@article{SchienleMaristanydelasCasasBlanco2019, author = {Schienle, Adam and Maristany de las Casas, Pedro and Blanco, Marco}, title = {A Priori Search Space Pruning in the Flight Planning Problem}, issn = {1438-0064}, doi = {https://doi.org/10.4230/OASIcs.ATMOS.2019.8}, year = {2019}, abstract = {We study the Flight Planning Problem for a single aircraft, where we look for a minimum cost path in the airway network, a directed graph. Arc evaluation, such as weather computation, is computationally expensive due to non-linear functions, but required for exactness. We propose several pruning methods to thin out the search space for Dijkstra's algorithm before the query commences. We do so by using innate problem characteristics such as an aircraft's tank capacity, lower and upper bounds on the total costs, and in particular, we present a method to reduce the search space even in the presence of regional crossing costs. We test all pruning methods on real-world instances, and show that incorporating crossing costs into the pruning process can reduce the number of nodes by 90\\% in our setting.}, language = {en} } @article{YokoyamaShinanoWakayamaetal.2019, author = {Yokoyama, Ryohei and Shinano, Yuji and Wakayama, Yuki and Wakui, Tetsuya}, title = {Model reduction by time aggregation for optimal design of energy supply systems by an MILP hierarchical branch and bound method}, volume = {181}, journal = {Energy}, doi = {https://doi.org/10.1016/j.energy.2019.04.066}, pages = {782 -- 792}, year = {2019}, abstract = {Mixed-integer linear programming (MILP) methods have been applied widely to optimal design of energy supply systems in consideration of multi-period operation. A hierarchical MILP method has been proposed to solve such optimal design problems efficiently. An original problem has been solved by dividing it into a relaxed optimal design problem at the upper level and optimal operation problems which are independent of one another at the lower level. In addition, some strategies have been proposed to enhance the computation efficiency furthermore. In this paper, a method of reducing model by time aggregation is proposed as a novel strategy to search design candidates efficiently in the relaxed optimal design problem at the upper level. In addition, the previous strategies are modified in accordance with the novel strategy. This method is realized only by clustering periods and averaging energy demands for clustered periods, while it guarantees to derive the optimal solution. Thus, it may decrease the computation time at the upper level. Through a case study on the optimal design of a gas turbine cogeneration system, it is clarified how the model reduction is effective to enhance the computation efficiency in comparison and combination with the modified previous strategies.}, language = {en} } @article{GamrathGleixnerKochetal.2019, author = {Gamrath, Gerald and Gleixner, Ambros and Koch, Thorsten and Miltenberger, Matthias and Kniasew, Dimitri and Schl{\"o}gel, Dominik and Martin, Alexander and Weninger, Dieter}, title = {Tackling Industrial-Scale Supply Chain Problems by Mixed-Integer Programming}, volume = {37}, journal = {Journal of Computational Mathematics}, doi = {10.4208/jcm.1905-m2019-0055}, pages = {866 -- 888}, year = {2019}, abstract = {The modeling flexibility and the optimality guarantees provided by mixed-integer programming greatly aid the design of robust and future-proof decision support systems. The complexity of industrial-scale supply chain optimization, however, often poses limits to the application of general mixed-integer programming solvers. In this paper we describe algorithmic innovations that help to ensure that MIP solver performance matches the complexity of the large supply chain problems and tight time limits encountered in practice. Our computational evaluation is based on a diverse set, modeling real-world scenarios supplied by our industry partner SAP.}, language = {en} } @article{TempLabuzNegreteetal.2019, author = {Temp, Julia and Labuz, Dominika and Negrete, Roger and Sunkara, Vikram and Machelska, Halina}, title = {Pain and knee damage in male and female mice in the medial meniscal transection-induced osteoarthritis}, journal = {Osteoarthritis and Cartilage}, doi = {10.1016/j.joca.2019.11.003}, year = {2019}, language = {en} } @article{Sunkara2019, author = {Sunkara, Vikram}, title = {On the Properties of the Reaction Counts Chemical Master Equation}, volume = {21}, journal = {Entropy}, number = {6}, doi = {10.3390/e21060607}, pages = {607}, year = {2019}, abstract = {The reaction counts chemical master equation (CME) is a high-dimensional variant of the classical population counts CME. In the reaction counts CME setting, we count the reactions which have fired over time rather than monitoring the population state over time. Since a reaction either fires or not, the reaction counts CME transitions are only forward stepping. Typically there are more reactions in a system than species, this results in the reaction counts CME being higher in dimension, but simpler in dynamics. In this work, we revisit the reaction counts CME framework and its key theoretical results. Then we will extend the theory by exploiting the reactions counts' forward stepping feature, by decomposing the state space into independent continuous-time Markov chains (CTMC). We extend the reaction counts CME theory to derive analytical forms and estimates for the CTMC decomposition of the CME. This new theory gives new insights into solving hitting times-, rare events-, and a priori domain construction problems.}, language = {en} } @article{HaaseSunkaraKohletal.2019, author = {Haase, Tobias and Sunkara, Vikram and Kohl, Benjamin and Meier, Carola and Bußmann, Patricia and Becker, Jessica and Jagielski, Michal and von Kleist, Max and Ertel, Wolfgang}, title = {Discerning the spatio-temporal disease patterns of surgically induced OA mouse models}, volume = {14}, journal = {PLOS One}, number = {4}, publisher = {PLOS One}, doi = {10.1371/journal.pone.0213734}, year = {2019}, abstract = {Osteoarthritis (OA) is the most common cause of disability in ageing societies, with no effective therapies available to date. Two preclinical models are widely used to validate novel OA interventions (MCL-MM and DMM). Our aim is to discern disease dynamics in these models to provide a clear timeline in which various pathological changes occur. OA was surgically induced in mice by destabilisation of the medial meniscus. Analysis of OA progression revealed that the intensity and duration of chondrocyte loss and cartilage lesion formation were significantly different in MCL-MM vs DMM. Firstly, apoptosis was seen prior to week two and was narrowly restricted to the weight bearing area. Four weeks post injury the magnitude of apoptosis led to a 40-60\% reduction of chondrocytes in the non-calcified zone. Secondly, the progression of cell loss preceded the structural changes of the cartilage spatio-temporally. Lastly, while proteoglycan loss was similar in both models, collagen type II degradation only occurred more prominently in MCL-MM. Dynamics of chondrocyte loss and lesion formation in preclinical models has important implications for validating new therapeutic strategies. Our work could be helpful in assessing the feasibility and expected response of the DMM- and the MCL-MM models to chondrocyte mediated therapies.}, language = {en} } @article{KlusHusicMollenhaueretal.2019, author = {Klus, Stefan and Husic, Brooke E. and Mollenhauer, Mattes and Noe, Frank}, title = {Kernel methods for detecting coherent structures in dynamical data}, volume = {29}, journal = {Chaos: An Interdisciplinary Journal of Nonlinear Science}, number = {12}, doi = {10.1063/1.5100267}, year = {2019}, language = {en} } @article{AlchikhConradMaetal.2019, author = {Alchikh, Maren and Conrad, Tim and Ma, Xiaolin and Broberg, Eeva K. and Penttinen, P. and Reiche, J. and Biere, Barbara and Schweiger, Brunhilde and Rath, Barbara and Hoppe, Christian}, title = {Are we missing respiratory viral infections in infants and children? Comparison of a hospital-based quality management system with standard of care}, volume = {25}, journal = {Clinical Microbiology and Infection}, number = {3}, issn = {1469-0691}, doi = {10.1016/j.cmi.2018.05.023}, pages = {380.e9 -- 380.e16}, year = {2019}, language = {en} } @article{KoltaiLiePlonka2019, author = {Koltai, P{\´e}ter and Lie, Han Cheng and Plonka, Martin}, title = {Fr{\´e}chet differentiable drift dependence of Perron-Frobenius and Koopman operators for non-deterministic dynamics}, volume = {32}, journal = {Nonlinearity}, number = {11}, doi = {10.1088/1361-6544/ab1f2a}, pages = {4232 -- 4257}, year = {2019}, abstract = {We prove the Fr{\´e}chet differentiability with respect to the drift of Perron-Frobenius and Koopman operators associated to time-inhomogeneous ordinary stochastic differential equations. This result relies on a similar differentiability result for pathwise expectations of path functionals of the solution of the stochastic differential equation, which we establish using Girsanov's formula. We demonstrate the significance of our result in the context of dynamical systems and operator theory, by proving continuously differentiable drift dependence of the simple eigen- and singular values and the corresponding eigen- and singular functions of the stochastic Perron-Frobenius and Koopman operators.}, language = {en} } @article{GoetschelWeiser2019, author = {G{\"o}tschel, Sebastian and Weiser, Martin}, title = {Compression Challenges in Large Scale Partial Differential Equation Solvers}, volume = {12}, journal = {Algorithms}, number = {9}, doi = {10.3390/a12090197}, pages = {197}, year = {2019}, abstract = {Solvers for partial differential equations (PDEs) are one of the cornerstones of computational science. For large problems, they involve huge amounts of data that need to be stored and transmitted on all levels of the memory hierarchy. Often, bandwidth is the limiting factor due to the relatively small arithmetic intensity, and increasingly due to the growing disparity between computing power and bandwidth. Consequently, data compression techniques have been investigated and tailored towards the specific requirements of PDE solvers over the recent decades. This paper surveys data compression challenges and discusses examples of corresponding solution approaches for PDE problems, covering all levels of the memory hierarchy from mass storage up to the main memory. We illustrate concepts for particular methods, with examples, and give references to alternatives.}, language = {en} } @article{StraubePagesTiernoetal.2019, author = {Straube, Arthur and Pag{\`e}s, Josep M. and Tierno, Pietro and Ign{\´e}s-Mullol, Jordi and Sagu{\´e}s, Francesc}, title = {Collective dynamics and conformal ordering in electrophoretically driven nematic colloids}, volume = {1}, journal = {Phys. Rev. Research}, doi = {10.1103/PhysRevResearch.1.022008}, pages = {022008}, year = {2019}, abstract = {We present a theoretical framework to understand the collective dynamics of an ensemble of electrophoretically driven colloidal particles that are forced to assemble around a single topological defect in a nematic liquid crystal by an alternating current electric field. Our generic model combines phoretic propulsion with electrostatic interactions and liquid-crystal-mediated hydrodynamics, which are effectively cast into a long-range interparticle repulsion, while nematic elasticity plays a subdominant role. Simulations based on this model fully capture the collective organization process observed in the experiments and other striking effects as the emergence of conformal ordering and a nearly frequency-independent repulsive interaction above 10Hz. Our results demonstrate the importance of hydrodynamic interactions on the assembly of driven microscale matter in anisotropic media.}, language = {en} } @article{AbbottStraubeAartsetal.2019, author = {Abbott, Joshua L. and Straube, Arthur and Aarts, Dirk G. A. L. and Dullens, Roel P. A.}, title = {Transport of a colloidal particle driven across a temporally oscillating optical potential energy landscape}, volume = {21}, journal = {New J. Phys.}, doi = {10.1088/1367-2630/ab3765}, pages = {083027}, year = {2019}, abstract = {A colloidal particle is driven across a temporally oscillating one-dimensional optical potential energy landscape and its particle motion is analysed. Different modes of dynamic mode locking are observed and are confirmed with the use of phase portraits. The effect of the oscillation frequency on the mode locked step width is addressed and the results are discussed in light of a high-frequency theory and compared to simulations. Furthermore, the influence of the coupling between the particle and the optical landscape on mode locking is probed by increasing the maximum depth of the optical landscape. Stronger coupling is seen to increase the width of mode locked steps. Finally, transport across the temporally oscillating landscape is studied by measuring the effective diffusion coefficient of a mobile particle, which is seen to be highly sensitive to the driving velocity and mode locking.}, language = {en} } @article{BraunPokuttaZink2019, author = {Braun, G{\´a}bor and Pokutta, Sebastian and Zink, Daniel}, title = {Affine Reductions for LPs and SDPs}, volume = {173}, journal = {Mathematical Programming A}, number = {1}, arxiv = {http://arxiv.org/abs/1410.8816}, pages = {281 -- 312}, year = {2019}, language = {en} } @article{BraunPokuttaZink2019, author = {Braun, G{\´a}bor and Pokutta, Sebastian and Zink, Daniel}, title = {Lazifying Conditional Gradient Algorithms}, volume = {20}, journal = {Journal of Machine Learning Research (JMLR)}, number = {71}, arxiv = {http://arxiv.org/abs/1610.05120}, pages = {1 -- 42}, year = {2019}, language = {en} } @article{SchulzYamamotoKlosseketal.2019, author = {Schulz, Robert and Yamamoto, Kenji and Klossek, Andr{\´e} and Rancan, Fiorenza and Vogt, Annika and Sch{\"u}tte, Christof and R{\"u}hl, Eckart and Netz, Roland R.}, title = {Modeling of Drug Diffusion Based on Concentration Profiles in Healthy and Damaged Human Skin}, volume = {117}, journal = {Biophysical Journal}, number = {5}, doi = {10.1016/j.bpj.2019.07.027}, pages = {998 -- 1008}, year = {2019}, abstract = {Based on experimental drug concentration profiles in healthy as well as tape-stripped ex vivo human skin, we model the penetration of the antiinflammatory drug dexamethasone into the skin layers by the one-dimensional generalized diffusion equation. We estimate the position-dependent free-energy and diffusivity profiles by solving the conjugated minimization problem, in which the only inputs are concentration profiles of dexamethasone in skin at three consecutive penetration times. The resulting free-energy profiles for damaged and healthy skin show only minor differences. In contrast, the drug diffusivity in the first 10 μm of the upper skin layer of damaged skin is 200-fold increased compared to healthy skin, which reflects the corrupted barrier function of tape-stripped skin. For the case of healthy skin, we examine the robustness of our method by analyzing the behavior of the extracted skin parameters when the number of input and output parameters are reduced. We also discuss techniques for the regularization of our parameter extraction method.}, language = {en} } @article{BanyassadyChiuKormanetal.2019, author = {Banyassady, Bahareh and Chiu, Man-Kwun and Korman, Matias and Mulzer, Wolfgang and van Renssen, Andr{\´e} and Roeloffzen, Marcel and Seiferth, Paul and Stein, Yannik and Vogtenhuber, Birgit and Willert, Max}, title = {Routing in polygonal domains}, volume = {87}, journal = {Computational Geometry, Theory and Applications}, publisher = {Elsevier}, doi = {10.1016/j.comgeo.2019.101593}, year = {2019}, abstract = {We consider the problem of routing a data packet through the visibility graph of a polygonal domain P with n vertices and h holes. We may preprocess P to obtain a "label" and a "routing table" for each vertex of P. Then, we must be able to route a data packet between any two vertices p and q of P, where each step must use only the label of the target node q and the routing table of the current node. For any fixed epsilon > 0, we present a routing scheme that always achieves a routing path whose length exceeds the shortest path by a factor of at most 1 + epsilon. The labels have O(log n) bits, and the routing tables are of size O(((epsilon^-1)+h)log n). The preprocessing time is O((n^2)log n). It can be improved to O(n^2) for simple polygons.}, language = {en} } @article{DelVecchioLabuzTempetal.2019, author = {Del Vecchio, Giovanna and Labuz, Dominika and Temp, Julia and Seitz, Viola and Kloner, Michael and Negrete, Roger and Rodriguez-Gaztelumendi, Antonio and Weber, Marcus and Machelska, Halina and Stein, Christoph}, title = {pKa of opioid ligands as a discriminating factor for side effects}, volume = {9}, journal = {Scientific Reports}, doi = {10.1038/s41598-019-55886-1}, pages = {19344}, year = {2019}, abstract = {The non-selective activation of central and peripheral opioid receptors is a major shortcoming of currently available opioids. Targeting peripheral opioid receptors is a promising strategy to preclude side effects. Recently, we showed that fentanyl-derived μ-opioid receptor (MOR) agonists with reduced acid dissociation constants (pKa) due to introducing single fluorine atoms produced injury-restricted antinociception in rat models of inflammatory, postoperative and neuropathic pain. Here, we report that a new double-fluorinated compound (FF6) and fentanyl show similar pKa, MOR affinity and [35S]-GTPγS binding at low and physiological pH values. In vivo, FF6 produced antinociception in injured and non-injured tissue, and induced sedation and constipation. The comparison of several fentanyl derivatives revealed a correlation between pKa values and pH-dependent MOR activation, antinociception and side effects. An opioid ligand's pKa value may be used as discriminating factor to design safer analgesics.}, language = {en} } @article{DibakFroehnerNoeetal.2019, author = {Dibak, Manuel and Fr{\"o}hner, Christoph and No{\´e}, Frank and H{\"o}fling, Felix}, title = {Diffusion-influenced reaction rates in the presence of pair interactions}, volume = {151}, journal = {The Journal of Chemical Physics}, arxiv = {http://arxiv.org/abs/1908.07764}, doi = {10.1063/1.5124728}, pages = {164105}, year = {2019}, abstract = {The kinetics of bimolecular reactions in solution depends, among other factors, on intermolecular forces such as steric repulsion or electrostatic interaction. Microscopically, a pair of molecules first has to meet by diffusion before the reaction can take place. In this work, we establish an extension of Doi's volume reaction model to molecules interacting via pair potentials, which is a key ingredient for interacting-particle-based reaction-diffusion (iPRD) simulations. As a central result, we relate model parameters and macroscopic reaction rate constants in this situation. We solve the corresponding reaction-diffusion equation in the steady state and derive semi- analytical expressions for the reaction rate constant and the local concentration profiles. Our results apply to the full spectrum from well-mixed to diffusion-limited kinetics. For limiting cases, we give explicit formulas, and we provide a computationally inexpensive numerical scheme for the general case, including the intermediate, diffusion-influenced regime. The obtained rate constants decompose uniquely into encounter and formation rates, and we discuss the effect of the potential on both subprocesses, exemplified for a soft harmonic repulsion and a Lennard-Jones potential. The analysis is complemented by extensive stochastic iPRD simulations, and we find excellent agreement with the theoretical predictions.}, language = {en} } @article{VenkatareddyWilkeErnstetal.2019, author = {Venkatareddy, Narendra Lagumaddepalli and Wilke, Patrick and Ernst, Natalia and Horch, Justus and Weber, Marcus and Dallmann, Andre and B{\"o}rner, Hans G.}, title = {Mussel-glue inspired adhesives: A study on the relevance of L-Dopa and the function of the sequence at nanomaterial-peptide interfaces}, volume = {6}, journal = {Advanced Materials Interfaces}, number = {13}, doi = {10.1002/admi.201900501}, pages = {1900501}, year = {2019}, abstract = {Mussel glue-proteins undergo structural transitions at material interfaces to optimize adhesive surface contacts. Those intriguing structure responses are mimicked by a mussel-glue mimetic peptide (HSY*SGWSPY*RSG (Y* = l-Dopa)) that was previously selected by phage-display to adhere to Al2O3 after enzymatic activation. Molecular level insights into the full-length adhesion domain at Al2O3 surfaces are provided by a divergent-convergent analysis, combining nuclear Overhauser enhancement based 2D NOESY and saturation transfer difference NMR analysis of submotifs along with molecular dynamics simulations of the full-length peptide. The peptide is divided into two submotifs, each containing one Dopa "anchor" (Motif-1 and 2). The analysis proves Motif-1 to constitute a dynamic Al2O3 binder and adopting an "M"-structure with multiple surface contacts. Motif-2 binds stronger by two surface contacts, forming a compact "C"-structure. Taking these datasets as constraints enables to predict the structure and propose a binding process model of the full-length peptide adhering to Al2O3.}, language = {en} } @article{Weber2019, author = {Weber, Marcus}, title = {Transformationsprodukte im Kl{\"a}rwerk: Mathematische Ans{\"a}tze der Bewertung}, volume = {7}, journal = {KA Korrespondenz Abwasser, Abfall}, pages = {551 -- 557}, year = {2019}, language = {de} }