Items 1-20 of 1826

    • Journal Article

      3D virtual pathohistology of lung tissue from Covid-19 patients based on phase contrast X-ray tomography 

      Eckermann, Marina; Frohn, Jasper; Reichardt, Marius; Osterhoff, Markus; Sprung, Michael; Westermeier, Fabian; Tzankov, Alexandar; Werlein, Christopher; Kühnel, Mark; Jonigk, Danny; et al.
      Salditt, Tim
      eLife 2020; 9 p.1-25: Art. e60408
      We present a three-dimensional (3D) approach for virtual histology and histopathology based on multi-scale phase contrast x-ray tomography, and use this to investigate the parenchymal architecture of unstained lung tissue from patients who succumbed to Covid-19. Based on this first proof-of-concept study, we propose multi-scale phase contrast x-ray tomography as a tool to unravel the pathophysiology of Covid-19, extending conventional histology by a third dimension and allowing for full quantification of tissue remodeling. By combining parallel and cone beam geometry, autopsy samples with a maximum cross section of 8 mm are scanned and reconstructed at a resolution and image quality, which allows for the segmentation of individual cells. Using the zoom capability of the cone beam geometry, regions-of-interest are reconstructed with a minimum voxel size of 167 nm. We exemplify the capability of this approach by 3D visualization of diffuse alveolar damage (DAD) with its prominent hyaline membrane formation, by mapping the 3D distribution and density of lymphocytes infiltrating the tissue, and by providing histograms of characteristic distances from tissue interior to the closest air compartment.
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    • Journal Article

      Time-continuous and time-discrete SIR models revisited: theory and applications 

      Wacker, Benjamin; Schlüter, Jan
      Advances in Difference Equations. 2020 Oct 07;2020(1):556
      Since Kermack and McKendrick have introduced their famous epidemiological SIR model in 1927, mathematical epidemiology has grown as an interdisciplinary research discipline including knowledge from biology, computer science, or mathematics. Due to current threatening epidemics such as COVID-19, this interest is continuously rising. As our main goal, we establish an implicit time-discrete SIR (susceptible people–infectious people–recovered people) model. For this purpose, we first introduce its continuous variant with time-varying transmission and recovery rates and, as our first contribution, discuss thoroughly its properties. With respect to these results, we develop different possible time-discrete SIR models, we derive our implicit time-discrete SIR model in contrast to many other works which mainly investigate explicit time-discrete schemes and, as our main contribution, show unique solvability and further desirable properties compared to its continuous version. We thoroughly show that many of the desired properties of the time-continuous case are still valid in the time-discrete implicit case. Especially, we prove an upper error bound for our time-discrete implicit numerical scheme. Finally, we apply our proposed time-discrete SIR model to currently available data regarding the spread of COVID-19 in Germany and Iran.
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    • Journal Article

      Cavitation bubble dynamics and sonochemiluminescence activity inside sonicated submerged flow tubes 

      Sarac, Busra Ekim; Stephens, Dwayne Savio; Eisener, Julian; Rosselló, Juan Manuel; Mettin, Robert
      Chemical Engineering and Processing - Process Intensification 2020; 150
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    • Journal Article

      Structure of Nanocrystalline, Partially Disordered MoS$_{2+δ}$ Derived from HRTEM—An Abundant Material for Efficient HER Catalysis 

      Ronge, Emanuel; Hildebrandt, Sonja; Grutza, Marie-Luise; Klein, Helmut; Kurz, Philipp; Jooss, Christian
      Catalysts 2020; 10(8) p.1-16: Art. 856
      Molybdenum sulfides (MoS$_x$, x > 2) are promising catalysts for the hydrogen evolution reaction (HER) that show high hydrogen evolution rates and potentially represent an abundant alternative to platinum. However, a complete understanding of the structure of the most active variants is still lacking. Nanocrystalline MoS$_{2+δ}$ was prepared by a solvothermal method and immobilized on graphene. The obtained electrodes exhibit stable HER current densities of 3 mA cm$^{−2}$ at an overpotential of ~200 mV for at least 7 h. A structural analysis of the material by high-resolution transmission electron microscopy (HRTEM) show partially disordered nanocrystals of a size between 5–10 nm. Both X-ray and electron diffraction reveal large fluctuations in lattice spacing, where the average c-axis stacking is increased and the in-plane lattice parameter is locally reduced in comparison to the layered structure of crystalline MoS$_2$. A three-dimensional structural model of MoS$_{2+δ}$ could be derived from the experiments, in which [Mo$_2$S$_{12}$]$^{2−}$ and [Mo$_3$S$_{13}$]$^{2−}$ clusters as well as disclinations represent the typical defects in the ideal MoS$_2$ structure. It is suggested that the partially disordered nanostructure leads to a high density of coordinatively modified Mo sites with lower Mo–Mo distances representing the active sites for HER catalysis, and, that these structural features are more important than the S:Mo ratio for the activity.
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    • Journal Article

      Environmental transmission electron microscopy study of hydrogen charging effect on a Cu-Zr metallic glass 

      Tian, Lin; Yang, Yue-Qing; Meyer, Tobias; Tönnies, Dominik; Roddatis, Vladimir; Voigt, Hendrik; Zhao, Xin-Ai; Wang, Zhang-Jie; Xie, De-Gang; Seibt, Michael; et al.
      Volkert, Cynthia A.Shan, Zhi-Wei
      Materials Research Letters 2020; 8(12) p.439-445
      Hydrogen induced plasticity has been found in metallic glasses; however, the underlying mechanism remains unclear. Herein, we studied a Cu-Zr metallic glass charged in a hydrogen atmosphere inside an environmental transmission electron microscope. Compression tests of hydrogen charged nanopillars show more controllable deformation compared to uncharged ones. A variable resolution fluctuation electron microscopy study of the hydrogen charged samples reveals an increase in the correlation length of the medium-range order. Our results provide experimental evidence for hydrogen-induced heterogeneity and support the idea that increasing the degree of heterogeneity leads to multiple local shear events and suppresses catastrophic shear banding.
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    • Journal Article

      Towards full surface Brillouin zone mapping by coherent multi-photon photoemission 

      Li, Andi; James, Namitha Ann; Wang, Tianyi; Wang, Zehua; Petek, Hrvoje; Reutzel, Marcel
      New Journal of Physics 2020; 22(7) p.1-6: Art. 073035
      We report a novel approach for coherent multi-photon photoemission in the entire Brillouin zone with infrared light that is readily implemented in a laboratory setting. We excite a solid state material, Ag(110), with intense femtosecond laser pulses to excite higher-order multi-photon photoemission; angle-resolved electron spectroscopic acquisition records photoemission at large in-plane momenta involving optical transitions from the occupied to unoccupied bands of the sample that otherwise might remain hidden by the photoemission horizon. We propose this as a complementary ultrafast method to time- and angle-resolved two-color, e.g. infrared pump and extreme ultraviolet probe, photoemission spectroscopy, with the advantage of being able to measure and control the coherent electron dynamics.
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    • Journal Article

      Upconversion photoluminescence of Ho$^{3+}$-Yb$^{3+}$ doped barium titanate nanocrystallites: Optical tools for structural phase detection and temperature probing 

      Mahata, Manoj Kumar; Koppe, Tristan; Kumar, Kaushal; Hofsäss, Hans; Vetter, Ulrich
      Scientific Reports 2020; 10(1) p.1-12: Art. 8775
      Authors have explored the photo-physical properties of Ho$^{3+}$-Yb$^{3+}$ doped BaTiO$_3$ nanocrystals and proposed an intuitive method to probe temperature and crystal phase structure of the matrix. Structural phase change of doped crystals was analyzed in terms of their X-ray diffraction, and it was confirmed through second harmonic generation. We give insights on upconversion of energy of light-emission in Ho$^{3+}$-Yb$^{3+}$: BaTiO$_3$ nanocrystals upon a 980 nm laser-light excitation and subsequently, the excited state dynamics were studied with the help of dependence of upconversion luminescence on excitation power and measuring-temperature. To understand the nature of occupancies of the Ho$^{3+}$ ions at the Ti- and Ba-sites, we performed site-selective, time-resolved spectroscopic measurements at various crystal phases. Based on the lifetime analysis, it is inferred that the Ho$^{3+}$ ions are present at two types of sites in barium titanate lattice. One of those is the 6-coordinated Ti-site of low symmetry, while the other one is the 12-coordinated Ba-site of higher symmetry. The upconversion emission of the nanocrystals are found to be temperature-sensitive (12 to 300 K), indicating possible use as a self-referenced temperature probe. An analysis of the temperature dependent emissions from $^5$F$_4$ and $^5$S$_2$ levels of Ho$^{3+}$ ions, gives a maximum value of temperature sensitivity ~ 0.0095 K$^{−1}$ at 12 K. Furthermore, we observe a sharp change in the luminescence intensity at ~180 K due to a ferroelectric phase change of the sample. The correlation of upconversion luminescence with the results of X-ray diffraction and second harmonic generation at different crystal phases implies that the frequency upconversion may be used as a probe of structural change of the lattice.
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    • Journal Article

      Hey, look over there: Distraction effects on rapid sequence recall 

      Miner, Daniel; Tetzlaff, Christian
      PLOS ONE 2020; 15(4) p.1-22: Art. e0223743
      In the course of everyday life, the brain must store and recall a huge variety of representations of stimuli which are presented in an ordered or sequential way. The processes by which the ordering of these various things is stored and recalled are moderately well understood. We use here a computational model of a cortex-like recurrent neural network adapted by a multitude of plasticity mechanisms. We first demonstrate the learning of a sequence. Then, we examine the influence of different types of distractors on the network dynamics during the recall of the encoded ordered information being ordered in a sequence. We are able to broadly arrive at two distinct effect-categories for distractors, arrive at a basic understanding of why this is so, and predict what distractors will fall into each category.
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    • Journal Article

      Modeling the Shape of Synaptic Spines by Their Actin Dynamics 

      Bonilla-Quintana, Mayte; Wörgötter, Florentin; Tetzlaff, Christian; Fauth, Michael
      Frontiers in Synaptic Neuroscience 2020; 12 p.1-19: Art. 9
      Dendritic spines are the morphological basis of excitatory synapses in the cortex and their size and shape correlates with functional synaptic properties. Recent experiments show that spines exhibit large shape fluctuations that are not related to activity-dependent plasticity but nonetheless might influence memory storage at their synapses. To investigate the determinants of such spontaneous fluctuations, we propose a mathematical model for the dynamics of the spine shape and analyze it in 2D—related to experimental microscopic imagery—and in 3D. We show that the spine shape is governed by a local imbalance between membrane tension and the expansive force from actin bundles that originates from discrete actin polymerization foci. Experiments have shown that only few such polymerization foci co-exist at any time in a spine, each having limited life time. The model shows that the momentarily existing set of such foci pushes the membrane along certain directions until foci are replaced and other directions may now be affected. We explore these relations in depth and use our model to predict shape and temporal characteristics of spines from the different biophysical parameters involved in actin polymerization. Approximating the model by a single recursive equation we finally demonstrate that the temporal evolution of the number of active foci is sufficient to predict the size of the model-spines. Thus, our model provides the first platform to study the relation between molecular and morphological properties of the spine with a high degree of biophysical detail.
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    • Journal Article

      Thermophysical properties of a Si$_{50}$Ge$_{50}$ melt measured on board the International Space Station 

      Luo, Yuansu; Damaschke, Bernd; Lohöfer, Georg; Samwer, Konrad
      npj Microgravity 2020; 6(1) p.1-9: Art. 10
      Thermophysical properties of highly doped Si$_{50}$Ge$_{50}$ melt were measured contactlessly in the electromagnetic levitation facility ISSEML on board the International Space Station. The sample could be melted, overheated by about 375 K, and cooled down in 350 mbar Argon atmosphere. A large undercooling of about 240 K was observed and a quasi-homogeneous nucleation on the droplet surface occurred. During the cooling phase, high-resolution videos were taken from the side and the top. The density and thermal expansion were evaluated with digital image processing; the viscosity and the surface tension were measured by means of the oscillating drop technique. Inductive measurements of the electrical resistivity were conducted by a dedicated electronics. All data were taken as a function of temperature T from the overheated melt down to the undercooled range. We found a nonlinear thermal expansion, suggesting a many body effect in the liquid beyond the regular pair interaction, an enhanced damping of surface oscillations likely related to an internal turbulent flow, and an increment of the electrical resistivity with decreased T in the undercooled range regarding a demixing of the components.
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    • Journal Article

      Exfoliated near infrared fluorescent silicate nanosheets for (bio)photonics 

      Selvaggio, Gabriele; Chizhik, Alexey; Nißler, Robert; Kuhlemann, llyas; Meyer, Daniel; Vuong, Loan; Preiß, Helen; Herrmann, Niklas; Mann, Florian A.; Lv, Zhiyi; et al.
      Oswald, Tabea A.Spreinat, AlexanderErpenbeck, LuiseGroßhans, JörgKarius, VolkerJanshoff, AndreasPablo Giraldo, JuanKruss, Sebastian
      Nature Communications 2020; 11(1) p.1-11: Art. 1495
      Imaging of complex (biological) samples in the near-infrared (NIR) is beneficial due toreduced light scattering, absorption, phototoxicity, and autofluorescence. However, there arefew NIRfluorescent materials known and suitable for biomedical applications. Here weexfoliate the layered pigment $CaCuSi_4O_{10}$ (Egyptian Blue, EB) via ball milling and facile tipsonication into NIRfluorescent nanosheets (EB-NS). The size of EB-NS can be tailored todiameters <20 nm and heights down to 1 nm. EB-NSfluoresce at 910 nm and thefluorescenceintensity correlates with the number of $Cu^{2+}$ ions. Furthermore, EB-NS display no bleachingand high brightness compared with other NIRfluorophores. The versatility of EB-NS isdemonstrated by in-vivo single-particle tracking and microrheology measurements inDro-sophila melanogasterembryos. EB-NS can be uptaken by plants and remotely detected in alow-cost stand-off detection setup. In summary, EB-NS have the potential for a wide range ofbioimaging applications.
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    • Journal Article

      Properties of a nonlinear bath: experiments, theory, and a stochastic Prandtl–Tomlinson model 

      Müller, Boris; Berner, Johannes; Bechinger, Clemens; Krüger, Matthias
      New Journal of Physics 2020; 22(2) p.1-19: Art. 023014
      A colloidal particle is a prominent example of a stochastic system, and, if suspended in a simple viscous liquid, very closely resembles the case of an ideal random walker. A variety of new phenomena have been observed when such colloid is suspended in a viscoelastic fluid instead, for example pronounced nonlinear responses when the viscoelastic bath is driven out of equilibrium. Here, using a micron-sized particle in a micellar solution, we investigate in detail, how these nonlinear bath properties leave their fingerprints already in equilibrium measurements, for the cases where the particle is unconfined or trapped in a harmonic potential. We find that the coefficients in an effective linear (generalized) Langevin equation show intriguing inter-dependencies, which can be shown to arise only in nonlinear baths: for example, the friction memory can depend on the external potential that acts only on the colloidal particle (as recently noted in simulations of molecular tracers in water in (2017 Phys. Rev. X 7 041065)), it can depend on the mass of the colloid, or, in an overdamped setting, on its bare diffusivity. These inter-dependencies, caused by so-called fluctuation renormalizations, are seen in an exact small time expansion of the friction memory based on microscopic starting points. Using linear response theory, they can be interpreted in terms of microrheological modes of force-controlled or velocity-controlled driving. The mentioned nonlinear markers are observed in our experiments, which are astonishingly well reproduced by a stochastic Prandtl–Tomlinson model mimicking the nonlinear viscoelastic bath. The pronounced nonlinearities seen in our experiments together with the good understanding in a simple theoretical model make this system a promising candidate for exploration of colloidal motion in nonlinear stochastic environments.
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    • Journal Article

      Substrate induced nanoscale resistance variation in epitaxial graphene 

      Sinterhauf, Anna; Traeger, Georg A.; Momeni Pakdehi, Davood; Schädlich, Philip; Willke, Philip; Speck, Florian; Seyller, Thomas; Tegenkamp, Christoph; Pierz, Klaus; Schumacher, Hans Werner; et al.
      Wenderoth, Martin
      Nature Communications 2020; 11(1) p.1-9: Art. 555
      Graphene, the first true two-dimensional material, still reveals the most remarkable transport properties among the growing class of two-dimensional materials. Although many studies have investigated fundamental scattering processes, the surprisingly large variation in the experimentally determined resistances is still an open issue. Here, we quantitatively investigate local transport properties of graphene prepared by polymer assisted sublimation growth using scanning tunneling potentiometry. These samples exhibit a spatially homogeneous current density, which allows to analyze variations in the local electrochemical potential with high precision. We utilize this possibility by examining the local sheet resistance finding a significant variation of up to 270% at low temperatures. We identify a correlation of the sheet resistance with the stacking sequence of the 6H silicon carbide substrate and with the distance between the graphene and the substrate. Our results experimentally quantify the impact of the graphene-substrate interaction on the local transport properties of graphene.
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    • Journal Article

      Determinants of customer satisfaction with a true door-to-door DRT service in rural Germany 

      Avermann, Niklas; Schlüter, Jan
      Research in Transportation Business & Management 2019; 32: Art. 100420
      The effects of demographic change and the lack of acceptance represent some of the main problems for the public transport infrastructure in rural areas. As a consequence, the development of new transport service options becomes especially relevant for rural communities. The Max-Planck-Institute for Dynamics and Self-Organization developed a new form of Demand Responsive Transport the EcoBus to examine the viability of new DRT systems in rural Germany. Our work draws on customer satisfaction data during the trial runs of the EcoBus. Based on the survey data, this paper develops regression models to explain the determinants of DRT customer satisfaction. Our main findings include the importance of waiting times and the ease of entry for overall customer satisfaction. Nevertheless, we found no evidence that the presence of other guests in the vehicle had any negative impact on customer satisfaction. Findings of other works that women are significantly more likely to use DRT services could not be validated from our data.
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    • Journal Article

      Interplay between myosin II and actin dynamics in chemotactic amoeba 

      Hsu, H. F.; Krekhov, A.; Tarantola, M.; Beta, C.; Bodenschatz, E.
      New Journal of Physics 2019; 21(11): Art. 113055
      The actin cytoskeleton and its response to external chemical stimuli is fundamental to the mechano-biology of eukaryotic cells and their functions. One of the key players that governs the dynamics of theactin network is the motor protein myosin II. Based on a phase space embedding we have identifiedfrom experiments three phases in the cytoskeletal dynamics of starvedDictyostelium discoideuminresponse to a precisely controlled chemotactic stimulation. In thefirst two phases the dynamics ofactin and myosin II in the cortex is uncoupled, while in the third phase the time scale for the recoveryof cortical actin is determined by the myosin II dynamics. We report a theoretical model that capturesthe experimental observations quantitatively. The model predicts an increase in the optimal responsetime of actin with decreasing myosin II-actin coupling strength highlighting the role of myosin II inthe robust control of cell contraction.
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    • Journal Article

      To Bud or Not to Bud: A Perspective on Molecular Simulations of Lipid Droplet Budding 

      Zoni, Valeria; Nieto, Vincent; Endter, Laura J.; Risselada, Herre J.; Monticelli, Luca; Vanni, Stefano
      Frontiers in Molecular Biosciences 2019; 6: Art. 124
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    • Journal Article

      The self-organized learning of noisy environmental stimuli requires distinct phases of plasticity 

      Krüppel, Steffen; Tetzlaff, Christian
      Network Neuroscience 2020; 4(1) p.174-199
      Along sensory pathways, representations of environmental stimuli become increasingly sparse and expanded. If additionally the feed-forward synaptic weights are structured according to the inherent organization of stimuli, the increase in sparseness and expansion leads to a reduction of sensory noise. However, it is unknown how the synapses in the brain form the required structure, especially given the omnipresent noise of environmental stimuli. Here, we employ a combination of synaptic plasticity and intrinsic plasticity-adapting the excitability of each neuron individually-and present stimuli with an inherent organization to a feed-forward network. We observe that intrinsic plasticity maintains the sparseness of the neural code and thereby allows synaptic plasticity to learn the organization of stimuli in low-noise environments. Nevertheless, even high levels of noise can be handled after a subsequent phase of readaptation of the neuronal excitabilities by intrinsic plasticity. Interestingly, during this phase the synaptic structure has to be maintained. These results demonstrate that learning and recalling in the presence of noise requires the coordinated interplay between plasticity mechanisms adapting different properties of the neuronal circuit.
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    • Journal Article

      Ultrafast optically induced spin transfer in ferromagnetic alloys 

      Hofherr, M.; Häuser, S.; Dewhurst, J. K.; Tengdin, P.; Sakshath, S.; Nembach, H. T.; Weber, S. T.; Shaw, J. M.; Silva, T. J.; Kapteyn, H. C.; et al.
      Cinchetti, M.Rethfeld, B.Murnane, M. M.Steil, D.Stadtmüller, B.Sharma, S.Aeschlimann, M.Mathias, S.
      Science Advances 2020; 6(3): Art. eaay8717
      The vision of using light to manipulate electronic and spin excitations in materials on their fundamental time and length scales requires new approaches in experiment and theory to observe and understand these excitations. The ultimate speed limit for all-optical manipulation requires control schemes for which the electronic or magnetic subsystems of the materials are coherently manipulated on the time scale of the laser excitation pulse. In our work, we provide experimental evidence of such a direct, ultrafast, and coherent spin transfer between two magnetic subsystems of an alloy of Fe and Ni. Our experimental findings are fully supported by time-dependent density functional theory simulations and, hence, suggest the possibility of coherently controlling spin dynamics on subfemtosecond time scales, i.e., the birth of the research area of attomagnetism.
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    • Journal Article

      Microtiming Deviations and Swing Feel in Jazz 

      Datseris, George; Ziereis, Annika; Albrecht, Thorsten; Hagmayer, York; Priesemann, Viola; Geisel, Theo
      Scientific Reports 2019; 9(1): Art. 19824
      Jazz music that swings has the fascinating power to elicit a pleasant sensation of flow in listeners and the desire to synchronize body movements with the music. Whether microtiming deviations (MTDs), i.e. small timing deviations below the bar or phrase level, enhance the swing feel is highly debated in the current literature. Studies on other groove related genres did not find evidence for a positive impact of MTDs. The present study addresses jazz music and swing in particular, as there is some evidence that microtiming patterns are genre-specific. We recorded twelve piano jazz standards played by a professional pianist and manipulated the natural MTDs of the recordings in systematic ways by quantizing, expanding and inverting them. MTDs were defined with respect to a grid determined by the average swing ratio. The original and manipulated versions were presented in an online survey and evaluated by 160 listeners with various musical skill levels and backgrounds. Across pieces the quantized versions (without MTDs) were rated slightly higher and versions with expanded MTDs were rated lower with regard to swing than the original recordings. Unexpectedly, inversion had no impact on swing ratings except for two pieces. Our results suggest that naturally fluctuating MTDs are not an essential factor for the swing feel.
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    • Journal Article

      Time-evolution methods for matrix-product states 

      Paeckel, Sebastian; Köhler, Thomas; Swoboda, Andreas; Manmana, Salvatore R.; Schollwöck, Ulrich; Hubig, Claudius
      Annals of Physics 2019; 411: Art. 167998
      Matrix-product states have become the de facto standard for the representation of one-dimensional quantum many body states. During the last few years, numerous new methods have been introduced to evaluate the time evolution of a matrix-product state. Here, we will review and summarize the recent work on this topic as applied to finite quantum systems. We will explain and compare the different methods available to construct a time-evolved matrix-product state, namely the time-evolving block decimation, the MPO method, the global Krylov method, the local Krylov method and the one- and two-site time-dependent variational principle. We will also apply these methods to four different representative examples of current problem settings in condensed matter physics.
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