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- Chemistry Development Kit, CDK, Molecule fragmentation, In silico fragmentation, Scaffolds, Functional groups, Glycosidic moieties, Rich client, Graphical user interface, GUI (1)
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Developing and implementing computational algorithms for the extraction of specific substructures from molecular graphs (in silico molecule fragmentation) is an iterative process. It involves repeated sequences of implementing a rule set, applying it to relevant structural data, checking the results, and adjusting the rules. This requires a computational workflow with data import, fragmentation algorithm integration, and result visualisation. The described workflow is normally unavailable for a new algorithm and must be set up individually. This work presents an open Java rich client Graphical User Interface (GUI) application to support the development of new in silico molecule fragmentation algorithms and make them readily available upon release. The MORTAR (MOlecule fRagmenTAtion fRamework) application visualises fragmentation results of a set of molecules in various ways and provides basic analysis features. Fragmentation algorithms can be integrated and developed within MORTAR by using a specific wrapper class. In addition, fragmentation pipelines with any combination of the available fragmentation methods can be executed. Upon release, three fragmentation algorithms are already integrated: ErtlFunctionalGroupsFinder, Sugar Removal Utility, and Scaffold Generator. These algorithms, as well as all cheminformatics functionalities in MORTAR, are implemented based on the Chemistry Development Kit (CDK).
The influence of molecular fragmentation and parameter settings on a mesoscopic dissipative particle dynamics (DPD) simulation of lamellar bilayer formation for a C10E4/water mixture is studied. A “bottom-up” decomposition of C10E4 into the smallest fragment molecules (particles) that satisfy chemical intuition leads to convincing simulation results which agree with experimental findings for bilayer formation and thickness. For integration of the equations of motion Shardlow’s S1 scheme proves to be a favorable choice with best overall performance. Increasing the integration time steps above the common setting of 0.04 DPD units leads to increasingly unphysical temperature drifts, but also to increasingly rapid formation of bilayer superstructures without significantly distorted particle distributions up to an integration time step of 0.12. A scaling of the mutual particle–particle repulsions that guide the dynamics has negligible influence within a considerable range of values but exhibits apparent lower thresholds beyond which a simulation fails. Repulsion parameter scaling and molecular particle decomposition show a mutual dependence. For mapping of concentrations to molecule numbers in the simulation box particle volume scaling should be taken into account. A repulsion parameter morphing investigation suggests to not overstretch repulsion parameter accuracy considerations.
Recent years have seen a sharp increase in the development of deep learning and artificial intelligence-based molecular informatics. There has been a growing interest in applying deep learning to several subfields, including the digital transformation of synthetic chemistry, extraction of chemical information from the scientific literature, and AI in natural product-based drug discovery. The application of AI to molecular informatics is still constrained by the fact that most of the data used for training and testing deep learning models are not available as FAIR and open data. As open science practices continue to grow in popularity, initiatives which support FAIR and open data as well as open-source software have emerged. It is becoming increasingly important for researchers in the field of molecular informatics to embrace open science and to submit data and software in open repositories. With the advent of open-source deep learning frameworks and cloud computing platforms, academic researchers are now able to deploy and test their own deep learning models with ease. With the development of new and faster hardware for deep learning and the increasing number of initiatives towards digital research data management infrastructures, as well as a culture promoting open data, open source, and open science, AI-driven molecular informatics will continue to grow. This review examines the current state of open data and open algorithms in molecular informatics, as well as ways in which they could be improved in future.
The German supply chain law ( Lieferkettensorgfaltspflichtengesetz, abbreviated: LkSG) which enters into force on 1 January 2023 is part of the developing legal framework for human rights in global supply chains. Like the French vigilance law, it represents a new generation of supply chain laws which impose mandatory human rights due diligence obligations. The LkSG requires enterprises to exercise a number of due diligence obligations – from conducting risk analysis to undertaking preventive measures or remedial actions. The law is based on public enforcement via a competent authority, the Federal Office for Economic Affairs and Export Control (BAFA). The BAFA monitors and enforces compliance with the due diligence obligations. Non-compliant enterprises can be fined with up to 800,000 Euros and, in some cases, up to 2% of the annual turnover. Whilst the LkSG is an important step towards achieving greater corporate sustainability, it also has limitations. It was a political compromise and, as such, it does not include a new civil liability for non-compliance. Moreover, by default, it only applies to the enterprise’s own business area and its direct suppliers, whereas indirect suppliers are only included where the enterprise has substantiated knowledge that an obligation has been violated.
Dephasing in quantum systems is typically the result of their interaction with environmental degrees of freedom. We investigate within a spin-boson model the influence of a super-Ohmic environment on the dynamics of a quantum two-state system. A super-Ohmic environment thereby models typical bulk phonons which are a common disturbance for solid state quantum systems as, for example, nitrogen-vacancy centers. By applying the numerically exact quasiadiabatic path-integral approach we show that for strong system-bath coupling, pseudocoherent dynamics emerges, i.e., oscillatory dynamics at short times due to slaving of the quantum system to the bath dynamics. We extend the phase diagram known for sub-Ohmic and Ohmic environments into the super-Ohmic regime and observe a pronounced nonmonotonous behavior. Super-Ohmic purely dephasing fluctuations strongly suppress the amplitude of coherent dynamics at very short times with no subsequent further decay at later times. Nevertheless, they render the dynamics overdamped. The corresponding phase separation line shows also a nonmonotonous behavior, very similar to the pseudocoherent dynamics.
We propose a quantum-mechanical model to calculate the current through a single molecular junction immersed in a solvent and surrounded by a thin shell of bound water under an applied ac voltage. The solvent plus hydration shell are captured by a dielectric continuum model for which the resulting spectral density is determined. Here the dielectric properties, e.g., the Debye relaxation time and the dielectric constant, of the bulk solvent and the hydration shell as well as the shell thickness directly enter. We determine the charge current through the molecular junction under an ac voltage in the sequential tunneling regime where we solve a quantum master equation by a real-time diagrammatic technique. Interestingly, the Fourier components of the charge current show an exponential-like decline when the hydration shell thickness increases. Finally, we apply our findings to binary solvent mixtures with varying volume fractions and find that the current is highly sensitive to both the hydration shell thickness as well as the volume fraction of the solvent mixture, giving rise to possible applications as shell and concentration sensors on the molecular scale.
Design and Development of a Bioreactor System for Mechanical Stimulation of Musculoskeletal Tissue
(2023)
We report on the development of a bioreactor system for mechanical stimulation of musculoskeletal tissues. The ultimate object is to improve the quality of medical treatment following injuries of the enthesis tissue. To this end, the tissue formation process through the effect of mechanical stimulation is investigated. A six-well system was designed, 3D printed and tested. An integrated actuator creates strain by applying a force. A contactless position sensor monitors the travels. An electronic circuit controls the bioreactor using a microcontroller. An IoT platform connects the microcontroller to a smartphone, enabling the user to alter variables, trigger actions and monitor the system. The system was stabilised by implementing two PID controllers and safety measures. The results show that the bioreactor design is suited to execute mechanical stimulation and to investigate the tissue formation and regeneration process …
In this paper, we investigate the influence of different disease groups on the size of different 1 anatomical structures. To this end, we first modify and improve an existing anatomical segmentation 2 model. Then, we use this model to segment 104 anatomical structures from computed tomography 3 (CT) scans and compute their volumes from the segmentation. After correlating the results with each 4 other, we find no new significant correlations. After correlating the volume data with known diseases 5 for each case, we find two weak correlations, one of which has not been described before and for 6 which we present a possible explanation.
The number of publications describing chemical structures has increased steadily over the last decades. However, the majority of published chemical information is currently not available in machine-readable form in public databases. It remains a challenge to automate the process of information extraction in a way that requires less manual intervention - especially the mining of chemical structure depictions. As an open-source platform that leverages recent advancements in deep learning, computer vision, and natural language processing, DECIMER.ai (Deep lEarning for Chemical IMagE Recognition) strives to automatically segment, classify, and translate chemical structure depictions from the printed literature. The segmentation and classification tools are the only openly available packages of their kind, and the optical chemical structure recognition (OCSR) core application yields outstanding performance on all benchmark datasets. The source code, the trained models and the datasets developed in this work have been published under permissive licences. An instance of the DECIMER web application is available at https://decimer.ai.
Among all additive manufacturing processes, Directed Energy Deposition-Arc (DED-Arc) shows significantly shorter production times and is particularly suitable for large-volume components of simple to medium complexity. To exploit the full potential of this process, the microstructural, mechanical and corrosion behavior have to be studied. High stickout distances lead to a large offset, which leads to an instable electric arc and thus defects such as lack of fusion. Since corrosion preferentially occurs at such defects, the main objective of this work is to investigate the influence of the stickout distance on the corrosion
behavior and microstructure of stainless steel manufactured by DED-Arc.
Within the heterogenous structure of the manufactured samples lack of fusion defects were detected. The quantity of such defects was reduced by applying a shorter stickout distance. The corrosion behavior of the additively manufactured specimens was investigated by means of potentiodynamic polarization measurements. The semi-logarithmic current density potential curves showed a similar course and thus similar corrosion resistance like that of the conventionally forged sample. The polarization curve of the reference material shows numerous current peaks, both in the anodic and cathodic regions. This metastable behavior is induced by the presence of manganese sulfides. On the sample surface a local attack by pitting corrosion was identified.
Among the FDM process variables, one of the less addressed in previous research is the filament color. Moreover, if not explicitly targeted, the filament color is usually not even mentioned.
Aiming to point out if, and to what extent, the color of the PLA filaments influences the dimensional precision and the mechanical strength of FDM prints, the authors of the present research carried out experiments on tensile specimens. The variable parameters were the layer height (0.05 mm, 0.10 mm, 0.15 mm, 0.20 mm) and the material color (natural, black, red, grey). The experimental results clearly showed that the filament color is an influential factor for the dimensional accuracy as well as for the tensile strength of the FDM printed PLA parts. Moreover, the two way ANOVA test performed revealed that the strongest effect on the tensile strength was exerted by the PLA color (2 = 97.3%), followed by the layer height (2 = 85.5%) and the interaction between the PLA color and the layer height (2 = 80.0%). Under the same printing conditions, the best dimensional accuracy was ensured by the black PLA (0.17% width deviations, respectively 5.48% height deviations), whilst the grey PLA showed the highest ultimate tensile strength values (between 57.10 MPa and 59.82 MPa).
Without proper post-processing (often using flame, furnace, laser remelting, and induction) or reinforcements’ addition, Ni-based flame-sprayed coatings generally manifest moderate adhesion to the substrate, high porosity, unmelted particles, undesirable oxides, or weak wear resistance and mechanical properties. The current research aimed to investigate the addition of ZrO2 as reinforcement to the self-fluxing alloy coatings. Mechanically mixed NiCrBSi-ZrO2 powders were thermally sprayed onto an industrially relevant high-grade steel. After thermal spraying, the samples were differently post-processed with a flame gun and with a vacuum furnace, respectively. Scanning electron microscopy showed a porosity reduction for the vacuum-heat-treated samples compared to that of the flame-post-processed ones. X-ray diffraction measurements showed differences in the main peaks of the patterns for the thermal processed samples compared to the as-sprayed ones, these having a direct influence on the mechanical behavior of the coatings. Although a slight microhardness decrease was observed in the case of vacuum-remelted samples, the overall low porosity and the phase differences helped the coating to perform better during wear-resistance testing, realized using a ball-on-disk arrangement, compared to the as-sprayed reference samples.
Ni-based alloys are among the materials of choice in developing high-quality coatings for ambient and high temperature applications that require protection against intense wear and corrosion. The current study aims to develop and characterize NiCrBSi coatings with high wear resistance and improved adhesion to the substrate. Starting with nickel-based feedstock powders, thermally sprayed coatings were initially fabricated. Prior to deposition, the powders were characterized in terms of microstructure, particle size, chemical composition, flowability, and density. For comparison, three types of powders with different chemical compositions and characteristics were deposited onto a 1.7227 tempered steel substrate using oxyacetylene flame spraying, and subsequently, the coatings were inductively remelted. Ball-on-disc sliding wear testing was chosen to investigate the tribological properties of both the as-sprayed and induction-remelted coatings. The results reveal that, in the case of as-sprayed coatings, the main wear mechanisms were abrasive, independent of powder chemical composition, and correlated with intense wear losses due to the poor intersplat cohesion typical of flame-sprayed coatings. The remelting treatment improved the performance of the coatings in terms of wear compared to that of the as-sprayed ones, and the density and lower porosity achieved during the induction post-treatment had a significant positive role in this behavior.