@article{ManleySegantiniAhibozetal.2021, author = {Manley, Phillip and Segantini, Michele and Ahiboz, Doguscan and Hammerschmidt, Martin and Arnaoutakis, Georgios and MacQueen, Rowan W. and Burger, Sven and Becker, Christiane}, title = {Double-layer metasurface for enhanced photon up-conversion}, volume = {6}, journal = {APL Photon.}, arxiv = {http://arxiv.org/abs/2012.03587}, doi = {10.1063/5.0040839}, pages = {036103}, year = {2021}, language = {en} } @article{PakhomovHammerschmidtBurgeretal.2021, author = {Pakhomov, Anton V. and Hammerschmidt, Martin and Burger, Sven and Pertsch, Thomas and Setzpfand, Frank}, title = {Modeling of surface-induced second-harmonic generation from multilayer structures by the transfer matrix method}, volume = {29}, journal = {Opt. Express}, doi = {10.1364/OE.417066}, pages = {9098}, year = {2021}, language = {en} } @article{BinkowskiWuLalanneetal.2021, author = {Binkowski, Felix and Wu, Tong and Lalanne, Philippe and Burger, Sven and Govorov, Alexander O.}, title = {Hot Electron Generation through Near-Field Excitation of Plasmonic Nanoresonators}, volume = {8}, journal = {ACS Photonics}, arxiv = {http://arxiv.org/abs/2103.06652}, doi = {10.1021/acsphotonics.1c00231}, pages = {1243}, year = {2021}, language = {en} } @article{CvetkovicConradLie2021, author = {Cvetkovic, Nada and Conrad, Tim and Lie, Han Cheng}, title = {A Convergent Discretisation Method for Transition Path Theory for Diffusion Processes}, volume = {19}, journal = {Multiscale Modeling \& Simulation}, number = {1}, publisher = {Society for Industrial and Applied Mathematics}, doi = {10.1137/20M1329354}, pages = {242 -- 266}, year = {2021}, language = {en} } @book{DeuflhardWeiser2020, author = {Deuflhard, Peter and Weiser, Martin}, title = {Numerische Mathematik 3. Adaptive L{\"o}sung partieller Differentialgleichungen}, edition = {2}, publisher = {de Gruyter}, isbn = {978-3-11-069168-9}, doi = {10.1515/9783110689655}, pages = {456}, year = {2020}, language = {de} } @article{SikorskiWeberSchuette2021, author = {Sikorski, Alexander and Weber, Marcus and Sch{\"u}tte, Christof}, title = {The Augmented Jump Chain}, volume = {4}, journal = {Advanced Theory and Simulations}, number = {4}, publisher = {Wiley-VCH}, arxiv = {http://arxiv.org/abs/2008.04624}, doi = {10.1002/adts.202000274}, year = {2021}, abstract = {Modern methods of simulating molecular systems are based on the mathematical theory of Markov operators with a focus on autonomous equilibrated systems. However, non-autonomous physical systems or non-autonomous simulation processes are becoming more and more important. A representation of non-autonomous Markov jump processes is presented as autonomous Markov chains on space-time. Augmenting the spatial information of the embedded Markov chain by the temporal information of the associated jump times, the so-called augmented jump chain is derived. The augmented jump chain inherits the sparseness of the infinitesimal generator of the original process and therefore provides a useful tool for studying time-dependent dynamics even in high dimensions. Furthermore, possible generalizations and applications to the computation of committor functions and coherent sets in the non-autonomous setting are discussed. After deriving the theoretical foundations, the concepts with a proof-of-concept Galerkin discretization of the transfer operator of the augmented jump chain applied to simple examples are illustrated.}, language = {en} } @article{SechiSikorskiWeber2021, author = {Sechi, Renata and Sikorski, Alexander and Weber, Marcus}, title = {Estimation of the Koopman Generator by Newton's Extrapolation}, volume = {19}, journal = {Multiscale Modeling and Simulation}, number = {2}, publisher = {SIAM}, doi = {10.1137/20M1333006}, pages = {758 -- 774}, year = {2021}, abstract = {This article addresses the problem of estimating the Koopman generator of a Markov process. The direct computation of the infinitesimal generator is not easy because of the discretization of the state space, in particular because of the trade-off inherent in the choice of the best lag time to study the process. Short lag times implies a strong discretization of the state space and a consequent loss of Markovianity. Large lag times bypass events on fast timescales. We propose a method to approximate the generator with the computation of the Newton polynomial extrapolation. This technique is a multistep approach which uses as its input Koopman transfer operators evaluated for a series of lag times. Thus, the estimated infinitesimal generator combines information from different time resolutions and does not bias only fast- or slow-decaying dynamics. We show that the multi-scale Newton method can improve the estimation of the generator in comparison to the computation using finite difference or matrix logarithm methods.}, language = {en} } @phdthesis{Venkatareddy2020, author = {Venkatareddy, Narendra Lagumaddepalli}, title = {Revealing secrets of mussel-glue mimetic peptides - From advanced NMR to computational process modelling}, year = {2020}, language = {en} } @phdthesis{Eshtewy2020, author = {Eshtewy, Neveen Ali Salem}, title = {Mathematical Modeling of Metabolic-Genetic Networks}, year = {2020}, language = {en} } @article{OettingerMontefuscoPeletier2021, author = {{\"O}ttinger, Hans Christian and Montefusco, Alberto and Peletier, Mark A.}, title = {A Framework of Nonequilibrium Statistical Mechanics. I. Role and Types of Fluctuations}, volume = {46}, journal = {Journal of Non-Equilibrium Thermodynamics}, number = {1}, publisher = {De Gruyter}, doi = {10.1515/jnet-2020-0068}, pages = {1 -- 13}, year = {2021}, abstract = {Understanding the fluctuations by which phenomenological evolution equations with thermodynamic structure can be enhanced is the key to a general framework of nonequilibrium statistical mechanics. These fluctuations provide an idealized representation of microscopic details. We consider fluctuation-enhanced equations associated with Markov processes and elaborate the general recipes for evaluating dynamic material properties, which characterize force-flux constitutive laws, by statistical mechanics. Markov processes with continuous trajectories are conveniently characterized by stochastic differential equations and lead to Green-Kubo-type formulas for dynamic material properties. Markov processes with discontinuous jumps include transitions over energy barriers with the rates calculated by Kramers. We describe a unified approach to Markovian fluctuations and demonstrate how the appropriate type of fluctuations (continuous versus discontinuous) is reflected in the mathematical structure of the phenomenological equations.}, language = {en} } @article{MontefuscoPeletierOettinger2021, author = {Montefusco, Alberto and Peletier, Mark A. and {\"O}ttinger, Hans Christian}, title = {A Framework of Nonequilibrium Statistical Mechanics. II. Coarse-Graining}, volume = {46}, journal = {Journal of Non-Equilibrium Thermodynamics}, number = {1}, publisher = {De Gruyter}, doi = {10.1515/jnet-2020-0069}, pages = {15 -- 33}, year = {2021}, abstract = {For a given thermodynamic system, and a given choice of coarse-grained state variables, the knowledge of a force-flux constitutive law is the basis for any nonequilibrium modeling. In the first paper of this series we established how, by a generalization of the classical fluctuation-dissipation theorem (FDT), the structure of a constitutive law is directly related to the distribution of the fluctuations of the state variables. When these fluctuations can be expressed in terms of diffusion processes, one may use Green-Kubo-type coarse-graining schemes to find the constitutive laws. In this paper we propose a coarse-graining method that is valid when the fluctuations are described by means of general Markov processes, which include diffusions as a special case. We prove the success of the method by numerically computing the constitutive law for a simple chemical reaction A⇄B. Furthermore, we show that, for such a system, one cannot find a consistent constitutive law by any Green-Kubo-like scheme.}, language = {en} } @article{SunkaraHeinzHeinrichetal.2020, author = {Sunkara, Vikram and Heinz, Gitta A. and Heinrich, Frederik F. and Durek, Pawel and Mobasheri, Ali and Mashreghi, Mir-Farzin and Lang, Annemarie}, title = {Combining segmental bulk- and single-cell RNA-sequencing to define the chondrocyte gene expression signature in the murine knee joint}, journal = {bioarxiv (Accepted in Osteoarthr. Cartil.)}, doi = {10.1101/2020.06.13.148056}, year = {2020}, language = {en} } @article{LangHelfmeierStefanowskietal.2020, author = {Lang, Annemarie and Helfmeier, Sarah and Stefanowski, Jonathan and Kuppe, Aditi and Sunkara, Vikram and Pfeiffenberger, Moritz and Wolter, Angelique and Damerau, Alexandra and Hemmati-Sadeghi, Shabnam and Ringe, Jochen and Haag, Rainer and Hauser, Anja E. and L{\"o}hning, Max and Perka, Carsten and Duda, Georg and Hoff, Paula and Schmidt-Bleek, Katharina and Gaber, Timo and Buttgereit, Frank}, title = {HIF-stabilization prevents delayed fracture healing}, journal = {bioarxiv}, doi = {10.1101/2020.07.02.182832}, year = {2020}, language = {en} } @article{LaydonSunkaraBoelenetal.2020, author = {Laydon, Daniel J. and Sunkara, Vikram and Boelen, Lies and Bangham, Charles R. M. and Asquith, Becca}, title = {The relative contributions of infectious and mitotic spread to HTLV-1 persistence}, journal = {PLOS Computational Biology}, doi = {10.1371/journal.pcbi.1007470}, year = {2020}, language = {en} } @article{SchielaStoeckleinWeiser2021, author = {Schiela, Anton and St{\"o}cklein, Matthias and Weiser, Martin}, title = {A primal dual projection algorithm for efficient constraint preconditioning}, volume = {43}, journal = {SIAM Journal on Scientific Computing}, number = {6}, doi = {10.1137/20M1380739}, pages = {A4095 -- A4120}, year = {2021}, abstract = {We consider a linear iterative solver for large scale linearly constrained quadratic minimization problems that arise, for example, in optimization with PDEs. By a primal-dual projection (PDP) iteration, which can be interpreted and analysed as a gradient method on a quotient space, the given problem can be solved by computing sulutions for a sequence of constrained surrogate problems, projections onto the feasible subspaces, and Lagrange multiplier updates. As a major application we consider a class of optimization problems with PDEs, where PDP can be applied together with a projected cg method using a block triangular constraint preconditioner. Numerical experiments show reliable and competitive performance for an optimal control problem in elasticity.}, language = {en} } @article{MielkeMontefuscoPeletier2021, author = {Mielke, Alexander and Montefusco, Alberto and Peletier, Mark A.}, title = {Exploring families of energy-dissipation landscapes via tilting: three types of EDP convergence}, volume = {33}, journal = {Continuum Mechanics and Thermodynamics}, publisher = {Springer}, doi = {10.1007/s00161-020-00932-x}, pages = {611 -- 637}, year = {2021}, abstract = {This paper revolves around a subtle distinction between two concepts: passing to the limit in a family of gradient systems, on one hand, and deriving effective kinetic relations on the other. The two concepts are strongly related, and in many examples they even appear to be the same. Our main contributions are to show that they are different, to show that well-known techniques developed for the former may give incorrect results for the latter, and to introduce new tools to remedy this. The approach is based on the Energy-Dissipation Principle that provides a variational formulation to gradient-flow equations that allows one to apply techniques from Γ-convergence of functional on states and functionals on trajectories.}, language = {en} } @phdthesis{Santiago2021, author = {Santiago, Xavier Garcia}, title = {Numerical methods for shape optimization of photonic nanostructures}, organization = {Karlsruher Institut f{\"u}r Technologie}, doi = {10.5445/IR/1000131006}, year = {2021}, language = {en} } @article{RamosLeiteZschiedrichKizilkayaetal.2022, author = {Ramos Leite, Tiago and Zschiedrich, Lin and Kizilkaya, Orhan and McPeak, Kevin M.}, title = {Resonant Plasmonic-Biomolecular Chiral Interactions in the Far-Ultraviolet: Enantiomeric Discrimination of sub-10 nm Amino Acid Films}, volume = {22}, journal = {Nano Lett.}, doi = {10.1021/acs.nanolett.2c01724}, pages = {7343}, year = {2022}, language = {en} } @article{RejSantiagoBaturinaetal.2022, author = {Rej, Sourav and Santiago, Eva Yazmin and Baturina, Olga and Zhang, Yu and Burger, Sven and Kment, Stepan and Govorov, Alexander O. and Naldoni, Alberto}, title = {Colloidal Titanium Nitride Nanobars for Broadband Inexpensive Plasmonics and Photochemistry from Visible to Mid-IR Wavelengths}, volume = {104}, journal = {Nano Energy}, arxiv = {http://arxiv.org/abs/2209.04678}, doi = {10.1016/j.nanoen.2022.107989}, pages = {107989}, year = {2022}, language = {en} } @article{RickertBetzPlocketal.2023, author = {Rickert, Lucas and Betz, Fridtjof and Plock, Matthias and Burger, Sven and Heindel, Tobias}, title = {High-performance designs for fiber-pigtailed quantum-light sources based on quantum dots in electrically-controlled circular Bragg gratings}, volume = {31}, journal = {Opt. Express}, arxiv = {http://arxiv.org/abs/2212.04883}, doi = {10.1364/OE.486060}, pages = {14750}, year = {2023}, language = {en} } @misc{RickertBetzPlocketal.2022, author = {Rickert, Lucas and Betz, Fridtjof and Plock, Matthias and Burger, Sven and Heindel, Tobias}, title = {Data publication for "High-performance designs for fiber-pigtailed quantum-light sources based on quantum dots in electrically-controlled circular Bragg gratings"}, journal = {Zenodo}, doi = {10.5281/zenodo.7360516}, pages = {7360516}, year = {2022}, language = {en} }