TY - CONF A1 - Weichert, D. A1 - Kister, Alexander A1 - Houben, S. A1 - Ernis, G. A1 - Wrobel, S. T1 - Robustness in Fatigue Strength Estimation N2 - Fatigue strength estimation is a costly manual material characterization process in which state-of-the-art approaches follow a standardized experiment and analysis procedure. In this paper, we examine a modular, Machine Learning-based approach for fatigue strength estimation that is likely to reduce the number of experiments and, thus, the overall experimental costs. Despite its high potential, deployment of a new approach in a real-life lab requires more than the theoretical definition and simulation. Therefore, we study the robustness of the approach against misspecification of the prior and discretization of the specified loads. We identify its applicability and its advantageous behavior over the state-of-the-art methods, potentially reducing the number of costly experiment. T2 - 2nd Annual AAAI Workshop on AI to Accelerate Science and Engineering CY - Washington DC, USA DA - 07.02.2023 KW - Active Learning KW - Gaussian Process KW - Fatigue Strength PY - 2022 AN - OPUS4-56684 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Monavari, M. A1 - Homaeigohar, S. A1 - Fuentes-Chandía, M. A1 - Nawaz, Q. A1 - Monavari, Mehran A1 - Venkatraman, A. A1 - Boccaccini, A. T1 - 3D printing of alginate dialdehyde-gelatin (ADA-GEL) hydrogels incorporating phytotherapeutic icariin loaded mesoporous SiO2-CaO nanoparticles for bone tissue engineering N2 - 3D printing enables a better control over the microstructure of bone restoring constructs, addresses the challenges seen in the preparation of patient-specific bone scaffolds, and overcomes the bottlenecks that can appear in delivering drugs/growth factors promoting bone regeneration. Here, 3D printing is employed for the fabrication of an osteogenic construct made of hydrogel nanocomposites. Alginate dialdehyde-gelatin (ADA-GEL) hydrogel is reinforced by the incorporation of bioactive glass nanoparticles, i.e. mesoporous silica-calcia nanoparticles (MSNs), in two types of drug (icariin) loading. The composites hydrogel is printed as superhydrated composite constructs in a grid structure. The MSNs not only improve the mechanical stiffness of the constructs but also induce formation of an apatite layer when the construct is immersed in simulated body fluid (SBF), thereby promoting cell adhesion and proliferation. The nanocomposite constructs can hold and deliver icariin efficiently, regardless of its incorporation mode, either as loaded into the MSNs or freely distributed within the hydrogel. Biocompatibility tests showed that the hydrogel nanocomposites assure enhanced osteoblast proliferation, adhesion, and differentiation. Such optimum biological properties stem from the superior biocompatibility of ADA-GEL, the bioactivity of the MSNs, and the supportive effect of icariin in relation to cell Proliferation and differentiation. Taken together, given the achieved structural and biological properties and effective drug delivery capability, the hydrogel nanocomposites show promising potential for bone tissue engineering. KW - 3D printed hydrogel KW - ADA-GEL KW - Drug delivery KW - Mesoporous SiO2-CaO nanoparticles KW - Bone tissue engineering PY - 2021 U6 - https://doi.org/10.1016/j.msec.2021.112470 VL - 131 SP - 1 EP - 11 PB - Elsevier B.V. AN - OPUS4-53848 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - CONF A1 - Pauw, Brian Richard A1 - Laskina, Sofya A1 - Naik, Aakash Ashok A1 - Smales, Glen Jacob A1 - George, Janine T1 - “Ultima Ratio”: Multi-scale, high-resolution 3D-FFT scattering pattern simulations N2 - This talk highlights a proof-of-concept that demonstrates the ability to calculate high-resolution Fourier transforms. These can be combined with multi-scale modeling to simulate scattering over a wide range, from small-angle scattering to XRD and PDF. T2 - Shapespyer/MuSSIC launch workshop CY - Didcot, UK DA - 20.02.2023 KW - X-ray scattering KW - Simulation KW - Fourier Transform KW - 3D KW - High resolution KW - Multi-scale PY - 2023 AN - OPUS4-57031 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Beslic, D. A1 - Tscheuschner, Georg A1 - Renard, B. Y. A1 - Weller, Michael G. A1 - Muth, Thilo T1 - Comprehensive evaluation of peptide de novo sequencing tools for monoclonal antibody assembly N2 - Monoclonal antibodies are biotechnologically produced proteins with various applications in research, therapeutics and diagnostics. Their ability to recognize and bind to specific molecule structures makes them essential research tools and therapeutic agents. Sequence information of antibodies is helpful for understanding antibody–antigen interactions and ensuring their affinity and specificity. De novo protein sequencing based on mass spectrometry is a valuable method to obtain the amino acid sequence of peptides and proteins without a priori knowledge. In this study, we evaluated six recently developed de novo peptide sequencing algorithms (Novor, pNovo 3, DeepNovo, SMSNet, PointNovo and Casanovo), which were not specifically designed for antibody data. We validated their ability to identify and assemble antibody sequences on three multi-enzymatic data sets. The deep learning-based tools Casanovo and PointNovo showed an increased peptide recall across different enzymes and data sets compared with spectrum-graph-based approaches. We evaluated different error types of de novo peptide sequencing tools and their performance for different numbers of missing cleavage sites, noisy spectra and peptides of various lengths. We achieved a sequence coverage of 97.69–99.53% on the light chains of three different antibody data sets using the de Bruijn assembler ALPS and the predictions from Casanovo. However, low sequence coverage and accuracy on the heavy chains demonstrate that complete de novo protein sequencing remains a challenging issue in proteomics that requires improved de novo error correction, alternative digestion strategies and hybrid approaches such as homology search to achieve high accuracy on long protein sequences. KW - De novo peptide sequencing KW - Bioinformatics KW - Benchmarking study KW - Monoclonal antibody KW - Mass spectrometry KW - Sequence coverage KW - Light chains KW - Heavy chains KW - IgG KW - Immunoglobulins KW - Error correction KW - Sequencing algorithm KW - Preprocessing KW - Missing fragmentation sites KW - Deep learning-based tools PY - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:b43-570363 VL - 24 IS - 1 SP - 1 EP - 12 PB - Oxford University Press AN - OPUS4-57036 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - CONF A1 - Amariamir, Sasan A1 - Benner, Philipp A1 - George, Janine T1 - Prediction of materials synthesizability N2 - In the pursuit of discovering materials with desirable properties, extending the available material libraries is crucial. High-throughput simulations have become an integral part in designing new materials in the past decades. However, there is no straightforward way of distinguishing synthesizable materials from all the proposed candidates. This project focuses on employing AI-driven methods to estimate synthesizability of materials. Up to now, material scientists and engineers have relied on domain knowledge as well as empirical heuristics to guess the stability and synthesizability of molecules and crystals. The famous Pauling rules of crystal stability are an example of such heuristics. However, after the accelerating material discovery in all the years since Pauling, these rules now fail to account for the stability of most known crystals. A new predictive set of heuristics for crystal stability/synthesizability is unlikely to be uncovered by human perception, given the magnitude and dimensionality of crystallographic data. Hence, a data-driven approach should be proposed to find a predictive model or set of heuristics which differentiate synthesizable crystal structures from the rest. The main challenge of this research problem is the lack of a negative set for classification. Here, there are two classes of data: the positive class which contains synthesizable materials and the negative class which contains materials which are not synthesizable. While the data from the positive class is simply the data of crystals which have been experimentally synthesized, we do not have access to data points which are certainly unsynthesizable. Strictly speaking, if an attempt of synthesizing a crystal fails, it does not necessarily follow that the crystal is not synthesizable. Also, there is no database available which contains the intended crystal structures of unsuccessful synthesis attempts. This project proposes a semi-supervised learning scheme to predict crystal synthesizability. The ML model is trained on experimental and theoretical crystal data. The initial featurization focuses on local environments which is inspired by the Pauling Rules. The experimental data points are downloaded through the Pymatgen API from the Materials Project database which contains relaxed structures recorded in Inorganic Crystal Structure Database – ICSD. The theoretical data is queried from select databases accessible through the Optimade project’s API. T2 - MSE Congress 2022 CY - Darmstadt, Germany DA - 27.09.2022 KW - Synthesizability KW - PU Learning KW - Cheminformatics PY - 2022 AN - OPUS4-56731 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - GEN A1 - Laskina, Sofya T1 - Computing the forward and inverse problem of X-ray scattering N2 - Continuing progress in the field of X-ray scattering methods empowers scientists with new possibilities to capture the most important piece of information about the structure of the sample - its 3D electron density. Although the first methods appeared almost a century ago, recovering the density structure of a sample is still very problematic. Most avail-able imaging techniques transform a 3D electron density of a realspace structure into the 2D Fourier Transform of the intensity of scattered waves in the reciprocal space. This process causes a loss of information. Firstly, instead of a 3D sample, a 2D image is created, and secondly, the phase information of the scattered waves is lost. The latter is known as the ”phase problem” and poses a serious obstacle on a way to recover a 3D electron density. In this work, we draw attention to the problem of forward and inverse Small Angle X-Ray Scattering. In the first, forward, part, we rethink the existing pipelines to computationally simulate such scattering experiments. Although there are efficient implementations of fast Fourier transformation, they often have some drawbacks. For instance, to calculate a 3D fast Fourier transform it is required to place its density in the RAM. For high-resolution structures of size > 1024 3 , this becomes very problematic, as the whole density structure requires more than 16 GB of memory. CUDA solution allows for a very fast and parallelizable implementation of high-resolution data on hundreds of last-generation machines. Such computations are very pricy and inaccessible for most scientists. To bypass this limitation, we propose a solution for a split-up 3D fast Fourier transform, which is implemented as a sequence of 2D and 1D operations. We compare our implementation on the simulated 3D shapes and show the result of a proof-of-concept on 4096 3 Metallorganic framework density structure. In the second, inverse problem, we train an invertible neural network, that given scattering data can predict the shape and its parameters. The architecture is built such, that the inverse problem is learned together with the forward process - the Fourier Transformation. We achieved very good results with this architecture, nonetheless, further testing is required, as the current training set only encompasses three simple shapes: sphere, hard sphere and cylinder. All code to reproduce and analyze the results is available at https: //github.com/sofyalaski/SAXS-simulations. KW - Machine Learning KW - SAXS KW - DFT PY - 2023 SP - 1 EP - 76 PB - Freie Universität Berlin CY - Berlin AN - OPUS4-56798 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - CONF A1 - Naik, Aakash Ashok A1 - Ertural, Christina A1 - Dhamrait, Nidal A1 - Benner, Phillip A1 - George, Janine T1 - A Quantum-Chemical Bonding Database for Solid-State Materials N2 - Understanding the chemistry and nature of individual chemical bonds is essential for materials design. Bonding analysis via the LOBSTER software package has provided valuable insights into the properties of materials for thermoelectric and catalysis applications. Thus, the data generated from bonding analysis becomes an invaluable asset that could be utilized as features in large-scale data analysis and machine learning of material properties. However, no systematic studies exist that conducted high-throughput materials simulations to curate and validate bonding data obtained from LOBSTER. Here we present an approach to constructing such a large database consisting of quantum-chemical bonding information. T2 - 16th International conference on materials chemistry (MC16) CY - Dublin, Ireland DA - 03.07.2023 KW - Bonding analysis KW - Automation KW - Materials Informatics KW - Computational Chemistry KW - Database PY - 2023 AN - OPUS4-57889 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Monavari, Mahshid A1 - Homaeigohar, Shahin A1 - Medhekar, Rucha A1 - Nawaz, Qaisar A1 - Monavari, Mehran A1 - Zheng, Kai A1 - Boccaccini, Aldo R. T1 - A 3D-Printed Wound-Healing Material Composed of Alginate Dialdehyde–Gelatin Incorporating Astaxanthin and Borate Bioactive Glass Microparticles N2 - In this study, a wound dressing composed of an alginate dialdehyde−gelatin (ADA-GEL) hydrogel incorporated by astaxanthin (ASX) and 70B (70:30 B2O3/CaO in mol %) borate bioactive glass (BBG) microparticles was developed through 3D printing. ASX and BBG particles sti.ened the composite hydrogel construct and delayed its in vitro degradation compared to the pristine hydrogel construct, mainly due to their cross-linking role, likely arising from hydrogen bonding between the ASX/BBG particles and ADA-GEL chains. Additionally, the composite hydrogel construct could hold and deliver ASX steadily. The composite hydrogel constructs codelivered biologically active ions (Ca and B) and ASX, which should lead to a faster, more e.ective wound-healing process. As shown through in vitro tests, the ASX-containing composite hydrogel promoted fibroblast (NIH 3T3) cell adhesion, proliferation, and vascular endothelial growth factor expression, as well as keratinocyte (HaCaT) migration, thanks to the antioxidant activity of ASX, the release of cell-supportive Ca2+ and B3+ ions, and the biocompatibility of ADA-GEL. Taken together, the results show that the ADA-GEL/BBG/ASX composite is an attractive biomaterial to develop multipurposed wound-healing constructs through 3D printing. KW - General Materials Science PY - 2023 U6 - https://doi.org/10.1021/acsami.2c23252 SP - 1 EP - 12 PB - American Chemical Society (ACS) AN - OPUS4-58548 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Nourinejhad Zarghani, Shaheen A1 - Ehlers, Jens A1 - Monavari, Mehran A1 - von Bargen, Susanne A1 - Hamacher, Joachim A1 - Büttner, Carmen A1 - Bandte, Martina T1 - Applicability of Different Methods for Quantifying Virucidal Efficacy Using MENNO Florades and Tomato Brown Rugose Fruit Virus as an Example N2 - After entry of a quarantine/regulated pathogen, infected plants shall be destroyed, and the cultivated area (e.g., greenhouse) shall be disinfected. Therefore, the selection of an effective disinfectant plays an important role. With the availability of different methods for virus quantification, we investigated the application of quantitative ELISA (qELISA), RT-qPCR (reverse transcription-quantitative polymerase chain reaction), and bioassays for the quantification of disinfectant efficacy. Therefore, we estimated the titer reduction in tomato brown rugose fruit virus (ToBRFV), a regulated pathogen, in plant sap and on germ carriers after treatment with MENNO Florades 4% for 16 h. The virus load before and after the treatment was measured with the mentioned methods. The RT-qPCR and qELISA methods showed very low efficacy in the presence of the disinfectant. Although bioassays are time-consuming, need purified particles for establishing the quantification models, and are less sensitive than RT-qPCR, they were able to quantify the differences in virus titer in the presence/absence of disinfectant. Interestingly, the bioassays reached at least the lower limit sensitivity of a qELISA. By being less sensitive to the presence of the disinfectant, bioassays proved to be the only technique for the determination of the disinfectant efficacy against ToBRFV on different germ carriers as well as on virus-infected plant sap. KW - Plant Science KW - Ecology KW - Evolution KW - Behavior and Systematics PY - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:b43-585497 VL - 12 IS - 4 SP - 1 EP - 18 PB - MDPI AG AN - OPUS4-58549 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Nourinejhad Zarghani, Shaheen A1 - Monavari, Mehran A1 - Ehlers, Jens A1 - Hamacher, Joachim A1 - Büttner, Carmen A1 - Bandte, Martina T1 - Comparison of Models for Quantification of Tomato Brown Rugose Fruit Virus Based on a Bioassay Using a Local Lesion Host N2 - Considering the availability of serological and molecular biological methods, the bioassay has been paled into insignificance, although it is the only experimental method that can be used to demonstrate the infectivity of a virus. We compared goodness-of-fit and predictability power of five models for the quantification of tomato brown rugose fruit virus (ToBRFV) based on local lesion assays: the Kleczkowski model, Furumoto and Mickey models I and II, the Gokhale and Bald model (growth curve model), and the modified Poisson model. For this purpose, mechanical inoculations onto Nicotiana tabacum L. cv. Xanthi nc and N. glutionosa L. with defined virus concentrations were first performed with half-leaf randomization in a Latin square design. Subsequently, models were implemented using Python software and fitted to the number of local lesions. All models could fit to the data for quantifying ToBRFV based on local lesions, among which the modified Poisson model had the best prediction of virus concentration in spike samples based on local lesions, although data of individual indicator plants showed variations. More accurate modeling was obtained from the test plant N. glutinosa than from N. tabacum cv. Xanthi nc. The position of the half-leaves on the test plants had no significant effect on the number of local lesions. KW - Plant Science KW - Ecology KW - Evolution KW - Behavior and Systematics PY - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:b43-585506 VL - 11 IS - 24 SP - 1 EP - 16 PB - MDPI AN - OPUS4-58550 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -