TY - JOUR A1 - Cherstvy, Andrey G. A1 - Wang, Wei A1 - Metzler, Ralf A1 - Sokolov, Igor M. T1 - Inertia triggers nonergodicity of fractional Brownian motion JF - Physical review : E, Statistical, nonlinear and soft matter physics N2 - How related are the ergodic properties of the over- and underdamped Langevin equations driven by fractional Gaussian noise? We here find that for massive particles performing fractional Brownian motion (FBM) inertial effects not only destroy the stylized fact of the equivalence of the ensemble-averaged mean-squared displacement (MSD) to the time-averaged MSD (TAMSD) of overdamped or massless FBM, but also dramatically alter the values of the ergodicity-breaking parameter (EB). Our theoretical results for the behavior of EB for underdamped or massive FBM for varying particle mass m, Hurst exponent H, and trace length T are in excellent agreement with the findings of stochastic computer simulations. The current results can be of interest for the experimental community employing various single-particle-tracking techniques and aiming at assessing the degree of nonergodicity for the recorded time series (studying, e.g., the behavior of EB versus lag time). To infer FBM as a realizable model of anomalous diffusion for a set single-particle-tracking data when massive particles are being tracked, the EBs from the data should be compared to EBs of massive (rather than massless) FBM. Y1 - 2021 U6 - https://doi.org/10.1103/PhysRevE.104.024115 SN - 2470-0045 SN - 2470-0053 VL - 104 IS - 2 PB - American Physical Society CY - College Park ER - TY - JOUR A1 - Zhao, Yuhang A1 - Opitz, Andreas A1 - Eljarrat, Alberto A1 - Kochovski, Zdravko A1 - Koch, Christoph A1 - Koch, Norbert A1 - Lu, Yan T1 - Kinetic study on the adsorption of 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane on Ag nanoparticles in chloroform BT - implications for the charge transfer complex of Ag-F(4)TCNQ JF - ACS applied nano materials N2 - In this study, the kinetics of the adsorption of 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F(4)TCNQ) on the surface of Ag nanoparticles (Ag NPs) in chloroform has been intensively investigated, as molecular doping is known to play a crucial role in organic electronic devices. Based on the results obtained from UV-visible (vis)-near-infrared (NIR) absorption spectroscopy, cryogenic transmission electron microscopy, scanning nanobeam electron diffraction, and electron energy loss spectroscopy, a two-step interaction kinetics has been proposed for the Ag NPs and F(4)TCNQ molecules, which includes the first step of electron transfer from Ag NPs to F(4)TCNQ indicated by the ionization of F(4)TCNQ and the second step of the formation of a Ag-F(4)TCNQ complex. The whole process has been followed via UV-vis-NIR absorption spectroscopy, which reveals distinct kinetics at two stages: the instantaneous ionization and the long-term complex formation. The kinetics and the influence of the molar ratio of Ag NPs/F(4)TCNQ molecules on the interaction between Ag NPs and F(4)TCNQ molecules in an organic solution are reported herein for the first time. Furthermore, the control experiment with silica-coated Ag NPs manifests that the charge transfer at the surface between Ag NPs and F(4)TCNQ molecules is prohibited by a silica layer of 18 nm. KW - Ag nanoparticles KW - F(4)TCNQ KW - phase transfer KW - kinetics KW - electron transfer KW - surface interaction Y1 - 2021 U6 - https://doi.org/10.1021/acsanm.1c02153 SN - 2574-0970 VL - 4 IS - 11 SP - 11625 EP - 11635 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Zhu, Chuanbin A1 - Cotton, Fabrice A1 - Kwak, Dong-Youp A1 - Ji, Kun A1 - Kawase, Hiroshi A1 - Pilz, Marco T1 - Within-site variability in earthquake site response JF - Geophysical journal international N2 - The within-site variability in site response is the randomness in site response at a given site from different earthquakes and is treated as aleatory variability in current seismic hazard/risk analyses. In this study, we investigate the single-station variability in linear site response at K-NET and KiK-net stations in Japan using a large number of earthquake recordings. We found that the standard deviation of the horizontal-to-vertical Fourier spectral ratio at individual sites, that is single-station horizontal-to-vertical spectral ratio (HVSR) sigma sigma(HV,s), approximates the within-site variability in site response quantified using surface-to-borehole spectral ratios (for oscillator frequencies higher than the site fundamental frequency) or empirical ground-motion models. Based on this finding, we then utilize the single-station HVSR sigma as a convenient tool to study the site-response variability at 697 KiK-net and 1169 K-NET sites. Our results show that at certain frequencies, stiff, rough and shallow sites, as well as small and local events tend to have a higher sigma(HV,s). However, when being averaged over different sites, the single-station HVSR sigma, that is sigma(HV), increases gradually with decreasing frequency. In the frequency range of 0.25-25 Hz, sigma(HV) is centred at 0.23-0.43 in ln scales (a linear scale factor of 1.26-1.54) with one standard deviation of less than 0.1. sigma(HV) is quite stable across different tectonic regions, and we present a constant, as well as earthquake magnitude- and distance-dependent sigma(HV) models. KW - earthquake ground motions KW - earthquake hazards KW - site effects Y1 - 2021 U6 - https://doi.org/10.1093/gji/ggab481 SN - 0956-540X SN - 1365-246X VL - 229 IS - 2 SP - 1268 EP - 1281 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Klett, Kolja A1 - Cherstvy, Andrey G. A1 - Shin, Jaeoh A1 - Sokolov, Igor M. A1 - Metzler, Ralf T1 - Non-Gaussian, transiently anomalous, and ergodic self-diffusion of flexible dumbbells in crowded two-dimensional environments BT - coupled translational and rotational motions JF - Physical review : E, Statistical, nonlinear and soft matter physics N2 - We employ Langevin-dynamics simulations to unveil non-Brownian and non-Gaussian center-of-mass self-diffusion of massive flexible dumbbell-shaped particles in crowded two-dimensional solutions. We study the intradumbbell dynamics of the relative motion of the two constituent elastically coupled disks. Our main focus is on effects of the crowding fraction phi and of the particle structure on the diffusion characteristics. We evaluate the time-averaged mean-squared displacement (TAMSD), the displacement probability-density function (PDF), and the displacement autocorrelation function (ACF) of the dimers. For the TAMSD at highly crowded conditions of dumbbells, e.g., we observe a transition from the short-time ballistic behavior, via an intermediate subdiffusive regime, to long-time Brownian-like spreading dynamics. The crowded system of dimers exhibits two distinct diffusion regimes distinguished by the scaling exponent of the TAMSD, the dependence of the diffusivity on phi, and the features of the displacement-ACF. We attribute these regimes to a crowding-induced transition from viscous to viscoelastic diffusion upon growing phi. We also analyze the relative motion in the dimers, finding that larger phi suppress their vibrations and yield strongly non-Gaussian PDFs of rotational displacements. For the diffusion coefficients D(phi) of translational and rotational motion of the dumbbells an exponential decay with phi for weak and a power-law variation D(phi) proportional to (phi - phi(star))(2.4) for strong crowding is found. A comparison of simulation results with theoretical predictions for D(phi) is discussed and some relevant experimental systems are overviewed. Y1 - 2021 U6 - https://doi.org/10.1103/PhysRevE.104.064603 SN - 2470-0045 SN - 2470-0053 VL - 104 IS - 6 PB - American Physical Society CY - College Park ER - TY - JOUR A1 - Simon, François-Xavier A1 - Papadopoulos, Nikos A1 - Guillemoteau, Julien A1 - Oikonomou, Dimitris A1 - Simirdanis, Kleanthis T1 - Multi-frequency loop electromagnetic system measurement on shallow offshore archaeological site of Oulos JF - ArcheoSciences : revue d'archéométrie / Groupe des Méthodes Pluridisciplinaires Contribuant à l'Archéologie (GMPCA) KW - hallow offshore KW - multi-frequency KW - electromagnetic KW - modelling KW - case study Y1 - 2021 U6 - https://doi.org/10.4000/archeosciences.9690 SN - 1960-1360 SN - 2104-3728 VL - 45 IS - 1 SP - 215 EP - 218 PB - Presses Universitaires de Rennes CY - Rennes ER - TY - JOUR A1 - Bolotov, Maxim I. A1 - Smirnov, Lev A. A1 - Bubnova, E. S. A1 - Osipov, Grigory V. A1 - Pikovskij, Arkadij T1 - Spatiotemporal regimes in the Kuramoto-Battogtokh system of nonidentical oscillators JF - Journal of experimental and theoretical physics N2 - We consider the spatiotemporal states of an ensemble of nonlocally coupled nonidentical phase oscillators, which correspond to different regimes of the long-term evolution of such a system. We have obtained homogeneous, twisted, and nonhomogeneous stationary solutions to the Ott-Antonsen equations corresponding to key variants of the realized collective rotational motion of elements of the medium in question with nonzero mesoscopic characteristics determining the degree of coherence of the dynamics of neighboring particles. We have described the procedures of the search for the class of nonhomogeneous solutions as stationary points of the auxiliary point map and of determining the stability based on analysis of the eigenvalue spectrum of the composite operator. Static and breather cluster regimes have been demonstrated and described, as well as the regimes with an irregular behavior of averaged complex fields including, in particular, the local order parameter. Y1 - 2021 U6 - https://doi.org/10.1134/S1063776121010106 SN - 1063-7761 SN - 1090-6509 VL - 132 IS - 1 SP - 127 EP - 147 PB - Springer CY - Heidelberg [u.a.] ER - TY - GEN A1 - Jauer, Nora A1 - Batura, Justine T1 - Don’t settle for less Y1 - 2021 UR - https://voelkerrechtsblog.org/dont-settle-for-less/ U6 - https://doi.org/10.17176/20210422-100928-0 SN - 2510-2567 PB - M. Riegner c/o Humboldt-Univ. CY - Berlin ER - TY - JOUR A1 - Omranian, Sara A1 - Angeleska, Angela A1 - Nikoloski, Zoran T1 - PC2P BT - parameter-free network-based prediction of protein complexes JF - Bioinformatics N2 - Motivation: Prediction of protein complexes from protein-protein interaction (PPI) networks is an important problem in systems biology, as they control different cellular functions. The existing solutions employ algorithms for network community detection that identify dense subgraphs in PPI networks. However, gold standards in yeast and human indicate that protein complexes can also induce sparse subgraphs, introducing further challenges in protein complex prediction. Results: To address this issue, we formalize protein complexes as biclique spanned subgraphs, which include both sparse and dense subgraphs. We then cast the problem of protein complex prediction as a network partitioning into biclique spanned subgraphs with removal of minimum number of edges, called coherent partition. Since finding a coherent partition is a computationally intractable problem, we devise a parameter-free greedy approximation algorithm, termed Protein Complexes from Coherent Partition (PC2P), based on key properties of biclique spanned subgraphs. Through comparison with nine contenders, we demonstrate that PC2P: (i) successfully identifies modular structure in networks, as a prerequisite for protein complex prediction, (ii) outperforms the existing solutions with respect to a composite score of five performance measures on 75% and 100% of the analyzed PPI networks and gold standards in yeast and human, respectively, and (iii,iv) does not compromise GO semantic similarity and enrichment score of the predicted protein complexes. Therefore, our study demonstrates that clustering of networks in terms of biclique spanned subgraphs is a promising framework for detection of complexes in PPI networks. Y1 - 2021 U6 - https://doi.org/10.1093/bioinformatics/btaa1089 SN - 1367-4803 SN - 1460-2059 VL - 37 IS - 1 SP - 73 EP - 81 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Tavakoli, Hamad A1 - Alirezazadeh, Pendar A1 - Hedayatipour, Ava A1 - Nasib, A. H. Banijamali A1 - Landwehr, Niels T1 - Leaf image-based classification of some common bean cultivars using discriminative convolutional neural networks JF - Computers and electronics in agriculture : COMPAG online ; an international journal N2 - In recent years, many efforts have been made to apply image processing techniques for plant leaf identification. However, categorizing leaf images at the cultivar/variety level, because of the very low inter-class variability, is still a challenging task. In this research, we propose an automatic discriminative method based on convolutional neural networks (CNNs) for classifying 12 different cultivars of common beans that belong to three various species. We show that employing advanced loss functions, such as Additive Angular Margin Loss and Large Margin Cosine Loss, instead of the standard softmax loss function for the classification can yield better discrimination between classes and thereby mitigate the problem of low inter-class variability. The method was evaluated by classifying species (level I), cultivars from the same species (level II), and cultivars from different species (level III), based on images from the leaf foreside and backside. The results indicate that the performance of the classification algorithm on the leaf backside image dataset is superior. The maximum mean classification accuracies of 95.86, 91.37 and 86.87% were obtained at the levels I, II and III, respectively. The proposed method outperforms the previous relevant works and provides a reliable approach for plant cultivars identification. KW - Bean KW - Plant identification KW - Digital image analysis KW - VGG16 KW - Loss KW - functions Y1 - 2021 U6 - https://doi.org/10.1016/j.compag.2020.105935 SN - 0168-1699 SN - 1872-7107 VL - 181 PB - Elsevier CY - Amsterdam [u.a.] ER - TY - JOUR A1 - Ben Dor, Yoav A1 - Flax, Tomer A1 - Levitan, Itamar A1 - Enzel, Yehouda A1 - Brauer, Achim A1 - Erel, Yigal T1 - The paleohydrological implications of aragonite precipitation under contrasting climates in the endorheic Dead Sea and its precursors revealed by experimental investigations JF - Chemical geology : official journal of the European Association for Geochemistry N2 - Carbonate minerals are common in both marine and lacustrine records, and are frequently used for paleoenvironmental reconstructions. The sedimentary sequence of the endorheic Dead Sea and its precursors contain aragonite laminae that provide a detailed sedimentary archive of climatic, hydrologic, limnologic and environmental conditions since the Pleistocene. However, the interpretation of these archives requires a detailed understanding of the constraints and mechanisms affecting CaCO3 precipitation, which are still debated. The implications of aragonite precipitation in the Dead Sea and in its late Pleistocene predecessor (Lake Lisan) were investigated in this study by mixing natural and synthetic brines with a synthetic bicarbonate solution that mimics flash-floods composition, with and without the addition of extracellular polymeric substances (EPS). Aragonite precipitation was monitored, and precipitation rates and carbonate yields were calculated and are discussed with respect to modern aquatic environments. The experimental insights on aragonite precipitation are then integrated with microfacies analyses in order to reconstruct and constrain prevailing limnogeological processes and their hydroclimatic drivers under low (interglacial) and high (glacial) lake level stands. Aragonite precipitation took place within days to several weeks after the mixing of the brines with a synthetic bicarbonate solution. Incubation time was proportional to bicarbonate concentration, and precipitation rates were partially influenced by ionic strength. Additionally, extracellular polymeric substances inhibited aragonite precipitation for several months. As for the lake's water budget, our calculations suggest that the precipitation of a typical aragonite lamina (0.5 mm thick) during high lake stand requires unreasonable freshwater inflow from either surface or subsurface sources. This discrepancy can be resolved by considering one or a combination of the following scenarios; (1) discontinuous aragonite deposition over parts of the lake floor; (2) supply of additional carbonate flux (or fluxes) to the lake from aeolian dust and the remobilization and dissolution of dust deposits at the watershed; (3) carbonate production via oxidation of organic carbon by sulfate-reducing bacteria. Altogether, it is suggested that aragonite laminae thickness cannot be directly interpreted for quantitatively reconstructing the hydrological balance for the entire lake, they may still prove valuable for identifying inherent hydroclimatic periodicities at a single site. KW - Dead Sea KW - Lake Lisan KW - Aragonite KW - Varves KW - Paleolimnology KW - Paleohydrology KW - Dead Sea deep drilling project KW - EPS KW - Extracellular polymeric substances KW - Levant climate KW - Eastern Mediterranean KW - Paleoclimate KW - Lacustrine carbonate Y1 - 2021 U6 - https://doi.org/10.1016/j.chemgeo.2021.120261 SN - 0009-2541 SN - 1872-6836 VL - 576 PB - Elsevier CY - Amsterdam ER -