Filtern
Erscheinungsjahr
- 2023 (38) (entfernen)
Dokumenttyp
- Wissenschaftlicher Artikel (12)
- Konferenzveröffentlichung (12)
- Teil eines Buches (Kapitel) (8)
- Video (2)
- Sonstiges (2)
- Preprint (2)
Sprache
- Englisch (38) (entfernen)
Schlagworte
- Dissipative Particle Dynamics (2)
- Field measurement (2)
- Solar modules (2)
- 360° Panorama (1)
- AI (1)
- Augmented Three-Phase AC-Railgun (1)
- Chemistry Development Kit, CDK, Molecule fragmentation, In silico fragmentation, Scaffolds, Functional groups, Glycosidic moieties, Rich client, Graphical user interface, GUI (1)
- Competency-Oriented Exams (1)
- Continuous Assessment (1)
- Dissipative particle dynamics, DPD, Surfactant, Bilayer, Lamellar, Simulation, Mesoscopic (1)
Institut
- Fachbereiche (8)
- Institut für biologische und chemische Informatik (8)
- Informatik und Kommunikation (5)
- Maschinenbau Bocholt (5)
- Westfälisches Energieinstitut (2)
- Wirtschaft und Informationstechnik Bocholt (2)
- Elektrotechnik und angewandte Naturwissenschaften (1)
- Institute (1)
- Strategische Projekte (1)
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.
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).
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 concept of “Internationalisation at Home“ has gained momentum with the increasing digitalization of education and limitations on mobility. Collaborative Online International Learning (COIL) is an innovative, cost-effective instructional method that promotes intercul-tural learning through online collaboration between faculty and students from different countries or locations. The benefits of using COIL courses have been widely recognized, with learners developing intercultural competencies, digital skills, international education experi-ence, and global awareness.
However, multicultural communication in project environments can be complex and demand awareness of cultural variations . The creation and development of effective cross-cultural collectivism, trust, communication, and empathy in leadership is an important ingredient for remote project collaborations success. This is an area that has been least explored in re-search on communication in virtual teams.
The GIPE projects are mainly carried out as so-called Collaborative Online International Learning (COIL) events. However, to gain a “real world“ experience abroad in an intercultural team, students from all partner universities can participate in the Spring School being held for two weeks in Germany and the Germany students present and hand-over the results in the country of the partner university. The main objective of this research was to examine the experiences of students participating in the GIPE project and to evaluate the effectiveness of the project in enhancing intercultural competencies and fostering collaboration among stu-dents from different continents. This paper will also explore the implications of the GIPE project for Education 2.0 considering the COVID-19 pandemic and the future of education delivery and administration transformation.
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 …