{ "types" : { "Bookmark" : { "pluralLabel" : "Bookmarks" }, "Publication" : { "pluralLabel" : "Publications" }, "GoldStandardPublication" : { "pluralLabel" : "GoldStandardPublications" }, "GoldStandardBookmark" : { "pluralLabel" : "GoldStandardBookmarks" }, "Tag" : { "pluralLabel" : "Tags" }, "User" : { "pluralLabel" : "Users" }, "Group" : { "pluralLabel" : "Groups" }, "Sphere" : { "pluralLabel" : "Spheres" } }, "properties" : { "count" : { "valueType" : "number" }, "date" : { "valueType" : "date" }, "changeDate" : { "valueType" : "date" }, "url" : { "valueType" : "url" }, "id" : { "valueType" : "url" }, "tags" : { "valueType" : "item" }, "user" : { "valueType" : "item" } }, "items" : [ { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/22db6760b6ada7530a16bb3516ae0048f/kpluhackova", "tags" : [ "myown","PN3-11","simtech","pn3","peerreviewed","updated","exc2075" ], "intraHash" : "2db6760b6ada7530a16bb3516ae0048f", "interHash" : "d1cceee8b5f4c0a8618480e7b74c9148", "label" : "Structural basis of NINJ1-mediated plasma membrane rupture in cell death", "user" : "kpluhackova", "description" : "", "date" : "2023-07-10 13:18:12", "changeDate" : "2023-11-16 09:32:52", "count" : 5, "pub-type": "article", "journal": "Nature", "year": "2023", "url": "https://doi.org/10.1038/s41586-023-05991-z", "author": [ "Morris Degen","José Carlos Santos","Kristyna Pluhackova","Gonzalo Cebrero","Saray Ramos","Gytis Jankevicius","Ella Hartenian","Undina Guillerm","Stefania A. Mari","Bastian Kohl","Daniel J. Müller","Paul Schanda","Timm Maier","Camilo Perez","Christian Sieben","Petr Broz","Sebastian Hiller" ], "authors": [ {"first" : "Morris", "last" : "Degen"}, {"first" : "José Carlos", "last" : "Santos"}, {"first" : "Kristyna", "last" : "Pluhackova"}, {"first" : "Gonzalo", "last" : "Cebrero"}, {"first" : "Saray", "last" : "Ramos"}, {"first" : "Gytis", "last" : "Jankevicius"}, {"first" : "Ella", "last" : "Hartenian"}, {"first" : "Undina", "last" : "Guillerm"}, {"first" : "Stefania A.", "last" : "Mari"}, {"first" : "Bastian", "last" : "Kohl"}, {"first" : "Daniel J.", "last" : "Müller"}, {"first" : "Paul", "last" : "Schanda"}, {"first" : "Timm", "last" : "Maier"}, {"first" : "Camilo", "last" : "Perez"}, {"first" : "Christian", "last" : "Sieben"}, {"first" : "Petr", "last" : "Broz"}, {"first" : "Sebastian", "last" : "Hiller"} ], "volume": "618","number": "7967","pages": "1065--1071","abstract": "Eukaryotic cells can undergo different forms of programmed cell death, many of which culminate in plasma membrane rupture as the defining terminal event1--7. Plasma membrane rupture was long thought to be driven by osmotic pressure, but it has recently been shown to be in many cases an active process, mediated by the protein ninjurin-18 (NINJ1). Here we resolve the structure of NINJ1 and the mechanism by which it ruptures membranes. Super-resolution microscopy reveals that NINJ1 clusters into structurally diverse assemblies in the membranes of dying cells, in particular large, filamentous assemblies with branched morphology. A cryo-electron microscopy structure of NINJ1 filaments shows a tightly packed fence-like array of transmembrane $\\alpha$-helices. Filament directionality and stability is defined by two amphipathic $\\alpha$-helices that interlink adjacent filament subunits. The NINJ1 filament features a hydrophilic side and a hydrophobic side, and molecular dynamics simulations show that it can stably cap membrane edges. The function of the resulting supramolecular arrangement was validated by site-directed mutagenesis. Our data thus suggest that, during lytic cell death, the extracellular $\\alpha$-helices of NINJ1 insert into the plasma membrane to polymerize NINJ1 monomers into amphipathic filaments that rupture the plasma membrane. The membrane protein NINJ1 is therefore an interactive component of the eukaryotic cell membrane that functions as an in-built breaking point in response to activation of cell death.", "issn" : "1476-4687", "doi" : "10.1038/s41586-023-05991-z", "bibtexKey": "Degen2023" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/25ddd950bf49c085783b3bed65686a7e0/kpluhackova", "tags" : [ "myown","PN3-11","CRC1333","simtech","pn3","peerreviewed","updated","exc2075" ], "intraHash" : "5ddd950bf49c085783b3bed65686a7e0", "interHash" : "53002411e3481886b8800a0d878f3b32", "label" : "Entropic barrier of water permeation through single-file channels", "user" : "kpluhackova", "description" : "", "date" : "2023-07-10 13:16:46", "changeDate" : "2025-11-19 15:26:38", "count" : 6, "pub-type": "article", "journal": "Communications Chemistry", "year": "2023", "url": "https://doi.org/10.1038/s42004-023-00919-0", "author": [ "Johann Wachlmayr","Gotthold Fläschner","Kristyna Pluhackova","Walter Sandtner","Christine Siligan","Andreas Horner" ], "authors": [ {"first" : "Johann", "last" : "Wachlmayr"}, {"first" : "Gotthold", "last" : "Fläschner"}, {"first" : "Kristyna", "last" : "Pluhackova"}, {"first" : "Walter", "last" : "Sandtner"}, {"first" : "Christine", "last" : "Siligan"}, {"first" : "Andreas", "last" : "Horner"} ], "volume": "6","number": "1","pages": "135","abstract": "Facilitated water permeation through narrow biological channels is fundamental for all forms of life. Despite its significance in health and disease as well as for biotechnological applications, the energetics of water permeation are still elusive. Gibbs free energy of activation is composed of an enthalpic and an entropic component. Whereas the enthalpic contribution is readily accessible via temperature dependent water permeability measurements, estimation of the entropic contribution requires information on the temperature dependence of the rate of water permeation. Here, we estimate, by means of accurate activation energy measurements of water permeation through Aquaporin-1 and by determining the accurate single channel permeability, the entropic barrier of water permeation through a narrow biological channel. Thereby the calculated value for \\$\\$\\backslashtriangle \\S\\^\\\\\\\\backslashddagger\\\\ \\\\$\\$þinspace=þinspace2.01þinspace±þinspace0.82þinspaceJ/(mol·K) links the activation energy of 3.75þinspace±þinspace0.16þinspacekcal/mol with its efficient water conduction rate of ˜1010 water molecules/second. This is a first step in understanding the energetic contributions in various biological and artificial channels exhibiting vastly different pore geometries.", "issn" : "2399-3669", "doi" : "10.1038/s42004-023-00919-0", "bibtexKey": "Wachlmayr2023" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2b2ba67bc06755ea9a9e84904d9340c6c/xiangxu", "tags" : [ "myown","simtech","pn3","peerreviewed","exc2075" ], "intraHash" : "b2ba67bc06755ea9a9e84904d9340c6c", "interHash" : "66e6cc8856b81837cb7ab3595b71f7cd", "label" : "Strong impact of spin fluctuations on the antiphase boundaries of weak itinerant ferromagnetic Ni3Al", "user" : "xiangxu", "description" : "", "date" : "2023-06-12 07:58:36", "changeDate" : "2024-07-17 10:52:59", "count" : 7, "pub-type": "article", "journal": "Acta Materialia","publisher":"Elsevier BV", "year": "2023", "url": "https://doi.org/10.1016%2Fj.actamat.2023.118986", "author": [ "Xiang Xu","Xi Zhang","Andrei Ruban","Siegfried Schmauder","Blazej Grabowski" ], "authors": [ {"first" : "Xiang", "last" : "Xu"}, {"first" : "Xi", "last" : "Zhang"}, {"first" : "Andrei", "last" : "Ruban"}, {"first" : "Siegfried", "last" : "Schmauder"}, {"first" : "Blazej", "last" : "Grabowski"} ], "volume": "255","pages": "118986", "doi" : "10.1016/j.actamat.2023.118986", "bibtexKey": "Xu_2023" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/250208e77b4197b9a139b28516b45c467/mschmitt", "tags" : [ "postPrint","graduateSchool","SimTech","graduateschool","peerReviewed","pn6","prePrint","EXC2075","exc2075" ], "intraHash" : "50208e77b4197b9a139b28516b45c467", "interHash" : "7efbe1d85ce6665f0065010c27e413a7", "label" : "Meta-Uncertainty in Bayesian Model Comparison", "user" : "mschmitt", "description" : "", "date" : "2023-04-20 13:53:02", "changeDate" : "2023-04-27 21:12:24", "count" : 2, "pub-type": "inproceedings", "booktitle": "Proceedings of The 26th International Conference on Artificial Intelligence and Statistics","series": "Proceedings of Machine Learning Research","publisher":"PMLR", "year": "2023", "url": "https://proceedings.mlr.press/v206/schmitt23a.html", "author": [ "Marvin Schmitt","Stefan T. Radev","Paul-Christian Bürkner" ], "authors": [ {"first" : "Marvin", "last" : "Schmitt"}, {"first" : "Stefan T.", "last" : "Radev"}, {"first" : "Paul-Christian", "last" : "Bürkner"} ], "volume": "206","pages": "11--29","abstract": "Bayesian model comparison (BMC) offers a principled probabilistic approach to study and rank competing models. In standard BMC, we construct a discrete probability distribution over the set of possible models, conditional on the observed data of interest. These posterior model probabilities (PMPs) are measures of uncertainty, but\u2014when derived from a finite number of observations\u2014are also uncertain themselves. In this paper, we conceptualize distinct levels of uncertainty which arise in BMC. We explore a fully probabilistic framework for quantifying meta-uncertainty, resulting in an applied method to enhance any BMC workflow. Drawing on both Bayesian and frequentist techniques, we represent the uncertainty over the uncertain PMPs via meta-models which combine simulated and observed data into a predictive distribution for PMPs on new data. We demonstrate the utility of the proposed method in the context of conjugate Bayesian regression, likelihood-based inference with Markov chain Monte Carlo, and simulation-based inference with neural networks.", "bibtexKey": "schmitt2023metauncertainty" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2acd0854050949710da06a9aa59258827/benjamin.weder", "tags" : [ "myown","simtech","pn7","peerreviewed","postprint","exc2075" ], "intraHash" : "acd0854050949710da06a9aa59258827", "interHash" : "2b3fd30bb974b920af1ec5d00696d69d", "label" : "Analysis and Rewrite of Quantum Workflows: Improving the Execution of Hybrid Quantum Algorithms", "user" : "benjamin.weder", "description" : "", "date" : "2023-02-09 16:12:30", "changeDate" : "2023-02-09 15:12:30", "count" : 3, "pub-type": "inproceedings", "booktitle": "Proceedings of the 12th International Conference on Cloud Computing and Services Science (CLOSER 2022)","publisher":"SciTePress", "year": "2022", "url": "https://www.scitepress.org/PublicationsDetail.aspx?ID=8gCNIWqSke0=", "author": [ "Benjamin Weder","Johanna Barzen","Martin Beisel","Frank Leymann" ], "authors": [ {"first" : "Benjamin", "last" : "Weder"}, {"first" : "Johanna", "last" : "Barzen"}, {"first" : "Martin", "last" : "Beisel"}, {"first" : "Frank", "last" : "Leymann"} ], "pages": "38--50", "doi" : "10.5220/0011035100003200", "bibtexKey": "Weder2022_QuantumWorkflowRewrite" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/270ce75dd2cd12e262f4a63aa38f52aee/benjamin.weder", "tags" : [ "myown","simtech","pn7","peerreviewed","postprint","exc2075" ], "intraHash" : "70ce75dd2cd12e262f4a63aa38f52aee", "interHash" : "98589b9975427f366f09e37d26d1f6df", "label" : "Quantum Software Development Lifecycle", "user" : "benjamin.weder", "description" : "", "date" : "2023-02-09 16:10:22", "changeDate" : "2023-02-09 15:10:22", "count" : 3, "pub-type": "inbook", "booktitle": "Quantum Software Engineering","publisher":"Springer International Publishing", "year": "2022", "url": "https://link.springer.com/chapter/10.1007/978-3-031-05324-5_4", "author": [ "Benjamin Weder","Johanna Barzen","Frank Leymann","Daniel Vietz" ], "authors": [ {"first" : "Benjamin", "last" : "Weder"}, {"first" : "Johanna", "last" : "Barzen"}, {"first" : "Frank", "last" : "Leymann"}, {"first" : "Daniel", "last" : "Vietz"} ], "editor": [ "Manuel A. Serrano","Ricardo Pérez-Castillo","Mario Piattini" ], "editors": [ {"first" : "Manuel A.", "last" : "Serrano"}, {"first" : "Ricardo", "last" : "Pérez-Castillo"}, {"first" : "Mario", "last" : "Piattini"} ], "pages": "61--83", "doi" : "10.1007/978-3-031-05324-5_4", "bibtexKey": "Weder2022_QuantumSoftwareDevLifecycle" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/22da0a4b3b8b50b9964bc7ada23fbce21/benjamin.weder", "tags" : [ "myown","simtech","pn7","peerreviewed","postprint","exc2075" ], "intraHash" : "2da0a4b3b8b50b9964bc7ada23fbce21", "interHash" : "150dcc6baf08719b719880665f18baf0", "label" : "QProv: A provenance system for quantum computing", "user" : "benjamin.weder", "description" : "", "date" : "2023-02-09 16:04:07", "changeDate" : "2023-02-09 15:07:38", "count" : 3, "pub-type": "article", "journal": "IET Quantum Communication","publisher":"Institution of Engineering and Technology (IET)", "year": "2021", "url": "https://doi.org/10.1049%2Fqtc2.12012", "author": [ "Benjamin Weder","Johanna Barzen","Frank Leymann","Marie Salm","Karoline Wild" ], "authors": [ {"first" : "Benjamin", "last" : "Weder"}, {"first" : "Johanna", "last" : "Barzen"}, {"first" : "Frank", "last" : "Leymann"}, {"first" : "Marie", "last" : "Salm"}, {"first" : "Karoline", "last" : "Wild"} ], "volume": "2","number": "4","pages": "171--181", "doi" : "10.1049/qtc2.12012", "bibtexKey": "Weder_2021" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/204782e4a5b543c181a29ff0b8066bec5/kpluhackova", "tags" : [ "myown","PN3-11","simtech","PN3","peerReviewed","EXC2075","updated" ], "intraHash" : "04782e4a5b543c181a29ff0b8066bec5", "interHash" : "a5066fa69245849b8d16b193902ad4a6", "label" : "The Hidden Intricacies of Aquaporins: Remarkable Details in a Common Structural Scaffold", "user" : "kpluhackova", "description" : "", "date" : "2022-11-23 20:49:12", "changeDate" : "2023-11-16 09:33:43", "count" : 6, "pub-type": "article", "journal": "Small", "year": "2022", "url": "https://onlinelibrary.wiley.com/doi/abs/10.1002/smll.202202056", "author": [ "Nikolaus Gössweiner-Mohr","Christine Siligan","Kristyna Pluhackova","Linnea Umlandt","Sabina Koefler","Natasha Trajkovska","Andreas Horner" ], "authors": [ {"first" : "Nikolaus", "last" : "Gössweiner-Mohr"}, {"first" : "Christine", "last" : "Siligan"}, {"first" : "Kristyna", "last" : "Pluhackova"}, {"first" : "Linnea", "last" : "Umlandt"}, {"first" : "Sabina", "last" : "Koefler"}, {"first" : "Natasha", "last" : "Trajkovska"}, {"first" : "Andreas", "last" : "Horner"} ], "volume": "18","number": "31","pages": "2202056","abstract": "Abstract Evolution turned aquaporins (AQPs) into the most efficient facilitators of passive water flow through cell membranes at no expense of solute discrimination. In spite of a plethora of solved AQP structures, many structural details remain hidden. Here, by combining extensive sequence- and structural-based analysis of a unique set of 20 non-redundant high-resolution structures and molecular dynamics simulations of four representatives, key aspects of AQP stability, gating, selectivity, pore geometry, and oligomerization, with a potential impact on channel functionality, are identified. The general view of AQPs possessing a continuous open water pore is challenged and it is depicted that AQPs\u2019 selectivity is not exclusively shaped by pore-lining residues but also by the relative arrangement of transmembrane helices. Moreover, this analysis reveals that hydrophobic interactions constitute the main determinant of protein thermal stability. Finally, a numbering scheme of the conserved AQP scaffold is established, facilitating direct comparison of, for example, disease-causing mutations and prediction of potential structural consequences. Additionally, the results pave the way for the design of optimized AQP water channels to be utilized in biotechnological applications.", "eprint" : "https://onlinelibrary.wiley.com/doi/pdf/10.1002/smll.202202056", "doi" : "https://doi.org/10.1002/smll.202202056", "bibtexKey": "https://doi.org/10.1002/smll.202202056" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2453d3bb69482a437ac0b847ebf80fd9f/kpluhackova", "tags" : [ "myown","PN3-11","simtech","PN3","peerReviewed","PN6","PN6-7","EXC2075","updated" ], "intraHash" : "453d3bb69482a437ac0b847ebf80fd9f", "interHash" : "db4618ba1f487d43517baad51a0d6bdb", "label" : "Multiple pore lining residues modulate water permeability of GlpF", "user" : "kpluhackova", "description" : "", "date" : "2022-11-23 19:07:57", "changeDate" : "2023-11-16 09:35:25", "count" : 6, "pub-type": "article", "journal": "Protein Science", "year": "2022", "url": "https://onlinelibrary.wiley.com/doi/abs/10.1002/pro.4431", "author": [ "Kristyna Pluhackova","Valentin Schittny","Paul-Christian Bürkner","Christine Siligan","Andreas Horner" ], "authors": [ {"first" : "Kristyna", "last" : "Pluhackova"}, {"first" : "Valentin", "last" : "Schittny"}, {"first" : "Paul-Christian", "last" : "Bürkner"}, {"first" : "Christine", "last" : "Siligan"}, {"first" : "Andreas", "last" : "Horner"} ], "volume": "31","number": "10","pages": "e4431","abstract": "Abstract The water permeability of aquaporins (AQPs) varies by more than an order of magnitude even though the pore structure, geometry, as well as the channel lining residues are highly conserved. However, channel gating by pH, divalent ions or phosphorylation was only shown for a minority of AQPs. Structural and in silico indications of water flux modulation by flexible side chains of channel lining residues have not been experimentally confirmed yet. Hence, the aquaporin \u201Copen state\u201D is still considered to be a continuously open pore with water molecules permeating in a single-file fashion. Using protein mutations outside the selectivity filter in the aqua(glycerol)facilitator GlpF of Escherichia coli we, to the best of our knowledge, for the first time, modulate the position of the highly conserved Arg in the selectivity filter. This in turn enhances or reduces the unitary water permeability of GlpF as shown in silico by molecular dynamics (MD) simulations and in vitro with purified and reconstituted GlpF. This finding suggests that AQP water permeability can indeed be regulated by lipid bilayer asymmetry and the transmembrane potential. Strikingly, our long-term MD simulations reveal that not only the conserved Arg in the selectivity filter, but the position and dynamics of multiple other pore lining residues modulate water passage through GlpF. This finding is expected to trigger a wealth of future investigations on permeability and regulation of AQPs among others with the aim to tune water permeability for biotechnological applications.", "eprint" : "https://onlinelibrary.wiley.com/doi/pdf/10.1002/pro.4431", "doi" : "https://doi.org/10.1002/pro.4431", "bibtexKey": "https://doi.org/10.1002/pro.4431" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2ce799e3e7728d7b320ea26282fe7f6cd/kpluhackova", "tags" : [ "myown","PN3-11","PN3","SimTech","peerReviewed","EXC2075","updated" ], "intraHash" : "ce799e3e7728d7b320ea26282fe7f6cd", "interHash" : "a07e4b1db56829d6178dc69b53dc0f37", "label" : "Not sorcery after all: Roles of multiple charged residues in membrane insertion of gasdermin-A3", "user" : "kpluhackova", "description" : "", "date" : "2022-11-23 19:03:17", "changeDate" : "2023-11-16 09:34:11", "count" : 7, "pub-type": "article", "journal": "Frontiers in Cell and Developmental Biology", "year": "2022", "url": "https://www.frontiersin.org/articles/10.3389/fcell.2022.958957", "author": [ "Viktoria Korn","Kristyna Pluhackova" ], "authors": [ {"first" : "Viktoria", "last" : "Korn"}, {"first" : "Kristyna", "last" : "Pluhackova"} ], "volume": "10","abstract": "Gasdermins execute programmatory cell death, known as pyroptosis, by forming medium-sized membrane pores. Recently, the molecular structure of those pores as well as the diversity in their shape and size have been revealed by cryoTEM and atomic force microscopy, respectively. Even though a growth of smaller to larger oligomers and reshaping from slits to rings could be documented, the initiation of the gasdermin pore formation remains a mystery. In one hypothesis, gasdermin monomers insert into membranes before associating into oligomeric pores. In the other hypothesis, gasdermin oligomers preassemble on the membrane surface prior to membrane insertion. Here, by studying the behavior of monomeric membrane-inserted gasdermin-A3 (GSDMA3), we unveil that a monomeric gasdermin prefers the membrane-adsorbed over the membrane-inserted state. Our results thus support the hypothesis of oligomers preassembling on the membrane surface before membrane penetration. At the same time, our simulations of small membrane-inserted arcs of GSDMA3 suggest that the inserting oligomer can be small and does not have to comprise a full ring of approximately 26--30 subunits. Moreover, our simulations have revealed an astonishingly large impact of salt-bridge formation and protein surroundings on the transmembrane passage of charged residues, reducing the energetic cost by up to 53% as compared to their free forms. The here observed free energy barrier of mere 5.6 kcal/mol for the membrane insertion of monomeric GSDMA3 explains the surprising ability of gasdermins to spontaneously self-insert into cellular membranes.", "issn" : "2296-634X", "bdsk-url-1" : "https://www.frontiersin.org/articles/10.3389/fcell.2022.958957", "bdsk-url-2" : "https://doi.org/10.3389/fcell.2022.958957", "doi" : "10.3389/fcell.2022.958957", "bibtexKey": "10.3389/fcell.2022.958957" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/23de1efd3564df7071a668a7e5c4039bb/bhillebrecht", "tags" : [ "myown","PN4","SimTech","peerReviewed","from:bhillebrecht","EXC2075" ], "intraHash" : "3de1efd3564df7071a668a7e5c4039bb", "interHash" : "4304a67819c757c85c5b19e1eec97200", "label" : "Certified machine learning: A posteriori error estimation for physics-informed neural networks", "user" : "bhillebrecht", "description" : "", "date" : "2022-10-25 16:29:09", "changeDate" : "2022-10-25 14:42:36", "count" : 6, "pub-type": "inproceedings", "booktitle": "2022 International Joint Conference on Neural Networks (IJCNN)", "year": "2022", "url": "", "author": [ "Birgit Hillebrecht","Benjamin Unger" ], "authors": [ {"first" : "Birgit", "last" : "Hillebrecht"}, {"first" : "Benjamin", "last" : "Unger"} ], "pages": "1-8","abstract": "Physics-informed neural networks (PINNs) are one popular approach to incorporate a priori knowledge about physical systems into the learning framework. PINNs are known to be robust for smaller training sets, derive better generalization problems, and are faster to train. In this paper, we show that using PINNs in comparison with purely data-driven neural networks is not only favorable for training performance but allows us to extract significant information on the quality of the approximated solution. Assuming that the underlying differential equation for the PINN training is an ordinary differential equation, we derive a rigorous upper limit on the PINN prediction error. This bound is applicable even for input data not included in the training phase and without any prior knowledge about the true solution. Therefore, our a posteriori error estimation is an essential step to certify the PINN. We apply our error estimator exemplarily to two academic toy problems, whereof one falls in the category of model-predictive control and thereby shows the practical use of the derived results.", "issn" : "2161-4407", "doi" : "10.1109/IJCNN55064.2022.9892569", "bibtexKey": "9892569" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2c3830c1dae95d399c1a98a86bcd15ed8/katharinafuchs", "tags" : [ "simtech","from:benjamin.weder","pn7","peerreviewed","postprint","exc2075" ], "intraHash" : "c3830c1dae95d399c1a98a86bcd15ed8", "interHash" : "c41bdbe8869e82fd121687520738b9c9", "label" : "SiDD: The Situation-Aware Distributed Deployment System", "user" : "katharinafuchs", "description" : "", "date" : "2021-12-08 17:10:08", "changeDate" : "2021-12-08 16:10:08", "count" : 3, "pub-type": "inproceedings", "booktitle": "Service-Oriented Computing -- ICSOC 2020 Workshops","publisher":"Springer International Publishing", "year": "2021", "url": "", "author": [ "Kálmán Képes","Frank Leymann","Benjamin Weder","Karoline Wild" ], "authors": [ {"first" : "Kálmán", "last" : "Képes"}, {"first" : "Frank", "last" : "Leymann"}, {"first" : "Benjamin", "last" : "Weder"}, {"first" : "Karoline", "last" : "Wild"} ], "editor": [ "Hakim Hacid","Fatma Outay","Hye-young Paik","Amira Alloum","Marinella Petrocchi","Mohamed Reda Bouadjenek","Amin Beheshti","Xumin Liu","Abderrahmane Maaradji" ], "editors": [ {"first" : "Hakim", "last" : "Hacid"}, {"first" : "Fatma", "last" : "Outay"}, {"first" : "Hye-young", "last" : "Paik"}, {"first" : "Amira", "last" : "Alloum"}, {"first" : "Marinella", "last" : "Petrocchi"}, {"first" : "Mohamed Reda", "last" : "Bouadjenek"}, {"first" : "Amin", "last" : "Beheshti"}, {"first" : "Xumin", "last" : "Liu"}, {"first" : "Abderrahmane", "last" : "Maaradji"} ], "pages": "72--76", "isbn" : "978-3-030-76352-7", "bibtexKey": "Kepes2020_DistChoreoDeployment" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/287f3a38e8d43c2711bff361e7c7e8a59/katharinafuchs", "tags" : [ "myown","simtech","peerReviewed","vis(us)","pn6","visus:ertl","visus:tkachegb","EXC2075","visus","from:gtkachev","visus:freysn" ], "intraHash" : "87f3a38e8d43c2711bff361e7c7e8a59", "interHash" : "347d569c3aae7cd4934c93a157da3cfe", "label" : "S4: Self-Supervised learning of Spatiotemporal Similarity", "user" : "katharinafuchs", "description" : "", "date" : "2021-12-08 17:10:08", "changeDate" : "2021-12-08 16:10:08", "count" : 11, "pub-type": "article", "journal": "IEEE Transactions on Visualization and Computer Graphics", "year": "2021", "url": "", "author": [ "Gleb Tkachev","Steffen Frey","Thomas Ertl" ], "authors": [ {"first" : "Gleb", "last" : "Tkachev"}, {"first" : "Steffen", "last" : "Frey"}, {"first" : "Thomas", "last" : "Ertl"} ], "abstract": "We introduce an ML-driven approach that enables interactive example-based queries for similar behavior in ensembles of spatiotemporal scientific data. This addresses an important use case in the visual exploration of simulation and experimental data, where data is often large, unlabeled and has no meaningful similarity measures available. We exploit the fact that nearby locations often exhibit similar behavior and train a Siamese Neural Network in a self-supervised fashion, learning an expressive latent space for spatiotemporal behavior. This space can be used to find similar behavior with just a few user-provided examples. We evaluate this approach on several ensemble datasets and compare with multiple existing methods, showing both qualitative and quantitative results.", "isbn" : "10.1109/TVCG.2021.3101418", "bibtexKey": "tkachev2021selfsupervised" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2ac32cf4b6d14e1517ea963f1aea480d0/katharinafuchs", "tags" : [ "myown","simtech","from:benjamin.weder","pn7","peerreviewed","postprint","exc2075" ], "intraHash" : "ac32cf4b6d14e1517ea963f1aea480d0", "interHash" : "12342f86dee8583bbcd4069c63669ce7", "label" : "Automated Quantum Hardware Selection for Quantum Workflows", "user" : "katharinafuchs", "description" : "", "date" : "2021-12-08 17:10:08", "changeDate" : "2021-12-08 16:10:08", "count" : 4, "pub-type": "article", "journal": "Electronics","publisher":"MDPI", "year": "2021", "url": "https://www.mdpi.com/2079-9292/10/8/984", "author": [ "Benjamin Weder","Johanna Barzen","Frank Leymann","Marie Salm" ], "authors": [ {"first" : "Benjamin", "last" : "Weder"}, {"first" : "Johanna", "last" : "Barzen"}, {"first" : "Frank", "last" : "Leymann"}, {"first" : "Marie", "last" : "Salm"} ], "volume": "10","number": "8", "iaaspdf" : "https://www.mdpi.com/2079-9292/10/8/984/pdf", "doi" : "10.3390/electronics10080984", "bibtexKey": "Weder2021_QuantumWorkflowHardwareSelection" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/20a1a436719a4f50611e70ff81344c148/katharinafuchs", "tags" : [ "myown","postPrint","simtech","from:benjamin.weder","pn7","peerreviewed","exc2075" ], "intraHash" : "0a1a436719a4f50611e70ff81344c148", "interHash" : "21f9b16048d09ca6269290a5c57b225e", "label" : "Data Flow Dependent Component Placement of Data Processing Cloud Applications", "user" : "katharinafuchs", "description" : "", "date" : "2021-12-08 17:10:08", "changeDate" : "2021-12-08 16:10:08", "count" : 3, "pub-type": "inproceedings", "booktitle": "2020 IEEE International Conference on Cloud Engineering (IC2E)", "year": "2020", "url": "https://ieeexplore.ieee.org/document/9096432/", "author": [ "M. Zimmermann","U. Breitenbücher","K. Képes","F. Leymann","B. Weder" ], "authors": [ {"first" : "M.", "last" : "Zimmermann"}, {"first" : "U.", "last" : "Breitenbücher"}, {"first" : "K.", "last" : "Képes"}, {"first" : "F.", "last" : "Leymann"}, {"first" : "B.", "last" : "Weder"} ], "pages": "83-94","abstract": "With the ongoing advances in the area of cloud computing, Internet of Things, Industry 4.0, and the increasing prevalence of cyber-physical systems and devices equipped with sensors, the amount of data generated every second is rising steadily. Thereby, the gathering of data and the creation of added value from this data is getting easier and easier. However, the increasing volume of data stored in the cloud leads to new challenges. Analytics software and scalable platforms are required to evaluate the data distributed all over the internet. But with distributed applications and large data sets to be handled, the network becomes a bottleneck. Therefore, in this work, we present an approach to automatically improve the deployment of such applications regarding the placement of data processing components dependent on the data flow of the application. To show the practical feasibility of our approach, we implemented a prototype based on the open-source ecosystem OpenTOSCA. Moreover, we evaluated our prototype using various scenarios.", "doi" : "10.1109/IC2E48712.2020.00016", "bibtexKey": "9096432" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2eecf093c61eb8d86eaff96bbebe69fe8/katharinafuchs", "tags" : [ "myown","simtech","from:benjamin.weder","pn7","peerreviewed","postprint","exc2075" ], "intraHash" : "eecf093c61eb8d86eaff96bbebe69fe8", "interHash" : "833d8c9b5a0b89152a6d0f7e626e6a79", "label" : "The Quantum Software Lifecycle", "user" : "katharinafuchs", "description" : "", "date" : "2021-12-08 17:10:08", "changeDate" : "2021-12-08 16:10:08", "count" : 4, "pub-type": "inproceedings", "booktitle": "Proceedings of the 1st ACM SIGSOFT International Workshop on Architectures and Paradigms for Engineering Quantum Software (APEQS 2020)","publisher":"ACM", "year": "2020", "url": "https://dl.acm.org/doi/10.1145/3412451.3428497", "author": [ "Benjamin Weder","Johanna Barzen","Frank Leymann","Marie Salm","Daniel Vietz" ], "authors": [ {"first" : "Benjamin", "last" : "Weder"}, {"first" : "Johanna", "last" : "Barzen"}, {"first" : "Frank", "last" : "Leymann"}, {"first" : "Marie", "last" : "Salm"}, {"first" : "Daniel", "last" : "Vietz"} ], "pages": "2--9", "doi" : "10.1145/3412451.3428497", "bibtexKey": "Weder2020_QuantumSoftwareLifecycle" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/299c86a4d30cb9392f618a01bc102fedd/katharinafuchs", "tags" : [ "myown","simtech","from:benjamin.weder","pn7","peerreviewed","postprint","exc2075" ], "intraHash" : "99c86a4d30cb9392f618a01bc102fedd", "interHash" : "5a337713f71edb20219b66c03fd7b622", "label" : "Automating the Comparison of Quantum Compilers for Quantum Circuits", "user" : "katharinafuchs", "description" : "", "date" : "2021-12-08 17:10:08", "changeDate" : "2021-12-08 16:10:08", "count" : 4, "pub-type": "inproceedings", "booktitle": "Proceedings of the 15th Symposium and Summer School on Service-Oriented Computing (SummerSOC 2021)","publisher":"Springer", "year": "2021", "url": "https://link.springer.com/chapter/10.1007/978-3-030-87568-8_4#citeas", "author": [ "Marie Salm","Johanna Barzen","Frank Leymann","Benjamin Weder","Karoline Wild" ], "authors": [ {"first" : "Marie", "last" : "Salm"}, {"first" : "Johanna", "last" : "Barzen"}, {"first" : "Frank", "last" : "Leymann"}, {"first" : "Benjamin", "last" : "Weder"}, {"first" : "Karoline", "last" : "Wild"} ], "pages": "64-80", "doi" : "10.1007/978-3-030-87568-8_4", "bibtexKey": "noauthororeditor" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/28b2c9006e55a886ca79f64b1302c9e1c/katharinafuchs", "tags" : [ "simtech","peerReviewed","vis(us)","pn6","visus:ertl","visus:tkachegb","EXC2075","visus","from:gtkachev","visus:freysn" ], "intraHash" : "8b2c9006e55a886ca79f64b1302c9e1c", "interHash" : "c658c4630195f65d590c2bf52b163201", "label" : "Local Prediction Models for Spatiotemporal Volume Visualization", "user" : "katharinafuchs", "description" : "", "date" : "2021-12-08 17:10:08", "changeDate" : "2021-12-08 16:10:08", "count" : 10, "pub-type": "article", "journal": "IEEE Transactions on Visualization and Computer Graphics", "year": "2019", "url": "http://ieeexplore.ieee.org/document/8941308", "author": [ "Gleb Tkachev","Steffen Frey","Thomas Ertl" ], "authors": [ {"first" : "Gleb", "last" : "Tkachev"}, {"first" : "Steffen", "last" : "Frey"}, {"first" : "Thomas", "last" : "Ertl"} ], "abstract": "We present a machine learning-based approach for detecting and visualizing complex behavior in spatiotemporal volumes. For this, we train models to predict future data values at a given position based on the past values in its neighborhood, capturing common temporal behavior in the data. We then evaluate the model's prediction on the same data. High prediction error means that the local behavior was too complex, unique or uncertain to be accurately captured during training, indicating spatiotemporal regions with interesting behavior. By training several models of varying capacity, we are able to detect spatiotemporal regions of various complexities. We aggregate the obtained prediction errors into a time series or spatial volumes and visualize them together to highlight regions of unpredictable behavior and how they differ between the models. We demonstrate two further volumetric applications: adaptive timestep selection and analysis of ensemble dissimilarity. We apply our technique to datasets from multiple application domains and demonstrate that we are able to produce meaningful results while making minimal assumptions about the underlying data.", "issn" : "2160-9306", "doi" : "10.1109/TVCG.2019.2961893", "bibtexKey": "tkachev2019local" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2684ba6cc33592f9ce01a7a3ac0069be2/katharinafuchs", "tags" : [ "myown","simtech","from:benjamin.weder","pn7","peerreviewed","postprint","exc2075" ], "intraHash" : "684ba6cc33592f9ce01a7a3ac0069be2", "interHash" : "cc51d89cf17e7e5b7a6951108baa75bc", "label" : "About a Criterion of Successfully Executing a Circuit in the NISQ Era: What $wd 1/\\epsilon_eff$ Really Means", "user" : "katharinafuchs", "description" : "", "date" : "2021-12-08 17:10:08", "changeDate" : "2021-12-08 16:10:08", "count" : 3, "pub-type": "inproceedings", "booktitle": "Proceedings of the 1st ACM SIGSOFT International Workshop on Architectures and Paradigms for Engineering Quantum Software","publisher":"ACM", "year": "2020", "url": "https://doi.org/10.1145%2F3412451.3428498", "author": [ "Marie Salm","Johanna Barzen","Frank Leymann","Benjamin Weder" ], "authors": [ {"first" : "Marie", "last" : "Salm"}, {"first" : "Johanna", "last" : "Barzen"}, {"first" : "Frank", "last" : "Leymann"}, {"first" : "Benjamin", "last" : "Weder"} ], "doi" : "10.1145/3412451.3428498", "bibtexKey": "Salm_2020" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/249d86bffd0542d056a4371906a64f6a0/katharinafuchs", "tags" : [ "simtech","from:benjamin.weder","pn7","peerreviewed","postprint","exc2075" ], "intraHash" : "49d86bffd0542d056a4371906a64f6a0", "interHash" : "4b6257a3be534da0867f72678c89ccd1", "label" : "Integrating Quantum Computing into Workflow Modeling and Execution", "user" : "katharinafuchs", "description" : "", "date" : "2021-12-08 17:10:08", "changeDate" : "2021-12-08 16:10:08", "count" : 4, "pub-type": "inproceedings", "booktitle": "2020 IEEE/ACM 13th International Conference on Utility and Cloud Computing (UCC)", "year": "2020", "url": "https://ieeexplore.ieee.org/document/9302814/", "author": [ "B. Weder","U. Breitenbücher","F. Leymann","K. Wild" ], "authors": [ {"first" : "B.", "last" : "Weder"}, {"first" : "U.", "last" : "Breitenbücher"}, {"first" : "F.", "last" : "Leymann"}, {"first" : "K.", "last" : "Wild"} ], "pages": "279-291","abstract": "Quantum computing has the potential to significantly impact many application domains, as several quantum algorithms are promising to solve problems more efficiently than possible on classical computers. However, various complex pre- and post-processing tasks have to be performed when executing a quantum circuit, which require immense mathematical and technical knowledge. For example, calculations on today\u2019s quantum computers are noisy and require an error mitigation task after the execution. Hence, integrating classical applications with quantum circuits is a difficult challenge. In this paper, we introduce a modeling extension for imperative workflow languages to enable the integration of quantum computations and ease the orchestration of classical applications and quantum circuits. Further, we show how the extension can be mapped to native modeling constructs of extended workflow languages to retain the portability of the workflows. We validate the practical feasibility of our approach by applying our proposed extension to BPMN and introduce Quantum4BPMN.", "doi" : "10.1109/UCC48980.2020.00046", "bibtexKey": "9302814" } ] }