TY - CHAP A1 - Igde, Sinaida A1 - Wölk, Hendrik A1 - Röblitz, Susanna A1 - Reidelbach, Marco A1 - Weber, Marcus A1 - Hartmann, Laura T1 - Identifying Multivalent Binding Kinetics of Precision Glycomacromolecules: A Kinetic Study Using kinITC T2 - Münster Symposium on Cooperative Effects 2015 - SFB 858, at Westfälische Wilhelms-Universität Münster, 2015 N2 - Multivalent sugar/protein interactions are well-known to proceed through different binding modes 1-5 which in turn can be described by their binding kinetics 3-5. This study provides additional insight into the association and dissociation reaction rates of complex multivalent sugar/protein interactions. Binding kinetics of recently introduced multivalent precision glycomacromolecules 6-8 to Concanavalin A (Con A) were studied by " kinetic Isothermal Titration Calorimetry " (kinITC) 9-11. The effect of multivalency is evaluated by comparing rate constants of glycomacromolecules obtaining the same and different valency of mannose ligands and by variation of the overall backbone properties, such as hydrophilic/ hydrophoboc. In addition, binding kinetics were studied using different conformations of Con A (homodimer vs.-tetramer) and thus a different protein valency. Our results show that precision glycomacromolecule/Con A binding proceeds non-cooperatively. Further, association and dissociation rates are mainly described by intermolecular complex formation. Together with the so-called functional valency, we can discriminate between " bound " and " unbound " states for macroscopic on-and off-rates, even for such complex glycooligomer/protein systems. By comparing e.g. a mono-to a divalent glycomacromolecule for their binding to dimeric Con A, we see a lower dissociation rate for the latter. As both bind monovalently to Con A, this is a strong indication for a statistical rebinding event. Further, there is a strong dependence of multivalent binding kinetics on the ligand density of glycomacromolecules as well as the Con A conformation and thus the overall on-and off-rates. Y1 - 2015 ER - TY - CHAP A1 - Schembera, Björn A1 - Wübbeling, Frank A1 - Kleikamp, Hendrik A1 - Schmidt, Burkhard A1 - Shehu, Aurela A1 - Reidelbach, Marco A1 - Biedinger, Christine A1 - Fiedler, Jochen A1 - Koprucki, Thomas A1 - Iglezakis, Dorothea A1 - Göddeke, Dominik T1 - Towards a Knowledge Graph for Models and Algorithms in Applied Mathematics T2 - Metadata and Semantic Research. MTSR 2024 N2 - Mathematical models and algorithms are an essential part of mathematical research data, as they are epistemically grounding numerical data. To make this research data FAIR, we present how two previously distinct ontologies, MathAlgoDB for algorithms and MathModDB for models, were merged and extended into a living knowledge graph as the key outcome. This was achieved by connecting the ontologies through computational tasks that correspond to algorithmic tasks. Moreover, we show how models and algorithms can be enriched with subject-specific metadata, such as matrix symmetry or model linearity, essential for defining workflows and determining suitable algorithms. Additionally, we propose controlled vocabularies to be added, along with a new class that differentiates base quantities from specific use case quantities. We illustrate the capabilities of the developed knowledge graph using two detailed examples from different application areas of applied mathematics, having already integrated over 250 research assets into the knowledge graph. Y1 - 2025 SN - 9783031819735 U6 - https://doi.org/10.1007/978-3-031-81974-2_8 SN - 1865-0929 VL - 2331 SP - 95 EP - 109 PB - Springer Nature Switzerland CY - Cham ER - TY - CHAP A1 - Schembera, Björn A1 - Wübbeling, Frank A1 - Kleikamp, Hendrik A1 - Biedinger, Christine A1 - Fiedler, Jochen A1 - Reidelbach, Marco A1 - Shehu, Aurela A1 - Schmidt, Burkhard A1 - Koprucki, Thomas A1 - Iglezakis, Dotothea A1 - Göddeke, Dominik T1 - Ontologies for Models and Algorithms in Applied Mathematics and Related Disciplines T2 - Metadata and Semantic Research - MTSR 2023 N2 - In applied mathematics and related disciplines, the modeling-simulation-optimization workflow is a prominent scheme, with mathematical models and numerical algorithms playing a crucial role. For these types of mathematical research data, the Mathematical Research Data Initiative has developed, merged and implemented ontologies and knowledge graphs. This contributes to making mathematical research data FAIR by introducing semantic technology and documenting the mathematical foundations accordingly. Using the concrete example of microfracture analysis of porous media, it is shown how the knowledge of the underlying mathematical model and the corresponding numerical algorithms for its solution can be represented by the ontologies. Y1 - 2023 U6 - https://doi.org/10.1007/978-3-031-65990-4_14 SP - 161 EP - 168 PB - Springer Nature Switzerland CY - Cham ET - Communications in Computer and Information Science ER - TY - CHAP A1 - Reidelbach, Marco A1 - Schembera, Björn A1 - Weber, Marcus T1 - Towards a FAIR Documentation of Workflows and Models in Applied Mathematics T2 - Mathematical Software – ICMS 2024 N2 - Modeling-Simulation-Optimization workflows play a fundamental role in applied mathematics. The Mathematical Research Data Initiative, MaRDI, responded to this by developing a FAIR and machine-interpretable template for a comprehensive documentation of such workflows. MaRDMO, a Plugin for the Research Data Management Organiser, enables scientists from diverse fields to document and publish their workflows on the MaRDI Portal seamlessly using the MaRDI template. Central to these workflows are mathematical models. MaRDI addresses them with the MathModDB ontology, offering a structured formal model description. Here, we showcase the interaction between MaRDMO and the MathModDB Knowledge Graph through an algebraic modeling workflow from the Digital Humanities. This demonstration underscores the versatility of both services beyond their original numerical domain. Y1 - 2024 U6 - https://doi.org/10.1007/978-3-031-64529-7_27 VL - 14749 SP - 254 EP - 262 PB - Springer Nature Switzerland CY - Cham ET - Lecture Notes in Computer Science ER -