Donated chemical probes for open science

Potent, selective and broadly characterized small molecule modulators of protein function (chemical probes) are powerful research reagents. The pharmaceutical industry has generated many high-quality chemical probes and several of these have been made available to academia. However, probe-associated data and control compounds, such as inactive structurally related molecules and their associated data, are generally not accessible. The lack of data and guidance makes it difficult for researchers to decide which chemical tools to choose. Several pharmaceutical companies (AbbVie, Bayer, Boehringer Ingelheim, Janssen, MSD, Pfizer, and Takeda) have therefore entered into a pre-competitive collaboration to make available a large number of innovative high-quality probes, including all probe-associated data, control compounds and recommendations on use (https://openscienceprobes.sgc-frankfurt.de/). Here we describe the chemical tools and target-related knowledge that have been made available, and encourage others to join the project

Magnetic field measurements and radiation simulation for a superconducting transverse-gradient undulator

The transverse gradient undulator (TGU) concept is a way to enable short-gain length free electron lasers with laser-plasma accelerated electron bunches, although their energy spread is typically in the percent range. In this contribution, we report on the magnetic field measurements on a 40-period superconducting TGU designed, manufactured and commissioned at the Karlsruhe Institute of Technology (KIT). As the figure of merit for the field quality, tracking and radiation field simulations, based on the measured fields, will be presented

Seasonal Differences in the Attenuation of Polar Trace Organics in the Hyporheic Zone of an Urban Stream

Attenuation of trace organic compounds (TrOCs) in a river occurs to a large extent in its hyporheic zone. A major part of the attenuation of polar TrOCs is of microbial origin. As microbial activity depends on temperature and redox conditions, seasonal differences in TrOC attenuation are likely. We investigated TrOC attenuation at a river influenced by treated wastewater during two sampling campaigns, one in summer and one in winter. In addition to redox conditions and temperature, we also determined residence times of porewater in sediment using three methods: (a) non‐parametric deconvolution of electrical conductivity time series, (b) the model VFLUX 2.0 based on temperature time series (only summer), and (c) applying Darcy's law to differences in hydraulic heads (only summer). Contrary to our expectations, we found higher attenuation for 12 out of 18 TrOCs in winter, while three TrOCs were better attenuated in summer. Sediment conditions varied between seasons as more of the top sandy layer with a higher hydraulic permeability accumulated on the river bed in summer. As a result, residence times in the sediment were shorter in summer. In winter, longer residence times, lower temperatures, and a steeper oxygen gradient in sediment coincided with higher TrOC attenuation. Further research is needed to understand our unexpected findings and underlying mechanisms.Key Points The attenuation of 12 out of 18 trace organic compounds (TrOCs) in the hyporheic zone was higher in winter while three TrOCs were attenuated better in summer Residence times in sediment were longer and more diverse in winter The extent of the oxic sediment was similar between seasons but the gradient from the oxic to anoxic zone was steeper in winterDeutsche Forschungsgemeinschaft (DFG) http://dx.doi.org/10.13039/501100001659EC | H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska‐Curie Actions (MSCA) http://dx.doi.org/10.13039/100010665University of Western Australia ‐ University Postgraduate AwardAustralian Government Research Training Program ScholarshipBundesministerium für Bildung und Forschung (BMBF) http://dx.doi.org/10.13039/501100002347Peer Reviewe

Simultaneous attenuation of trace organics and change in organic matter composition in the hyporheic zone of urban streams

Trace organic compounds (TrOCs) enter rivers with discharge of treated wastewater. These effluents can contain high loads of dissolved organic matter (DOM). In a 48 h field study, we investigated changes in molecular composition of seven DOM compound classes (FTICR-MS) and attenuation of 17 polar TrOCs in a small urban stream receiving treated wastewater. Correlations between TrOCs and DOM were used to identify simultaneous changes in surface water and the hyporheic zone. Changes in TrOC concentrations in surface water ranged between a decrease of 29.2% for methylbenzotriazole and an increase of 152.2% for the transformation product gabapentin-lactam. In the hyporheic zone, only decreasing TrOC concentrations were observed, ranging from 4.9% for primidone to 93.8% for venlafaxine . TrOC attenuation coincided with a decline of molecular diversity of easily biodegradable DOM compound classes while molecular diversity of poorly biodegradable DOM compound classes increased. This concurrence indicates similar or linked attenuation pathways for biodegradable DOM and TrOCs. Strong correlations between TrOCs and DOM compound classes as well as high attenuation of TrOCs primarily occurred in the hyporheic zone. This suggests high potential for DOM turnover and TrOC mitigation in rivers if hyporheic exchange is sufficient.German Research Foundation (DFG)European Union's Horizon 2020 research and innovation programme under Marie Sklodowska-Curie grant agreementBattelle Memorial Institute for the U.S. Department of EnergyPeer Reviewe

Microbunching threshold manipulation by a corrugated structure impedance at KARA

Two parallel corrugated plates can be used to manipulate the impedance of an electron storage ring such as the KIT storage ring KARA (KArlsruhe Research Accelerator). This impedance manipulation structure opens up the possibility to eventually control the electron beam dynamics and the emitted coherent synchrotron radiation (CSR). In this contribution, we present the impedance that is most effective to manipulate the threshold of the microbunching instability for different machine settings. Furthermore, it will be shown, how the resonance frequency of this impedance is related to the spectrum of the substructures in the electron bunches

Netzwerkmanagement und Hochleistungskommunikation. Teil XXIV. Seminar SS 2001

This Technical Report includes student papers produced within a seminar of "Network Management and High Performance Communications". For the 24nd time this seminar has attracted a large number of diligent students, proving the broad interest in topics of network management and high performance ommunications. The topics of this report may be coarsely divided into two blocks: One block is devoted to high speed and high performance technology. At first, the concept of modern High Speed Switches and Routers with quality-of-service support is described. Subsequently, Efficient Methods and Algorithms for Routing Table Lookups as well as Classification of IP Packets and multiprotocol Label Switching (MPLS) are presented. A second block deals with various topics such as wireless communications, network management and security. The first article shows advantages of the Policy-based Networks to manage todays networks. Furthermore, Security Extensions of DNS for secure use of the domain name service are examined and presented. The next article describes how to use mobility profiles in mobile ad-hoc networks. Methods for watermarking of multimedia data are discussed in a subsequent article. Moreover, Technical Challenges and Solutions for IP-telephony are also presented, whereby the Stream Control Transmission Protocol is described separately as an approach to achieve a better transport of signaling messages over the Internet. The last article deals with group communication and shows New Approaches for Multicast Routing as well as an overview of some Multicast transport protocols

Enzyme-functionalized biomimetic apatites: concept and perspectives in view of innovative medical approaches

Biomimetic nanocrystalline calcium-deficient apatite compounds are particularly attractive for the setup of bioactive bone-repair scaffolds due to their high similarity to bone mineral in terms of chemical composition, structural and substructural features. As such, along with the increasingly appealing development of moderate temperature engineered routes for sample processing, they have widened the armamentarium of orthopedic and maxillofacial surgeons in the field of bone tissue engineering. This was made possible by exploiting the exceptional surface reactivity of biomimetic apatite nanocrystals, capable of easily exchanging ions or adsorbing (bio)molecules, thus leading to highly-versatile drug delivery systems. In this contribution we focus on the preparation of hybrid materials combining biomimetic nanocrystalline apatites and enzymes (lysozyme and subtilisin). This paper reports physico-chemical data as well as cytotoxicity evaluations towards Cal-72 osteoblast-like cells and finally antimicrobial assessments towards selected strains of interest in bone surgery. Biomimetic apatite/enzyme hybrids could be prepared in varying buffers. They were found to be non-cytotoxic toward osteoblastic cells and the enzymes retained their biological activity (e.g. bond cleavage or antibacterial properties) despite the immobilization and drying processes. Release properties were also examined. Beyond these illustrative examples, the concept of biomimetic apatites functionalized with enzymes is thus shown to be useable in practice, e.g. for antimicrobial purposes, thus widening possible therapeutic perspectives

Characterizing optical synchrotron radiation in the geometric optical phase space and optimizing the energy transport to a photo detector

At the Karlsruhe Research Accelerator (KARA) facility, an electron beam is generated by a thermionic electron gun, pre-accelerated to 53 MeV by a microtron and then ramped up to 500 MeV in a booster synchrotron before being injected into the storage ring, where a final electron energy of 2.5 GeV is reached. Compared to a 2D camera, when using 1D photodetectors either directly at the synchrotron light port or after a fiber optics segment, the optic design goal is to maximize the optical intensity at the photo detector, rather than to keep spacial coherence. In this field of non-imaging optics the emitter, optical setup and sink can be modeled in the optical phase space, with the etendue being the conserved quantity and position and angle the independent variables. In this contribution we describe the synchrotron radiation emitted at a dipole in the KARA booster synchrotron and the imaging setup into an optical multimode fiber with this formalism and compare the results with measurements at the synchrotron light port of the booster synchrotron

Longitudinal phase space density tomography constrained by the Vlasov-Fokker-Planck equation

Understanding the evolution of complex systems with numerous interacting particles requires advanced analytical tools capable of capturing the intricate dynamics of the phase space. This study introduces a novel approach to longitudinal phase space density tomography in an electron storage ring, leveraging constraints imposed by the Vlasov-Fokker-Planck equation. The Vlasov-Fokker-Planck equation provides a comprehensive description of the evolution of density functions in phase space, accounting for both deterministic and stochastic processes. Measurements of the turn-by-turn bunch profile offer a time-dependent projection of the phase space. Observing the bunch profile evolution of charged particles in regimes characterized by a rich phase space dynamics presents a challenging inverse problem for reconstructing the phase space densities. In this work, we present a tomographic framework for reconstructing the longitudinal phase space density of an electron bunch at the Karlsruhe Research Accelerator (KARA). This framework utilizes simulated data and applies the Vlasov-Fokker-Planck equation to drive the reconstruction process

Resonator design optimization for a compact transverse-deflecting system

Various design options have been studied and simulated using CST MICROWAVE STUDIO for a compact transverse-deflecting system proposed for diagnostics of extremely short electron bunches. The idea of the method is to use terahertz radiation, produced from optical rectification of the facility’s electron gun laser pulse. The proposed system is to be checked experimentally at the test facility FLUTE (Ferninfrarot Linac- und Test-Experiment) at Karlsruhe Institute of Technology (KIT). The present paper is focused on the simulations of the resonator providing interaction between the electron bunch and the terahertz pulse. Two types of resonators and their arrays have been studied for this purpose: inverse split-ring resonator and tilted slit resonator. Different types of terahertz pulse structure have been studied, including plane wave and transversely focused (Gaussian) beam. Useful analytical models have been proposed to systematize the results of the simulations