TY - JOUR A1 - Sajulga, R. A1 - Easterly, C. A1 - Riffle, M. A1 - Mesuere, B. A1 - Muth, Thilo A1 - Mehta, S. A1 - Kumar, P. A1 - Johnson, J. A1 - Gruening, B. A1 - Schiebenhoefer, H. A1 - Kolmeder, C. A1 - Fuchs, S. A1 - Nunn, B. A1 - Rudney, J. A1 - Griffin, T. A1 - Jagtap, P. T1 - Survey of metaproteomics software tools for functional microbiome analysis N2 - To gain a thorough appreciation of microbiome dynamics, researchers characterize the functional relevance of expressed microbial genes or proteins. This can be accomplished through metaproteomics, which characterizes the protein expression of microbiomes. Several software tools exist for analyzing microbiomes at the functional level by measuring their combined proteome-level response to environmental perturbations. In this survey, we explore the performance of six available tools, to enable researchers to make informed decisions regarding software choice based on their research goals. Tandem mass spectrometry-based proteomic data obtained from dental caries plaque samples grown with and without sucrose in paired biofilm reactors were used as representative data for this evaluation. Microbial peptides from one sample pair were identified by the X! tandem search algorithm via SearchGUI and subjected to functional analysis using software tools including eggNOG-mapper, MEGAN5, MetaGOmics, MetaProteomeAnalyzer (MPA), ProPHAnE, and Unipept to generate functional annotation through Gene Ontology (GO) terms. Among these software tools, notable differences in functional annotation were detected after comparing differentially expressed protein functional groups. Based on the generated GO terms of these tools we performed a peptide-level comparison to evaluate the quality of their functional annotations. A BLAST analysis against the NCBI non-redundant database revealed that the sensitivity and specificity of functional annotation varied between tools. For example, eggNOG-mapper mapped to the most number of GO terms, while Unipept generated more accurate GO terms. Based on our evaluation, metaproteomics researchers can choose the software according to their analytical needs and developers can use the resulting feedback to further optimize their algorithms. To make more of these tools accessible via scalable metaproteomics workflows, eggNOG-mapper and Unipept 4.0 were incorporated into the Galaxy platform. KW - Bioinformatics KW - Metaproteomics KW - Mass spectrometry PY - 2020 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-516358 DO - https://doi.org/10.1371/journal.pone.0241503 SP - e0241503 AN - OPUS4-51635 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Sadowski, A. A1 - Seidel, M. A1 - Al-Lawati, H. A1 - Azizi, E. A1 - Balscheit, Hagen A1 - Böhm, M. A1 - Chen, Lei A1 - van Dijk, I. A1 - Doerich-Stavridis, C. A1 - Kunle Fajuyitan, O. A1 - Filippidis, A. A1 - Winther Fischer, A. A1 - Fischer, C. A1 - Gerasimidis, S. A1 - Karampour, H. A1 - Kathirkamanathan, L. A1 - Subramanian, S. A1 - Topkaya, Cem A1 - Wagner, H. N. R. A1 - Wang, J. A1 - Wang, J. A1 - Kumar Yadav, K. A1 - Yun, X. A1 - Zhang, P. T1 - 8-MW wind turbine tower computational shell buckling benchmark - Part 1: An international ‘round-robin’ exercise N2 - An assessment of the elastic-plastic buckling limit state for multi-strake wind turbine support towers poses a particular challenge for the modern finite element analyst, who must competently navigate numerous modelling choices related to the tug-of-war between meshing and computational cost, the use of solvers that are robust to highly nonlinear behaviour, the potential for multiple near-simultaneously critical failure locations, the complex issue of imperfection sensitivity and finally the interpretation of the data into a safe and economic design. This paper reports on an international ‘round-robin’ exercise conducted in 2022 aiming to take stock of the computational shell buckling expertise around the world which attracted 29 submissions. Participants were asked to perform analyses of increasing complexity on a standardised benchmark of an 8-MW multi-strake steel wind turbine support tower segment, from a linear elastic stress analysis to a linear bifurcation analysis to a geometrically and materially nonlinear buckling analysis with imperfections. The results are a showcase of the significant shell buckling expertise now available in both industry and academia. This paper is the first of a pair. The second paper presents a detailed reference solution to the benchmark, including an illustration of the Eurocode-compliant calibration of two important imperfection forms. KW - Wind turbine tower KW - Computational KW - Shell buckling KW - Benchmark PY - 2023 DO - https://doi.org/10.1016/j.engfailanal.2023.107124 SN - 1350-6307 VL - 148 SP - 1 EP - 23 PB - Elsevier Science CY - Oxford AN - OPUS4-57019 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Anker, Andy S. A1 - Aspuru-Guzik, Alán A1 - Bechtel, Tim A1 - Bigi, Filippo A1 - Briling, Ksenia R. A1 - Das, Basita A1 - David, Nicholas A1 - Day, Graeme M. A1 - Deringer, Volker L. A1 - Dyer, Matthew A1 - Eardley-Brunt, Annabel A1 - Evans, Matthew L. A1 - Evans, Rob A1 - Franklin, Barnabas A. A1 - Ganose, Alex M. A1 - George, Janine A1 - Goulding, Mark A1 - Hickey, Niamh A1 - James, Gillian A1 - Kalikadien, Adarsh V. A1 - Kapil, Venkat A1 - Kulik, Heather J. A1 - Kumar, Vishank A1 - Kuttner, Christian A1 - Lam, Erwin A1 - Lederbauer, Magdalena A1 - Lou, Yuchen A1 - Martin, Jennie A1 - Marulanda Bran, Andres A1 - Mathea, Miriam A1 - Pickard, Chris J. A1 - Ruscic, Branko A1 - Ryder, Matthew R. A1 - Sabanza Gil, Victor A1 - Schwaller, Philippe A1 - Segler, Marwin H. S. A1 - Sun, Wenhao A1 - Tanovic, Sara A1 - Treyde, Wojtek A1 - Walsh, Aron A1 - Wu, Ruiqi T1 - Discovering synthesis targets: General discussion N2 - This article is a discussion of the paper "Analysis of uncertainty of neural fingerprint-based models" by Christian W. Feldmann, Jochen Sieg and Miriam Mathea (Faraday discussions, 2025, DOI: 10.1039/D4FD00095A). KW - Automation KW - Materials acceleration platforms KW - Machine learning KW - Materials design KW - Materials discovery KW - Density functional theory KW - Ab initio PY - 2025 DO - https://doi.org/10.1039/D4FD90064B SN - 1359-6640 SN - 1364-5498 VL - 256 IS - Themed collection: Data-driven discovery in the chemical sciences SP - 639 EP - 663 PB - Royal Society of Chemistry (RSC) CY - Cambridge AN - OPUS4-62317 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Fareed, Adnan A1 - Rosalie, Julian A1 - Kumar, Sourabh A1 - Kar, S. A1 - Hickel, Tilmann A1 - Fähler, S. A1 - Maaß, Robert T1 - Constrained incipient phase transformation in Ni-Mn-Ga films: A small-scale design challenge N2 - Ni-Mn-Ga shape-memory alloys are promising candidates for large strain actuation and magnetocaloric cooling devices. In view of potential small-scale applications, we probe here nanomechanically the stress-induced austenite–martensite transition in single crystalline austenitic thin films as a function of temperature. In 0.5 μm thin films, a marked incipient phase transformation to martensite is observed during nanoindentation, leaving behind pockets of residual martensite after unloading. These nanomechanical instabilities occur irrespective of deformation rate and temperature, are Weibull distributed, and reveal large spatial variations in transformation stress. In contrast, at a larger film thickness of 2 μm fully reversible transformations occur, and mechanical loading remains entirely smooth. Ab-initio simulations demonstrate how an in-plane constraint can considerably increase the martensitic transformation stress, explaining the thickness-dependent nanomechanical behavior. These findings for a shape-memory Heusler alloy give insights into how reduced dimensions and constraints can lead to unexpectedly large transformation stresses that need to be considered in small-scale actuation design. KW - Shape-memory alloys KW - Nanoindentation KW - Incipient plasticity KW - NiMaGa PY - 2023 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-581422 DO - https://doi.org/10.1016/j.matdes.2023.112259 VL - 233 SP - 1 EP - 8 PB - Elsevier B.V. AN - OPUS4-58142 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Naresh-Kumar, G. A1 - Vilalta-Clemente, A. A1 - Jussila, H. A1 - Winkelmann, Aimo A1 - Nolze, Gert A1 - Vespucci, S. A1 - Nagarajan, S. A1 - Wilkinson, A. J. A1 - Trager-Cowan, C. T1 - Quantitative imaging of anti-phase domains by polarity sensitive orientation mapping using electron backscatter diffraction N2 - Advanced structural characterisation techniques which are rapid to use, non-destructive and structurally definitive on the nanoscale are in demand, especially for a detailed understanding of extended-defects and their influence on the properties of materials. We have applied the electron backscatter diffraction (EBSD) technique in a scanning electron microscope to non-destructively characterise and quantify antiphase domains (APDs) in GaP thin films grown on different (001)Si substrates with different offcuts. We were able to image and quantify APDs by relating the asymmetrical intensity distributions observed in the EBSD patterns acquired experimentally and comparing the same with the dynamical electron diffraction simulations. Additionally mean angular error maps were also plotted using automated cross-correlation based approaches to image APDs. Samples grown on substrates with a 4° offcut from the [110] do not show any APDs, whereas samples grown on the exactly oriented substrates contain APDs. The procedures described in our work can be adopted for characterising a wide range of other material systems possessing non-centrosymmetric point groups. KW - Polarity KW - Semiconductor KW - Antiphase boundary PY - 2017 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-420167 SN - 2045-2322 VL - 7 SP - Article 10916, 1 EP - 10 AN - OPUS4-42016 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Anker, Andy S. A1 - Aspuru-Guzik, Alán A1 - Ben Mahmoud, Chiheb A1 - Bennett, Sophie A1 - Briling, Ksenia R. A1 - Changiarath, Arya A1 - Chong, Sanggyu A1 - Collins, Christopher M. A1 - Cooper, Andrew I. A1 - Crusius, Daniel A1 - Darmawan, Kevion K. A1 - Das, Basita A1 - David, Nicholas A1 - Day, Graeme M. A1 - Deringer, Volker L. A1 - Duarte, Fernanda A1 - Eardley-Brunt, Annabel A1 - Evans, Matthew L. A1 - Evans, Rob A1 - Fairlamb, Ian A1 - Franklin, Barnabas A. A1 - Frey, Jeremy A1 - Ganose, Alex M. A1 - Goulding, Mark A1 - Hafizi, Roohollah A1 - Hakkennes, Matthijs A1 - Hickey, Niamh A1 - James, Gillian A1 - Jelfs, Kim E. A1 - Kalikadien, Adarsh V. A1 - Kapil, Venkat A1 - Koczor-Benda, Zsuzsanna A1 - Krammer, Ferdinand A1 - Kulik, Heather J. A1 - Kumar, Vishank A1 - Kuttner, Christian A1 - Lam, Erwin A1 - Lou, Yuchen A1 - Mante, Eltjo A1 - Martin, Jennie A1 - Mroz, Austin M. A1 - Nematiaram, Tahereh A1 - Pare, Charles W. P. A1 - Patra, Sarbani A1 - Proudfoot, James A1 - Ruscic, Branko A1 - Ryder, Matthew R. A1 - Sakaushi, Ken A1 - Saßmannshausen, Jörg A1 - Savoie, Brett M. A1 - Schneider, Nadine A1 - Schwaller, Philippe A1 - Skjelstad, Bastian Bjerkem A1 - Sun, Wenhao A1 - Szczypiński, Filip T. A1 - Torrisi, Steven A1 - Ueltzen, Katharina A1 - Vishnoi, Shubham A1 - Walsh, Aron A1 - Wang, Xinwei A1 - Wilson, Chloe A1 - Wu, Ruiqi A1 - Zeitler, Jakob T1 - Discovering structure–property correlations: General discussion N2 - This article is a discussion of the paper "Web-BO: Towards increased accessibility of Bayesian optimisation (BO) for chemistry" by Austin M. Mroz, Piotr N. Toka, Ehecatl Antonio del Río Chanona and Kim E. Jelfs (Faraday discussions, 2025, 256, 221-234). KW - Materials design KW - Machine learning KW - Automation KW - Materials discovery PY - 2025 DO - https://doi.org/10.1039/d4fd90062f SN - 1359-6640 SN - 1364-5498 VL - 256 IS - Themed collection: Data-driven discovery in the chemical sciences SP - 373 EP - 412 PB - Royal Society of Chemistry (RSC) CY - Cambridge AN - OPUS4-62208 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Baynosa, M. L. A1 - Mady, A. H. A1 - Nguyen, V. Q. A1 - Kumar, D. R. A1 - Sayed, M. S. A1 - Tuma, Dirk A1 - Shim, J.-J. T1 - Eco-friendly synthesis of recyclable mesoporous zinc ferrite@reduced graphene oxide nanocomposite for efficient photocatalytic dye degradation under solar radiation N2 - Zinc ferrite and graphene composites have attracted considerable attention in wastewater treatment. In this work, a magnetically separable mesoporous composite of ZnFe2O4 nanoparticles (NPs) and reduced graphene oxide (rGO) was prepared through a simple and eco-friendly method with pure water as solvent and without the need for subsequent thermal treatment. Uniformly dispersed ZnFe2O4 NPs on the surface of rGO sheets exhibited good crystallinity and a large BET specific surface area. These factors contributed to good photocatalytic performance of the composite for the degradation of methylene blue (MB) under simulated solar-light radiation, increased adsorptivity, increased separation efficiency of the photo-excited charges on the surface of the catalyst, and broadened light-absorption range of the composite. Efficient interfacial interaction between the ZnFe2O4 NPs and rGO sheets resulted in synergistic effects. The magnetically separable ZnFe2O4@rGO nanocomposite proved an efficient and stable catalyst in three consecutive photodegradation cycles for MB dye in aqueous solution under solar radiation. In addition, the synthesis method proposed in this study could be scaled-up easily due to the simplicity of the process, the lack of a toxic reagent, and the use of low temperatures. KW - Zinc ferrite KW - Reduced graphene oxide KW - Nanocomposite KW - Wastewater PY - 2020 DO - https://doi.org/10.1016/j.jcis.2019.11.018 SN - 0021-9797 VL - 561 SP - 459 EP - 469 PB - Elsevier B. V. CY - Amsterdam AN - OPUS4-50211 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Schürmann, Robin Mathis A1 - Tsering, Thupten A1 - Tanzer, Katrin A1 - Denifl, Stephan A1 - Kumar, S.V.K. A1 - Bald, Ilko T1 - Resonant Formation of Strand Breaks in Sensitized Oligonucleotides Induced by Low-Energy Electrons (0.5–9 eV) N2 - Halogenated nucleobases are used as radiosensitizers in cancer radiation therapy, enhancing the reactivity of DNA to secondary low-energy electrons (LEEs). LEEs induce DNA strand breaks at specific energies (resonances) by dissociative electron attachment (DEA). Although halogenated nucleobases show intense DEA resonances at various electron energies in the gas phase, it is inherently difficult to investigate the influence of halogenated nucleobases on the actual DNA strand breakage over the broad range of electron energies at which DEA can take place (<12 eV). By using DNA origami nanostructures, we determined the energy dependence of the strand break cross-section for oligonucleotides modified with 8-bromoadenine ((8Br)A). These results were evaluated against DEA measurements with isolated (8Br)A in the gas phase. Contrary to expectations, the major contribution to strand breaks is from resonances at around 7 eV while resonances at very low energy (<2 eV) have little influence on strand breaks. KW - Dissociative electron attachment KW - DNA damage KW - DNA nanotechnology KW - Low energy electrons PY - 2017 DO - https://doi.org/10.1002/anie.201705504 SN - 1433-7851 SN - 1521-3773 VL - 56 IS - 36 SP - 10952 EP - 10955 PB - Wiley AN - OPUS4-41850 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -