chemf : a purely functional chemistry toolkit

Background: Although programming in a type-safe and referentially transparent style offers several advantages over working with mutable data structures and side effects, this style of programming has not seen much use in chemistry-related software. Since functional programming languages were designed with referential transparency in mind, these languages offer a lot of support when writing immutable data structures and side-effects free code. We therefore started implementing our own toolkit based on the above programming paradigms in a modern, versatile programming language. Results: We present our initial results with functional programming in chemistry by first describing an immutable data structure for molecular graphs together with a couple of simple algorithms to calculate basic molecular properties before writing a complete SMILES parser in accordance with the OpenSMILES specification. Along the way we show how to deal with input validation, error handling, bulk operations, and parallelization in a purely functional way. At the end we also analyze and improve our algorithms and data structures in terms of performance and compare it to existing toolkits both object-oriented and purely functional. All code was written in Scala, a modern multi-paradigm programming language with a strong support for functional programming and a highly sophisticated type system. Conclusions: We have successfully made the first important steps towards a purely functional chemistry toolkit. The data structures and algorithms presented in this article perform well while at the same time they can be safely used in parallelized applications, such as computer aided drug design experiments, without further adjustments. This stands in contrast to existing object-oriented toolkits where thread safety of data structures and algorithms is a deliberate design decision that can be hard to implement. Finally, the level of type-safety achieved by Scala highly increased the reliability of our code as well as the productivity of the programmers involved in this project

Report of the Workshop on Concepts and Methods of Identifying Digital Potentials in Information Management

Recently a discussion has been instigated in the scientific community on whether our understanding of information management (IM) is still up to date[1]. A workshop on the concepts and methods of an additional IM perspective which intends to identify possible technology applications (by putting the primary focus on the possibilities offered by information technology rather than on the support of existing organisational functions and task structures) was held at the WI Conference 2019. This paper summarizes the conceptual input of the workshop and provides an overview of the initial workshop contributions

Stark Effect of Hybrid Charge Transfer States at Planar ZnO/Organic Interfaces

We investigate the bias-dependence of the hybrid charge transfer state emission at planar heterojunctions between the metal oxide acceptor ZnO and three donor molecules. The electroluminescence peak energy linearly increases with the applied bias, saturating at high fields. Variation of the organic layer thickness and deliberate change of the ZnO conductivity through controlled photo-doping allow us to confirm that this bias-induced spectral shifts relate to the internal electric field in the organic layer rather than the filling of states at the hybrid interface. We show that existing continuum models overestimate the hole delocalization and propose a simple electrostatic model in which the linear and quadratic Stark effects are explained by the electrostatic interaction of a strongly polarizable molecular cation with its mirror image

CyBy2 : a strongly typed, purely functional framework for chemical data management

We present the development of CyBy2, a versatile framework for chemical data management written in purely functional style in Scala, a modern multi-paradigm programming language. Together with the core libraries we provide a fully functional example implementation of a HTTP server together with a single page web client with powerful querying and visualization capabilities, providing essential functionality for people working in the field of organic and medicinal chemistry. The main focus of CyBy2 are the diverse needs of different research groups in the field and therefore the flexibility required from the underlying data model. Techniques for writing type level specifications giving strong guarantees about the correctness of the implementation are described, together with the resulting gain in confidence during refactoring. Finally we talk about the advantages of using a single code base from which the server, the client and the software's documentation pages are being generated. We conclude with a comparison with existing open source solutions. All code described in this article is published under version 3 of the GNU General Public License and available from GitHub including an example implementation of both backend and frontend together with documentation how to download and compile the software (available at https://github.com/stefan-hoeck/cyby2)

Aktivierung und Optimierung beruflicher Handlungskompetenzen durch komplexe Projektaufgaben. Ein Erfahrungsbericht aus dem zweisemestrigen "Mastermodell Höxter"

Wie kann man Studierende auf die Berufspraxis in Planungsbüros vorbereiten? Die Landschaftsarchitektur-Studierenden der Technischen Hochschule Ostwestfalen-Lippe in Höxter haben im Rahmen ihres Masterprojekts "Klimavorsorge Stadt Höxter" eine Antwort gefunden. Das zweisemestrige Projekt verlangt den Studierenden ein hohes Maß an eigenständigem, erforschendem und projektorientiertem Studieren ab. Dabei spielen die fünf didaktischen Phasen - Information, Durchdringung, Expertengespräche, Synthese und Präsentation - eine wichtige Rolle. Ziel ist es, berufliche und reflektierte Handlungskompetenz zu vermitteln. Das Projekt wurde im Rahmen des energy awards 2019 der "Westfalen Weser Energie" prämiert und die Studierenden wurden von der örtlichen Volkshochschule eingeladen, einen Themenabend zum Klimawandel mit ihren Erkenntnissen zu gestalten. (Herausgeber)How can students be prepared for professional practice in planning offices? The landscape architecture students at the Ostwestfalen-Lippe University of Applied Sciences and Arts in Höxter have found an answer as part of their Master\u27s project "Climate Precaution City of Höxter". The two-semester project demands a high degree of independent, exploratory and project-oriented study from the students. The five didactic phases - information, penetration, expert discussion, synthesis and presentation - play an important role. The aim is to impart professional and reflective action competence. The project was awarded a prize in the "Westfalen Weser Energie" energy awards 2019 and the students were invited by the local adult education center to design a themed evening on climate change with their findings. (Editor

Bose-Einstein condensate as a quantum memory for a photonic polarization qubit

A scheme based on electromagnetically induced transparency is used to store light in a Bose-Einstein condensate. In this process, a photonic polarization qubit is stored in atomic Zeeman states. The performance of the storage process is characterized and optimized. The average process fidelity is 1.000 +/- 0.004. For long storage times, temporal fluctuations of the magnetic field reduce this value, yielding a lifetime of the fidelity of 1.1 +/- 0.2 ms. The write-read efficiency of the pulse energy can reach 0.53 +/- 0.05

The Nod-Like Receptor (NLR) Family: A Tale of Similarities and Differences

Innate immunity represents an important system with a variety of vital processes at the core of many diseases. In recent years, the central role of the Nod-like receptor (NLR) protein family became increasingly appreciated in innate immune responses. NLRs are classified as part of the signal transduction ATPases with numerous domains (STAND) clade within the AAA+ ATPase family. They typically feature an N-terminal effector domain, a central nucleotide-binding domain (NACHT) and a C-terminal ligand-binding region that is composed of several leucine-rich repeats (LRRs). NLRs are believed to initiate or regulate host defense pathways through formation of signaling platforms that subsequently trigger the activation of inflammatory caspases and NF-kB. Despite their fundamental role in orchestrating key pathways in innate immunity, their mode of action in molecular terms remains largely unknown. Here we present the first comprehensive sequence and structure modeling analysis of NLR proteins, revealing that NLRs posses a domain architecture similar to the apoptotic initiator protein Apaf-1. Apaf-1 performs its cellular function by the formation of a heptameric platform, dubbed apoptosome, ultimately triggering the controlled demise of the affected cell. The mechanism of apoptosome formation by Apaf-1 potentially offers insight into the activation mechanisms of NLR proteins. Multiple sequence alignment analysis and homology modeling revealed Apaf-1-like structural features in most members of the NLR family, suggesting a similar biochemical behaviour in catalytic activity and oligomerization. Evolutionary tree comparisons substantiate the conservation of characteristic functional regions within the NLR family and are in good agreement with domain distributions found in distinct NLRs. Importantly, the analysis of LRR domains reveals surprisingly low conservation levels among putative ligand-binding motifs. The same is true for the effector domains exhibiting distinct interfaces ensuring specific interactions with downstream target proteins. All together these factors suggest specific biological functions for individual NLRs

Fracture properties of CrN hard coatings: Influence of the microstructure, alloying elements, and coating architecture

Transition metal nitrides are well known and applied as protective coating materials based on their unique refractory characteristics, such as high hardness or Young’s modulus. However, for long-term applications, the fracture toughness KIC is an essential factor as the integrity of the coating-substrate interface is impaired by cracking and subsequent environmental attacks. Please click Download on the upper right corner to see the full abstract