@article{SorgenfreiGiangrisostomiKuehnetal.2022, author = {Sorgenfrei, Nomi and Giangrisostomi, Erika and K{\"u}hn, Danilo and Ovsyannikov, Ruslan and F{\"o}hlisch, Alexander}, title = {Time and angle-resolved time-of-flight electron spectroscopy for functional materials science}, series = {Molecules : a journal of synthetic chemistry and natural product chemistry}, volume = {27}, journal = {Molecules : a journal of synthetic chemistry and natural product chemistry}, number = {24}, publisher = {MDPI}, address = {Basel}, issn = {1420-3049}, doi = {10.3390/molecules27248833}, pages = {14}, year = {2022}, abstract = {Electron spectroscopy with the unprecedented transmission of angle-resolved time-of-flight detection, in combination with pulsed X-ray sources, brings new impetus to functional materials science. We showcase recent developments towards chemical sensitivity from electron spectroscopy for chemical analysis and structural information from photoelectron diffraction using the phase transition properties of 1T-TaS2. Our development platform is the SurfaceDynamics instrument located at the Femtoslicing facility at BESSY II, where femtosecond and picosecond X-ray pulses can be generated and extracted. The scientific potential is put into perspective to the current rapidly developing pulsed X-ray source capabilities from Lasers and Free-Electron Lasers.}, language = {en} } @article{GrasslRitterSchulz2022, author = {Grassl, Sandra and Ritter, Christoph and Schulz, Alexander}, title = {The nature of the Ny-Alesund wind field analysed by high-resolution windlidar data}, series = {Remote sensing}, volume = {14}, journal = {Remote sensing}, number = {15}, publisher = {MDPI}, address = {Basel}, issn = {2072-4292}, doi = {10.3390/rs14153771}, pages = {24}, year = {2022}, abstract = {In this work we present windlidar data for the research village Ny-Alesund located on Svalbard in the European Arctic (78.923 degrees N, 11.928 degrees F) from 2013 to 2021. The data have a resolution of 50 m and 10 min with an overlapping height of about 150 m. The maximum range depends on the meteorologic situation. Up to 1000 m altitude the data availability is better than 71\%. We found that the highest wind speeds occur in November and December, the lowest ones in June and July, up to 500 m altitude the wind is channelled strongly in ESE to NW direction parallel to the fjord axis and the synoptic conditions above 1000 m altitude already dominate. While the fraction of windy days (v > 10 m/s) varies significantly from month to month, there is no overall trend of the wind visible in our data set. We define gusts and jets by the requirement of wind maxima v > 2 m/s above and below a wind maximum. In total, more than 24,000 of these events were identified (corresponding to 6\% of the time), of which 223 lasted for at least 100 min ("Long Jets"). All of these events are fairly equally distributed over the months relatively to the available data. Further, gusts and jets follow different distributions (in terms of altitude or depths) and occur more frequently for synoptic flow from roughly a southerly direction. Jets do not show a clear correlation between occurrence and synoptic flow. Gusts and jets are not related to cloud cover. We conclude that the atmosphere from 400 m to 1000 m above Ny-Alesund is dominated by a turbulent wind shear zone, which connects the micrometeorology in the atmospheric boundary layer (ABL) with the synoptic flow.}, language = {en} } @article{LeproGrossmannPanahetal.2022, author = {Lepro, Valentino and Großmann, Robert and Panah, Setareh Sharifi and Nagel, Oliver and Klumpp, Stefan and Lipowsky, Reinhard and Beta, Carsten}, title = {Optimal cargo size for active diffusion of biohybrid microcarriers}, series = {Physical Review Applied}, volume = {18}, journal = {Physical Review Applied}, number = {3}, publisher = {American Physical Society}, address = {College Park}, issn = {2331-7019}, doi = {10.1103/PhysRevApplied.18.034014}, pages = {13}, year = {2022}, abstract = {As society paves its way towards device miniaturization and precision medicine, microscale actuation and transport become increasingly prominent research fields with high impact in both technological and clinical contexts. In order to accomplish movement of micron-sized objects towards specific target sites, active biohybrid transport systems, such as motile living cells that act as smart biochemically powered microcarriers, have been suggested as an alternative to synthetic microrobots. Inspired by the motility of leukocytes, we propose the amoeboid crawling of eukaryotic cells as a promising mechanism for transport of micron-sized cargoes and present an in-depth study of this type of composite active matter. Its transport properties result from the interactions of an active element (cell) and a passive one (cargo) and reveal an optimal cargo size that enhances the locomotion of the load-carrying cells, even exceeding their motility in the absence of cargo. The experimental findings are rationalized in terms of a biohybrid active particle model that describes the emergent cell-cargo dynamics and enables us to derive the long-time diffusive transport of amoeboid microcarriers. As amoeboid locomotion is commonly observed for mammalian cells such as leukocytes, our results lay the foundations for the study of transport performance of other medically relevant cell types and for extending our findings to more advanced transport tasks in complex environments, such as tissues.}, language = {en} } @article{YanLiangXu2022, author = {Yan, Shengjie and Liang, Yingjie and Xu, Wei}, title = {Characterization of chloride ions diffusion in concrete using fractional Brownian motion run with power law clock}, series = {Fractals : complex geometry, patterns, and scaling in nature and society}, volume = {30}, journal = {Fractals : complex geometry, patterns, and scaling in nature and society}, number = {9}, publisher = {World Scient. Publ.}, address = {Singapore [u.a.]}, issn = {0218-348X}, doi = {10.1142/S0218348X22501778}, pages = {9}, year = {2022}, abstract = {In this paper, we propose a revised fractional Brownian motion run with a nonlinear clock (fBm-nlc) model and utilize it to illustrate the microscopic mechanism analysis of the fractal derivative diffusion model with variable coefficient (VC-FDM). The power-law mean squared displacement (MSD) links the fBm-nlc model and the VC-FDM via the two-parameter power law clock and the Hurst exponent is 0.5. The MSD is verified by using the experimental points of the chloride ions diffusion in concrete. When compared to the linear Brownian motion, the results show that the power law MSD of the fBm-nlc is much better in fitting the experimental points of chloride ions in concrete. The fBm-nlc clearly interprets the VC-FDM and provides a microscopic strategy in characterizing different types of non-Fickian diffusion processes with more different nonlinear functions.}, language = {en} } @article{SavchenkoLomadzeSanteretal.2022, author = {Savchenko, Vladyslav and Lomadze, Nino and Santer, Svetlana and Guskova, Olga}, title = {Spiropyran/merocyanine amphiphile in various solvents}, series = {International journal of molecular sciences}, volume = {23}, journal = {International journal of molecular sciences}, number = {19}, publisher = {MDPI}, address = {Basel}, issn = {1422-0067}, doi = {10.3390/ijms231911535}, pages = {24}, year = {2022}, abstract = {This joint experimental-theoretical work focuses on molecular and photophysical properties of the spiropyran-containing amphiphilic molecule in organic and aqueous solutions. Being dissolved in tested organic solvents, the system demonstrates positive photochromism, i.e., upon UV stimulus the colorless spiropyran form is transformed into colorful merocyanine isomer. However, the aqueous solution of the amphiphile possesses a negative photochromism: the orange-red merocyanine form becomes thermodynamically more stable in water, and both UV and vis stimuli lead to the partial or complete photobleaching of the solution. The explanation of this phenomenon is given on the basis of density functional theory calculations and classical modeling including thermodynamic integration. The simulations reveal that stabilization of merocyanine in water proceeds with the energy of ca. 70 kJ mol-1, and that the Helmholtz free energy of hydration of merocyanine form is 100 kJ mol-1 lower as compared to the behavior of SP isomer in water. The explanation of such a difference lies in the molecular properties of the merocyanine: after ring-opening reaction this molecule transforms into a zwitterionic form, as evidenced by the electrostatic potential plotted around the opened form. The presence of three charged groups on the periphery of a flat conjugated backbone stimulates the self-assembly of merocyanine molecules in water, ending up with the formation of elongated associates with stack-like building blocks, as shown in molecular dynamics simulations of the aqueous solution with the concentration above critical micelle concentration. Our quantitative evaluation of the hydrophilicity switching in spiropyran/merocyanine containing surfactants may prompt the search for new systems, including colloidal and polymeric ones, aiming at remote tuning of their morphology, which could give new promising shapes and patterns for the needs of modern nanotechnology.}, language = {en} } @article{OdziomekGiustoKossmannetal.2022, author = {Odziomek, Mateusz and Giusto, Paolo and Kossmann, Janina and Tarakina, Nadezda and Heske, Julian and Rivadeneira, Salvador M. and Keil, Waldemar and Schmidt, Claudia and Mazzanti, Stefano and Savateev, Oleksandr and Perdigon-Toro, Lorena and Neher, Dieter and K{\"u}hne, Thomas D. and Antonietti, Markus and Lopez-Salas, Nieves}, title = {"Red Carbon": a rediscovered covalent crystalline semiconductor}, series = {Advanced materials}, volume = {34}, journal = {Advanced materials}, number = {40}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {0935-9648}, doi = {10.1002/adma.202206405}, pages = {13}, year = {2022}, abstract = {Carbon suboxide (C3O2) is a unique molecule able to polymerize spontaneously into highly conjugated light-absorbing structures at temperatures as low as 0 degrees C. Despite obvious advantages, little is known about the nature and the functional properties of this carbonaceous material. In this work, the aim is to bring "red carbon," a forgotten polymeric semiconductor, back to the community's attention. A solution polymerization process is adapted to simplify the synthesis and control the structure. This allows one to obtain this crystalline covalent material at low temperatures. Both spectroscopic and elemental analyses support the chemical structure represented as conjugated ladder polypyrone ribbons. Density functional theory calculations suggest a crystalline structure of AB stacks of polypyrone ribbons and identify the material as a direct bandgap semiconductor with a medium bandgap that is further confirmed by optical analysis. The material shows promising photocatalytic performance using blue light. Moreover, the simple condensation-aromatization route described here allows the straightforward fabrication of conjugated ladder polymers and can be inspiring for the synthesis of carbonaceous materials at low temperatures in general.}, language = {en} } @article{YochelisFlemmingBeta2022, author = {Yochelis, Arik and Flemming, Sven and Beta, Carsten}, title = {Versatile patterns in the actin cortex of motile cells}, series = {Physical review letters}, volume = {129}, journal = {Physical review letters}, number = {8}, publisher = {American Physical Society}, address = {College Park}, issn = {0031-9007}, doi = {10.1103/PhysRevLett.129.088101}, pages = {6}, year = {2022}, abstract = {Self-organized patterns in the actin cytoskeleton are essential for eukaryotic cellular life. They are the building blocks of many functional structures that often operate simultaneously to facilitate, for example, nutrient uptake and movement of cells. However, identifying how qualitatively distinct actin patterns can coexist remains a challenge. Using bifurcation theory of a mass conserved activator-inhibitor system, we uncover a generic mechanism of how different actin waves-traveling waves and excitable pulses- organize and simultaneously emerge. Live-cell imaging experiments indeed reveal that narrow, planar, and fast-moving excitable pulses may coexist with ring-shaped macropinocytic actin waves in the cortex of motile amoeboid cells.}, language = {en} } @article{VazdaCruzMascarenhasBuechneretal.2022, author = {Vaz da Cruz, Vinicius and Mascarenhas, Eric J. and B{\"u}chner, Robby and Jay, Raphael M. and Fondell, Mattis and Eckert, Sebastian and Foehlisch, Alexander}, title = {Metal-water covalency in the photo-aquated ferrocyanide complex as seen by multi-edge picosecond X-ray absorption}, series = {Physical chemistry, chemical physics : a journal of European Chemical Societies}, volume = {24}, journal = {Physical chemistry, chemical physics : a journal of European Chemical Societies}, number = {45}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1463-9076}, doi = {10.1039/d2cp04084k}, pages = {27819 -- 27826}, year = {2022}, abstract = {In this work, we investigate the photo-aquation reaction of the ferrocyanide anion with multi-edge picosecond soft X-ray spectroscopy. Combining the information of the iron L-edge with nitrogen and oxygen K-edges, we carry out a complete characterization of the bonding channels in the [Fe(CN)(5)(H2O)](3-) photo-product. We observe clear spectral signatures of covalent bonding between water and the metal, reflecting the mixing of the Fe d(z)(2) orbital with the 3a(1) and 4a(1) orbitals of H2O. Additional fingerprints related to the symmetry reduction and the resulting loss in orbital degeneracy are also reported. The implications of the elucidated fingerprints in the context of future ultra-fast experiments are also discussed.}, language = {en} } @article{BohdanWeidlMorrisetal.2022, author = {Bohdan, Artem and Weidl, Martin S. and Morris, Paul J. and Pohl, Martin}, title = {The electron foreshock at high-Mach-number non-relativistic oblique shocks}, series = {Physics of plasmas}, volume = {29}, journal = {Physics of plasmas}, number = {5}, publisher = {AIP Publishing}, address = {Melville}, issn = {1070-664X}, doi = {10.1063/5.0084544}, pages = {13}, year = {2022}, abstract = {In the Universe, matter outside of stars and compact objects is mostly composed of collisionless plasma. The interaction of a supersonic plasma flow with an obstacle results in collisionless shocks that are often associated with intense nonthermal radiation and the production of cosmic ray particles. Motivated by simulations of non-relativistic high-Mach-number shocks in supernova remnants, we investigate the instabilities excited by relativistic electron beams in the extended foreshock of oblique shocks. The phase-space distributions in the inner and outer foreshock regions are derived with a particle-in-cell simulation of the shock and used as initial conditions for simulations with periodic boundary conditions to study their relaxation toward equilibrium. We find that the observed electron-beam instabilities agree very well with the predictions of a linear dispersion analysis: the electrostatic electron-acoustic instability dominates in the outer region of the foreshock, while the denser electron beams in the inner foreshock drive the gyroresonant oblique-whistler instability.}, language = {en} } @article{JeonChechkinMetzler2014, author = {Jeon, Jae-Hyung and Chechkin, Aleksei and Metzler, Ralf}, title = {Scaled Brownian motion: a paradoxical process with a time dependent diffusivity for the description of anomalous diffusion}, series = {Physical chemistry, chemical physics : PCCP}, volume = {30}, journal = {Physical chemistry, chemical physics : PCCP}, number = {16}, publisher = {The Royal Society of Chemistry}, address = {Cambridge}, doi = {10.1039/C4CP02019G}, pages = {15811 -- 15817}, year = {2014}, abstract = {Anomalous diffusion is frequently described by scaled Brownian motion (SBM){,} a Gaussian process with a power-law time dependent diffusion coefficient. Its mean squared displacement is ?x2(t)? [similar{,} equals] 2K(t)t with K(t) [similar{,} equals] t[small alpha]-1 for 0 < [small alpha] < 2. SBM may provide a seemingly adequate description in the case of unbounded diffusion{,} for which its probability density function coincides with that of fractional Brownian motion. Here we show that free SBM is weakly non-ergodic but does not exhibit a significant amplitude scatter of the time averaged mean squared displacement. More severely{,} we demonstrate that under confinement{,} the dynamics encoded by SBM is fundamentally different from both fractional Brownian motion and continuous time random walks. SBM is highly non-stationary and cannot provide a physical description for particles in a thermalised stationary system. Our findings have direct impact on the modelling of single particle tracking experiments{,} in particular{,} under confinement inside cellular compartments or when optical tweezers tracking methods are used.}, language = {en} } @article{MetzlerCherstvyChechkinetal.2015, author = {Metzler, Ralf and Cherstvy, Andrey G. and Chechkin, Aleksei and Bodrova, Anna S.}, title = {Ultraslow scaled Brownian motion}, series = {New journal of physics : the open-access journal for physics}, volume = {17}, journal = {New journal of physics : the open-access journal for physics}, number = {063038}, publisher = {Dt. Physikalische Ges., IOP}, address = {Bad Honnef, London}, issn = {1367-2630}, doi = {10.1088/1367-2630/17/6/063038}, year = {2015}, abstract = {We define and study in detail utraslow scaled Brownian motion (USBM) characterized by a time dependent diffusion coefficient of the form . For unconfined motion the mean squared displacement (MSD) of USBM exhibits an ultraslow, logarithmic growth as function of time, in contrast to the conventional scaled Brownian motion. In a harmonic potential the MSD of USBM does not saturate but asymptotically decays inverse-proportionally to time, reflecting the highly non-stationary character of the process. We show that the process is weakly non-ergodic in the sense that the time averaged MSD does not converge to the regular MSD even at long times, and for unconfined motion combines a linear lag time dependence with a logarithmic term. The weakly non-ergodic behaviour is quantified in terms of the ergodicity breaking parameter. The USBM process is also shown to be ageing: observables of the system depend on the time gap between initiation of the test particle and start of the measurement of its motion. Our analytical results are shown to agree excellently with extensive computer simulations.}, language = {en} } @article{DebMolhoBarbara2021, author = {Deb, Marwan and Molho, Pierre and Barbara, Bernard}, title = {Tunable exchange-bias-like effect in bi-substituted Gadolinium iron garnet film}, series = {Physical review applied}, volume = {15}, journal = {Physical review applied}, number = {5}, publisher = {American Physical Society}, address = {College Park}, issn = {2331-7019}, doi = {10.1103/PhysRevApplied.15.054064}, pages = {7}, year = {2021}, abstract = {Using magneto-optical Faraday and Kerr measurements, we investigate the magnetic and magnetooptical properties of a thick Bi-substituted gadolinium iron garnet film over a broad range of wavelengths (250-850 nm) and temperatures (150-300 K), including the magnetization compensation point, TM. We observe an exchange-bias-like effect in the vicinity of TM. By slightly changing the sample temperature, we can precisely tune the bias field, which reaches a magnitude 6 times higher than the coercive field. We explain this phenomenon by considering the short-range superexchange interaction and a change in the magnetic behavior when moving from the surface to the bulk of the film. This finding may lead to the development of single-film magneto-optical devices based on the exchange-bias effect.}, language = {en} } @article{MeyerCherstvySeckleretal.2023, author = {Meyer, Philipp and Cherstvy, Andrey G. and Seckler, Henrik and Hering, Robert and Blaum, Niels and Jeltsch, Florian and Metzler, Ralf}, title = {Directedeness, correlations, and daily cycles in springbok motion}, series = {Physical review research}, volume = {5}, journal = {Physical review research}, number = {4}, publisher = {APS}, address = {College Park}, issn = {2643-1564}, doi = {10.1103/PhysRevResearch.5.043129}, pages = {17}, year = {2023}, abstract = {How predictable is the next move of an animal? Specifically, which factors govern the short- and long-term motion patterns and the overall dynamics of land-bound, plant-eating animals in general and ruminants in particular? To answer this question, we here study the movement dynamics of springbok antelopes Antidorcas marsupialis. We propose several complementary statistical-analysis techniques combined with machine-learning approaches to analyze—across multiple time scales—the springbok motion recorded in long-term GPS tracking of collared springboks at a private wildlife reserve in Namibia. As a result, we are able to predict the springbok movement within the next hour with a certainty of about 20\%. The remaining about 80\% are stochastic in nature and are induced by unaccounted factors in the modeling algorithm and by individual behavioral features of springboks. We find that directedness of motion contributes approximately 17\% to this predicted fraction. We find that the measure for directedeness is strongly dependent on the daily cycle of springbok activity. The previously known daily affinity of springboks to their water points, as predicted from our machine-learning algorithm, overall accounts for only about 3\% of this predicted deterministic component of springbok motion. Moreover, the resting points are found to affect the motion of springboks at least as much as the formally studied effects of water points. The generality of these statements for the motion patterns and their underlying behavioral reasons for other ruminants can be examined on the basis of our statistical-analysis tools in the future.}, language = {en} } @article{WangBalcerekBurneckietal.2023, author = {Wang, Wei and Balcerek, Michał and Burnecki, Krzysztof and Chechkin, Aleksei and Janušonis, Skirmantas and Ślęzak, Jakub and Vojta, Thomas and Wyłomańska, Agnieszka and Metzler, Ralf}, title = {Memory-multi-fractional Brownian motion with continuous correlations}, series = {Physical review research}, volume = {5}, journal = {Physical review research}, number = {3}, publisher = {APS}, address = {College Park}, issn = {2643-1564}, doi = {10.1103/PhysRevResearch.5.L032025}, pages = {8}, year = {2023}, abstract = {We propose a generalization of the widely used fractional Brownian motion (FBM), memory-multi-FBM (MMFBM), to describe viscoelastic or persistent anomalous diffusion with time-dependent memory exponent α(t ) in a changing environment. In MMFBM the built-in, long-range memory is continuously modulated by α(t ). We derive the essential statistical properties of MMFBM such as its response function, mean-squared displacement (MSD), autocovariance function, and Gaussian distribution. In contrast to existing forms of FBM with time-varying memory exponents but a reset memory structure, the instantaneous dynamic of MMFBM is influenced by the process history, e.g., we show that after a steplike change of α(t ) the scaling exponent of the MSD after the α step may be determined by the value of α(t ) before the change. MMFBM is a versatile and useful process for correlated physical systems with nonequilibrium initial conditions in a changing environment.}, language = {en} } @article{MatternReppertZeuschneretal.2023, author = {Mattern, Maximilian and Reppert, Alexander von and Zeuschner, Steffen Peer and Herzog, Marc and Pudell, Jan-Etienne and Bargheer, Matias}, title = {Concepts and use cases for picosecond ultrasonics with x-rays}, series = {Photoacoustics}, volume = {31}, journal = {Photoacoustics}, publisher = {Elsevier}, address = {Amsterdam}, issn = {2213-5979}, doi = {10.1016/j.pacs.2023.100503}, pages = {22}, year = {2023}, abstract = {This review discusses picosecond ultrasonics experiments using ultrashort hard x-ray probe pulses to extract the transient strain response of laser-excited nanoscopic structures from Bragg-peak shifts. This method provides direct, layer-specific, and quantitative information on the picosecond strain response for structures down to few-nm thickness. We model the transient strain using the elastic wave equation and express the driving stress using Gruneisen parameters stating that the laser-induced stress is proportional to energy density changes in the microscopic subsystems of the solid, i.e., electrons, phonons and spins. The laser-driven strain response can thus serve as an ultrafast proxy for local energy-density and temperature changes, but we emphasize the importance of the nanoscale morphology for an accurate interpretation due to the Poisson effect. The presented experimental use cases encompass ultrathin and opaque metal-heterostructures, continuous and granular nanolayers as well as negative thermal expansion materials, that each pose a challenge to established all-optical techniques.}, language = {en} } @article{RosenblumPikovsky2023, author = {Rosenblum, Michael and Pikovsky, Arkady}, title = {Inferring connectivity of an oscillatory network via the phase dynamics reconstruction}, series = {Frontiers in network physiology}, volume = {3}, journal = {Frontiers in network physiology}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {2674-0109}, doi = {10.3389/fnetp.2023.1298228}, pages = {10}, year = {2023}, abstract = {We review an approach for reconstructing oscillatory networks' undirected and directed connectivity from data. The technique relies on inferring the phase dynamics model. The central assumption is that we observe the outputs of all network nodes. We distinguish between two cases. In the first one, the observed signals represent smooth oscillations, while in the second one, the data are pulse-like and can be viewed as point processes. For the first case, we discuss estimating the true phase from a scalar signal, exploiting the protophase-to-phase transformation. With the phases at hand, pairwise and triplet synchronization indices can characterize the undirected connectivity. Next, we demonstrate how to infer the general form of the coupling functions for two or three oscillators and how to use these functions to quantify the directional links. We proceed with a different treatment of networks with more than three nodes. We discuss the difference between the structural and effective phase connectivity that emerges due to high-order terms in the coupling functions. For the second case of point-process data, we use the instants of spikes to infer the phase dynamics model in the Winfree form directly. This way, we obtain the network's coupling matrix in the first approximation in the coupling strength.}, language = {en} } @article{FernandezCharcharCherstvyetal.2020, author = {Fernandez, Amanda Diez and Charchar, Patrick and Cherstvy, Andrey G. and Metzler, Ralf and Finnis, Michael W.}, title = {The diffusion of doxorubicin drug molecules in silica nanoslits is non-Gaussian, intermittent and anticorrelated}, series = {Physical chemistry, chemical physics}, volume = {22}, journal = {Physical chemistry, chemical physics}, number = {48}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1463-9076}, doi = {10.1039/d0cp03849k}, pages = {27955 -- 27965}, year = {2020}, abstract = {In this study we investigate, using all-atom molecular-dynamics computer simulations, the in-plane diffusion of a doxorubicin drug molecule in a thin film of water confined between two silica surfaces. We find that the molecule diffuses along the channel in the manner of a Gaussian diffusion process, but with parameters that vary according to its varying transversal position. Our analysis identifies that four Gaussians, each describing particle motion in a given transversal region, are needed to adequately describe the data. Each of these processes by itself evolves with time at a rate slower than that associated with classical Brownian motion due to a predominance of anticorrelated displacements. Long adsorption events lead to ageing, a property observed when the diffusion is intermittently hindered for periods of time with an average duration which is theoretically infinite. This study presents a simple system in which many interesting features of anomalous diffusion can be explored. It exposes the complexity of diffusion in nanoconfinement and highlights the need to develop new understanding.}, language = {en} } @article{MardoukhiJeonChechkinetal.2018, author = {Mardoukhi, Yousof and Jeon, Jae-Hyung and Chechkin, Aleksei and Metzler, Ralf}, title = {Fluctuations of random walks in critical random environments}, series = {Physical chemistry, chemical physics : a journal of European Chemical Societies}, volume = {20}, journal = {Physical chemistry, chemical physics : a journal of European Chemical Societies}, number = {31}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1463-9076}, doi = {10.1039/c8cp03212b}, pages = {20427 -- 20438}, year = {2018}, abstract = {Percolation networks have been widely used in the description of porous media but are now found to be relevant to understand the motion of particles in cellular membranes or the nucleus of biological cells. Random walks on the infinite cluster at criticality of a percolation network are asymptotically ergodic. On any finite size cluster of the network stationarity is reached at finite times, depending on the cluster's size. Despite of this we here demonstrate by combination of analytical calculations and simulations that at criticality the disorder and cluster size average of the ensemble of clusters leads to a non-vanishing variance of the time averaged mean squared displacement, regardless of the measurement time. Fluctuations of this relevant experimental quantity due to the disorder average of such ensembles are thus persistent and non-negligible. The relevance of our results for single particle tracking analysis in complex and biological systems is discussed.}, language = {en} } @article{ŚlęzakMetzlerMagdziarz2019, author = {Ślęzak, Jakub and Metzler, Ralf and Magdziarz, Marcin}, title = {Codifference can detect ergodicity breaking and non-Gaussianity}, series = {New Journal of Physics}, volume = {21}, journal = {New Journal of Physics}, publisher = {Deutsche Physikalische Gesellschaft}, address = {Bad Honnef}, issn = {1367-2630}, doi = {10.1088/1367-2630/ab13f3}, pages = {25}, year = {2019}, abstract = {We show that the codifference is a useful tool in studying the ergodicity breaking and non-Gaussianity properties of stochastic time series. While the codifference is a measure of dependence that was previously studied mainly in the context of stable processes, we here extend its range of applicability to random-parameter and diffusing-diffusivity models which are important in contemporary physics, biology and financial engineering. We prove that the codifference detects forms of dependence and ergodicity breaking which are not visible from analysing the covariance and correlation functions. We also discuss a related measure of dispersion, which is a nonlinear analogue of the mean squared displacement.}, language = {en} } @article{HouCherstvyMetzleretal.2018, author = {Hou, Ru and Cherstvy, Andrey G. and Metzler, Ralf and Akimoto, Takuma}, title = {Biased continuous-time random walks for ordinary and equilibrium cases}, series = {Physical chemistry, chemical physics : a journal of European Chemical Societies}, volume = {20}, journal = {Physical chemistry, chemical physics : a journal of European Chemical Societies}, number = {32}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1463-9076}, doi = {10.1039/c8cp01863d}, pages = {20827 -- 20848}, year = {2018}, abstract = {We examine renewal processes with power-law waiting time distributions (WTDs) and non-zero drift via computing analytically and by computer simulations their ensemble and time averaged spreading characteristics. All possible values of the scaling exponent alpha are considered for the WTD psi(t) similar to 1/t(1+alpha). We treat continuous-time random walks (CTRWs) with 0 < alpha < 1 for which the mean waiting time diverges, and investigate the behaviour of the process for both ordinary and equilibrium CTRWs for 1 < alpha < 2 and alpha > 2. We demonstrate that in the presence of a drift CTRWs with alpha < 1 are ageing and non-ergodic in the sense of the non-equivalence of their ensemble and time averaged displacement characteristics in the limit of lag times much shorter than the trajectory length. In the sense of the equivalence of ensemble and time averages, CTRW processes with 1 < alpha < 2 are ergodic for the equilibrium and non-ergodic for the ordinary situation. Lastly, CTRW renewal processes with alpha > 2-both for the equilibrium and ordinary situation-are always ergodic. For the situations 1 < alpha < 2 and alpha > 2 the variance of the diffusion process, however, depends on the initial ensemble. For biased CTRWs with alpha > 1 we also investigate the behaviour of the ergodicity breaking parameter. In addition, we demonstrate that for biased CTRWs the Einstein relation is valid on the level of the ensemble and time averaged displacements, in the entire range of the WTD exponent alpha.}, language = {en} } @article{OzturkMarwanKorupetal.2018, author = {Ozturk, Ugur and Marwan, Norbert and Korup, Oliver and Saito, H. and Agarwa, Ankit and Grossman, M. J. and Zaiki, M. and Kurths, J{\"u}rgen}, title = {Complex networks for tracking extreme rainfall during typhoons}, series = {Chaos : an interdisciplinary journal of nonlinear science}, volume = {28}, journal = {Chaos : an interdisciplinary journal of nonlinear science}, number = {7}, publisher = {American Institute of Physics}, address = {Melville}, issn = {1054-1500}, doi = {10.1063/1.5004480}, pages = {8}, year = {2018}, abstract = {Reconciling the paths of extreme rainfall with those of typhoons remains difficult despite advanced forecasting techniques. We use complex networks defined by a nonlinear synchronization measure termed event synchronization to track extreme rainfall over the Japanese islands. Directed networks objectively record patterns of heavy rain brought by frontal storms and typhoons but mask out contributions of local convective storms. We propose a radial rank method to show that paths of extreme rainfall in the typhoon season (August-November, ASON) follow the overall southwest-northeast motion of typhoons and mean rainfall gradient of Japan. The associated eye-of-the-typhoon tracks deviate notably and may thus distort estimates of heavy typhoon rainfall. We mainly found that the lower spread of rainfall tracks in ASON may enable better hindcasting than for westerly-fed frontal storms in June and July.}, language = {en} } @article{KurilovichMantsevichStevensonetal.2020, author = {Kurilovich, Aleksandr A. and Mantsevich, Vladimir and Stevenson, Keith J. and Chechkin, Aleksei and Palyulin, V. V.}, title = {Complex diffusion-based kinetics of photoluminescence in semiconductor nanoplatelets}, series = {Physical chemistry, chemical physics : a journal of European Chemical Societies}, volume = {22}, journal = {Physical chemistry, chemical physics : a journal of European Chemical Societies}, number = {42}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1463-9076}, doi = {10.1039/d0cp03744c}, pages = {24686 -- 24696}, year = {2020}, abstract = {We present a diffusion-based simulation and theoretical models for explanation of the photoluminescence (PL) emission intensity in semiconductor nanoplatelets. It is shown that the shape of the PL intensity curves can be reproduced by the interplay of recombination, diffusion and trapping of excitons. The emission intensity at short times is purely exponential and is defined by recombination. At long times, it is governed by the release of excitons from surface traps and is characterized by a power-law tail. We show that the crossover from one limit to another is controlled by diffusion properties. This intermediate region exhibits a rich behaviour depending on the value of diffusivity. The proposed approach reproduces all the features of experimental curves measured for different nanoplatelet systems.}, language = {en} } @article{DybiecCapalaChechkinetal.2018, author = {Dybiec, Bartlomiej and Capala, Karol and Chechkin, Aleksei and Metzler, Ralf}, title = {Conservative random walks in confining potentials}, series = {Journal of physics : A, Mathematical and theoretical}, volume = {52}, journal = {Journal of physics : A, Mathematical and theoretical}, number = {1}, publisher = {IOP Publ. Ltd.}, address = {Bristol}, issn = {1751-8113}, doi = {10.1088/1751-8121/aaefc2}, pages = {25}, year = {2018}, abstract = {Levy walks are continuous time random walks with spatio-temporal coupling of jump lengths and waiting times, often used to model superdiffusive spreading processes such as animals searching for food, tracer motion in weakly chaotic systems, or even the dynamics in quantum systems such as cold atoms. In the simplest version Levy walks move with a finite speed. Here, we present an extension of the Levy walk scenario for the case when external force fields influence the motion. The resulting motion is a combination of the response to the deterministic force acting on the particle, changing its velocity according to the principle of total energy conservation, and random velocity reversals governed by the distribution of waiting times. For the fact that the motion stays conservative, that is, on a constant energy surface, our scenario is fundamentally different from thermal motion in the same external potentials. In particular, we present results for the velocity and position distributions for single well potentials of different steepness. The observed dynamics with its continuous velocity changes enriches the theory of Levy walk processes and will be of use in a variety of systems, for which the particles are externally confined.}, language = {en} } @article{AgarwalMaheswaranMarwanetal.2018, author = {Agarwal, Ankit and Maheswaran, Rathinasamy and Marwan, Norbert and Caesar, Levke and Kurths, J{\"u}rgen}, title = {Wavelet-based multiscale similarity measure for complex networks}, series = {The European physical journal : B, Condensed matter and complex systems}, volume = {91}, journal = {The European physical journal : B, Condensed matter and complex systems}, number = {11}, publisher = {Springer}, address = {New York}, issn = {1434-6028}, doi = {10.1140/epjb/e2018-90460-6}, pages = {12}, year = {2018}, abstract = {In recent years, complex network analysis facilitated the identification of universal and unexpected patterns in complex climate systems. However, the analysis and representation of a multiscale complex relationship that exists in the global climate system are limited. A logical first step in addressing this issue is to construct multiple networks over different timescales. Therefore, we propose to apply the wavelet multiscale correlation (WMC) similarity measure, which is a combination of two state-of-the-art methods, viz. wavelet and Pearson's correlation, for investigating multiscale processes through complex networks. Firstly we decompose the data over different timescales using the wavelet approach and subsequently construct a corresponding network by Pearson's correlation. The proposed approach is illustrated and tested on two synthetics and one real-world example. The first synthetic case study shows the efficacy of the proposed approach to unravel scale-specific connections, which are often undiscovered at a single scale. The second synthetic case study illustrates that by dividing and constructing a separate network for each time window we can detect significant changes in the signal structure. The real-world example investigates the behavior of the global sea surface temperature (SST) network at different timescales. Intriguingly, we notice that spatial dependent structure in SST evolves temporally. Overall, the proposed measure has an immense potential to provide essential insights on understanding and extending complex multivariate process studies at multiple scales.}, language = {en} } @article{MaheswaranAgarwalSivakumaretal.2019, author = {Maheswaran, Rathinasamy and Agarwal, Ankit and Sivakumar, Bellie and Marwan, Norbert and Kurths, J{\"u}rgen}, title = {Wavelet analysis of precipitation extremes over India and teleconnections to climate indices}, series = {Stochastic Environmental Research and Risk Assessment}, volume = {33}, journal = {Stochastic Environmental Research and Risk Assessment}, number = {11-12}, publisher = {Springer}, address = {New York}, issn = {1436-3240}, doi = {10.1007/s00477-019-01738-3}, pages = {2053 -- 2069}, year = {2019}, abstract = {Precipitation patterns and extremes are significantly influenced by various climatic factors and large-scale atmospheric circulation patterns. This study uses wavelet coherence analysis to detect significant interannual and interdecadal oscillations in monthly precipitation extremes across India and their teleconnections to three prominent climate indices, namely, Nino 3.4, Pacific Decadal Oscillation, and Indian Ocean Dipole (IOD). Further, partial wavelet coherence analysis is used to estimate the standalone relationship between the climate indices and precipitation after removing the effect of interdependency. The wavelet analysis of monthly precipitation extremes at 30 different locations across India reveals that (a) interannual (2-8 years) and interdecadal (8-32 years) oscillations are statistically significant, and (b) the oscillations vary in both time and space. The results from the partial wavelet coherence analysis reveal that Nino 3.4 and IOD are the significant drivers of Indian precipitation at interannual and interdecadal scales. Intriguingly, the study also confirms that the strength of influence of large-scale atmospheric circulation patterns on Indian precipitation extremes varies with spatial physiography of the region.}, language = {en} } @article{PalyulinBlackburnLomholtetal.2019, author = {Palyulin, Vladimir V and Blackburn, George and Lomholt, Michael A and Watkins, Nicholas W and Metzler, Ralf and Klages, Rainer and Chechkin, Aleksei}, title = {First passage and first hitting times of L{\´e}vy flights and L{\´e}vy walks}, series = {New Journal of Physics}, volume = {21}, journal = {New Journal of Physics}, publisher = {Dt. Physikalische Ges.}, address = {Bad Honnef}, issn = {1367-2630}, doi = {10.1088/1367-2630/ab41bb}, pages = {24}, year = {2019}, abstract = {For both L{\´e}vy flight and L{\´e}vy walk search processes we analyse the full distribution of first-passage and first-hitting (or first-arrival) times. These are, respectively, the times when the particle moves across a point at some given distance from its initial position for the first time, or when it lands at a given point for the first time. For L{\´e}vy motions with their propensity for long relocation events and thus the possibility to jump across a given point in space without actually hitting it ('leapovers'), these two definitions lead to significantly different results. We study the first-passage and first-hitting time distributions as functions of the L{\´e}vy stable index, highlighting the different behaviour for the cases when the first absolute moment of the jump length distribution is finite or infinite. In particular we examine the limits of short and long times. Our results will find their application in the mathematical modelling of random search processes as well as computer algorithms.}, language = {en} } @article{LandaUshakovKurths2006, author = {Landa, Polina S. and Ushakov, Vladimir and Kurths, J{\"u}rgen}, title = {Rigorous theory of stochastic resonance in overdamped bistable oscillators for weak signals}, series = {Chaos, solitons \& fractals : applications in science and engineering}, volume = {30}, journal = {Chaos, solitons \& fractals : applications in science and engineering}, number = {3}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0960-0779}, doi = {10.1016/j.chaos.2005.08.116}, pages = {574 -- 578}, year = {2006}, abstract = {The results of the theoretical consideration of stochastic resonance in overdamped bistable oscillators are given. These results are founded not on the model of two states as in [McNamara B, Wiesenfeld K. Theory of stochastic resonance. Phys Rev A 1989;39:4854-69], but on splitting of motion into regular and random and the rigorous solution of the Fokker-Planck equation for the random component. We show that this resonance is caused by a change, under the influence of noise, of the system's effective stiffness and damping factor contained in the equation for the regular component. For a certain value of the noise intensity the effective stiffness is minimal, and this fact causes non-monotonic change of the output signal amplitude as the noise intensity changes. It is important that the location of the minimum and its value depend essentially on the signal frequency.}, language = {en} } @article{GandhimathiRajasekarKurths2006, author = {Gandhimathi, V. M. and Rajasekar, S. and Kurths, J{\"u}rgen}, title = {Vibrational and stochastic resonances in two coupled overdamped anharmonic oscillators}, series = {Modern physics letters : A, Particles and fields, gravitation, cosmology, nuclear physics}, volume = {360}, journal = {Modern physics letters : A, Particles and fields, gravitation, cosmology, nuclear physics}, number = {2}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0375-9601}, doi = {10.1016/j.physleta.2006.08.051}, pages = {279 -- 286}, year = {2006}, abstract = {We study the overdamped version of two coupled anharmonic oscillators under the influence of both low- and high-frequency forces respectively and a Gaussian noise term added to one of the two state variables of the system. The dynamics of the system is first studied in the presence of both forces separately without noise. In the presence of only one of the forces, no resonance behaviour is observed, however, hysteresis happens there. Then the influence of the high-frequency force in the presence of a low-frequency, i.e. biharmonic forcing, is studied. Vibrational resonance is found to occur when the amplitude of the high-frequency force is varied. The resonance curve resembles a stochastic resonance-like curve. It is maximum at the value of g at which the orbit lies in one well during one half of the drive cycle of the low-frequency force and in the other for the remaining half cycle. Vibrational resonance is characterized using the response amplitude and mean residence time. We show the occurrence of stochastic resonance behaviour in the overdamped system by replacing the high-frequency force by Gaussian noise. Similarities and differences between both types of resonance are presented. (c) 2006 Elsevier B.V. All rights reserved.}, language = {en} } @article{ZouThielRomanoetal.2006, author = {Zou, Yong and Thiel, M. and Romano, Maria Carmen and Kurths, J{\"u}rgen and Bi, Q.}, title = {Shrimp structure and associated dynamics in parametrically excited oscillators}, series = {International journal of bifurcation and chaos : in applied sciences and engineering}, volume = {16}, journal = {International journal of bifurcation and chaos : in applied sciences and engineering}, number = {12}, publisher = {World Scientific Publ. Co}, address = {Singapore}, issn = {0218-1274}, doi = {10.1142/S0218127406016987}, pages = {3567 -- 3579}, year = {2006}, abstract = {We investigate the bifurcation structures in a two-dimensional parameter space (PS) of a parametrically excited system with two degrees of freedom both analytically and numerically. By means of the Renyi entropy of second order K-2, which is estimated from recurrence plots, we uncover that regions of chaotic behavior are intermingled with many complex periodic windows, such as shrimp structures in the PS. A detailed numerical analysis shows that, the stable solutions lose stability either via period doubling, or via intermittency when the parameters leave these shrimps in different directions, indicating different bifurcation properties of the boundaries. The shrimps of different sizes offer promising ways to control the dynamics of such a complex system.}, language = {en} } @article{ZhouZemanovaZamoraetal.2006, author = {Zhou, Changsong and Zemanova, Lucia and Zamora, Gorka and Hilgetag, Claus C. and Kurths, J{\"u}rgen}, title = {Hierarchical organization unveiled by functional connectivity in complex brain networks}, series = {Physical review letters}, volume = {97}, journal = {Physical review letters}, publisher = {American Physical Society}, address = {College Park}, issn = {0031-9007}, doi = {10.1103/PhysRevLett.97.238103}, pages = {4}, year = {2006}, abstract = {How do diverse dynamical patterns arise from the topology of complex networks? We study synchronization dynamics in the cortical brain network of the cat, which displays a hierarchically clustered organization, by modeling each node (cortical area) with a subnetwork of interacting excitable neurons. We find that in the biologically plausible regime the dynamics exhibits a hierarchical modular organization, in particular, revealing functional clusters coinciding with the anatomical communities at different scales. Our results provide insights into the relationship between network topology and functional organization of complex brain networks.}, language = {en} } @article{CherstvyThapaWagneretal.2019, author = {Cherstvy, Andrey G. and Thapa, Samudrajit and Wagner, Caroline E. and Metzler, Ralf}, title = {Non-Gaussian, non-ergodic, and non-Fickian diffusion of tracers in mucin hydrogels}, series = {Soft matter}, volume = {15}, journal = {Soft matter}, number = {12}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1744-683X}, doi = {10.1039/c8sm02096e}, pages = {2526 -- 2551}, year = {2019}, abstract = {Native mucus is polymer-based soft-matter material of paramount biological importance. How non-Gaussian and non-ergodic is the diffusive spreading of pathogens in mucus? We study the passive, thermally driven motion of micron-sized tracers in hydrogels of mucins, the main polymeric component of mucus. We report the results of the Bayesian analysis for ranking several diffusion models for a set of tracer trajectories [C. E. Wagner et al., Biomacromolecules, 2017, 18, 3654]. The models with "diffusing diffusivity', fractional and standard Brownian motion are used. The likelihood functions and evidences of each model are computed, ranking the significance of each model for individual traces. We find that viscoelastic anomalous diffusion is often most probable, followed by Brownian motion, while the model with a diffusing diffusion coefficient is only realised rarely. Our analysis also clarifies the distribution of time-averaged displacements, correlations of scaling exponents and diffusion coefficients, and the degree of non-Gaussianity of displacements at varying pH levels. Weak ergodicity breaking is also quantified. We conclude that-consistent with the original study-diffusion of tracers in the mucin gels is most non-Gaussian and non-ergodic at low pH that corresponds to the most heterogeneous networks. Using the Bayesian approach with the nested-sampling algorithm, together with the quantitative analysis of multiple statistical measures, we report new insights into possible physical mechanisms of diffusion in mucin gels.}, language = {en} } @article{PadashChechkinDybiecetal.2019, author = {Padash, Amin and Chechkin, Aleksei and Dybiec, Bartlomiej and Pavlyukevich, Ilya and Shokri, Babak and Metzler, Ralf}, title = {First-passage properties of asymmetric Levy flights}, series = {Journal of physics : A, Mathematical and theoretical}, volume = {52}, journal = {Journal of physics : A, Mathematical and theoretical}, number = {45}, publisher = {IOP Publ. Ltd.}, address = {Bristol}, issn = {1751-8113}, doi = {10.1088/1751-8121/ab493e}, pages = {48}, year = {2019}, abstract = {L{\´e}vy flights are paradigmatic generalised random walk processes, in which the independent stationary increments—the 'jump lengths'—are drawn from an -stable jump length distribution with long-tailed, power-law asymptote. As a result, the variance of L{\´e}vy flights diverges and the trajectory is characterised by occasional extremely long jumps. Such long jumps significantly decrease the probability to revisit previous points of visitation, rendering L{\´e}vy flights efficient search processes in one and two dimensions. To further quantify their precise property as random search strategies we here study the first-passage time properties of L{\´e}vy flights in one-dimensional semi-infinite and bounded domains for symmetric and asymmetric jump length distributions. To obtain the full probability density function of first-passage times for these cases we employ two complementary methods. One approach is based on the space-fractional diffusion equation for the probability density function, from which the survival probability is obtained for different values of the stable index and the skewness (asymmetry) parameter . The other approach is based on the stochastic Langevin equation with -stable driving noise. Both methods have their advantages and disadvantages for explicit calculations and numerical evaluation, and the complementary approach involving both methods will be profitable for concrete applications. We also make use of the Skorokhod theorem for processes with independent increments and demonstrate that the numerical results are in good agreement with the analytical expressions for the probability density function of the first-passage times.}, language = {en} } @article{KurthsAgarwalShuklaetal.2019, author = {Kurths, J{\"u}rgen and Agarwal, Ankit and Shukla, Roopam and Marwan, Norbert and Maheswaran, Rathinasamy and Caesar, Levke and Krishnan, Raghavan and Merz, Bruno}, title = {Unravelling the spatial diversity of Indian precipitation teleconnections via a non-linear multi-scale approach}, series = {Nonlinear processes in geophysics}, volume = {26}, journal = {Nonlinear processes in geophysics}, number = {3}, publisher = {Copernicus}, address = {G{\"o}ttingen}, issn = {1023-5809}, doi = {10.5194/npg-26-251-2019}, pages = {251 -- 266}, year = {2019}, abstract = {A better understanding of precipitation dynamics in the Indian subcontinent is required since India's society depends heavily on reliable monsoon forecasts. We introduce a non-linear, multiscale approach, based on wavelets and event synchronization, for unravelling teleconnection influences on precipitation. We consider those climate patterns with the highest relevance for Indian precipitation. Our results suggest significant influences which are not well captured by only the wavelet coherence analysis, the state-of-the-art method in understanding linkages at multiple timescales. We find substantial variation across India and across timescales. In particular, El Ni{\~n}o-Southern Oscillation (ENSO) and the Indian Ocean Dipole (IOD) mainly influence precipitation in the south-east at interannual and decadal scales, respectively, whereas the North Atlantic Oscillation (NAO) has a strong connection to precipitation, particularly in the northern regions. The effect of the Pacific Decadal Oscillation (PDO) stretches across the whole country, whereas the Atlantic Multidecadal Oscillation (AMO) influences precipitation particularly in the central arid and semi-arid regions. The proposed method provides a powerful approach for capturing the dynamics of precipitation and, hence, helps improve precipitation forecasting.}, language = {en} } @article{BodrovaChechkinSokolov2019, author = {Bodrova, Anna S. and Chechkin, Aleksei and Sokolov, Igor M.}, title = {Scaled Brownian motion with renewal resetting}, series = {Physical review : E, Statistical, nonlinear and soft matter physics}, volume = {100}, journal = {Physical review : E, Statistical, nonlinear and soft matter physics}, number = {1}, publisher = {American Physical Society}, address = {College Park}, issn = {2470-0045}, doi = {10.1103/PhysRevE.100.012120}, pages = {13}, year = {2019}, abstract = {We investigate an intermittent stochastic process in which the diffusive motion with time-dependent diffusion coefficient D(t)∼tα-1 with α>0 (scaled Brownian motion) is stochastically reset to its initial position, and starts anew. In the present work we discuss the situation in which the memory on the value of the diffusion coefficient at a resetting time is erased, so that the whole process is a fully renewal one. The situation when the resetting of the coordinate does not affect the diffusion coefficient's time dependence is considered in the other work of this series [A. S. Bodrova et al., Phys. Rev. E 100, 012119 (2019)]. We show that the properties of the probability densities in such processes (erasing or retaining the memory on the diffusion coefficient) are vastly different. In addition we discuss the first-passage properties of the scaled Brownian motion with renewal resetting and consider the dependence of the efficiency of search on the parameters of the process.}, language = {en} } @article{WangCherstvyChechkinetal.2020, author = {Wang, Wei and Cherstvy, Andrey G. and Chechkin, Aleksei and Thapa, Samudrajit and Seno, Flavio and Liu, Xianbin and Metzler, Ralf}, title = {Fractional Brownian motion with random diffusivity}, series = {Journal of physics : A, Mathematical and theoretical}, volume = {53}, journal = {Journal of physics : A, Mathematical and theoretical}, number = {47}, publisher = {IOP Publ. Ltd.}, address = {Bristol}, issn = {1751-8113}, doi = {10.1088/1751-8121/aba467}, pages = {34}, year = {2020}, abstract = {Numerous examples for a priori unexpected non-Gaussian behaviour for normal and anomalous diffusion have recently been reported in single-particle tracking experiments. Here, we address the case of non-Gaussian anomalous diffusion in terms of a random-diffusivity mechanism in the presence of power-law correlated fractional Gaussian noise. We study the ergodic properties of this model via examining the ensemble- and time-averaged mean-squared displacements as well as the ergodicity breaking parameter EB quantifying the trajectory-to-trajectory fluctuations of the latter. For long measurement times, interesting crossover behaviour is found as function of the correlation time tau characterising the diffusivity dynamics. We unveil that at short lag times the EB parameter reaches a universal plateau. The corresponding residual value of EB is shown to depend only on tau and the trajectory length. The EB parameter at long lag times, however, follows the same power-law scaling as for fractional Brownian motion. We also determine a corresponding plateau at short lag times for the discrete representation of fractional Brownian motion, absent in the continuous-time formulation. These analytical predictions are in excellent agreement with results of computer simulations of the underlying stochastic processes. Our findings can help distinguishing and categorising certain nonergodic and non-Gaussian features of particle displacements, as observed in recent single-particle tracking experiments.}, language = {en} } @article{AydinerCherstvyMetzler2018, author = {Aydiner, Ekrem and Cherstvy, Andrey G. and Metzler, Ralf}, title = {Wealth distribution, Pareto law, and stretched exponential decay of money}, series = {Physica : europhysics journal ; A, Statistical mechanics and its applications}, volume = {490}, journal = {Physica : europhysics journal ; A, Statistical mechanics and its applications}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0378-4371}, doi = {10.1016/j.physa.2017.08.017}, pages = {278 -- 288}, year = {2018}, abstract = {We study by Monte Carlo simulations a kinetic exchange trading model for both fixed and distributed saving propensities of the agents and rationalize the person and wealth distributions. We show that the newly introduced wealth distribution - that may be more amenable in certain situations - features a different power-law exponent, particularly for distributed saving propensities of the agents. For open agent-based systems, we analyze the person and wealth distributions and find that the presence of trap agents alters their amplitude, leaving however the scaling exponents nearly unaffected. For an open system, we show that the total wealth - for different trap agent densities and saving propensities of the agents - decreases in time according to the classical Kohlrausch-Williams-Watts stretched exponential law. Interestingly, this decay does not depend on the trap agent density, but rather on saving propensities. The system relaxation for fixed and distributed saving schemes are found to be different.}, language = {en} } @article{ChechkinSokolov2018, author = {Chechkin, Aleksei and Sokolov, Igor M.}, title = {Random search with resetting}, series = {Physical review letters}, volume = {121}, journal = {Physical review letters}, number = {5}, publisher = {American Physical Society}, address = {College Park}, issn = {0031-9007}, doi = {10.1103/PhysRevLett.121.050601}, pages = {5}, year = {2018}, abstract = {We provide a unified renewal approach to the problem of random search for several targets under resetting. This framework does not rely on specific properties of the search process and resetting procedure, allows for simpler derivation of known results, and leads to new ones. Concentrating on minimizing the mean hitting time, we show that resetting at a constant pace is the best possible option if resetting helps at all, and derive the equation for the optimal resetting pace. No resetting may be a better strategy if without resetting the probability of not finding a target decays with time to zero exponentially or faster. We also calculate splitting probabilities between the targets, and define the limits in which these can be manipulated by changing the resetting procedure. We moreover show that the number of moments of the hitting time distribution under resetting is not less than the sum of the numbers of moments of the resetting time distribution and the hitting time distribution without resetting.}, language = {en} } @article{CiemerRehmKurthsetal.2020, author = {Ciemer, Catrin and Rehm, Lars and Kurths, J{\"u}rgen and Donner, Reik Volker and Winkelmann, Ricarda and Boers, Niklas}, title = {An early-warning indicator for Amazon droughts exclusively based on tropical Atlantic sea surface temperatures}, series = {Environmental Research Letters}, volume = {15}, journal = {Environmental Research Letters}, number = {9}, publisher = {IOP - Institute of Physics Publishing}, address = {Bristol}, pages = {10}, year = {2020}, abstract = {Droughts in tropical South America have an imminent and severe impact on the Amazon rainforest and affect the livelihoods of millions of people. Extremely dry conditions in Amazonia have been previously linked to sea surface temperature (SST) anomalies in the adjacent tropical oceans. Although the sources and impacts of such droughts have been widely studied, establishing reliable multi-year lead statistical forecasts of their occurrence is still an ongoing challenge. Here, we further investigate the relationship between SST and rainfall anomalies using a complex network approach. We identify four ocean regions which exhibit the strongest overall SST correlations with central Amazon rainfall, including two particularly prominent regions in the northern and southern tropical Atlantic. Based on the time-dependent correlation between SST anomalies in these two regions alone, we establish a new early-warning method for droughts in the central Amazon basin and demonstrate its robustness in hindcasting past major drought events with lead-times up to 18 months.}, language = {en} } @article{LiuCherstvyMetzler2017, author = {Liu, Lin and Cherstvy, Andrey G. and Metzler, Ralf}, title = {Facilitated Diffusion of Transcription Factor Proteins with Anomalous Bulk Diffusion}, series = {The journal of physical chemistry : B, Condensed matter, materials, surfaces, interfaces \& biophysical chemistry}, volume = {121}, journal = {The journal of physical chemistry : B, Condensed matter, materials, surfaces, interfaces \& biophysical chemistry}, publisher = {American Chemical Society}, address = {Washington}, issn = {1520-6106}, doi = {10.1021/acs.jpcb.6b12413}, pages = {1284 -- 1289}, year = {2017}, abstract = {What are the physical laws of the diffusive search of proteins for their specific binding sites on DNA in the presence of the macromolecular crowding in cells? We performed extensive computer simulations to elucidate the protein target search on DNA. The novel feature is the viscoelastic non-Brownian protein bulk diffusion recently observed experimentally. We examine the influence of the protein-DNA binding affinity and the anomalous diffusion exponent on the target search time. In all cases an optimal search time is found. The relative contribution of intermittent three-dimensional bulk diffusion and one-dimensional sliding of proteins along the DNA is quantified. Our results are discussed in the light of recent single molecule tracking experiments, aiming at a better understanding of the influence of anomalous kinetics of proteins on the facilitated diffusion mechanism.}, language = {en} } @article{CrovettoHempelRusuetal.2020, author = {Crovetto, Andrea and Hempel, Hannes and Rusu, Marin and Choubrac, Leo and Kojda, Sandrino Danny and Habicht, Klaus and Unold, Thomas}, title = {Water adsorption enhances electrical conductivity in transparent p-type CuI}, series = {ACS applied materials \& interfaces}, volume = {12}, journal = {ACS applied materials \& interfaces}, number = {43}, publisher = {American Chemical Society}, address = {Washington, DC}, issn = {1944-8244}, doi = {10.1021/acsami.0c11040}, pages = {48741 -- 48747}, year = {2020}, abstract = {CuI has been recently rediscovered as a p-type transparent conductor with a high figure of merit. Even though many metal iodides are hygroscopic, the effect of moisture on the electrical properties of CuI has not been clarified. In this work, we observe a 2-fold increase in the conductivity of CuI after exposure to ambient humidity for 5 h, followed by slight long-term degradation. Simultaneously, the work function of CuI decreases by almost 1 eV, which can explain the large spread in the previously reported work function values. The conductivity increase is partially reversible and is maximized at intermediate humidity levels. On the basis of the large intragrain mobility measured by THz spectroscopy, we suggest that hydration of grain boundaries may be beneficial for the overall hole mobility.}, language = {en} } @article{KojdaHofmannGostkowskaLekneretal.2022, author = {Kojda, Sandrino Danny and Hofmann, Tommy and Gostkowska-Lekner, Natalia Katarzyna and Habicht, Klaus}, title = {Characterization and modeling of the temperature-dependent thermal conductivity in sintered porous silicon-aluminum nanomaterials}, series = {Nano research}, volume = {15}, journal = {Nano research}, number = {6}, publisher = {Tsinghua Univ. Press}, address = {Beijing}, issn = {1998-0124}, doi = {10.1007/s12274-022-4123-y}, pages = {5663 -- 5670}, year = {2022}, abstract = {Nanostructured silicon and silicon-aluminum compounds are synthesized by a novel synthesis strategy based on spark plasma sintering (SPS) of silicon nanopowder, mesoporous silicon (pSi), and aluminum nanopowder. The interplay of metal-assisted crystallization and inherent porosity is exploited to largely suppress thermal conductivity. Morphology and temperature-dependent thermal conductivity studies allow us to elucidate the impact of porosity and nanostructure on the macroscopic heat transport. Analytic electron microscopy along with quantitative image analysis is applied to characterize the sample morphology in terms of domain size and interpore distance distributions. We demonstrate that nanostructured domains and high porosity can be maintained in densified mesoporous silicon samples. In contrast, strong grain growth is observed for sintered nanopowders under similar sintering conditions. We observe that aluminum agglomerations induce local grain growth, while aluminum diffusion is observed in porous silicon and dispersed nanoparticles. A detailed analysis of the measured thermal conductivity between 300 and 773 K allows us to distinguish the effect of reduced thermal conductivity caused by porosity from the reduction induced by phonon scattering at nanosized domains. With a modified Landauer/Lundstrom approach the relative thermal conductivity and the scattering length are extracted. The relative thermal conductivity confirms the applicability of Kirkpatrick's effective medium theory. The extracted scattering lengths are in excellent agreement with the harmonic mean of log-normal distributed domain sizes and the interpore distances combined by Matthiessen's rule.}, language = {en} } @article{ShpritsKellermanAseevetal.2017, author = {Shprits, Yuri and Kellerman, Adam C . and Aseev, Nikita and Drozdov, Alexander and Michaelis, Ingo}, title = {Multi-MeV electron loss in the heart of the radiation belts}, series = {Geophysical research letters}, volume = {44}, journal = {Geophysical research letters}, number = {3}, publisher = {American Geophysical Union}, address = {Washington}, issn = {0094-8276}, doi = {10.1002/2016GL072258}, pages = {1204 -- 1209}, year = {2017}, abstract = {Significant progress has been made in recent years in understanding acceleration mechanisms in the Earth's radiation belts. In particular, a number of studies demonstrated the importance of the local acceleration by analyzing the radial profiles of phase space density (PSD) and observing building up peaks in PSD. In this study, we focus on understanding of the local loss using very similar tools. The profiles of PSD for various values of the first adiabatic invariants during the previously studied 17 January 2013 storm are presented and discussed. The profiles of PSD show clear deepening minimums consistent with the scattering by electromagnetic ion cyclotron waves. Long-term evolution shows that local minimums in PSD can persist for relatively long times. During considered interval of time the deepening minimums were observed around L* = 4 during 17 January 2013 storm and around L* = 3.5 during 1 March 2013 storm. This study shows a new method that can help identify the location, magnitude, and time of the local loss and will help quantify local loss in the future. This study also provides additional clear and definitive evidence that local loss plays a major role for the dynamics of the multi-MeV electrons.}, language = {en} } @article{SteigertKojdaIbacetaJanaetal.2022, author = {Steigert, Alexander and Kojda, Sandrino Danny and Ibaceta-Ja{\~n}a, Josefa Fernanda and Abou-Ras, Daniel and Gunder, Ren{\´e} and Alktash, Nivin and Habicht, Klaus and Wagner, Markus Raphael and Klenk, Reiner and Raoux, Simone and Szyszka, Bernd and Lauermann, Iver and Muydinov, Ruslan}, title = {Water-assisted crystallization of amorphous indium zinc oxide films}, series = {Materials today. Communications}, volume = {31}, journal = {Materials today. Communications}, publisher = {Elsevier}, address = {Amsterdam}, issn = {2352-4928}, doi = {10.1016/j.mtcomm.2022.103213}, pages = {10}, year = {2022}, abstract = {Transparent conductive materials based on indium oxide remain yet irreplaceable in various optoelectronic applications. Amorphous oxides appear especially attractive for technology as they are isotropic, demonstrate relatively high electron mobility and can be processed at low temperatures. Among them is indium zinc oxide (IZO) with a large zinc content that is crucial for keeping the amorphous state but redundant for the doping. In this work we investigated water-free and water containing IZO films obtained by radio frequency sputtering. The correlation between temperature driven changes of the chemical state, the optical and electrical properties as well as the progression of crystallization was in focus. Such characterization methods as: scanning electron microscopy, X-ray diffraction, X-ray photoelectron spectroscopy, Raman spectroscopy, temperature dependent Hall-effect measurements and others were applied. Temperature dependent electrical properties of amorphous IZO and IZO:H2O films were found to evolve similarly. Based on our experience in In2O3:H2O (In2O3:H or IOH) we proposed an explanation for the changes observed. Water admixture was found to decrease crystallization temperature of IZO significantly from similar to 550 degrees C to similar to 280 degrees C. Herewith, the presence and concentration of water and/or hydroxyls was found to determine Zn distribution in the film. In particular, Zn enrichment was detected at the film's surface respective to the high water and/or hydroxyl amount. Raman spectra revealed a two-dimensional crystallization of w-ZnO which precedes regardless water presence an extensive In2O3 crystallization. An abrupt loss of electron mobility as a result of crystallization was attributed to the formation of ZnO interlayer on grain boundaries.}, language = {en} } @article{KlugeLevermannSchewe2022, author = {Kluge, Lucas and Levermann, Anders and Schewe, Jacob}, title = {Radiation model for migration with directional preferences}, series = {Physical review : E, Statistical, nonlinear and soft matter physics}, volume = {106}, journal = {Physical review : E, Statistical, nonlinear and soft matter physics}, number = {6}, publisher = {American Physical Society}, address = {College Park}, issn = {2470-0045}, doi = {10.1103/PhysRevE.106.064138}, pages = {10}, year = {2022}, abstract = {The radiation model is a parameter-free model of human mobility that has been applied primarily for short-distance moves, such as commuting. When applied to migration, it underestimates the number of long-range moves, such as between different US states. Here we show that it additionally suffers from a conceptual inconsistency that can have substantial numerical effects on long-distance moves. We propose a modification of the radiation model that introduces a dependence on the angle between any two alternative potential destinations, accounting for the possibility that migrants may have preferences about the approximate direction of their move. We demonstrate that this modification mitigates the conceptual inconsistency and improves the model fit to observational migration data, without introducing any fitting parameters.}, language = {en} } @article{HenkelFolman2022, author = {Henkel, Carsten and Folman, Ron}, title = {Internal decoherence in nano-object interferometry due to phonons}, series = {AVS Quantum Science}, volume = {4}, journal = {AVS Quantum Science}, number = {2}, publisher = {AIP Publishing}, address = {Melville}, issn = {2639-0213}, doi = {10.1116/5.0080503}, pages = {9}, year = {2022}, abstract = {We discuss the coherent splitting and recombining of a nanoparticle in a mesoscopic "closed-loop" Stern-Gerlach interferometer in which the observable is the spin of a single impurity embedded in the particle. This spin, when interacting with a pulsed magnetic gradient, generates the force on the particle. We calculate the internal decoherence, which arises as the displaced impurity excites internal degrees of freedom (phonons) that may provide WelcherWeg information and preclude interference. We estimate the constraints this decoherence channel puts on future interference experiments with massive objects. We find that for a wide range of masses, forces, and temperatures, phonons do not inhibit Stern-Gerlach interferometry with micro-scale objects. However, phonons do constitute a fundamental limit on the splitting of larger macroscopic objects if the applied force induces phonons.}, language = {en} } @article{KamlahVermaDierckeetal.2021, author = {Kamlah, Robert and Verma, Meetu and Diercke, Andrea and Denker, Carsten}, title = {Wavelength dependence of image quality metrics and seeing parameters and their relation to adaptive optics performance}, series = {Solar physics : a journal for solar and solar-stellar research and the study of solar terrestrial physics}, volume = {296}, journal = {Solar physics : a journal for solar and solar-stellar research and the study of solar terrestrial physics}, number = {2}, publisher = {Springer Science + Business Media B.V}, address = {Dordrecht [u.a.]}, issn = {1573-093X}, doi = {10.1007/s11207-021-01771-y}, pages = {29}, year = {2021}, abstract = {Ground-based solar observations are severely affected by Earth's turbulent atmosphere. As a consequence, observed image quality and prevailing seeing conditions are closely related. Partial correction of image degradation is nowadays provided in real time by adaptive optics (AO) systems. In this study, different metrics of image quality are compared with parameters characterizing the prevailing seeing conditions, i.e. Median Filter Gradient Similarity (MFGS), Median Filter Laplacian Similarity (MFLS), Helmli-Scherer mean, granular rms-contrast, differential image motion, and Fried-parameter r(0). The quiet-Sun observations at disk center were carried out at the Vacuum Tower Telescope (VTT), Observatorio del Teide (OT), Izana, Tenerife, Spain. In July and August 2016, time series of short-exposure images were recorded with the High-resolution Fast Imager (HiFI) at various wavelengths in the visible and near-infrared parts of the spectrum. Correlation analysis yields the wavelength dependence of the image quality metrics and seeing parameters, and Uniform Manifold Approximation and Projection (UMAP) is employed to characterize the seeing on a particular observing day. In addition, the image quality metrics and seeing parameters are used to determine the field dependence of the correction provided by the AO system. Management of high-resolution imaging data from large-aperture, ground-based telescopes demands reliable image quality metrics and meaningful characterization of prevailing seeing conditions and AO performance. The present study offers guidance on how retrieving such information ex post facto.}, language = {en} } @article{JonesWiesner2022, author = {Jones, Chris and Wiesner, Karoline}, title = {Clarifying how degree entropies and degree-degree correlations relate to network robustness}, series = {Entropy : an international and interdisciplinary journal of entropy and information studies}, volume = {24}, journal = {Entropy : an international and interdisciplinary journal of entropy and information studies}, number = {9}, publisher = {MDPI}, address = {Basel}, issn = {1099-4300}, doi = {10.3390/e24091182}, pages = {13}, year = {2022}, abstract = {It is often claimed that the entropy of a network's degree distribution is a proxy for its robustness. Here, we clarify the link between degree distribution entropy and giant component robustness to node removal by showing that the former merely sets a lower bound to the latter for randomly configured networks when no other network characteristics are specified. Furthermore, we show that, for networks of fixed expected degree that follow degree distributions of the same form, the degree distribution entropy is not indicative of robustness. By contrast, we show that the remaining degree entropy and robustness have a positive monotonic relationship and give an analytic expression for the remaining degree entropy of the log-normal distribution. We also show that degree-degree correlations are not by themselves indicative of a network's robustness for real networks. We propose an adjustment to how mutual information is measured which better encapsulates structural properties related to robustness.}, language = {en} } @article{NadammalCabezaMishurovaetal.2017, author = {Nadammal, Naresh and Cabeza, Sandra and Mishurova, Tatiana and Thiede, Tobias and Kromm, Arne and Seyfert, Christoph and Farahbod, Lena and Haberland, Christoph and Schneider, Judith Ann and Portella, Pedro Dolabella and Bruno, Giovanni}, title = {Effect of hatch length on the development of microstructure, texture and residual stresses in selective laser melted superalloy Inconel 718}, series = {Materials \& Design}, volume = {134}, journal = {Materials \& Design}, publisher = {Elsevier}, address = {Oxford}, issn = {0264-1275}, doi = {10.1016/j.matdes.2017.08.049}, pages = {139 -- 150}, year = {2017}, abstract = {In the present study, samples fabricated by varying the deposition hatch length during selective laser melting of nickel based superalloy Inconel 718 were investigated. Microstructure and texture of these samples was characterized using scanning electron microscopy, combined with electron back-scattered diffraction, and residual stress assessment, using neutron diffraction method. Textured columnar grains oriented along the sample building direction were observed in the shorter hatch length processed sample. A ten-fold increase in the hatch length reduced the texture intensity by a factor of two attributed to the formation of finer grains in the longer hatch length sample. Larger gradients of transverse residual stress in the longer hatch length sample were also observed. Along the build direction, compressive stresses in the shorter hatch length and negligible stresses for the longer hatch length specimen were observed. Changes to the temperature gradient (G) in response to the hatch length variation, influenced the G to growth rate (R) ratio and the product GxR, in agreement with the microstructures and textures formed. For the residual stress development, geometry of the part also played an important role. In summary, tailored isotropy could be induced in Inconel 718 by a careful selection of parameters during selective laser melting.}, language = {en} } @article{LeverMayerMetjeetal.2021, author = {Lever, Fabiano and Mayer, Dennis and Metje, Jan and Alisauskas, Skirmantas and Calegari, Francesca and D{\"u}sterer, Stefan and Feifel, Raimund and Niebuhr, Mario and Manschwetus, Bastian and Kuhlmann, Marion and Mazza, Tommaso and Robinson, Matthew Scott and Squibb, Richard J. and Trabattoni, Andrea and Wallner, M{\aa}ns and Wolf, Thomas J. A. and G{\"u}hr, Markus}, title = {Core-level spectroscopy of 2-thiouracil at the sulfur L1 and L2,3 edges utilizing a SASE free-electron-laser}, series = {Molecules}, volume = {26}, journal = {Molecules}, number = {21}, publisher = {MDPI}, address = {Basel}, issn = {1420-3049}, doi = {10.3390/molecules26216469}, pages = {11}, year = {2021}, abstract = {In this paper, we report X-ray absorption and core-level electron spectra of the nucleobase derivative 2-thiouracil at the sulfur L1- and L2,3-edges. We used soft X-rays from the free-electron laser FLASH2 for the excitation of isolated molecules and dispersed the outgoing electrons with a magnetic bottle spectrometer. We identified photoelectrons from the 2p core orbital, accompanied by an electron correlation satellite, as well as resonant and non-resonant Coster-Kronig and Auger-Meitner emission at the L1- and L2,3-edges, respectively. We used the electron yield to construct X-ray absorption spectra at the two edges. The experimental data obtained are put in the context of the literature currently available on sulfur core-level and 2-thiouracil spectroscopy.}, language = {en} } @article{TianLiang2022, author = {Tian, Peibo and Liang, Yingjie}, title = {Material coordinate driven variable-order fractal derivative model of water anomalous adsorption in swelling soil}, series = {Chaos, solitons \& fractals}, volume = {164}, journal = {Chaos, solitons \& fractals}, publisher = {Elsevier}, address = {Oxford}, issn = {0960-0779}, doi = {10.1016/j.chaos.2022.112754}, pages = {8}, year = {2022}, abstract = {The diffusion process of water in swelling (expansive) soil often deviates from normal Fick diffusion and belongs to anomalous diffusion. The process of water adsorption by swelling soil often changes with time, in which the microstructure evolves with time and the absorption rate changes along a fractal dimension gradient function. Thus, based on the material coordinate theory, this paper proposes a variable order derivative fractal model to describe the cumulative adsorption of water in the expansive soil, and the variable order is time dependent linearly. The cumulative adsorption is a power law function of the anomalous sorptivity, and patterns of the variable order. The variable-order fractal derivative model is tested to describe the cumulative adsorption in chernozemic surface soil, Wunnamurra clay and sandy loam. The results show that the fractal derivative model with linearly time dependent variable-order has much better accuracy than the fractal derivative model with a constant derivative order and the integer order model in the application cases. The derivative order can be used to distinguish the evolution of the anomalous adsorption process. The variable-order fractal derivative model can serve as an alternative approach to describe water anomalous adsorption in swelling soil.}, language = {en} } @article{SchneiderBytyqiKohautetal.2022, author = {Schneider, Sebastian and Bytyqi, Kushtrim and Kohaut, Stephan and B{\"u}gel, Patrick and Weinschenk, Benjamin and Marz, Michael and Kimouche, Amina and Fink, Karin and Hoffmann-Vogel, Regina}, title = {Molecular self-assembly of DBBA on Au(111) at room temperature}, series = {Physical chemistry, chemical physics : a journal of European Chemical Societies}, volume = {24}, journal = {Physical chemistry, chemical physics : a journal of European Chemical Societies}, number = {46}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1463-9076}, doi = {10.1039/d2cp02268k}, pages = {28371 -- 28380}, year = {2022}, abstract = {We have investigated the self-assembly of the graphene nanoribbon molecular precursor 10,10'-dibromo-9,9'-bianthryl (DBBA) on Au(111) with frequency modulation scanning force microscopy (FM-SFM) at room temperature combined with ab initio calculations. For low molecular coverages, the molecules aggregate along the substrate herringbone reconstruction main directions while remaining mobile. At intermediate coverage, two phases coexist, zigzag stripes of monomer chains and decorated herringbones. For high coverage, the molecules assemble in a dimer-striped phase. The adsorption behaviour of DBBA molecules and their interactions are discussed and compared with the results from ab initio calculations.}, language = {en} } @article{RotheZhaoHalimetal.2022, author = {Rothe, Martin and Zhao, Yuhang and Halim, Henry and Lu, Yan and Benson, Oliver}, title = {Spatial mapping of bleaching in a metal-organic plasmon converter}, series = {Optics continuum}, volume = {1}, journal = {Optics continuum}, number = {8}, publisher = {Optica Publishing Group}, address = {Washington}, issn = {2770-0208}, doi = {10.1364/OPTCON.454911}, pages = {1730 -- 1740}, year = {2022}, abstract = {Hybrid nanophotonic elements, fabricated by organic and inorganic materials, are going to be key components of modern devices. Coupled systems of photoemitters with a plasmonic waveguide serve the demand for nanoscopic frequency converters. However, processes like the degradation of the photoemitters via photobleaching occur and need to be monitored and controlled, to realize future successful devices. We introduce a hybrid perylene-diimide / silver nanowire as plasmon frequency converter. A versatile method is presented to monitor and analyze the bleaching process. It is based on a time series of photoluminescence images, during the operation of a single converter. An analytical model is applied on the data and unveils that the photobleaching rate is constant and independent of the operation of the plasmon converter.}, language = {en} } @article{SliusarenkoVitaliSposinietal.2019, author = {Sliusarenko, Oleksii Yu and Vitali, Silvia and Sposini, Vittoria and Paradisi, Paolo and Chechkin, Aleksei and Castellani, Gastone and Pagnini, Gianni}, title = {Finite-energy Levy-type motion through heterogeneous ensemble of Brownian particles}, series = {Journal of physics : A, Mathematical and theoretical}, volume = {52}, journal = {Journal of physics : A, Mathematical and theoretical}, number = {9}, publisher = {IOP Publ. Ltd.}, address = {Bristol}, issn = {1751-8113}, doi = {10.1088/1751-8121/aafe90}, pages = {27}, year = {2019}, abstract = {Complex systems are known to display anomalous diffusion, whose signature is a space/time scaling x similar to t(delta) with delta not equal 1/2 in the probability density function (PDF). Anomalous diffusion can emerge jointly with both Gaussian, e.g. fractional Brownian motion, and power-law decaying distributions, e.g. Levy Flights or Levy Walks (LWs). Levy flights get anomalous scaling, but, being jumps of any size allowed even at short times, have infinite position variance, infinite energy and discontinuous paths. LWs, which are based on random trapping events, overcome these limitations: they resemble a Levy-type power-law distribution that is truncated in the large displacement range and have finite moments, finite energy and, even with discontinuous velocity, they are continuous. However, LWs do not take into account the role of strong heterogeneity in many complex systems, such as biological transport in the crowded cell environment. In this work we propose and discuss a model describing a heterogeneous ensemble of Brownian particles (HEBP). Velocity of each single particle obeys a standard underdamped Langevin equation for the velocity, with linear friction term and additive Gaussian noise. Each particle is characterized by its own relaxation time and velocity diffusivity. We show that, for proper distributions of relaxation time and velocity diffusivity, the HEBP resembles some LW statistical features, in particular power-law decaying PDF, long-range correlations and anomalous diffusion, at the same time keeping finite position moments and finite energy. The main differences between the HEBP model and two different LWs are investigated, finding that, even when both velocity and position PDFs are similar, they differ in four main aspects: (i) LWs are biscaling, while HEBP is monoscaling; (ii) a transition from anomalous (delta = 1/2) to normal (delta = 1/2) diffusion in the long-time regime is seen in the HEBP and not in LWs; (iii) the power-law index of the position PDF and the space/time diffusion scaling are independent in the HEBP, while they both depend on the scaling of the interevent time PDF in LWs; (iv) at variance with LWs, our HEBP model obeys a fluctuation-dissipation theorem.}, language = {en} } @article{WangCherstvyMetzleretal.2022, author = {Wang, Wei and Cherstvy, Andrey G. and Metzler, Ralf and Sokolov, Igor M.}, title = {Restoring ergodicity of stochastically reset anomalous-diffusion processes}, series = {Physical Review Research}, volume = {4}, journal = {Physical Review Research}, edition = {1}, publisher = {American Physical Society}, address = {College Park, Maryland, United States}, issn = {2643-1564}, doi = {10.1103/PhysRevResearch.4.013161}, pages = {013161-1 -- 013161-13}, year = {2022}, abstract = {How do different reset protocols affect ergodicity of a diffusion process in single-particle-tracking experiments? We here address the problem of resetting of an arbitrary stochastic anomalous-diffusion process (ADP) from the general mathematical points of view and assess ergodicity of such reset ADPs for an arbitrary resetting protocol. The process of stochastic resetting describes the events of the instantaneous restart of a particle's motion via randomly distributed returns to a preset initial position (or a set of those). The waiting times of such resetting events obey the Poissonian, Gamma, or more generic distributions with specified conditions regarding the existence of moments. Within these general approaches, we derive general analytical results and support them by computer simulations for the behavior of the reset mean-squared displacement (MSD), the new reset increment-MSD (iMSD), and the mean reset time-averaged MSD (TAMSD). For parental nonreset ADPs with the MSD(t)∝ tμ we find a generic behavior and a switch of the short-time growth of the reset iMSD and mean reset TAMSDs from ∝ _μ for subdiffusive to ∝ _1 for superdiffusive reset ADPs. The critical condition for a reset ADP that recovers its ergodicity is found to be more general than that for the nonequilibrium stationary state, where obviously the iMSD and the mean TAMSD are equal. The consideration of the new statistical quantifier, the iMSD—as compared to the standard MSD—restores the ergodicity of an arbitrary reset ADP in all situations when the μth moment of the waiting-time distribution of resetting events is finite. Potential applications of these new resetting results are, inter alia, in the area of biophysical and soft-matter systems.}, language = {en} } @article{CherstvyVinodAghionetal.2017, author = {Cherstvy, Andrey G. and Vinod, Deepak and Aghion, Erez and Chechkin, Aleksei and Metzler, Ralf}, title = {Time averaging, ageing and delay analysis of financial time series}, series = {New journal of physics}, volume = {19}, journal = {New journal of physics}, publisher = {IOP}, address = {London}, issn = {1367-2630}, doi = {10.1088/1367-2630/aa7199}, pages = {1 -- 11}, year = {2017}, abstract = {We introduce three strategies for the analysis of financial time series based on time averaged observables. These comprise the time averaged mean squared displacement (MSD) as well as the ageing and delay time methods for varying fractions of the financial time series. We explore these concepts via statistical analysis of historic time series for several Dow Jones Industrial indices for the period from the 1960s to 2015. Remarkably, we discover a simple universal law for the delay time averaged MSD. The observed features of the financial time series dynamics agree well with our analytical results for the time averaged measurables for geometric Brownian motion, underlying the famed Black-Scholes-Merton model. The concepts we promote here are shown to be useful for financial data analysis and enable one to unveil new universal features of stock market dynamics.}, language = {en} } @article{GhoshCherstvyPetrovetal.2016, author = {Ghosh, Surya K. and Cherstvy, Andrey G. and Petrov, Eugene P. and Metzler, Ralf}, title = {Interactions of rod-like particles on responsive elastic sheets}, series = {Soft matter}, journal = {Soft matter}, publisher = {RSC}, address = {London}, issn = {1744-6848}, doi = {10.1039/C6SM01522K}, year = {2016}, abstract = {What are the physical laws of the mutual interactions of objects bound to cell membranes, such as various membrane proteins or elongated virus particles? To rationalise this, we here investigate by extensive computer simulations mutual interactions of rod-like particles adsorbed on the surface of responsive elastic two-dimensional sheets. Specifically, we quantify sheet deformations as a response to adhesion of such filamentous particles. We demonstrate that tip-to-tip contacts of rods are favoured for relatively soft sheets, while side-by-side contacts are preferred for stiffer elastic substrates. These attractive orientation-dependent substrate-mediated interactions between the rod-like particles on responsive sheets can drive their aggregation and self-assembly. The optimal orientation of the membrane-bound rods is established via responding to the elastic energy profiles created around the particles. We unveil the phase diagramme of attractive-repulsive rod-rod interactions in the plane of their separation and mutual orientation. Applications of our results to other systems featuring membrane-associated particles are also discussed.}, language = {en} } @article{CaetanoCarvalhoMetzleretal.2020, author = {Caetano, Daniel L. Z. and Carvalho, Sidney Jurado de and Metzler, Ralf and Cherstvy, Andrey G.}, title = {Critical adsorption of multiple polyelectrolytes onto a nanosphere}, series = {Interface : journal of the Royal Society}, volume = {17}, journal = {Interface : journal of the Royal Society}, number = {167}, publisher = {Royal Society}, address = {London}, issn = {1742-5689}, doi = {10.1098/rsif.2020.0199}, pages = {10}, year = {2020}, abstract = {Employing extensive Monte Carlo computer simulations, we investigate in detail the properties of multichain adsorption of charged flexible polyelectrolytes (PEs) onto oppositely charged spherical nanoparticles (SNPs). We quantify the conditions of critical adsorption-the phase-separation curve between the adsorbed and desorbed states of the PEs-as a function of the SNP surface-charge density and the concentration of added salt. We study the degree of fluctuations of the PE-SNP electrostatic binding energy, which we use to quantify the emergence of the phase subtransitions, including a series of partially adsorbed PE configurations. We demonstrate how the phase-separation adsorption-desorption boundary shifts and splits into multiple subtransitions at low-salt conditions, thereby generalizing and extending the results for critical adsorption of a single PE onto the SNP. The current findings are relevant for finite concentrations of PEs around the attracting SNP, such as the conditions for PE adsorption onto globular proteins carrying opposite electric charges.}, language = {en} } @article{BodrovaChechkinSokolov2019, author = {Bodrova, Anna S. and Chechkin, Aleksei and Sokolov, Igor M.}, title = {Nonrenewal resetting of scaled Brownian motion}, series = {Physical review : E, Statistical, nonlinear and soft matter physics}, volume = {100}, journal = {Physical review : E, Statistical, nonlinear and soft matter physics}, number = {1}, publisher = {American Physical Society}, address = {College Park}, issn = {2470-0045}, doi = {10.1103/PhysRevE.100.012119}, pages = {10}, year = {2019}, abstract = {We investigate an intermittent stochastic process in which diffusive motion with a time-dependent diffusion coefficient, D(t)∼tα-1, α>0 (scaled Brownian motion), is stochastically reset to its initial position and starts anew. The resetting follows a renewal process with either an exponential or a power-law distribution of the waiting times between successive renewals. The resetting events, however, do not affect the time dependence of the diffusion coefficient, so that the whole process appears to be a nonrenewal one. We discuss the mean squared displacement of a particle and the probability density function of its positions in this process. We show that scaled Brownian motion with resetting demonstrates rich behavior whose properties essentially depend on the interplay of the parameters of the resetting process and the particle's displacement infree motion. The motion of particles can remain almost unaffected by resetting but can also get slowed down or even be completely suppressed. Especially interesting are the nonstationary situations in which the mean squared displacement stagnates but the distribution of positions does not tend to any steady state. This behavior is compared to the situation [discussed in the companion paper; A. S. Bodrova et al., Phys. Rev. E 100, 012120 (2019)] in which the memory of the value of the diffusion coefficient at a resetting time is erased, so that the whole process is a fully renewal one. We show that the properties of the probability densities in such processes (erasing or retaining the memory on the diffusion coefficient) are vastly different.}, language = {en} } @article{WangMetzlerCherstvy2022, author = {Wang, Wei and Metzler, Ralf and Cherstvy, Andrey G.}, title = {Anomalous diffusion, aging, and nonergodicity of scaled Brownian motion with fractional Gaussian noise: overview of related experimental observations and models}, series = {Physical chemistry, chemical physics : PCCP ; a journal of European chemical societies}, volume = {24}, journal = {Physical chemistry, chemical physics : PCCP ; a journal of European chemical societies}, number = {31}, publisher = {RSC Publ.}, address = {Cambridge}, issn = {1463-9076}, doi = {10.1039/d2cp01741e}, pages = {18482 -- 18504}, year = {2022}, abstract = {How does a systematic time-dependence of the diffusion coefficient D(t) affect the ergodic and statistical characteristics of fractional Brownian motion (FBM)? Here, we answer this question via studying the characteristics of a set of standard statistical quantifiers relevant to single-particle-tracking (SPT) experiments. We examine, for instance, how the behavior of the ensemble- and time-averaged mean-squared displacements-denoted as the standard MSD < x(2)(Delta)> and TAMSD <<(delta(2)(Delta))over bar>> quantifiers-of FBM featuring < x(2) (Delta >> = <<(delta(2)(Delta >)over bar>> proportional to Delta(2H) (where H is the Hurst exponent and Delta is the [lag] time) changes in the presence of a power-law deterministically varying diffusivity D-proportional to(t) proportional to t(alpha-1) -germane to the process of scaled Brownian motion (SBM)-determining the strength of fractional Gaussian noise. The resulting compound "scaled-fractional" Brownian motion or FBM-SBM is found to be nonergodic, with < x(2)(Delta >> proportional to Delta(alpha+)(2H)(-1) and <(delta 2(Delta >) over bar > proportional to Delta(2H). We also detect a stalling behavior of the MSDs for very subdiffusive SBM and FBM, when alpha + 2H - 1 < 0. The distribution of particle displacements for FBM-SBM remains Gaussian, as that for the parent processes of FBM and SBM, in the entire region of scaling exponents (0 < alpha < 2 and 0 < H < 1). The FBM-SBM process is aging in a manner similar to SBM. The velocity autocorrelation function (ACF) of particle increments of FBM-SBM exhibits a dip when the parent FBM process is subdiffusive. Both for sub- and superdiffusive FBM contributions to the FBM-SBM process, the SBM exponent affects the long-time decay exponent of the ACF. Applications of the FBM-SBM-amalgamated process to the analysis of SPT data are discussed. A comparative tabulated overview of recent experimental (mainly SPT) and computational datasets amenable for interpretation in terms of FBM-, SBM-, and FBM-SBM-like models of diffusion culminates the presentation. The statistical aspects of the dynamics of a wide range of biological systems is compared in the table, from nanosized beads in living cells, to chromosomal loci, to water diffusion in the brain, and, finally, to patterns of animal movements.}, language = {en} } @article{VojtaSkinnerMetzler2019, author = {Vojta, Thomas and Skinner, Sarah and Metzler, Ralf}, title = {Probability density of the fractional Langevin equation with reflecting walls}, series = {Physical review : E, Statistical, nonlinear and soft matter physics}, volume = {100}, journal = {Physical review : E, Statistical, nonlinear and soft matter physics}, number = {4}, publisher = {American Physical Society}, address = {College Park}, issn = {2470-0045}, doi = {10.1103/PhysRevE.100.042142}, pages = {11}, year = {2019}, abstract = {We investigate anomalous diffusion processes governed by the fractional Langevin equation and confined to a finite or semi-infinite interval by reflecting potential barriers. As the random and damping forces in the fractional Langevin equation fulfill the appropriate fluctuation-dissipation relation, the probability density on a finite interval converges for long times towards the expected uniform distribution prescribed by thermal equilibrium. In contrast, on a semi-infinite interval with a reflecting wall at the origin, the probability density shows pronounced deviations from the Gaussian behavior observed for normal diffusion. If the correlations of the random force are persistent (positive), particles accumulate at the reflecting wall while antipersistent (negative) correlations lead to a depletion of particles near the wall. We compare and contrast these results with the strong accumulation and depletion effects recently observed for nonthermal fractional Brownian motion with reflecting walls, and we discuss broader implications.}, language = {en} } @article{SposiniChechkinSenoetal.2018, author = {Sposini, Vittoria and Chechkin, Aleksei and Seno, Flavio and Pagnini, Gianni and Metzler, Ralf}, title = {Random diffusivity from stochastic equations}, series = {New Journal of Physics}, journal = {New Journal of Physics}, publisher = {Deutsche Physikalische Gesellschaft / Institute of Physics}, address = {Bad Honnef und London}, issn = {1367-2630}, doi = {10.1088/1367-2630/aab696}, pages = {1 -- 33}, year = {2018}, abstract = {A considerable number of systems have recently been reported in which Brownian yet non-Gaussian dynamics was observed. These are processes characterised by a linear growth in time of the mean squared displacement, yet the probability density function of the particle displacement is distinctly non-Gaussian, and often of exponential(Laplace) shape. This apparently ubiquitous behaviour observed in very different physical systems has been interpreted as resulting from diffusion in inhomogeneous environments and mathematically represented through a variable, stochastic diffusion coefficient. Indeed different models describing a fluctuating diffusivity have been studied. Here we present a new view of the stochastic basis describing time dependent random diffusivities within a broad spectrum of distributions. Concretely, our study is based on the very generic class of the generalised Gamma distribution. Two models for the particle spreading in such random diffusivity settings are studied. The first belongs to the class of generalised grey Brownian motion while the second follows from the idea of diffusing diffusivities. The two processes exhibit significant characteristics which reproduce experimental results from different biological and physical systems. We promote these two physical models for the description of stochastic particle motion in complex environments.}, language = {en} } @article{VinodCherstvyMetzleretal.2022, author = {Vinod, Deepak and Cherstvy, Andrey G. and Metzler, Ralf and Sokolov, Igor M.}, title = {Time-averaging and nonergodicity of reset geometric Brownian motion with drift}, series = {Physical review : E, Statistical, nonlinear and soft matter physics}, volume = {106}, journal = {Physical review : E, Statistical, nonlinear and soft matter physics}, number = {3}, publisher = {American Physical Society}, address = {College Park}, issn = {2470-0045}, doi = {10.1103/PhysRevE.106.034137}, pages = {36}, year = {2022}, abstract = {How do near-bankruptcy events in the past affect the dynamics of stock-market prices in the future? Specifically, what are the long-time properties of a time-local exponential growth of stock-market prices under the influence of stochastically occurring economic crashes? Here, we derive the ensemble- and time-averaged properties of the respective "economic" or geometric Brownian motion (GBM) with a nonzero drift exposed to a Poissonian constant-rate price-restarting process of "resetting." We examine-based both on thorough analytical calculations and on findings from systematic stochastic computer simulations-the general situation of reset GBM with a nonzero [positive] drift and for all special cases emerging for varying parameters of drift, volatility, and reset rate in the model. We derive and summarize all short- and long-time dependencies for the mean-squared displacement (MSD), the variance, and the mean time-averaged MSD (TAMSD) of the process of Poisson-reset GBM under the conditions of both rare and frequent resetting. We consider three main regions of model parameters and categorize the crossovers between different functional behaviors of the statistical quantifiers of this process. The analytical relations are fully supported by the results of computer simulations. In particular, we obtain that Poisson-reset GBM is a nonergodic stochastic process, with generally MSD(Delta) not equal TAMSD(Delta) and Variance(Delta) not equal TAMSD(Delta) at short lag times Delta and for long trajectory lengths T. We investigate the behavior of the ergodicity-breaking parameter in each of the three regions of parameters and examine its dependence on the rate of reset at Delta/T << 1. Applications of these theoretical results to the analysis of prices of reset-containing options are pertinent.}, language = {en} } @article{SafdariCherstvyChechkinetal.2017, author = {Safdari, Hadiseh and Cherstvy, Andrey G. and Chechkin, Aleksei and Bodrova, Anna and Metzler, Ralf}, title = {Aging underdamped scaled Brownian motion}, series = {Physical review : E, Statistical, nonlinear and soft matter physics}, volume = {95}, journal = {Physical review : E, Statistical, nonlinear and soft matter physics}, publisher = {American Physical Society}, address = {College Park}, issn = {2470-0045}, doi = {10.1103/PhysRevE.95.012120}, pages = {15}, year = {2017}, abstract = {We investigate both analytically and by computer simulations the ensemble- and time-averaged, nonergodic, and aging properties of massive particles diffusing in a medium with a time dependent diffusivity. We call this stochastic diffusion process the (aging) underdamped scaled Brownian motion (UDSBM). We demonstrate how the mean squared displacement (MSD) and the time-averaged MSD of UDSBM are affected by the inertial term in the Langevin equation, both at short, intermediate, and even long diffusion times. In particular, we quantify the ballistic regime for the MSD and the time-averaged MSD as well as the spread of individual time-averaged MSD trajectories. One of the main effects we observe is that, both for the MSD and the time-averaged MSD, for superdiffusive UDSBM the ballistic regime is much shorter than for ordinary Brownian motion. In contrast, for subdiffusive UDSBM, the ballistic region extends to much longer diffusion times. Therefore, particular care needs to be taken under what conditions the overdamped limit indeed provides a correct description, even in the long time limit. We also analyze to what extent ergodicity in the Boltzmann-Khinchin sense in this nonstationary system is broken, both for subdiffusive and superdiffusive UDSBM. Finally, the limiting case of ultraslow UDSBM is considered, with a mixed logarithmic and power-law dependence of the ensemble-and time-averaged MSDs of the particles. In the limit of strong aging, remarkably, the ordinary UDSBM and the ultraslow UDSBM behave similarly in the short time ballistic limit. The approaches developed here open ways for considering other stochastic processes under physically important conditions when a finite particle mass and aging in the system cannot be neglected.}, language = {en} } @article{SandevMetzlerChechkin2018, author = {Sandev, Trifce and Metzler, Ralf and Chechkin, Aleksei}, title = {From continuous time random walks to the generalized diffusion equation}, series = {Fractional calculus and applied analysis : an international journal for theory and applications}, volume = {21}, journal = {Fractional calculus and applied analysis : an international journal for theory and applications}, number = {1}, publisher = {De Gruyter}, address = {Berlin}, issn = {1311-0454}, doi = {10.1515/fca-2018-0002}, pages = {10 -- 28}, year = {2018}, abstract = {We obtain a generalized diffusion equation in modified or Riemann-Liouville form from continuous time random walk theory. The waiting time probability density function and mean squared displacement for different forms of the equation are explicitly calculated. We show examples of generalized diffusion equations in normal or Caputo form that encode the same probability distribution functions as those obtained from the generalized diffusion equation in modified form. The obtained equations are general and many known fractional diffusion equations are included as special cases.}, language = {en} } @article{PalyulinBlackburnLomholtetal.2019, author = {Palyulin, Vladimir V. and Blackburn, George and Lomholt, Michael A. and Watkins, Nicholas W. and Metzler, Ralf and Klages, Rainer and Chechkin, Aleksei}, title = {First passage and first hitting times of Levy flights and Levy walks}, series = {New journal of physics : the open-access journal for physics}, volume = {21}, journal = {New journal of physics : the open-access journal for physics}, number = {10}, publisher = {IOP Publ. Ltd.}, address = {Bristol}, issn = {1367-2630}, doi = {10.1088/1367-2630/ab41bb}, pages = {23}, year = {2019}, abstract = {For both L{\´e}vy flight and L{\´e}vy walk search processes we analyse the full distribution of first-passage and first-hitting (or first-arrival) times. These are, respectively, the times when the particle moves across a point at some given distance from its initial position for the first time, or when it lands at a given point for the first time. For L{\´e}vy motions with their propensity for long relocation events and thus the possibility to jump across a given point in space without actually hitting it ('leapovers'), these two definitions lead to significantly different results. We study the first-passage and first-hitting time distributions as functions of the L{\´e}vy stable index, highlighting the different behaviour for the cases when the first absolute moment of the jump length distribution is finite or infinite. In particular we examine the limits of short and long times. Our results will find their application in the mathematical modelling of random search processes as well as computer algorithms.}, language = {en} } @article{DietrichHindererSamajdar2021, author = {Dietrich, Tim and Hinderer, Tanja and Samajdar, Anuradha}, title = {Interpreting binary neutron star mergers}, series = {General relativity and gravitation : GRG journal}, volume = {53}, journal = {General relativity and gravitation : GRG journal}, number = {3}, publisher = {Springer Science + Business Media B.V.}, address = {New York, NY [u.a.]}, issn = {0001-7701}, doi = {10.1007/s10714-020-02751-6}, pages = {76}, year = {2021}, abstract = {Gravitational waves emitted from the coalescence of neutron star binaries open a new window to probe matter and fundamental physics in unexplored, extreme regimes. To extract information about the supranuclear matter inside neutron stars and the properties of the compact binary systems, robust theoretical prescriptions are required. We give an overview about general features of the dynamics and the gravitational wave signal during the binary neutron star coalescence. We briefly describe existing analytical and numerical approaches to investigate the highly dynamical, strong-field region during the merger. We review existing waveform approximants and discuss properties and possible advantages and shortcomings of individual waveform models, and their application for real gravitational-wave data analysis.}, language = {en} } @article{DenkerKuckeinVermaetal.2018, author = {Denker, Carsten and Kuckein, Christoph and Verma, Meetu and Manrique Gonzalez, Sergio Javier Gonzalez and Diercke, Andrea and Enke, Harry and Klar, Jochen and Balthasar, Horst and Louis, Rohan E. and Dineva, Ekaterina Ivanova}, title = {High-cadence Imaging and Imaging Spectroscopy at the GREGOR Solar Telescope-A Collaborative Research Environment for High-resolution Solar Physics}, series = {The astrophysical journal : an international review of spectroscopy and astronomical physics ; Supplement series}, volume = {236}, journal = {The astrophysical journal : an international review of spectroscopy and astronomical physics ; Supplement series}, number = {1}, publisher = {IOP Publ. Ltd.}, address = {Bristol}, issn = {0067-0049}, doi = {10.3847/1538-4365/aab773}, pages = {12}, year = {2018}, abstract = {In high-resolution solar physics, the volume and complexity of photometric, spectroscopic, and polarimetric ground-based data significantly increased in the last decade, reaching data acquisition rates of terabytes per hour. This is driven by the desire to capture fast processes on the Sun and the necessity for short exposure times "freezing" the atmospheric seeing, thus enabling ex post facto image restoration. Consequently, large-format and high-cadence detectors are nowadays used in solar observations to facilitate image restoration. Based on our experience during the "early science" phase with the 1.5 m GREGOR solar telescope (2014-2015) and the subsequent transition to routine observations in 2016, we describe data collection and data management tailored toward image restoration and imaging spectroscopy. We outline our approaches regarding data processing, analysis, and archiving for two of GREGOR's post-focus instruments (see http://gregor.aip.de), i.e., the GREGOR Fabry-P{\´e}rot Interferometer (GFPI) and the newly installed High-Resolution Fast Imager (HiFI). The heterogeneous and complex nature of multidimensional data arising from high-resolution solar observations provides an intriguing but also a challenging example for "big data" in astronomy. The big data challenge has two aspects: (1) establishing a workflow for publishing the data for the whole community and beyond and (2) creating a collaborative research environment (CRE), where computationally intense data and postprocessing tools are colocated and collaborative work is enabled for scientists of multiple institutes. This requires either collaboration with a data center or frameworks and databases capable of dealing with huge data sets based on virtual observatory (VO) and other community standards and procedures.}, language = {en} } @article{DierckeKuckeinDenker2019, author = {Diercke, Andrea and Kuckein, Christoph and Denker, Carsten}, title = {Dynamics and connectivity of an extended arch filament system}, series = {Astronomy and astrophysics : an international weekly journal}, volume = {629}, journal = {Astronomy and astrophysics : an international weekly journal}, publisher = {EDP Sciences}, address = {Les Ulis}, issn = {1432-0746}, doi = {10.1051/0004-6361/201935583}, pages = {14}, year = {2019}, abstract = {Aims. In this study, we analyzed a filament system, which expanded between moving magnetic features (MMFs) of a decaying sunspot and opposite flux outside of the active region from the nearby quiet-Sun network. This configuration deviated from a classical arch filament system (AFS), which typically connects two pores in an emerging flux region. Thus, we called this system an extended AFS. We contrasted classical and extended AFSs with an emphasis on the complex magnetic structure of the latter. Furthermore, we examined the physical properties of the extended AFS and described its dynamics and connectivity. Methods. The extended AFS was observed with two instruments at the Dunn Solar Telescope (DST). The Rapid Oscillations in the Solar Atmosphere (ROSA) imager provided images in three different wavelength regions, which covered the dynamics of the extended AFS at different atmospheric heights. The Interferometric Bidimensional Spectropolarimeter (IBIS) provided spectroscopic Ha data and spectropolarimetric data that was obtained in the near-infrared (NIR) Call lambda 8542 angstrom line. We derived the corresponding line-of-sight (LOS) velocities and used He II lambda 304 angstrom extreme ultraviolet (EUV) images of the Atmospheric Imaging Assembly (AIA) and LOS magnetograms of the Helioseismic and Magnetic Imager (HMI) on board the Solar Dynamics Observatory (SDO) as context data. Results. The NIR Call Stokes-V maps are not suitable to definitively define a clear polarity inversion line and to classify this chromospheric structure. Nevertheless, this unusual AFS connects the MMFs of a decaying sunspot with the network field. At the southern footpoint, we measured that the flux decreases over time. We find strong downflow velocities at the footpoints of the extended AFS, which increase in a time period of 30 min. The velocities are asymmetric at both footpoints with higher velocities at the southern footpoint. An EUV brigthening appears in one of the arch filaments, which migrates from the northern footpoint toward the southern one. This activation likely influences the increasing redshift at the southern footpoint. Conclusions. The extended AFS exhibits a similar morphology as classical AFSs, for example, threaded filaments of comparable length and width. Major differences concern the connection from MMFs around the sunspot with the flux of the neighboring quietSun network, converging footpoint motions, and longer lifetimes of individual arch filaments of about one hour, while the extended AFS is still very dynamic.}, language = {en} } @article{DoerriesChechkinMetzler2022, author = {Doerries, Timo J. and Chechkin, Aleksei and Metzler, Ralf}, title = {Apparent anomalous diffusion and non-Gaussian distributions in a simple mobile-immobile transport model with Poissonian switching}, series = {Interface : journal of the Royal Society}, volume = {19}, journal = {Interface : journal of the Royal Society}, number = {192}, publisher = {Royal Society}, address = {London}, issn = {1742-5689}, doi = {10.1098/rsif.2022.0233}, pages = {14}, year = {2022}, abstract = {We analyse mobile-immobile transport of particles that switch between the mobile and immobile phases with finite rates. Despite this seemingly simple assumption of Poissonian switching, we unveil a rich transport dynamics including significant transient anomalous diffusion and non-Gaussian displacement distributions. Our discussion is based on experimental parameters for tau proteins in neuronal cells, but the results obtained here are expected to be of relevance for a broad class of processes in complex systems. Specifically, we obtain that, when the mean binding time is significantly longer than the mean mobile time, transient anomalous diffusion is observed at short and intermediate time scales, with a strong dependence on the fraction of initially mobile and immobile particles. We unveil a Laplace distribution of particle displacements at relevant intermediate time scales. For any initial fraction of mobile particles, the respective mean squared displacement (MSD) displays a plateau. Moreover, we demonstrate a short-time cubic time dependence of the MSD for immobile tracers when initially all particles are immobile.}, language = {en} } @article{HartmannGoetzkeDuestereretal.2022, author = {Hartmann, Gregor and Goetzke, Gesa and D{\"u}sterer, Stefan and Feuer-Forson, Peter and Lever, Fabiano and Meier, David and M{\"o}ller, Felix and Ramirez, Luis Vera and G{\"u}hr, Markus and Tiedtke, Kai and Viefhaus, Jens and Braune, Markus}, title = {Unsupervised real-world knowledge extraction via disentangled variational autoencoders for photon diagnostics}, series = {Scientific reports}, volume = {12}, journal = {Scientific reports}, number = {1}, publisher = {Springer Nature}, address = {London}, issn = {2045-2322}, doi = {10.1038/s41598-022-25249-4}, pages = {10}, year = {2022}, abstract = {We present real-world data processing on measured electron time-of-flight data via neural networks. Specifically, the use of disentangled variational autoencoders on data from a diagnostic instrument for online wavelength monitoring at the free electron laser FLASH in Hamburg. Without a-priori knowledge the network is able to find representations of single-shot FEL spectra, which have a low signal-to-noise ratio. This reveals, in a directly human-interpretable way, crucial information about the photon properties. The central photon energy and the intensity as well as very detector-specific features are identified. The network is also capable of data cleaning, i.e. denoising, as well as the removal of artefacts. In the reconstruction, this allows for identification of signatures with very low intensity which are hardly recognisable in the raw data. In this particular case, the network enhances the quality of the diagnostic analysis at FLASH. However, this unsupervised method also has the potential to improve the analysis of other similar types of spectroscopy data.}, language = {en} } @article{GoswamiChakiChakrabarti2022, author = {Goswami, Koushik and Chaki, Subhasish and Chakrabarti, Rajarshi}, title = {Reconfiguration, swelling and tagged monomer dynamics of a single polymer chain in Gaussian and non-Gaussian active baths}, series = {Journal of physics : concerned with the fundamental mathematical and computational methods underpinning physics, the journal is particularly relevant to statistical physics, chaotic and complex systems, classical and quantum mechanics and classical and quantum field theory. A, Mathematical and theoretical}, volume = {55}, journal = {Journal of physics : concerned with the fundamental mathematical and computational methods underpinning physics, the journal is particularly relevant to statistical physics, chaotic and complex systems, classical and quantum mechanics and classical and quantum field theory. A, Mathematical and theoretical}, number = {42}, publisher = {IOP Publ. Ltd.}, address = {Bristol}, issn = {1751-8113}, doi = {10.1088/1751-8121/ac96db}, pages = {48}, year = {2022}, abstract = {In this topical review, we give an overview of the structure and dynamics of a single polymer chain in active baths, Gaussian or non-Gaussian. The review begins with the discussion of single flexible or semiflexible linear polymer chains subjected to two noises, thermal and active. The active noise has either Gaussian or non-Gaussian distribution but has a memory, accounting for the persistent motion of the active bath particles. This finite persistence makes the reconfiguration dynamics of the chain slow as compared to the purely thermal case and the chain swells. The active noise also results superdiffusive or ballistic motion of the tagged monomer. We present all the calculations in details but mainly focus on the analytically exact or almost exact results on the topic, as obtained from our group in recent years. In addition, we briefly mention important works of other groups and include some of our new results. The review concludes with pointing out the implications of polymer chains in active bath in biologically relevant context and its future directions.}, language = {en} } @article{KraemerHellmannAnvarietal.2022, author = {Kr{\"a}mer, Kai Hauke and Hellmann, Frank and Anvari, Mehrnaz and Kurths, J{\"u}rgen and Marwan, Norbert}, title = {Spike spectra for recurrences}, series = {Entropy : an international and interdisciplinary journal of entropy and information studies}, volume = {24}, journal = {Entropy : an international and interdisciplinary journal of entropy and information studies}, number = {11}, publisher = {MDPI}, address = {Basel}, issn = {1099-4300}, doi = {10.3390/e24111689}, pages = {18}, year = {2022}, abstract = {In recurrence analysis, the tau-recurrence rate encodes the periods of the cycles of the underlying high-dimensional time series. It, thus, plays a similar role to the autocorrelation for scalar time-series in encoding temporal correlations. However, its Fourier decomposition does not have a clean interpretation. Thus, there is no satisfactory analogue to the power spectrum in recurrence analysis. We introduce a novel method to decompose the tau-recurrence rate using an over-complete basis of Dirac combs together with sparsity regularization. We show that this decomposition, the inter-spike spectrum, naturally provides an analogue to the power spectrum for recurrence analysis in the sense that it reveals the dominant periodicities of the underlying time series. We show that the inter-spike spectrum correctly identifies patterns and transitions in the underlying system in a wide variety of examples and is robust to measurement noise.}, language = {en} } @article{MardoukhiChechkinMetzler2020, author = {Mardoukhi, Yousof and Chechkin, Aleksei and Metzler, Ralf}, title = {Spurious ergodicity breaking in normal and fractional Ornstein-Uhlenbeck process}, series = {New Journal of Physics}, volume = {22}, journal = {New Journal of Physics}, publisher = {IOP}, address = {London}, issn = {1367-2630}, doi = {10.1088/1367-2630/ab950b}, pages = {18}, year = {2020}, abstract = {The Ornstein-Uhlenbeck process is a stationary and ergodic Gaussian process, that is fully determined by its covariance function and mean. We show here that the generic definitions of the ensemble- and time-averaged mean squared displacements fail to capture these properties consistently, leading to a spurious ergodicity breaking. We propose to remedy this failure by redefining the mean squared displacements such that they reflect unambiguously the statistical properties of any stochastic process. In particular we study the effect of the initial condition in the Ornstein-Uhlenbeck process and its fractional extension. For the fractional Ornstein-Uhlenbeck process representing typical experimental situations in crowded environments such as living biological cells, we show that the stationarity of the process delicately depends on the initial condition.}, language = {en} } @article{deCarvalhoMetzlerCherstvy2016, author = {de Carvalho, Sidney J. and Metzler, Ralf and Cherstvy, Andrey G.}, title = {Critical adsorption of polyelectrolytes onto planar and convex highly charged surfaces}, series = {New journal of physics : the open-access journal for physics}, volume = {18}, journal = {New journal of physics : the open-access journal for physics}, publisher = {IOP Publ.}, address = {London}, issn = {1367-2630}, doi = {10.1088/1367-2630/18/8/083037}, year = {2016}, abstract = {We study the adsorption-desorption transition of polyelectrolyte chains onto planar, cylindrical and spherical surfaces with arbitrarily high surface charge densities by massive Monte Carlo computer simulations. We examine in detail how the well known scaling relations for the threshold transition—demarcating the adsorbed and desorbed domains of a polyelectrolyte near weakly charged surfaces—are altered for highly charged interfaces. In virtue of high surface potentials and large surface charge densities, the Debye-H{\"u}ckel approximation is often not feasible and the nonlinear Poisson-Boltzmann approach should be implemented. At low salt conditions, for instance, the electrostatic potential from the nonlinear Poisson-Boltzmann equation is smaller than the Debye-H{\"u}ckel result, such that the required critical surface charge density for polyelectrolyte adsorption σc increases. The nonlinear relation between the surface charge density and electrostatic potential leads to a sharply increasing critical surface charge density with growing ionic strength, imposing an additional limit to the critical salt concentration above which no polyelectrolyte adsorption occurs at all. We contrast our simulations findings with the known scaling results for weak critical polyelectrolyte adsorption onto oppositely charged surfaces for the three standard geometries. Finally, we discuss some applications of our results for some physical-chemical and biophysical systems.}, language = {en} } @article{BodrovaChechkinCherstvyetal.2016, author = {Bodrova, Anna S. and Chechkin, Aleksei and Cherstvy, Andrey G. and Safdari, Hadiseh and Sokolov, Igor M. and Metzler, Ralf}, title = {Underdamped scaled Brownian motion}, series = {Scientific reports}, volume = {6}, journal = {Scientific reports}, publisher = {Nature Publishing Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/srep30520}, year = {2016}, abstract = {It is quite generally assumed that the overdamped Langevin equation provides a quantitative description of the dynamics of a classical Brownian particle in the long time limit. We establish and investigate a paradigm anomalous diffusion process governed by an underdamped Langevin equation with an explicit time dependence of the system temperature and thus the diffusion and damping coefficients. We show that for this underdamped scaled Brownian motion (UDSBM) the overdamped limit fails to describe the long time behaviour of the system and may practically even not exist at all for a certain range of the parameter values. Thus persistent inertial effects play a non-negligible role even at significantly long times. From this study a general questions on the applicability of the overdamped limit to describe the long time motion of an anomalously diffusing particle arises, with profound consequences for the relevance of overdamped anomalous diffusion models. We elucidate our results in view of analytical and simulations results for the anomalous diffusion of particles in free cooling granular gases.}, language = {en} } @article{CherstvyThapaMardoukhietal.2018, author = {Cherstvy, Andrey G. and Thapa, Samudrajit and Mardoukhi, Yousof and Chechkin, Aleksei and Metzler, Ralf}, title = {Time averages and their statistical variation for the Ornstein-Uhlenbeck process}, series = {Physical review : E, Statistical, nonlinear and soft matter physics}, volume = {98}, journal = {Physical review : E, Statistical, nonlinear and soft matter physics}, number = {2}, publisher = {American Physical Society}, address = {College Park}, issn = {2470-0045}, doi = {10.1103/PhysRevE.98.022134}, pages = {15}, year = {2018}, abstract = {How ergodic is diffusion under harmonic confinements? How strongly do ensemble- and time-averaged displacements differ for a thermally-agitated particle performing confined motion for different initial conditions? We here study these questions for the generic Ornstein-Uhlenbeck (OU) process and derive the analytical expressions for the second and fourth moment. These quantifiers are particularly relevant for the increasing number of single-particle tracking experiments using optical traps. For a fixed starting position, we discuss the definitions underlying the ensemble averages. We also quantify effects of equilibrium and nonequilibrium initial particle distributions onto the relaxation properties and emerging nonequivalence of the ensemble- and time-averaged displacements (even in the limit of long trajectories). We derive analytical expressions for the ergodicity breaking parameter quantifying the amplitude scatter of individual time-averaged trajectories, both for equilibrium and outof-equilibrium initial particle positions, in the entire range of lag times. Our analytical predictions are in excellent agreement with results of computer simulations of the Langevin equation in a parabolic potential. We also examine the validity of the Einstein relation for the ensemble- and time-averaged moments of the OU-particle. Some physical systems, in which the relaxation and nonergodic features we unveiled may be observable, are discussed.}, language = {en} } @article{SandevTomovskiDubbeldametal.2018, author = {Sandev, Trifce and Tomovski, Zivorad and Dubbeldam, Johan L. A. and Chechkin, Aleksei}, title = {Generalized diffusion-wave equation with memory kernel}, series = {Journal of physics : A, Mathematical and theoretical}, volume = {52}, journal = {Journal of physics : A, Mathematical and theoretical}, number = {1}, publisher = {IOP Publ. Ltd.}, address = {Bristol}, issn = {1751-8113}, doi = {10.1088/1751-8121/aaefa3}, pages = {22}, year = {2018}, abstract = {We study generalized diffusion-wave equation in which the second order time derivative is replaced by an integro-differential operator. It yields time fractional and distributed order time fractional diffusion-wave equations as particular cases. We consider different memory kernels of the integro-differential operator, derive corresponding fundamental solutions, specify the conditions of their non-negativity and calculate the mean squared displacement for all cases. In particular, we introduce and study generalized diffusion-wave equations with a regularized Prabhakar derivative of single and distributed orders. The equations considered can be used for modeling the broad spectrum of anomalous diffusion processes and various transitions between different diffusion regimes.}, language = {en} } @article{AryaUmlandtJelkenetal.2021, author = {Arya, Pooja and Umlandt, Maren and Jelken, Joachim and Feldmann, David and Lomadze, Nino and Asmolov, Evgeny S. and Vinogradova, Olga I. and Santer, Svetlana}, title = {Light-induced manipulation of passive and active microparticles}, series = {The European physical journal. E, Soft matter}, volume = {44}, journal = {The European physical journal. E, Soft matter}, number = {4}, publisher = {Springer}, address = {Berlin}, issn = {1292-8941}, doi = {10.1140/epje/s10189-021-00032-x}, pages = {10}, year = {2021}, abstract = {We consider sedimented at a solid wall particles that are immersed in water containing small additives of photosensitive ionic surfactants. It is shown that illumination with an appropriate wavelength, a beam intensity profile, shape and size could lead to a variety of dynamic, both unsteady and steady state, configurations of particles. These dynamic, well-controlled and switchable particle patterns at the wall are due to an emerging diffusio-osmotic flow that takes its origin in the adjacent to the wall electrostatic diffuse layer, where the concentration gradients of surfactant are induced by light. The conventional nonporous particles are passive and can move only with already generated flow. However, porous colloids actively participate themselves in the flow generation mechanism at the wall, which also sets their interactions that can be very long ranged. This light-induced diffusio-osmosis opens novel avenues to manipulate colloidal particles and assemble them to various patterns. We show in particular how to create and split optically the confined regions of particles of tunable size and shape, where well-controlled flow-induced forces on the colloids could result in their crystalline packing, formation of dilute lattices of well-separated particles, and other states.}, language = {en} } @article{CherstvyVinodAghionetal.2021, author = {Cherstvy, Andrey G. and Vinod, Deepak and Aghion, Erez and Sokolov, Igor M. and Metzler, Ralf}, title = {Scaled geometric Brownian motion features sub- or superexponential ensemble-averaged, but linear time-averaged mean-squared displacements}, series = {Physical review : E, Statistical, nonlinear and soft matter physics}, volume = {103}, journal = {Physical review : E, Statistical, nonlinear and soft matter physics}, number = {6}, publisher = {American Physical Society}, address = {College Park}, issn = {2470-0045}, doi = {10.1103/PhysRevE.103.062127}, pages = {11}, year = {2021}, abstract = {Various mathematical Black-Scholes-Merton-like models of option pricing employ the paradigmatic stochastic process of geometric Brownian motion (GBM). The innate property of such models and of real stock-market prices is the roughly exponential growth of prices with time [on average, in crisis-free times]. We here explore the ensemble- and time averages of a multiplicative-noise stochastic process with power-law-like time-dependent volatility, sigma(t) similar to t(alpha), named scaled GBM (SGBM). For SGBM, the mean-squared displacement (MSD) computed for an ensemble of statistically equivalent trajectories can grow faster than exponentially in time, while the time-averaged MSD (TAMSD)-based on a sliding-window averaging along a single trajectory-is always linear at short lag times Delta. The proportionality factor between these the two averages of the time series is Delta/T at short lag times, where T is the trajectory length, similarly to GBM. This discrepancy of the scaling relations and pronounced nonequivalence of the MSD and TAMSD at Delta/T << 1 is a manifestation of weak ergodicity breaking for standard GBM and for SGBM with s (t)-modulation, the main focus of our analysis. The analytical predictions for the MSD and mean TAMSD for SGBM are in quantitative agreement with the results of stochastic computer simulations.}, language = {en} } @article{RitschelCherstvyMetzler2021, author = {Ritschel, Stefan and Cherstvy, Andrey G. and Metzler, Ralf}, title = {Universality of delay-time averages for financial time series}, series = {Journal of physics. Complexity}, volume = {2}, journal = {Journal of physics. Complexity}, number = {4}, publisher = {IOP Publ. Ltd.}, address = {Bristol}, issn = {2632-072X}, doi = {10.1088/2632-072X/ac2220}, pages = {30}, year = {2021}, abstract = {We analyze historical data of stock-market prices for multiple financial indices using the concept of delay-time averaging for the financial time series (FTS). The region of validity of our recent theoretical predictions [Cherstvy A G et al 2017 New J. Phys. 19 063045] for the standard and delayed time-averaged mean-squared 'displacements' (TAMSDs) of the historical FTS is extended to all lag times. As the first novel element, we perform extensive computer simulations of the stochastic differential equation describing geometric Brownian motion (GBM) which demonstrate a quantitative agreement with the analytical long-term price-evolution predictions in terms of the delayed TAMSD (for all stock-market indices in crisis-free times). Secondly, we present a robust procedure of determination of the model parameters of GBM via fitting the features of the price-evolution dynamics in the FTS for stocks and cryptocurrencies. The employed concept of single-trajectory-based time averaging can serve as a predictive tool (proxy) for a mathematically based assessment and rationalization of probabilistic trends in the evolution of stock-market prices.}, language = {en} } @article{PadashAghionSchulzetal.2022, author = {Padash, Amin and Aghion, Erez and Schulz, Alexander and Barkai, Eli and Chechkin, Aleksei and Metzler, Ralf and Kantz, Holger}, title = {Local equilibrium properties of ultraslow diffusion in the Sinai model}, series = {New journal of physics}, volume = {24}, journal = {New journal of physics}, number = {7}, publisher = {IOP Publishing}, address = {Bristol}, issn = {1367-2630}, doi = {10.1088/1367-2630/ac7df8}, pages = {14}, year = {2022}, abstract = {We perform numerical studies of a thermally driven, overdamped particle in a random quenched force field, known as the Sinai model. We compare the unbounded motion on an infinite 1-dimensional domain to the motion in bounded domains with reflecting boundaries and show that the unbounded motion is at every time close to the equilibrium state of a finite system of growing size. This is due to time scale separation: inside wells of the random potential, there is relatively fast equilibration, while the motion across major potential barriers is ultraslow. Quantities studied by us are the time dependent mean squared displacement, the time dependent mean energy of an ensemble of particles, and the time dependent entropy of the probability distribution. Using a very fast numerical algorithm, we can explore times up top 10(17) steps and thereby also study finite-time crossover phenomena.}, language = {en} } @article{VinodCherstvyWangetal.2022, author = {Vinod, Deepak and Cherstvy, Andrey G. and Wang, Wei and Metzler, Ralf and Sokolov, Igor M.}, title = {Nonergodicity of reset geometric Brownian motion}, series = {Physical review : E, Statistical, nonlinear and soft matter physics}, volume = {105}, journal = {Physical review : E, Statistical, nonlinear and soft matter physics}, number = {1}, publisher = {American Physical Society}, address = {College Park}, issn = {2470-0045}, doi = {10.1103/PhysRevE.105.L012106}, pages = {4}, year = {2022}, abstract = {We derive. the ensemble-and time-averaged mean-squared displacements (MSD, TAMSD) for Poisson-reset geometric Brownian motion (GBM), in agreement with simulations. We find MSD and TAMSD saturation for frequent resetting, quantify the spread of TAMSDs via the ergodicity-breaking parameter and compute distributions of prices. General MSD-TAMSD nonequivalence proves reset GBM nonergodic.}, language = {en} } @article{ŚlęzakBurneckiMetzler2019, author = {Ślęzak, Jakub and Burnecki, Krzysztof and Metzler, Ralf}, title = {Random coefficient autoregressive processes describe Brownian yet non-Gaussian diffusion in heterogeneous systems}, series = {New Journal of Physics}, volume = {21}, journal = {New Journal of Physics}, publisher = {Deutsche Physikalische Gesellschaft ; IOP, Institute of Physics}, address = {Bad Honnef und London}, issn = {1367-2630}, doi = {10.1088/1367-2630/ab3366}, pages = {18}, year = {2019}, abstract = {Many studies on biological and soft matter systems report the joint presence of a linear mean-squared displacement and a non-Gaussian probability density exhibiting, for instance, exponential or stretched-Gaussian tails. This phenomenon is ascribed to the heterogeneity of the medium and is captured by random parameter models such as 'superstatistics' or 'diffusing diffusivity'. Independently, scientists working in the area of time series analysis and statistics have studied a class of discrete-time processes with similar properties, namely, random coefficient autoregressive models. In this work we try to reconcile these two approaches and thus provide a bridge between physical stochastic processes and autoregressive models.Westart from the basic Langevin equation of motion with time-varying damping or diffusion coefficients and establish the link to random coefficient autoregressive processes. By exploring that link we gain access to efficient statistical methods which can help to identify data exhibiting Brownian yet non-Gaussian diffusion.}, language = {en} } @article{LiMeiXuetal.2020, author = {Li, Yongge and Mei, Ruoxing and Xu, Yong and Kurths, J{\"u}rgen and Duan, Jinqiao and Metzler, Ralf}, title = {Particle dynamics and transport enhancement in a confined channel with position-dependent diffusivity}, series = {New Journal of Physics}, volume = {22}, journal = {New Journal of Physics}, publisher = {Dt. Physikalische Ges.}, address = {Bad Honnef}, issn = {1367-2630}, doi = {10.1088/1367-2630/ab81b9}, pages = {27}, year = {2020}, abstract = {This work focuses on the dynamics of particles in a confined geometry with position-dependent diffusivity, where the confinement is modelled by a periodic channel consisting of unit cells connected by narrow passage ways. We consider three functional forms for the diffusivity, corresponding to the scenarios of a constant (D ₀), as well as a low (D ₘ) and a high (D d) mobility diffusion in cell centre of the longitudinally symmetric cells. Due to the interaction among the diffusivity, channel shape and external force, the system exhibits complex and interesting phenomena. By calculating the probability density function, mean velocity and mean first exit time with the It{\^o} calculus form, we find that in the absence of external forces the diffusivity D d will redistribute particles near the channel wall, while the diffusivity D ₘ will trap them near the cell centre. The superposition of external forces will break their static distributions. Besides, our results demonstrate that for the diffusivity D d, a high dependence on the x coordinate (parallel with the central channel line) will improve the mean velocity of the particles. In contrast, for the diffusivity D ₘ, a weak dependence on the x coordinate will dramatically accelerate the moving speed. In addition, it shows that a large external force can weaken the influences of different diffusivities; inversely, for a small external force, the types of diffusivity affect significantly the particle dynamics. In practice, one can apply these results to achieve a prominent enhancement of the particle transport in two- or three-dimensional channels by modulating the local tracer diffusivity via an engineered gel of varying porosity or by adding a cold tube to cool down the diffusivity along the central line, which may be a relevant effect in engineering applications. Effects of different stochastic calculi in the evaluation of the underlying multiplicative stochastic equation for different physical scenarios are discussed.}, language = {en} } @article{RamosBuilesJaramilloPovedaetal.2017, author = {Ramos, Antonio M. T. and Builes-Jaramillo, Alejandro and Poveda, German and Goswami, Bedartha and Macau, Elbert E. N. and Kurths, J{\"u}rgen and Marwan, Norbert}, title = {Recurrence measure of conditional dependence and applications}, series = {Physical review : E, Statistical, nonlinear and soft matter physics}, volume = {95}, journal = {Physical review : E, Statistical, nonlinear and soft matter physics}, publisher = {American Physical Society}, address = {College Park}, issn = {2470-0045}, doi = {10.1103/PhysRevE.95.052206}, pages = {8}, year = {2017}, abstract = {Identifying causal relations from observational data sets has posed great challenges in data-driven causality inference studies. One of the successful approaches to detect direct coupling in the information theory framework is transfer entropy. However, the core of entropy-based tools lies on the probability estimation of the underlying variables. Herewe propose a data-driven approach for causality inference that incorporates recurrence plot features into the framework of information theory. We define it as the recurrence measure of conditional dependence (RMCD), and we present some applications. The RMCD quantifies the causal dependence between two processes based on joint recurrence patterns between the past of the possible driver and present of the potentially driven, excepting the contribution of the contemporaneous past of the driven variable. Finally, it can unveil the time scale of the influence of the sea-surface temperature of the Pacific Ocean on the precipitation in the Amazonia during recent major droughts.}, language = {en} } @article{WangSenoSokolovetal.2020, author = {Wang, Wei and Seno, Flavio and Sokolov, Igor M. and Chechkin, Aleksei and Metzler, Ralf}, title = {Unexpected crossovers in correlated random-diffusivity processes}, series = {New Journal of Physics}, volume = {22}, journal = {New Journal of Physics}, publisher = {Dt. Physikalische Ges.}, address = {Bad Honnef}, issn = {1367-2630}, doi = {10.1088/1367-2630/aba390}, pages = {17}, year = {2020}, abstract = {The passive and active motion of micron-sized tracer particles in crowded liquids and inside living biological cells is ubiquitously characterised by 'viscoelastic' anomalous diffusion, in which the increments of the motion feature long-ranged negative and positive correlations. While viscoelastic anomalous diffusion is typically modelled by a Gaussian process with correlated increments, so-called fractional Gaussian noise, an increasing number of systems are reported, in which viscoelastic anomalous diffusion is paired with non-Gaussian displacement distributions. Following recent advances in Brownian yet non-Gaussian diffusion we here introduce and discuss several possible versions of random-diffusivity models with long-ranged correlations. While all these models show a crossover from non-Gaussian to Gaussian distributions beyond some correlation time, their mean squared displacements exhibit strikingly different behaviours: depending on the model crossovers from anomalous to normal diffusion are observed, as well as a priori unexpected dependencies of the effective diffusion coefficient on the correlation exponent. Our observations of the non-universality of random-diffusivity viscoelastic anomalous diffusion are important for the analysis of experiments and a better understanding of the physical origins of 'viscoelastic yet non-Gaussian' diffusion.}, language = {en} } @article{ThapaWyłomańskaSikoraetal.2021, author = {Thapa, Samudrajit and Wyłomańska, Agnieszka and Sikora, Grzegorz and Wagner, Caroline E. and Krapf, Diego and Kantz, Holger and Chechkin, Aleksei and Metzler, Ralf}, title = {Leveraging large-deviation statistics to decipher the stochastic properties of measured trajectories}, series = {New Journal of Physics}, volume = {23}, journal = {New Journal of Physics}, publisher = {Dt. Physikalische Ges. ; IOP}, address = {Bad Honnef ; London}, issn = {1367-2630}, doi = {10.1088/1367-2630/abd50e}, pages = {22}, year = {2021}, abstract = {Extensive time-series encoding the position of particles such as viruses, vesicles, or individualproteins are routinely garnered insingle-particle tracking experiments or supercomputing studies.They contain vital clues on how viruses spread or drugs may be delivered in biological cells.Similar time-series are being recorded of stock values in financial markets and of climate data.Such time-series are most typically evaluated in terms of time-averaged mean-squareddisplacements (TAMSDs), which remain random variables for finite measurement times. Theirstatistical properties are different for differentphysical stochastic processes, thus allowing us toextract valuable information on the stochastic process itself. To exploit the full potential of thestatistical information encoded in measured time-series we here propose an easy-to-implementand computationally inexpensive new methodology, based on deviations of the TAMSD from itsensemble average counterpart. Specifically, we use the upper bound of these deviations forBrownian motion (BM) to check the applicability of this approach to simulated and real data sets.By comparing the probability of deviations fordifferent data sets, we demonstrate how thetheoretical bound for BM reveals additional information about observed stochastic processes. Weapply the large-deviation method to data sets of tracer beads tracked in aqueous solution, tracerbeads measured in mucin hydrogels, and of geographic surface temperature anomalies. Ouranalysis shows how the large-deviation properties can be efficiently used as a simple yet effectiveroutine test to reject the BM hypothesis and unveil relevant information on statistical propertiessuch as ergodicity breaking and short-time correlations.}, language = {en} } @article{ŚlęzakMetzlerMagdziarz2018, author = {Ślęzak, Jakub and Metzler, Ralf and Magdziarz, Marcin}, title = {Superstatistical generalised Langevin equation}, series = {New Journal of Physics}, volume = {20}, journal = {New Journal of Physics}, number = {023026}, publisher = {Deutsche Physikalische Gesellschaft / Institute of Physics}, address = {Bad Honnef und London}, issn = {1367-2630}, doi = {10.1088/1367-2630/aaa3d4}, pages = {1 -- 25}, year = {2018}, abstract = {Recent advances in single particle tracking and supercomputing techniques demonstrate the emergence of normal or anomalous, viscoelastic diffusion in conjunction with non-Gaussian distributions in soft, biological, and active matter systems. We here formulate a stochastic model based on a generalised Langevin equation in which non-Gaussian shapes of the probability density function and normal or anomalous diffusion have a common origin, namely a random parametrisation of the stochastic force. We perform a detailed analysis demonstrating how various types of parameter distributions for the memory kernel result in exponential, power law, or power-log law tails of the memory functions. The studied system is also shown to exhibit a further unusual property: the velocity has a Gaussian one point probability density but non-Gaussian joint distributions. This behaviour is reflected in the relaxation from a Gaussian to a non-Gaussian distribution observed for the position variable. We show that our theoretical results are in excellent agreement with stochastic simulations.}, language = {en} } @article{CapałaPadashChechkinetal.2020, author = {Capała, Karol and Padash, Amin and Chechkin, Aleksei and Shokri, Babak and Metzler, Ralf and Dybiec, Bartłomiej}, title = {Levy noise-driven escape from arctangent potential wells}, series = {Chaos : an interdisciplinary journal of nonlinear science}, volume = {30}, journal = {Chaos : an interdisciplinary journal of nonlinear science}, number = {12}, publisher = {American Institute of Physics}, address = {Woodbury, NY}, issn = {1054-1500}, doi = {10.1063/5.0021795}, pages = {15}, year = {2020}, abstract = {The escape from a potential well is an archetypal problem in the study of stochastic dynamical systems, representing real-world situations from chemical reactions to leaving an established home range in movement ecology. Concurrently, Levy noise is a well-established approach to model systems characterized by statistical outliers and diverging higher order moments, ranging from gene expression control to the movement patterns of animals and humans. Here, we study the problem of Levy noise-driven escape from an almost rectangular, arctangent potential well restricted by two absorbing boundaries, mostly under the action of the Cauchy noise. We unveil analogies of the observed transient dynamics to the general properties of stationary states of Levy processes in single-well potentials. The first-escape dynamics is shown to exhibit exponential tails. We examine the dependence of the escape on the shape parameters, steepness, and height of the arctangent potential. Finally, we explore in detail the behavior of the probability densities of the first-escape time and the last-hitting point.}, language = {en} } @article{SposiniChechkinMetzler2018, author = {Sposini, Vittoria and Chechkin, Aleksei and Metzler, Ralf}, title = {First passage statistics for diffusing diffusivity}, series = {Journal of physics : A, Mathematical and theoretical}, volume = {52}, journal = {Journal of physics : A, Mathematical and theoretical}, number = {4}, publisher = {IOP Publ. Ltd.}, address = {Bristol}, issn = {1751-8113}, doi = {10.1088/1751-8121/aaf6ff}, pages = {11}, year = {2018}, abstract = {A rapidly increasing number of systems is identified in which the stochastic motion of tracer particles follows the Brownian law < r(2)(t)> similar or equal to Dt yet the distribution of particle displacements is strongly non-Gaussian. A central approach to describe this effect is the diffusing diffusivity (DD) model in which the diffusion coefficient itself is a stochastic quantity, mimicking heterogeneities of the environment encountered by the tracer particle on its path. We here quantify in terms of analytical and numerical approaches the first passage behaviour of the DD model. We observe significant modifications compared to Brownian-Gaussian diffusion, in particular that the DD model may have a faster first passage dynamics. Moreover we find a universal crossover point of the survival probability independent of the initial condition.}, language = {en} } @article{GuggenbergerPagniniVojtaetal.2019, author = {Guggenberger, Tobias and Pagnini, Gianni and Vojta, Thomas and Metzler, Ralf}, title = {Fractional Brownian motion in a finite interval}, series = {New Journal of Physics}, volume = {21}, journal = {New Journal of Physics}, publisher = {Deutsche Physikalische Gesellschaft ; IOP, Institute of Physics}, address = {Bad Honnef und London}, issn = {1367-2630}, doi = {10.1088/1367-2630/ab075f}, pages = {13}, year = {2019}, abstract = {Fractional Brownian motion (FBM) is a Gaussian stochastic process with stationary, long-time correlated increments and is frequently used to model anomalous diffusion processes. We study numerically FBM confined to a finite interval with reflecting boundary conditions. The probability density function of this reflected FBM at long times converges to a stationary distribution showing distinct deviations from the fully flat distribution of amplitude 1/L in an interval of length L found for reflected normal Brownian motion. While for superdiffusion, corresponding to a mean squared displacement (MSD) 〈X² (t)〉 ⋍ tᵅ with 1 < α < 2, the probability density function is lowered in the centre of the interval and rises towards the boundaries, for subdiffusion (0 < α < 1) this behaviour is reversed and the particle density is depleted close to the boundaries. The MSD in these cases at long times converges to a stationary value, which is, remarkably, monotonically increasing with the anomalous diffusion exponent α. Our a priori surprising results may have interesting consequences for the application of FBM for processes such as molecule or tracer diffusion in the confines of living biological cells or organelles, or other viscoelastic environments such as dense liquids in microfluidic chambers.}, language = {en} } @article{ThapaLomholtKrogetal.2018, author = {Thapa, Samudrajit and Lomholt, Michael Andersen and Krog, Jens and Cherstvy, Andrey G. and Metzler, Ralf}, title = {Bayesian analysis of single-particle tracking data using the nested-sampling algorithm: maximum-likelihood model selection applied to stochastic-diffusivity data}, series = {Physical chemistry, chemical physics : PCCP ; a journal of European Chemical Societies}, volume = {20}, journal = {Physical chemistry, chemical physics : PCCP ; a journal of European Chemical Societies}, number = {46}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1463-9076}, doi = {10.1039/c8cp04043e}, pages = {29018 -- 29037}, year = {2018}, abstract = {We employ Bayesian statistics using the nested-sampling algorithm to compare and rank multiple models of ergodic diffusion (including anomalous diffusion) as well as to assess their optimal parameters for in silico-generated and real time-series. We focus on the recently-introduced model of Brownian motion with "diffusing diffusivity'-giving rise to widely-observed non-Gaussian displacement statistics-and its comparison to Brownian and fractional Brownian motion, also for the time-series with some measurement noise. We conduct this model-assessment analysis using Bayesian statistics and the nested-sampling algorithm on the level of individual particle trajectories. We evaluate relative model probabilities and compute best-parameter sets for each diffusion model, comparing the estimated parameters to the true ones. We test the performance of the nested-sampling algorithm and its predictive power both for computer-generated (idealised) trajectories as well as for real single-particle-tracking trajectories. Our approach delivers new important insight into the objective selection of the most suitable stochastic model for a given time-series. We also present first model-ranking results in application to experimental data of tracer diffusion in polymer-based hydrogels.}, language = {en} } @article{ZemanovaZhouKurths2006, author = {Zemanova, Lucia and Zhou, Changsong and Kurths, J{\"u}rgen}, title = {Structural and functional clusters of complex brain networks}, series = {Physica, D, Nonlinear phenomena}, volume = {224}, journal = {Physica, D, Nonlinear phenomena}, number = {1-2}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0167-2789}, doi = {10.1016/j.physd.2006.09.008}, pages = {202 -- 212}, year = {2006}, abstract = {Recent research using the complex network approach has revealed a rich and complicated network topology in the cortical connectivity of mammalian brains. It is of importance to understand the implications of such complex network structures in the functional organization of the brain activities. Here we study this problem from the viewpoint of dynamical complex networks. We investigate synchronization dynamics on the corticocortical network of the cat by modeling each node (cortical area) of the network with a sub-network of interacting excitable neurons. We find that the network displays clustered synchronization behavior, and the dynamical clusters coincide with the topological community structures observed in the anatomical network. Our results provide insights into the relationship between the global organization and the functional specialization of the brain cortex.}, language = {en} } @article{MeucciSalvadoriIvanchenkoetal.2006, author = {Meucci, Riccardo and Salvadori, Francesco and Ivanchenko, Mikhail V. and Al Naimee, Kais and Zhou, Chansong and Arecchi, Fortunato Tito and Boccaletti, Stefano and Kurths, J{\"u}rgen}, title = {Synchronization of spontaneous bursting in a CO2 laser}, series = {Physical review : E, Statistical, nonlinear and soft matter physics}, volume = {74}, journal = {Physical review : E, Statistical, nonlinear and soft matter physics}, publisher = {American Physical Society}, address = {College Park}, issn = {2470-0045}, doi = {10.1103/PhysRevE.74.066207}, pages = {6}, year = {2006}, abstract = {We present experimental and numerical evidence of synchronization of burst events in two different modulated CO2 lasers. Bursts appear randomly in each laser as trains of large amplitude spikes intercalated by a small amplitude chaotic regime. Experimental data and model show the frequency locking of bursts in a suitable interval of coupling strength. We explain the mechanism of this phenomenon and demonstrate the inhibitory properties of the implemented coupling.}, language = {en} } @article{ZaikinKurths2006, author = {Zaikin, Alexey and Kurths, J{\"u}rgen}, title = {Optimal length transportation hypothesis to model proteasome product size distribution}, series = {Journal of biological physics : emphasizing physical principles in biological research ; an international journal for the formulation and application of mathematical models in the biological sciences}, volume = {32}, journal = {Journal of biological physics : emphasizing physical principles in biological research ; an international journal for the formulation and application of mathematical models in the biological sciences}, number = {3-4}, publisher = {Springer}, address = {Dordrecht}, issn = {0092-0606}, doi = {10.1007/s10867-006-9014-z}, pages = {231 -- 243}, year = {2006}, abstract = {This paper discusses translocation features of the 20S proteasome in order to explain typical proteasome length distributions. We assume that the protein transport depends significantly on the fragment length with some optimal length which is transported most efficiently. By means of a simple one-channel model, we show that this hypothesis can explain both the one- and the three-peak length distributions found in experiments. A possible mechanism of such translocation is provided by so-called fluctuation-driven transport.}, language = {en} } @article{ThapaLukatSelhuberUnkeletal.2019, author = {Thapa, Samudrajit and Lukat, Nils and Selhuber-Unkel, Christine and Cherstvy, Andrey G. and Metzler, Ralf}, title = {Transient superdiffusion of polydisperse vacuoles in highly motile amoeboid cells}, series = {The journal of chemical physics : bridges a gap between journals of physics and journals of chemistr}, volume = {150}, journal = {The journal of chemical physics : bridges a gap between journals of physics and journals of chemistr}, number = {14}, publisher = {American Institute of Physics}, address = {Melville}, issn = {0021-9606}, doi = {10.1063/1.5086269}, pages = {18}, year = {2019}, abstract = {We perform a detailed statistical analysis of diffusive trajectories of membrane-enclosed vesicles (vacuoles) in the supercrowded cytoplasm of living Acanthamoeba castellanii cells. From the vacuole traces recorded in the center-of-area frame of moving amoebae, we examine the statistics of the time-averaged mean-squared displacements of vacuoles, their generalized diffusion coefficients and anomalous scaling exponents, the ergodicity breaking parameter, the non-Gaussian features of displacement distributions of vacuoles, the displacement autocorrelation function, as well as the distributions of speeds and positions of vacuoles inside the amoeba cells. Our findings deliver novel insights into the internal dynamics of cellular structures in these infectious pathogens. Published under license by AIP Publishing.}, language = {en} } @article{AkimotoCherstvyMetzler2018, author = {Akimoto, Takuma and Cherstvy, Andrey G. and Metzler, Ralf}, title = {Ergodicity, rejuvenation, enhancement, and slow relaxation of diffusion in biased continuous-time random walks}, series = {Physical review : E, Statistical, nonlinear and soft matter physics}, volume = {98}, journal = {Physical review : E, Statistical, nonlinear and soft matter physics}, number = {2}, publisher = {American Physical Society}, address = {College Park}, issn = {2470-0045}, doi = {10.1103/PhysRevE.98.022105}, pages = {6}, year = {2018}, abstract = {Bias plays an important role in the enhancement of diffusion in periodic potentials. Using the continuous-time random walk in the presence of a bias, we report on an interesting phenomenon for the enhancement of diffusion by the start of the measurement in a random energy landscape. When the variance of the waiting time diverges, in contrast to the bias-free case, the dynamics with bias becomes superdiffusive. In the superdiffusive regime, we find a distinct initial ensemble dependence of the diffusivity. Moreover, the diffusivity can be increased by the aging time when the initial ensemble is not in equilibrium. We show that the time-averaged variance converges to the corresponding ensemble-averaged variance; i.e., ergodicity is preserved. However, trajectory-to-trajectory fluctuations of the time-averaged variance decay unexpectedly slowly. Our findings provide a rejuvenation phenomenon in the superdiffusive regime, that is, the diffusivity for a nonequilibrium initial ensemble gradually increases to that for an equilibrium ensemble when the start of the measurement is delayed.}, language = {en} } @article{GajdaWylomanskaKantzetal.2018, author = {Gajda, J. and Wylomanska, Agnieszka and Kantz, Holger and Chechkin, Aleksei and Sikora, Grzegorz}, title = {Large deviations of time-averaged statistics for Gaussian processes}, series = {Statistics \& Probability Letters}, volume = {143}, journal = {Statistics \& Probability Letters}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0167-7152}, doi = {10.1016/j.spl.2018.07.013}, pages = {47 -- 55}, year = {2018}, abstract = {In this paper we study the large deviations of time averaged mean square displacement (TAMSD) for Gaussian processes. The theory of large deviations is related to the exponential decay of probabilities of large fluctuations in random systems. From the mathematical point of view a given statistics satisfies the large deviation principle, if the probability that it belongs to a certain range decreases exponentially. The TAMSD is one of the main statistics used in the problem of anomalous diffusion detection. Applying the theory of generalized chi-squared distribution and sub-gamma random variables we prove the upper bound for large deviations of TAMSD for Gaussian processes. As a special case we consider fractional Brownian motion, one of the most popular models of anomalous diffusion. Moreover, we derive the upper bound for large deviations of the estimator for the anomalous diffusion exponent. (C) 2018 Elsevier B.V. All rights reserved.}, language = {en} } @article{DieterichLindemannMoskoppetal.2022, author = {Dieterich, Peter and Lindemann, Otto and Moskopp, Mats Leif and Tauzin, Sebastien and Huttenlocher, Anna and Klages, Rainer and Chechkin, Aleksei and Schwab, Albrecht}, title = {Anomalous diffusion and asymmetric tempering memory in neutrophil chemotaxis}, series = {PLoS Computational Biology : a new community journal}, volume = {18}, journal = {PLoS Computational Biology : a new community journal}, number = {5}, publisher = {PLoS}, address = {San Fransisco}, issn = {1553-734X}, doi = {10.1371/journal.pcbi.1010089}, pages = {26}, year = {2022}, abstract = {Neutrophil granulocytes are essential for the first host defense. After leaving the blood circulation they migrate efficiently towards sites of inflammation. They are guided by chemoattractants released from cells within the inflammatory foci. On a cellular level, directional migration is a consequence of cellular front-rear asymmetry which is induced by the concentration gradient of the chemoattractants. The generation and maintenance of this asymmetry, however, is not yet fully understood. Here we analyzed the paths of chemotacting neutrophils with different stochastic models to gain further insight into the underlying mechanisms. Wildtype chemotacting neutrophils show an anomalous superdiffusive behavior. CXCR2 blockade and TRPC6-knockout cause the tempering of temporal correlations and a reduction of chemotaxis. Importantly, such tempering is found both in vitro and in vivo. These findings indicate that the maintenance of anomalous dynamics is crucial for chemotactic behavior and the search efficiency of neutrophils. The motility of neutrophils and their ability to sense and to react to chemoattractants in their environment are of central importance for the innate immunity. Neutrophils are guided towards sites of inflammation following the activation of G-protein coupled chemoattractant receptors such as CXCR2 whose signaling strongly depends on the activity of Ca2+ permeable TRPC6 channels. It is the aim of this study to analyze data sets obtained in vitro (murine neutrophils) and in vivo (zebrafish neutrophils) with a stochastic mathematical model to gain deeper insight into the underlying mechanisms. The model is based on the analysis of trajectories of individual neutrophils. Bayesian data analysis, including the covariances of positions for fractional Brownian motion as well as for exponentially and power-law tempered model variants, allows the estimation of parameters and model selection. Our model-based analysis reveals that wildtype neutrophils show pure superdiffusive fractional Brownian motion. This so-called anomalous dynamics is characterized by temporal long-range correlations for the movement into the direction of the chemotactic CXCL1 gradient. Pure superdiffusion is absent vertically to this gradient. This points to an asymmetric 'memory' of the migratory machinery, which is found both in vitro and in vivo. CXCR2 blockade and TRPC6-knockout cause tempering of temporal correlations in the chemotactic gradient. This can be interpreted as a progressive loss of memory, which leads to a marked reduction of chemotaxis and search efficiency of neutrophils. In summary, our findings indicate that spatially differential regulation of anomalous dynamics appears to play a central role in guiding efficient chemotactic behavior.}, language = {en} } @article{EmanuelCherstvyMetzleretal.2020, author = {Emanuel, Marc D. and Cherstvy, Andrey G. and Metzler, Ralf and Gompper, Gerhard}, title = {Buckling transitions and soft-phase invasion of two-component icosahedral shells}, series = {Physical review / publ. by The American Physical Society. E, Statistical, nonlinear, and soft matter physics}, volume = {102}, journal = {Physical review / publ. by The American Physical Society. E, Statistical, nonlinear, and soft matter physics}, number = {6}, publisher = {Woodbury}, address = {New York}, issn = {2470-0045}, doi = {10.1103/PhysRevE.102.062104}, pages = {26}, year = {2020}, abstract = {What is the optimal distribution of two types of crystalline phases on the surface of icosahedral shells, such as of many viral capsids? We here investigate the distribution of a thin layer of soft material on a crystalline convex icosahedral shell. We demonstrate how the shapes of spherical viruses can be understood from the perspective of elasticity theory of thin two-component shells. We develop a theory of shape transformations of an icosahedral shell upon addition of a softer, but still crystalline, material onto its surface. We show how the soft component "invades" the regions with the highest elastic energy and stress imposed by the 12 topological defects on the surface. We explore the phase diagram as a function of the surface fraction of the soft material, the shell size, and the incommensurability of the elastic moduli of the rigid and soft phases. We find that, as expected, progressive filling of the rigid shell by the soft phase starts from the most deformed regions of the icosahedron. With a progressively increasing soft-phase coverage, the spherical segments of domes are filled first (12 vertices of the shell), then the cylindrical segments connecting the domes (30 edges) are invaded, and, ultimately, the 20 flat faces of the icosahedral shell tend to be occupied by the soft material. We present a detailed theoretical investigation of the first two stages of this invasion process and develop a model of morphological changes of the cone structure that permits noncircular cross sections. In conclusion, we discuss the biological relevance of some structures predicted from our calculations, in particular for the shape of viral capsids.}, language = {en} }