@masterthesis{Zoufahl2012, type = {Bachelor Thesis}, author = {Zoufahl, Andre}, title = {Explorative Analysis of Vortex Structures in 2D Flows}, year = {2012}, language = {en} } @misc{ZonkerPadillaIglesiasDjurdjevacConrad2023, author = {Zonker, Johannes and Padilla-Iglesias, Cecilia and Djurdjevac Conrad, Natasa}, title = {Supplementary code and data for Royal Society Open Science Manuscript rsos.230495}, doi = {10.12752/9254}, year = {2023}, abstract = {In this repository are all files necessary to run the agent-based model of the paper "Insights into drivers of mobility and cultural dynamics of African hunter-gatherers over the past 120 000 years", Royal Society Open Science, 10(11), 2023.}, language = {en} } @article{ZonkerPadillaIglesiasDjurdjevacConrad2023, author = {Zonker, Johannes and Padilla-Iglesias, Cecilia and Djurdjevac Conrad, Natasa}, title = {Insights into drivers of mobility and cultural dynamics of African hunter-gatherers over the past 120 000 years}, volume = {10}, journal = {Royal Society Open Science}, number = {11}, doi = {10.1098/rsos.230495}, year = {2023}, abstract = {Humans have a unique capacity to innovate, transmit and rely on complex, cumulative culture for survival. While an important body of work has attempted to explore the role of changes in the size and interconnectedness of populations in determining the persistence, diversity and complexity of material culture, results have achieved limited success in explaining the emergence and spatial distribution of cumulative culture over our evolutionary trajectory. Here, we develop a spatio-temporally explicit agent-based model to explore the role of environmentally driven changes in the population dynamics of hunter-gatherer communities in allowing the development, transmission and accumulation of complex culture. By modelling separately demography- and mobility-driven changes in interaction networks, we can assess the extent to which cultural change is driven by different types of population dynamics. We create and validate our model using empirical data from Central Africa spanning 120 000 years. We find that populations would have been able to maintain diverse and elaborate cultural repertoires despite abrupt environmental changes and demographic collapses by preventing isolation through mobility. However, we also reveal that the function of cultural features was also an essential determinant of the effects of environmental or demographic changes on their dynamics. Our work can therefore offer important insights into the role of a foraging lifestyle on the evolution of cumulative culture.}, language = {en} } @phdthesis{Zonker2023, author = {Zonker, Johannes}, title = {Coarse Graining of Agent-Based Models and Spatio-Temporal Modeling of Spreading Processes}, year = {2023}, language = {en} } @misc{ZobelReininghausHotz2013, author = {Zobel, Valentin and Reininghaus, Jan and Hotz, Ingrid}, title = {Visualization of Two-Dimensional Symmetric Tensor Fields Using the Heat Kernel Signature}, journal = {Topological Methods in Data Analysis and Visualization III}, address = {Davis, CA, USA}, pages = {249 -- 262}, year = {2013}, language = {en} } @article{ZobelReininghausHotz2011, author = {Zobel, Valentin and Reininghaus, Jan and Hotz, Ingrid}, title = {Generalized Heat Kernel Signature}, journal = {Journal of WSCG, International Conference on Computer Graphics, Visualization and Computer Vision}, pages = {93 -- 100target}, year = {2011}, language = {en} } @misc{Zobel2010, type = {Master Thesis}, author = {Zobel, Valentin}, title = {Spectral Analysis of the Hodge Laplacian on Discrete Manifolds}, year = {2010}, language = {en} } @article{ZittelPetkovicEinck2025, author = {Zittel, Janina and Petkovic, Milena and Einck, Mathias}, title = {Forecasting Hourly Gas Flows}, volume = {79}, journal = {Foresight - The International Journal of Applied Forecasting}, pages = {40 -- 44}, year = {2025}, language = {en} } @inproceedings{ZittelClarnerTawfiketal.2024, author = {Zittel, Janina and Clarner, Jan-Patrick and Tawfik, Christine and Dykes, Maxwell and Rivetta, Fabian and Riedm{\"u}ller, Stephanie}, title = {A multi-objective optimization strategy for district heating production portfolio planning}, booktitle = {37th International Conference on Efficiency, Cost, Optimization, Simulation and Environmental Impact of Energy Systems (ECOS 2024)}, doi = {10.52202/077185-0066}, pages = {764 -- 775}, year = {2024}, abstract = {The imperative to decarbonize energy systems has intensified the need for efficient transformations within the heating sector, with a particular focus on district heating networks. This study addresses this challenge by proposing a comprehensive optimization approach evaluated on the district heating network of the M{\"a}rkisches Viertel of Berlin. Our objective is to simultaneously optimize heat production with three targets: minimizing costs, minimizing CO2-emissions, and maximizing heat generation from Combined Heat and Power (CHP) plants for enhanced efficiency. To tackle this optimization problem, we employed a Mixed-Integer Linear Program (MILP) that encompasses the conversion of various fuels into heat and power, integration with relevant markets, and considerations for technical constraints on power plant operation. These constraints include startup and minimum downtime, activation costs, and storage limits. The ultimate goal is to delineate the Pareto front, representing the optimal trade-offs between the three targets. We evaluate variants of the 𝜖-constraint algorithm for their effectiveness in coordinating these objectives, with a simultaneous focus on the quality of the estimated Pareto front and computational efficiency. One algorithm explores solutions on an evenly spaced grid in the objective space, while another dynamically adjusts the grid based on identified solutions. Initial findings highlight the strengths and limitations of each algorithm, providing guidance on algorithm selection depending on desired outcomes and computational constraints. Our study emphasizes that the optimal choice of algorithm hinges on the density and distribution of solutions in the feasible space. Whether solutions are clustered or evenly distributed significantly influences algorithm performance. These insights contribute to a nuanced understanding of algorithm selection for multi-objective multi-energy system optimization, offering valuable guidance for future research and practical applications for planning sustainable district heating networks.}, language = {en} } @article{ZinserZachowSailer2013, author = {Zinser, Max and Zachow, Stefan and Sailer, Hermann}, title = {Bimaxillary "rotation advancement" procedures in patients with obstructive sleep apnea: A 3-dimensional airway analysis of morphological changes}, volume = {42}, journal = {International Journal of Oral \& Maxillofacial Surgery}, number = {5}, doi = {10.1016/j.ijom.2012.08.002}, pages = {569 -- 578}, year = {2013}, language = {en} } @inproceedings{ZinkEkteraiMartinetal.2023, author = {Zink, Christof and Ekterai, Michael and Martin, Dominik and Clemens, William and Maennel, Angela and Mundinger, Konrad and Richter, Lorenz and Crump, Paul and Knigge, Andrea}, title = {Deep-learning-based visual inspection of facets and p-sides for efficient quality control of diode lasers}, volume = {12403}, booktitle = {High-Power Diode Laser Technology XXI}, publisher = {SPIE}, doi = {10.1117/12.2648691}, pages = {94 -- 112}, year = {2023}, abstract = {The optical inspection of the surfaces of diode lasers, especially the p-sides and facets, is an essential part of the quality control in the laser fabrication procedure. With reliable, fast, and flexible optical inspection processes, it is possible to identify and eliminate defects, accelerate device selection, reduce production costs, and shorten the cycle time for product development. Due to a vast range of rapidly changing designs, structures, and coatings, however, it is impossible to realize a practical inspection with conventional software. In this work, we therefore suggest a deep learning based defect detection algorithm that builds on a Faster Regional Convolutional Neural Network (Faster R-CNN) as a core component. While for related, more general object detection problems, the application of such models is straightforward, it turns out that our task exhibits some additional challenges. On the one hand, a sophisticated pre- and postprocessing of the data has to be deployed to make the application of the deep learning model feasible. On the other hand, we find that creating labeled training data is not a trivial task in our scenario, and one has to be extra careful with model evaluation. We can demonstrate in multiple empirical assessments that our algorithm can detect defects in diode lasers accurately and reliably in most cases. We analyze the results of our production-ready pipeline in detail, discuss its limitations and provide some proposals for further improvements.}, language = {en} } @article{ZimperDjurdjevacHartmannetal.2025, author = {Zimper, Sebastian and Djurdjevac, Ana and Hartmann, Carsten and Sch{\"u}tte, Christof and Conrad, Natasa Djurdjevac}, title = {Mean-field optimal control with stochastic leaders}, arxiv = {http://arxiv.org/abs/2512.19201}, year = {2025}, abstract = {We consider interacting agent systems with a large number of stochastic agents (or particles) influenced by a fixed number of external stochastic lead agents. Such examples arise, for example in models of opinion dynamics, where a small number of leaders (influencers) can steer the behaviour of a large population of followers. In this context, we study a partial mean-field limit where the number of followers tends to infinity, while the number of leaders stays constant. The partial mean-field limit dynamics is then given by a McKean-Vlasov stochastic differential equation (SDE) for the followers, coupled to a controlled It{\^o}-SDE governing the dynamics of the lead agents. For a given cost functional that the lead agents seek to minimise, we show that the unique optimal control of the finite agent system convergences to the optimal control of the limiting system. This establishes that the low-dimensional control of the partial (mean-field) system provides an effective approximation for controlling the high-dimensional finite agent system. In addition, we propose a stochastic gradient descent algorithm that can efficiently approximate the mean-field control. Our theoretical results are illustrated on opinion dynamics model with lead agents, where the control objective is to drive the followers to reach consensus in finite time.}, language = {en} } @article{ZimperCornalbaDjurdjevacConradetal.2025, author = {Zimper, Sebastian and Cornalba, Federico and Djurdjevac Conrad, Natasa and Djurdjevac, Ana}, title = {On reduced inertial PDE models for Cucker-Smale flocking dynamics}, volume = {481}, journal = {Proceedings of the Royal Society A}, publisher = {Royal Society}, arxiv = {http://arxiv.org/abs/2407.18717}, doi = {https://doi.org/10.1098/rspa.2024.0675}, year = {2025}, abstract = {In particle systems, flocking refers to the phenomenon where particles' individual velocities eventually align. The Cucker-Smale model is a well-known mathematical framework that describes this behaviour. Many continuous descriptions of the Cucker-Smale model use PDEs with both particle position and velocity as independent variables, thus providing a full description of the particles mean-field limit (MFL) dynamics. In this paper, we introduce a novel reduced inertial PDE model consisting of two equations that depend solely on particle position. In contrast to other reduced models, ours is not derived from the MFL, but directly includes the model reduction at the level of the empirical densities, thus allowing for a straightforward connection to the underlying particle dynamics. We present a thorough analytical investigation of our reduced model, showing that: firstly, our reduced PDE satisfies a natural and interpretable continuous definition of flocking; secondly, in specific cases, we can fully quantify the discrepancy between PDE solution and particle system. Our theoretical results are supported by numerical simulations.}, language = {en} } @inproceedings{ZimmerSpiegelPokutta2023, author = {Zimmer, Max and Spiegel, Christoph and Pokutta, Sebastian}, title = {How I Learned to Stop Worrying and Love Retraining}, booktitle = {Proceedings of International Conference on Learning Representations}, year = {2023}, language = {en} } @inproceedings{ZimmerSpiegelPokutta2024, author = {Zimmer, Max and Spiegel, Christoph and Pokutta, Sebastian}, title = {Sparse Model Soups}, booktitle = {12th International Conference on Learning Representations (ICLR 2024)}, publisher = {Curran Associates, Inc.}, isbn = {9781713898658}, year = {2024}, language = {en} } @incollection{ZimmerSpiegelPokutta2025, author = {Zimmer, Max and Spiegel, Christoph and Pokutta, Sebastian}, title = {Compression-aware training of neural networks using Frank-Wolfe}, booktitle = {Mathematical Optimization for Machine Learning: Proceedings of the MATH+ Thematic Einstein Semester 2023}, editor = {Fackeldey, K.}, publisher = {De Gruyter}, doi = {10.1515/9783111376776-010}, pages = {137 -- 168}, year = {2025}, language = {en} } @misc{ZilskeLameckerZachow2007, author = {Zilske, Michael and Lamecker, Hans and Zachow, Stefan}, title = {Adaptive Remeshing of Non-Manifold Surfaces}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-9445}, number = {07-01}, year = {2007}, abstract = {We present a unified approach for consistent remeshing of arbitrary non-manifold triangle meshes with additional user-defined feature lines, which together form a feature skeleton. Our method is based on local operations only and produces meshes of high regularity and triangle quality while preserving the geometry as well as topology of the feature skeleton and the input mesh.}, language = {en} } @inproceedings{ZilskeLameckerZachow2008, author = {Zilske, Michael and Lamecker, Hans and Zachow, Stefan}, title = {Adaptive Remeshing of Non-Manifold Surfaces}, booktitle = {Eurographics 2008 Annex to the Conf. Proc.}, pages = {207 -- 211}, year = {2008}, language = {en} } @misc{Zilske2007, type = {Master Thesis}, author = {Zilske, Michael}, title = {Adaptive remeshing of non-manifold triangulations}, year = {2007}, language = {en} } @misc{Zilske2008, type = {Master Thesis}, author = {Zilske, Michael}, title = {Adaptives Remeshing von nicht-mannigfaltigen Dreiecksnetzen}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-474}, school = {Zuse Institute Berlin (ZIB)}, year = {2008}, abstract = {In dieser Arbeit wird eine Serie von Remeshing-Verfahren um die Ber{\"u}cksichtigung von nicht-mannigfaltigen Dreiecksvernetzungen und Merkmalskantenz{\"u}gen erweitert. Die betrachteten Verfahren arbeiten im Wesentlichen lokal. Daher k{\"o}nnen die im Rahmen dieser Arbeit entwickelten Erweiterungen, die nicht-mannigfaltige Kantenz{\"u}ge und Merkmalskantenz{\"u}ge betreffen, separat beschrieben werden. Dabei wird ein Ansatz verfolgt, beide Arten von besonderen Kantenz{\"u}gen aufgrund ihrer Gemeinsamkeiten einheitlich zu behandeln. Dieser besteht zum einen darin, eine Korrespondenz zwischen Kantenz{\"u}gen auf der Eingabe- und der Ausgabefl{\"a}che zu erhalten, indem die Remeshing-Operationen auf den Kantenz{\"u}gen in entsprechend eingeschr{\"a}nkter Weise verwendet werden. Zum anderen wird beschrieben, wie die Abtastdichte der Kantenz{\"u}ge dynamisch an die Abtastdichte der Umgebung angepasst werden kann, um f{\"u}r weitgehende Isotropie in der N{\"a}he von Merkmalskantenz{\"u}gen zu sorgen.}, language = {de} } @article{ZiescheArltFineganetal.2020, author = {Ziesche, Ralf F. and Arlt, Tobias and Finegan, Donal P. and Heenan, Thomas M.M. and Tengattini, Alessandro and Baum, Daniel and Kardjilov, Nikolay and Mark{\"o}tter, Henning and Manke, Ingo and Kockelmann, Winfried and Brett, Dan J.L. and Shearing, Paul R.}, title = {4D imaging of lithium-batteries using correlative neutron and X-ray tomography with a virtual unrolling technique}, volume = {11}, journal = {Nature Communications}, doi = {10.1038/s41467-019-13943-3}, pages = {777}, year = {2020}, abstract = {The temporally and spatially resolved tracking of lithium intercalation and electrode degradation processes are crucial for detecting and understanding performance losses during the operation of lithium-batteries. Here, high-throughput X-ray computed tomography has enabled the identification of mechanical degradation processes in a commercial Li/MnO2 primary battery and the indirect tracking of lithium diffusion; furthermore, complementary neutron computed tomography has identified the direct lithium diffusion process and the electrode wetting by the electrolyte. Virtual electrode unrolling techniques provide a deeper view inside the electrode layers and are used to detect minor fluctuations which are difficult to observe using conventional three dimensional rendering tools. Moreover, the 'unrolling' provides a platform for correlating multi-modal image data which is expected to find wider application in battery science and engineering to study diverse effects e.g. electrode degradation or lithium diffusion blocking during battery cycling.}, language = {en} } @misc{ZieglerZivaljevic1991, author = {Ziegler, G{\"u}nter M. and Zivaljevic, R. T.}, title = {Homotopy Types of Subspace Arrangements via Diagrams of Spaces.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-658}, number = {SC-91-15}, year = {1991}, abstract = {We prove combinatorial formulas for the homotopy type of the union of the subspaces in an (affine, compactified affine, spherical or projective) subspace arrangement. From these formulas we derive results of Goresky \& MacPherson on the homology of the arrangement and the cohomology of its complement. The union of an arrangement can be interpreted as the direct limit of a diagram of spaces over the intersection poset. A closely related space is obtained by taking the homotopy direct limit of this diagram. Our method consists in constructing a combinatorial model diagram over the same poset, whose homotopy limit can be compared to the original one by usual homotopy comparison results for diagrams of spaces.}, language = {en} } @article{ZieglerHegeDuda2005, author = {Ziegler, G{\"u}nter M. and Hege, Hans-Christian and Duda, Georg}, title = {Neue Bilder f{\"u}r die Medizin?}, volume = {13(3)}, journal = {DFN-Mitteilungen}, pages = {163 -- 167}, year = {2005}, language = {en} } @misc{Ziegler1992, author = {Ziegler, G{\"u}nter M.}, title = {Shellability of Chessboard Complexes.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-890}, number = {SC-92-19}, year = {1992}, abstract = {The matchings in a complete bipartite graph form a simplicial complex, which in many cases has strong structural properties. We use an equivalent description as chessboard complexes: the complexes of all non-taking rook positions on chessboards of various shapes. In this paper we construct `certificate \$k\$-shapes' \$\Sigma(m,n,k)\$ such that if the shape \$A\$ contains some \$\Sigma(m,n,k)\$, then the \$(k{-}1)\$-skeleton of the chessboard complex \$\Delta(A)\$ is vertex decomposable in the sense of Provan \& Billera. This covers, in particular, the case of rectangular chessboards \$A=[m]{\times}[n]\$, for which \$\Delta(A)\$ is vertex decomposable if \$n\ge 2m{-}1\$, and the \$(\lfloor{m+n+1\over3}\rfloor{-}1)\$-skeleton is vertex decomposable in general. The notion of vertex decomposability is a very convenient tool to prove shellability of such combinatorially defined simplicial complexes. We establish a relation between vertex decomposability and the CL-shellability technique (for posets) of Bj{\"o}rner \& Wachs.}, language = {en} } @misc{Ziegler1991, author = {Ziegler, G{\"u}nter M.}, title = {On the Difference Between Real and Complex Arrangements.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-648}, number = {SC-91-14}, year = {1991}, abstract = {If \$B\$ is an arrangement of linear complex Hyperplanes in \$C^d\$, then the following can be constructed from knowledge of its intersection lattice: (a) the cohomology groups of the complement [Br], (b) the cohomology algebra of the complement [OS], (c) the fundamental group of the complement, if \$d\le2\$, (d) the singularity link up to homeomorphism, if \$d\le3\$, (e) the singularity link up to homotopy type [ZZ]. If \$B'\$ is, more generally, a 2-arrangement in \$ R^{2d}\$ (an arrangement of real subspaces of codimension 2 with even-dimensional intersections), then the intersection lattice still determines (a) the cohomology groups of the complement [GM] and (e) the homotopy type of the singularity link [ZZ]. We show, however, that for 2-arrangements the data (b), (c) and (d) are not determined by the intersection lattice. They require the knowledge of extra information on sign patterns, which can be computed as determinants of linear relations, or (equivalently) as linking coefficients in the sense of knot theory.}, language = {en} } @misc{Ziegler1991, author = {Ziegler, G{\"u}nter M.}, title = {Higher Bruhat Orders and Cyclic Hyperplane Arrangements.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-607}, number = {SC-91-10}, year = {1991}, abstract = {We study the higher Bruhat orders \$B(n,k)\$ of Manin \& Schechtman [MaS] and - characterize them in terms of inversion sets, - identify them with the posets \$U(C^{n+1,r},n+1)\$ of uniform extensions of the alternating oriented matroids \$C^{n,r}\$ for \$r:=n-k\$ (that is, with the extensions of a cyclic hyperplane arrangement by a new oriented pseudoplane), - show that \$B(n,k)\$ is a lattice for \$k =1\$ and for \$r\le 3\$, but not in general, - show that \$B(n,k)\$ is ordered by inclusion of inversion sets for \$k=1\$ and for \$r\le 4\$. However, \$B(8,3)\$ is not ordered by inclusion. This implies that the partial order \$B_\subseteq (n,k)\$ defined by inclusion of inversion sets differs from \$B(n,k)\$ in general. We show that the proper part of \$B_\subseteq (n,k)\$ is homotopy equivalent to \$S^{r-2}\$. Consequently, - \$B(n,k)\simeq S^{r-2}\$ for \$k=1\$ and for \$r\le 4\$. In contrast to this, we find that the uniform extension poset of an affine hyperplane arrangement is in general not graded and not a lattice even for \$r=3\$, and that the proper part is not always homotopy equivalent to \$S^{r(M)-2}\$.}, language = {en} } @misc{Ziegler1993, author = {Ziegler, G{\"u}nter M.}, title = {Lectures on Polytopes.}, number = {TR-93-06}, year = {1993}, abstract = {These lecture notes have several aims: \begin{itemize} \item to give an introduction to some basic facts about convex polytopes, with an emphasis on the basic methods that yield them (Fourier-Motzkin elimination, Schlegel diagrams, shellability, Gale transforms and oriented matroids), \item to discuss some important examples and elegant constructions (cyclic and neighborly polytopes, zonotopes, Minkowski sums, permutahedra and associahedra, fiber polytopes, the Lawrence construction) \item and to illustrate why polytope theory is exciting, with highlights like Kalai's new diameter bounds, the construction of non-rational polytopes, the Bohne-Dress tiling theorem, shellability and the upper bound theorem, .... \end{itemize} For several of these topics the decisive break-through is very recent, which suggests that there is much more discovered.}, language = {en} } @article{ZieglerOgurreckSteinkeetal.2010, author = {Ziegler, Alexander and Ogurreck, Malte and Steinke, Thomas and Beckmann, Felix and Prohaska, Steffen and Ziegler, Andreas}, title = {Opportunities and challenges for digital morphology}, volume = {5}, journal = {Biology Direct}, number = {1}, doi = {10.1186/1745-6150-5-45}, pages = {45}, year = {2010}, language = {en} } @article{ZhukovaHiepenKnausetal.2017, author = {Zhukova, Yulia and Hiepen, Christian and Knaus, Petra and Osterland, Marc and Prohaska, Steffen and Dunlop, John W. C. and Fratzl, Peter and Skorb, Ekaterina V.}, title = {The role of titanium surface nanotopography on preosteoblast morphology, adhesion and migration}, journal = {Advanced Healthcare Materials}, doi = {10.1002/adhm.201601244}, year = {2017}, abstract = {Surface structuring of titanium-based implants with appropriate nanotopographies can significantly modulate their impact on the biological behavior of cells populating these implants. Implant assisted bone tissue repair and regeneration require functional adhesion and expansion of bone progenitors. The surface nanotopography of implant materials used to support bone healing and its effect on cell behavior, in particular cell adhesion, spreading, expansion, and motility, is still not clearly understood. The aim of this study is to investigate preosteoblast proliferation, adhesion, morphology, and migration on different titanium materials with similar surface chemistry, but distinct nanotopographical features. Sonochemical treatment and anodic oxidation were employed to fabricate disordered - mesoporous titania (TMS), and ordered - titania nanotubular (TNT) topographies respectively. The morphological evaluation revealed a surface dependent shape, thickness, and spreading of cells owing to different adherence behavior. Cells were polygonal-shaped and well-spread on glass and TMS, but displayed an elongated fibroblast-like morphology on TNT surfaces. The cells on glass however, were much flatter than on nanostructured surfaces. Both nanostructured surfaces impaired cell adhesion, but TMS was more favorable for cell growth due to its support of cell attachment and spreading in contrast to TNT. Quantitative wound healing assay in combination with live-cell imaging revealed that cells seeded on TMS surfaces migrated in close proximity to neighboring cells and less directed when compared to the migratory behavior on other surfaces. The results indicate distinctly different cell adhesion and migration on ordered and disordered titania nanotopographies, providing important information that could be used in optimizing titanium-based scaffold design to foster bone tissue growth and repair.}, language = {en} } @misc{ZhukovaHiepenKnausetal.2017, author = {Zhukova, Yulia and Hiepen, Christian and Knaus, Petra and Osterland, Marc and Prohaska, Steffen and Dunlop, John W. C. and Fratzl, Peter and Skorb, Ekaterina V.}, title = {The role of titanium surface nanotopography on preosteoblast morphology, adhesion and migration}, issn = {1438-0064}, doi = {10.1002/adhm.201601244}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-63053}, year = {2017}, abstract = {Surface structuring of titanium-based implants with appropriate nanotopographies can significantly modulate their impact on the biological behavior of cells populating these implants. Implant assisted bone tissue repair and regeneration require functional adhesion and expansion of bone progenitors. The surface nanotopography of implant materials used to support bone healing and its effect on cell behavior, in particular cell adhesion, spreading, expansion, and motility, is still not clearly understood. The aim of this study is to investigate preosteoblast proliferation, adhesion, morphology, and migration on different titanium materials with similar surface chemistry, but distinct nanotopographical features. Sonochemical treatment and anodic oxidation were employed to fabricate disordered - mesoporous titania (TMS), and ordered - titania nanotubular (TNT) topographies respectively. The morphological evaluation revealed a surface dependent shape, thickness, and spreading of cells owing to different adherence behavior. Cells were polygonal-shaped and well-spread on glass and TMS, but displayed an elongated fibroblast-like morphology on TNT surfaces. The cells on glass however, were much flatter than on nanostructured surfaces. Both nanostructured surfaces impaired cell adhesion, but TMS was more favorable for cell growth due to its support of cell attachment and spreading in contrast to TNT. Quantitative wound healing assay in combination with live-cell imaging revealed that cells seeded on TMS surfaces migrated in close proximity to neighboring cells and less directed when compared to the migratory behavior on other surfaces. The results indicate distinctly different cell adhesion and migration on ordered and disordered titania nanotopographies, providing important information that could be used in optimizing titanium-based scaffold design to foster bone tissue growth and repair.}, language = {en} } @article{ZhouChenPengetal.2025, author = {Zhou, Lei and Chen, Ying and Peng, Hanqiu and Koch, Thorsten}, title = {Is innovation slowing down? Insights from the AIMS framework of patent values}, volume = {280}, journal = {Expert Systems with Applications}, doi = {10.1016/j.eswa.2025.127355}, pages = {127355}, year = {2025}, abstract = {Amidst the unprecedented expansion of scientific and technological knowledge over the past century, concerns persist regarding a slowdown in innovation. To address this, we introduce the AIMS framework, which categorizes patents into four types—Aurora, Invisible, Mirage, and Success—based on their respective inherent scientific values and market-recognized economic values. Utilizing USPTO patent and citation data from 1976 to 2022, our analysis reveals an increasing volume of patent issuances but a concerning dilution in scientific quality starting in the 2000s. This trend is primarily attributed to the rise of low scientific value patents—categorized as Mirage and Invisible—and a modest decline in high-impact scientific patents—categorized as Success and Aurora. Meanwhile, the economic value of patents has risen, especially noted with the growth in Mirage patents since the 2010s, indicating a shift towards strategies that prioritize market-driven patenting. This study highlights the evolving nature of patents from mere indicators of scientific innovation to strategic tools for market dominance, providing an alternative understanding of patent value and its implications for firms' strategic decisions over patent issuance across different sectors.}, language = {en} } @article{ZhongHoeflingJohn2025, author = {Zhong, Xin and H{\"o}fling, Felix and John, Timm}, title = {Hydrogen diffusion in garnet: insights from atomistic simulations}, volume = {26}, journal = {Geochemistry Geophysics Geosystems}, arxiv = {http://arxiv.org/abs/2410.07724}, doi = {10.1029/2024GC011951}, pages = {e2024GC011951}, year = {2025}, abstract = {Garnet has been widely used to decipher the pressure-temperature-time history of rocks, but its physical properties such as elasticity and diffusion are strongly affected by trace amounts of hydrogen. Experimental measurements of H diffusion in garnet are limited to room pressure. We use atomistic simulations to study H diffusion in perfect and defective garnet lattices, focusing on protonation defects at the Si and Mg sites, which are shown to be energetically favored. Transient trapping of H renders ab-initio simulations of H diffusion computationally challenging, which is overcome with machine learning techniques by training a deep neural network that encodes the interatomic potential. Our results from such deep potential molecular dynamics (DeePMD) simulations show high mobility of hydrogen in defect-free garnet lattices, whereas H diffusivity is significantly diminished in defective lattices. Tracer simulations focusing on H alone highlight the vital role of atomic vibrations of heavier atoms like Mg on the release of H atoms. Two regimes of H diffusion are identified: a diffuser-dominated regime at high hydrogen content with low activation energies due to saturation of vacancies by hydrogen, and a vacancy-dominated regime at low hydrogen content with high activation energies due to trapping of H atoms at vacancy sites. These regimes account for experimental observations, such as a H-concentration dependent diffusivity and the discrepancy in activation energy between deprotonation and D-H exchange experiments. This study underpins the crucial role of vacancies in H diffusion and demonstrates the utility of machine-learned interatomic potentials in studying kinetic processes in the Earth's interior.}, language = {en} } @inproceedings{ZhaoMarsmanWendeetal.2017, author = {Zhao, Zhengji and Marsman, Martijn and Wende, Florian and Kim, Jeongnim}, title = {Performance of Hybrid MPI/OpenMP VASP on Cray XC40 Based on Intel Knights Landing Many Integrated Core Architecture}, year = {2017}, abstract = {With the recent installation of Cori, a Cray XC40 system with Intel Xeon Phi Knights Landing (KNL) many integrated core (MIC) architecture, NERSC is transitioning from the multi-core to the more energy-efficient many-core era. The developers of VASP, a widely used materials science code, have adopted MPI/OpenMP parallelism to better exploit the increased on-node parallelism, wider vector units, and the high bandwidth on-package memory (MCDRAM) of KNL. To achieve optimal performance, KNL specifics relevant for the build, boot and run time setup must be explored. In this paper, we present the performance analysis of representative VASP workloads on Cori, focusing on the effects of the compilers, libraries, and boot/run time options such as the NUMA/MCDRAM modes, Hyper-Threading, huge pages, core specialization, and thread scaling. The paper is intended to serve as a KNL performance guide for VASP users, but it will also benefit other KNL users.}, language = {en} } @article{ZhaoZhangLi2024, author = {Zhao, Yue and Zhang, Wei and Li, Tiejun}, title = {EPR-Net: Constructing non-equilibrium potential landscape via a variational force projection formulation}, volume = {11}, journal = {National Science Review}, number = {7}, doi = {10.1093/nsr/nwae052}, year = {2024}, abstract = {We present EPR-Net, a novel and effective deep learning approach that tackles a crucial challenge in biophysics: constructing potential landscapes for high-dimensional non-equilibrium steady-state (NESS) systems. EPR-Net leverages a nice mathematical fact that the desired negative potential gradient is simply the orthogonal projection of the driving force of the underlying dynamics in a weighted inner-product space. Remarkably, our loss function has an intimate connection with the steady entropy production rate (EPR), enabling simultaneous landscape construction and EPR estimation. We introduce an enhanced learning strategy for systems with small noise, and extend our framework to include dimensionality reduction and state-dependent diffusion coefficient case in a unified fashion. Comparative evaluations on benchmark problems demonstrate the superior accuracy, effectiveness, and robustness of EPR-Net compared to existing methods. We apply our approach to challenging biophysical problems, such as an 8D limit cycle and a 52D multi-stability problem, which provide accurate solutions and interesting insights on constructed landscapes. With its versatility and power, EPR-Net offers a promising solution for diverse landscape construction problems in biophysics.}, language = {en} } @article{ZhaoFrankBurgeretal.2011, author = {Zhao, J. and Frank, B. and Burger, Sven and Giessen, H.}, title = {Large-Area High-Quality Plasmonic Oligomers Fabricated by Angle-Controlled Colloidal Nanolithography}, volume = {5}, journal = {ACS Nano}, number = {11}, doi = {10.1021/nn203177s}, pages = {9009}, year = {2011}, language = {en} } @article{ZhangWangHartmannetal.2014, author = {Zhang, Wei and Wang, Han and Hartmann, Carsten and Weber, Marcus and Sch{\"u}tte, Christof}, title = {Applications of the cross-entropy method to importance sampling and optimal control of diffusions}, volume = {36}, journal = {Siam Journal on Scientific Computing}, number = {6}, doi = {10.1137/14096493X}, pages = {A2654 -- A2672}, year = {2014}, language = {en} } @misc{ZhangWangHartmannetal.2014, author = {Zhang, Wei and Wang, Han and Hartmann, Carsten and Weber, Marcus and Sch{\"u}tte, Christof}, title = {Applications of the cross-entropy method to importance sampling and optimal control of diffusions}, issn = {1438-0064}, doi = {10.1137/14096493X}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-49720}, year = {2014}, abstract = {We study the cross-entropy method for diffusions. One of the results is a versatile cross-entropy algorithm that can be used to design efficient importance sampling strategies for rare events or to solve optimal control problems. The approach is based on the minimization of a suitable cross-entropy functional, with a parametric family of exponentially tilted probability distributions. We illustrate the new algorithm with several numerical examples and discuss algorithmic issues and possible extensions of the method.}, language = {en} } @article{ZhangSchuette2017, author = {Zhang, Wei and Sch{\"u}tte, Christof}, title = {Reliable approximation of long relaxation timescales in molecular dynamics}, volume = {19}, journal = {Entropy}, number = {7}, doi = {10.3390/e19070367}, year = {2017}, language = {en} } @misc{ZhangSchuette2017, author = {Zhang, Wei and Sch{\"u}tte, Christof}, title = {Reliable approximation of long relaxation timescales in molecular dynamics}, issn = {1438-0064}, doi = {10.3390/e19070367}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-63718}, year = {2017}, abstract = {Many interesting rare events in molecular systems like ligand association, protein folding or con- formational changes happen on timescales that often are not accessible by direct numerical simulation. Therefore rare event approximation approaches like interface sampling, Markov state model building or advanced reaction coordinate based free energy estimation have attracted huge attention recently. In this article we analyze the reliability of such approaches: How precise is an estimate of long relaxation timescales of molecular systems resulting from various forms of rare event approximation methods? Our results give a theoretical answer to this question by relating it with the transfer operator approach to molecular dynamics. By doing so they also allow for understanding deep connections between the different approaches.}, language = {en} } @article{ZhangSchuette2025, author = {Zhang, Wei and Sch{\"u}tte, Christof}, title = {On finding optimal collective variables for complex systems by minimizing the deviation between effective and full dynamics}, volume = {23}, journal = {Multiscale Modeling and Simulation}, number = {2}, arxiv = {http://arxiv.org/abs/2405.02001}, doi = {10.1137/24M1658917}, pages = {924 -- 958}, year = {2025}, abstract = {This paper is concerned with collective variables, or reaction coordinates, that map a discrete-in-time Markov process X_n in R^d to a (much) smaller dimension k≪d. We define the effective dynamics under a given collective variable map ξ as the best Markovian representation of X_n under ξ. The novelty of the paper is that it gives strict criteria for selecting optimal collective variables via the properties of the effective dynamics. In particular, we show that the transition density of the effective dynamics of the optimal collective variable solves a relative entropy minimization problem from certain family of densities to the transition density of X_n. We also show that many transfer operator-based data-driven numerical approaches essentially learn quantities of the effective dynamics. Furthermore, we obtain various error estimates for the effective dynamics in approximating dominant timescales / eigenvalues and transition rates of the original process X_n and how optimal collective variables minimize these errors. Our results contribute to the development of theoretical tools for the understanding of complex dynamical systems, e.g. molecular kinetics, on large timescales. These results shed light on the relations among existing data-driven numerical approaches for identifying good collective variables, and they also motivate the development of new methods.}, language = {en} } @article{ZhangSchuette2023, author = {Zhang, Wei and Sch{\"u}tte, Christof}, title = {Understanding recent deep-learning techniques for identifying collective variables of molecular dynamics}, volume = {23}, journal = {Proceedings in Applied Mathematics and Mechanics}, number = {4}, doi = {10.1002/pamm.202300189}, year = {2023}, abstract = {High-dimensional metastable molecular dynamics (MD) can often be characterised by a few features of the system, that is, collective variables (CVs). Thanks to the rapid advance in the area of machine learning and deep learning, various deep learning-based CV identification techniques have been developed in recent years, allowing accurate modelling and efficient simulation of complex molecular systems. In this paper, we look at two different categories of deep learning-based approaches for finding CVs, either by computing leading eigenfunctions of transfer operator associated to the underlying dynamics, or by learning an autoencoder via minimisation of reconstruction error. We present a concise overview of the mathematics behind these two approaches and conduct a comparative numerical study of these two approaches on illustrative examples.}, language = {en} } @article{ZhangLiSchuette2022, author = {Zhang, Wei and Li, Tiejun and Sch{\"u}tte, Christof}, title = {Solving eigenvalue PDEs of metastable diffusion processes using artificial neural networks}, volume = {465}, journal = {Journal of Computational Physics}, arxiv = {http://arxiv.org/abs/2110.14523}, doi = {10.1016/j.jcp.2022.111377}, year = {2022}, abstract = {In this paper, we consider the eigenvalue PDE problem of the infinitesimal generators of metastable diffusion processes. We propose a numerical algorithm based on training artificial neural networks for solving the leading eigenvalues and eigenfunctions of such high-dimensional eigenvalue problem. The algorithm is useful in understanding the dynamical behaviors of metastable processes on large timescales. We demonstrate the capability of our algorithm on a high-dimensional model problem, and on the simple molecular system alanine dipeptide.}, language = {en} } @article{ZhangKlusConradetal.2019, author = {Zhang, Wei and Klus, Stefan and Conrad, Tim and Sch{\"u}tte, Christof}, title = {Learning chemical reaction networks from trajectory data}, volume = {18}, journal = {SIAM Journal on Applied Dynamical Systems (SIADS)}, number = {4}, arxiv = {http://arxiv.org/abs/1902.04920}, doi = {10.1137/19M1265880}, pages = {2000 -- 2046}, year = {2019}, abstract = {We develop a data-driven method to learn chemical reaction networks from trajectory data. Modeling the reaction system as a continuous-time Markov chain and assuming the system is fully observed,our method learns the propensity functions of the system with predetermined basis functions by maximizing the likelihood function of the trajectory data under l^1 sparse regularization. We demonstrate our method with numerical examples using synthetic data and carry out an asymptotic analysis of the proposed learning procedure in the infinite-data limit.}, language = {en} } @article{ZhangHartmannvonKleist2018, author = {Zhang, Wei and Hartmann, Carsten and von Kleist, Max}, title = {Optimal control of Markov jump processes: Asymptotic analysis, algorithms and applications to the modeling of chemical reaction systems}, journal = {Communications in Mathematical Sciences}, doi = {10.4310/CMS.2018.v16.n2.a1}, pages = {293 -- 331}, year = {2018}, abstract = {Markov jump processes are widely used to model natural and engineered processes. In the context of biological or chemical applications one typically refers to the chemical master equation (CME), which models the evolution of the probability mass of any copy-number combination of the interacting particles. When many interacting particles ("species") are considered, the complexity of the CME quickly increases, making direct numerical simulations impossible. This is even more problematic when one aims at controlling the Markov jump processes defined by the CME. In this work, we study both open loop and feedback optimal control problems of the Markov jump processes in the case that the controls can only be switched at fixed control stages. Based on Kurtz's limit theorems, we prove the convergence of the respective control value functions of the underlying Markov decision problem as the copy numbers of the species go to infinity. In the case of the optimal control problem on a finite time-horizon, we propose a hybrid control policy algorithm to overcome the difficulties due to the curse of dimensionality when the copy number of the involved species is large. Two numerical examples demonstrate the suitability of both the analysis and the proposed algorithms.}, language = {en} } @misc{ZhangHartmannSchuette2016, author = {Zhang, Wei and Hartmann, Carsten and Sch{\"u}tte, Christof}, title = {Effective Dynamics Along Given Reaction Coordinates, and Reaction Rate Theory}, issn = {1438-0064}, doi = {10.1039/C6FD00147E}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-59706}, year = {2016}, abstract = {In molecular dynamics and related fields one considers dynamical descriptions of complex systems in full (atomic) detail. In order to reduce the overwhelming complexity of realistic systems (high dimension, large timescale spread, limited computational resources) the projection of the full dynamics onto some reaction coordinates is examined in order to extract statistical information like free energies or reaction rates. In this context, the effective dynamics that is induced by the full dynamics on the reaction coordinate space has attracted considerable attention in the literature. In this article, we contribute to this discussion: We first show that if we start with an ergodic diffusion processes whose invariant measure is unique then these properties are inherited by the effective dynamics. Then, we give equations for the effective dynamics, discuss whether the dominant timescales and reaction rates inferred from the effective dynamics are accurate approximations of such quantities for the full dynamics, and compare our findings to results from approaches like Zwanzig-Mori, averaging, or homogenization. Finally, by discussing the algorithmic realization of the effective dynamics, we demonstrate that recent algorithmic techniques like the "equation-free" approach and the "heterogeneous multiscale method" can be seen as special cases of our approach.}, language = {en} } @article{ZhangHartmannSchuette2016, author = {Zhang, Wei and Hartmann, Carsten and Sch{\"u}tte, Christof}, title = {Effective dynamics along given reaction coordinates, and reaction rate theory}, journal = {Faraday Discussions}, number = {195}, doi = {10.1039/C6FD00147E}, pages = {365 -- 394}, year = {2016}, language = {en} } @article{Zhang2021, author = {Zhang, Wei}, title = {Some new results on relative entropy production, time reversal, and optimal control of time-inhomogeneous diffusion processes}, volume = {62}, journal = {Journal of Mathematical Physics}, number = {4}, arxiv = {http://arxiv.org/abs/2006.11212}, doi = {10.1063/5.0038740}, pages = {26}, year = {2021}, abstract = {This paper studies time-inhomogeneous nonequilibrium diffusion processes, including both Brownian dynamics and Langevin dynamics. We derive upper bounds of the relative entropy production of the time-inhomogeneous process with respect to the transient invariant probability measures. We also study the time reversal of the reverse process in Crooks' fluctuation theorem. We show that the time reversal of the reverse process coincides with the optimally controlled forward process that leads to zero variance importance sampling estimator based on Jarzynski's equality.}, language = {en} } @article{Zhang2019, author = {Zhang, Wei}, title = {Ergodic SDEs on submanifolds and related numerical sampling schemes}, journal = {ESAIM: Mathematical Modelling and Numerical Analysis}, arxiv = {http://arxiv.org/abs/1702.08064}, year = {2019}, abstract = {In many applications, it is often necessary to sample the mean value of certain quantity with respect to a probability measure \$\mu\$ on the level set of a smooth function ξ:R^d→R^k, 1≤k