@inproceedings{IgdeWoelkRoeblitzetal., author = {Igde, Sinaida and W{\"o}lk, Hendrik and R{\"o}blitz, Susanna and Reidelbach, Marco and Weber, Marcus and Hartmann, Laura}, title = {Identifying Multivalent Binding Kinetics of Precision Glycomacromolecules: A Kinetic Study Using kinITC}, series = {M{\"u}nster Symposium on Cooperative Effects 2015 - SFB 858, at Westf{\"a}lische Wilhelms-Universit{\"a}t M{\"u}nster, 2015}, booktitle = {M{\"u}nster Symposium on Cooperative Effects 2015 - SFB 858, at Westf{\"a}lische Wilhelms-Universit{\"a}t M{\"u}nster, 2015}, abstract = {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.}, language = {en} } @misc{WeberDurmazSabrietal., author = {Weber, Marcus and Durmaz, Vedat and Sabri, Peggy and Reidelbach, Marco}, title = {Supplementary simulation data for Science Manuscript ai8636}, doi = {10.12752/5.MWB.1.0}, abstract = {The simulation data has been produced by Vedat Durmaz, Peggy Sabri and Marco Reidelbach inside the "Computational Molecular Design" Group headed by Marcus Weber at Zuse-Institut Berlin, Takustr. 7, D-14195 Berlin, Germany. The file contains classical simulation data for different fentanyl derivates in the MOR binding pocket at different pHs. It also includes instruction files for quantum-chemical pKa-value estimations and a description of how we derived the pKa-values from the Gaussian09 log-files.}, language = {en} } @article{SpahnDelVecchioLabuzetal., author = {Spahn, Viola and Del Vecchio, Giovanna and Labuz, Dominika and Rodriguez-Gaztelumendi, Antonio and Massaly, N. and Temp, Julia and Durmaz, Vedat and Sabri, P. and Reidelbach, Marco and Machelska, Halina and Weber, Marcus and Stein, Christoph}, title = {A nontoxic pain killer designed by modeling of pathological receptor conformations}, series = {Science}, volume = {355}, journal = {Science}, number = {6328}, doi = {10.1126/science.aai8636}, pages = {966 -- 969}, language = {en} } @article{ReidelbachWeberImhof, author = {Reidelbach, Marco and Weber, Marcus and Imhof, Petra}, title = {Prediction of perturbed proton transfer networks}, series = {PLoS ONE}, volume = {13}, journal = {PLoS ONE}, number = {12}, doi = {https://doi.org/10.1371/journal.pone.0207718}, pages = {e0207718 -- e0207718}, abstract = {The transfer of protons through proton translocating channels is a complex process, for which direct samplings of different protonation states and side chain conformations in a transition network calculation provide an efficient, bias-free description. In principle, a new transition network calculation is required for every unsampled change in the system of interest, e.g. an unsampled protonation state change, which is associated with significant computational costs. Transition networks void of or including an unsampled change are termed unperturbed or perturbed, respectively. Here, we present a prediction method, which is based on an extensive coarse-graining of the underlying transition networks to speed up the calculations. It uses the minimum spanning tree and a corresponding sensitivity analysis of an unperturbed transition network as initial guess and refinement parameter for the determination of an unknown, perturbed transition network. Thereby, the minimum spanning tree defines a sub-network connecting all nodes without cycles and minimal edge weight sum, while the sensitivity analysis analyzes the stability of the minimum spanning tree towards individual edge weight reductions. Using the prediction method, we are able to reduce the calculation costs in a model system by up to 80\%, while important network properties are maintained in most predictions.}, language = {en} } @phdthesis{Reidelbach, author = {Reidelbach, Marco}, title = {Optimal Network Generation for the Simulation of Proton Transfer Processes}, language = {en} } @article{SpahnDelVecchioRodriguezGaztelumendietal., author = {Spahn, Viola and Del Vecchio, Giovanna and Rodriguez-Gaztelumendi, Antonio and Temp, Julia and Labuz, Dominika and Kloner, Michael and Reidelbach, Marco and Machelska, Halina and Weber, Marcus and Stein, Christoph}, title = {Opioid receptor signaling, analgesic and side effects induced by a computationally designed pH-dependent agonist}, series = {Scientific Reports}, volume = {8}, journal = {Scientific Reports}, publisher = {Springer Nature}, pages = {8965}, abstract = {Novel pain killers without adverse effects are urgently needed.}, language = {en} } @misc{ReidelbachWeber, author = {Reidelbach, Marco and Weber, Marcus}, title = {MaRDI - The mathematical Research Data Initiative}, series = {Aktionstag Forschungsdaten}, journal = {Aktionstag Forschungsdaten}, doi = {10.5281/zenodo.7397588}, language = {en} } @article{ReidelbachBaiZoellneretal., author = {Reidelbach, Marco and Bai, Mei and Z{\"o}llner, Martin Sebastian and Schneeberger, Michaela and Kubicek, Katharina and Kirchberg, Henning and Bressler, Christian and Thorwart, Michael and Herrmann, Carmen}, title = {Solvent dynamics of aqueous halides before and after photoionization}, series = {Journal of Physical Chemistry}, journal = {Journal of Physical Chemistry}, language = {en} } @article{BoegeFritzeGoergenetal., author = {Boege, Tobias and Fritze, Ren{\´e} and G{\"o}rgen, Christiane and Hanselmann, Jeroen and Iglezakis, Dorothea and Kastner, Lars and Koprucki, Thomas and Krause, Tabea and Lehrenfeld, Christoph and Polla, Silvia and Reidelbach, Marco and Riedel, Christian and Saak, Jens and Schembera, Bj{\"o}rn and Tabelow, Karsten and Weber, Marcus}, title = {Research-Data Management Planning in the German Mathematical Community}, series = {Eur. Math. Soc. Mag.}, volume = {130}, journal = {Eur. Math. Soc. Mag.}, doi = {10.4171/mag/152}, pages = {40 -- 47}, abstract = {In this paper we discuss the notion of research data for the field of mathematics and report on the status quo of research-data management and planning. A number of decentralized approaches are presented and compared to needs and challenges faced in three use cases from different mathematical subdisciplines. We highlight the importance of tailoring research-data management plans to mathematicians' research processes and discuss their usage all along the data life cycle.}, language = {en} } @article{SchemberaWuebbelingKopruckietal., author = {Schembera, Bj{\"o}rn and W{\"u}bbeling, Frank and Koprucki, Thomas and Biedinger, Christine and Reidelbach, Marco and Schmidt, Burkhard and G{\"o}ddeke, Dominik and Fiedler, Jochen}, title = {Building Ontologies and Knowledge Graphs for Mathematics and its Applications}, series = {Proceedings of the Conference on Research Data Infrastructure}, volume = {1}, journal = {Proceedings of the Conference on Research Data Infrastructure}, publisher = {TIB Open Publishing}, issn = {2941-296X}, doi = {10.52825/cordi.v1i.255}, abstract = {Ontologies and knowledge graphs for mathematical algorithms and models are presented, that have been developed by the Mathematical Research Data Initiative. This enables FAIR data handling in mathematics and the applied disciplines. Moreover, challenges of harmonization during the ontology development are discussed.}, language = {en} } @article{ReidelbachFerrerWeber, author = {Reidelbach, Marco and Ferrer, Eloi and Weber, Marcus}, title = {MaRDMO Plugin}, series = {Proceedings of the Conference on Research Data Infrastructure}, volume = {1}, journal = {Proceedings of the Conference on Research Data Infrastructure}, publisher = {TIB Open Publishing}, issn = {2941-296X}, doi = {10.52825/cordi.v1i.254}, abstract = {MaRDMO, a plugin for the Research Data Management Organiser, was developed in the Mathematical Research Data Initiative to document interdisciplinary workflows using a standardised scheme. Interdisciplinary workflows recorded this way are published directly on the MaRDI portal. In addition, central information is integrated into the MaRDI knowledge graph. Next to the documentation, MaRDMO offers the possibility to retrieve existing interdisciplinary workflows from the MaRDI Knowledge Graph to allow the reproduction of the initial work and to provide scientists with new researchimpulses. Thus, MaRDMO creates a community-driven knowledge loop that could help to overcome the replication crisis.}, language = {en} } @article{BennerDanabalanGoedekkeetal., author = {Benner, Peter and Danabalan, Renita and G{\"o}dekke, Dominik and Kastner, Lars and Krause, Tabea and Mietchen, Daniel and Reidelbach, Marco and Schembera, Bj{\"o}rn and Schubotz, Moritz and Sinn, Rainer and Tabelow, Karsten}, title = {Research Data Management Planning in Mathematics}, doi = {10.5281/zenodo.10018245}, abstract = {Research data are crucial in mathematics and all scientific disciplines, as they form the foundation for empirical evidence, by enabling the validation and reproducibility of scientific findings. Mathematical research data (MathRD) have become vast and complex, and their interdisciplinary potential and abstract nature make them ubiquitous in various scientific fields. The volume of data and the velocity of its creation are rapidly increasing due to advancements in data science and computing power. This complexity extends to other disciplines, resulting in diverse research data and computational models. Thus, proper handling of research data is crucial both within mathematics and for its manifold connections and exchange with other disciplines. The National Research Data Infrastructure (NFDI), funded by the federal and state governments of Germany, consists of discipline-oriented consortia, including the Mathematical Research Data Initiative (MaRDI). MaRDI has been established to develop services, guidelines and outreach measures for all aspects of MathRD, and thus support the mathematical research community. Research data management (RDM) should be an integral component of every scientific project, and is becoming a mandatory component of grants with funding bodies such as the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation). At the core of RDM are the FAIR (Findable, Accessible, Interoperable, and Reusable) principles. This document aims to guide mathematicians and researchers from related disciplines who create RDM plans. It highlights the benefits and opportunities of RDM in mathematics and interdisciplinary studies, showcases examples of diverse MathRD, and suggests technical solutions that meet the requirements of funding agencies with specific examples. The document is regularly updated to reflect the latest developments within the mathematical community represented by MaRDI.}, language = {en} } @article{DiederichsKrauseLemaireetal., author = {Diederichs, Katja and Krause, Celia and Lemaire, Marina and Reidelbach, Marco and Windeck, J{\"u}rgen}, title = {A Vision for Data Management Plans in the NFDI}, doi = {10.5281/zenodo.10570653}, abstract = {At present, data management plans (DMPs) are still often perceived as mere documents for funding agencies providing clarity on how research data will be handled during a funded project, but are not usually actively involved in the processes. However, they contain a great deal of information that can be shared automatically to facilitate active research data management (RDM) by providing metadata to research infrastructures and supporting communication between all involved stakeholders. This position paper brings together a number of ideas developed and collected during interdisciplinary workshops of the Data Management Planning Working Group (infra-dmp), which is part of the section Common Infrastructures of the National Research Data Infrastructure (NFDI) in Germany. We present our vision of a possible future role of DMPs, templates, and tools in the upcoming NFDI service architecture.}, language = {en} } @inproceedings{SchemberaWuebbelingKleikampetal., author = {Schembera, Bj{\"o}rn and W{\"u}bbeling, Frank and Kleikamp, Hendrik and Biedinger, Christine and Fiedler, Jochen and Reidelbach, Marco and Shehu, Aurela and Schmidt, Burkhard and Koprucki, Thomas and Iglezakis, Dotothea and G{\"o}ddeke, Dominik}, title = {Ontologies for Models and Algorithms in Applied Mathematics and Related Disciplines}, abstract = {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.}, language = {en} } @inproceedings{ReidelbachSchemberaWeber, author = {Reidelbach, Marco and Schembera, Bj{\"o}rn and Weber, Marcus}, title = {Towards a FAIR Documentation of Workflows and Models in Applied Mathematics}, abstract = {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.}, language = {en} }