\pi_1(X)$ spans an induced subrepresentation in $H_1(Y;\mathbb{C})$, and we show that this property is never sufficient to characterize such homology classes if $G$ is Abelian. We study $H_1^{\textrm{comm}}(Y;\mathbb{C}) \leq H_1(Y;\mathbb{C})$ -- the subrepresentation spanned by homology classes of lifts of commutators of primitive elements in $\pi_1(X)$. Concretely, we prove that the span of such a homology class is isomorphic to the quotient of two induced representations. Furthermore, we construct examples of finite covers with $H_1^{\textrm{comm}}(Y;\mathbb{C}) \neq \ker(p_*)$., Comment: 14 pages. Comments welcome! Second version: Minor corrections and implementation of referee's recommendations (a proof of Corollary 2.5 (former Corollary 2.4) and an explanation of Example 4.1 were added), accepted for publication by Glasgow Mathematical Journal

Autocatalysis is a deceptively simple concept, referring to the situation that a chemical species $X$ catalyzes its own formation. From the perspective of chemical kinetics, autocatalysts show a regime of super-linear growth. Given a chemical reaction network, however, it is not at all straightforward to identify species that are autocatalytic in the sense that there is a sub-network that takes $X$ as input and produces more than one copy of $X$ as output. The difficulty arises from the need to distinguish autocatalysis e.g. from the superposition of a cycle that consumes and produces equal amounts of $X$ and a pathway that produces $X$. To deal with this issue, a number of competing notions, such as exclusive autocatalysis and autocatalytic cycles, have been introduced. A closer inspection of concepts and their usage by different authors shows, however, that subtle differences in the definitions often makes conceptually matching ideas difficult to bring together formally. In this contribution we make some of the available approaches comparable by translating them into a common formal framework that uses integer hyperflows as a basis to study autocatalysis in large chemical reaction networks. As an application we investigate the prevalence of autocatalysis in metabolic networks.

The separation of complex inner and outer contours of glass articles with curved surfaces using ultrashort pulsed lasers is reported. Single-pass, full-thickness modifications along the entire substrate are achieved using a processing optics that allows for beam shaping of non-diffracting beams and, additionally, for aberration compensation of phase distortions occurring at the curved interface. The glass articles finally separated by thermal stress or via selective etching meet the demands of the medical industry in terms of micro-debris, surface quality and processing speed., Comment: Accepted manuscript, 10 pages, 8 figures, 2 visualizations