TY - JOUR A1 - Boggio, Jose M. Chavez A1 - Bodenmueller, D. A1 - Fremberg, T. A1 - Haynes, R. A1 - Roth, Martin M. A1 - Eisermann, R. A1 - Lisker, M. A1 - Zimmermann, L. A1 - Boehm, Michael T1 - Dispersion engineered silicon nitride waveguides by geometrical and refractive-index optimization JF - Journal of the Optical Society of America : B, Optical physics N2 - Dispersion engineering in silicon nitride (SiXNY) waveguides is investigated through the optimization of the waveguide transversal dimensions and refractive indices in a multicladding arrangement. Ultraflat dispersion of -84.0 +/- 0.5 ps/nm/km between 1700 and 2440 nm and 1.5 +/- 3 ps/nm/km between 1670 and 2500 nm is numerically demonstrated. It is shown that typical refractive index fluctuations as well as dimension fluctuations during fabrication of the SiXNY waveguides are a limitation for obtaining ultraflat dispersion profiles. Single- and multicladding waveguides are fabricated and their dispersion profiles measured (over nearly 1000 nm) using a low-coherence frequency domain interferometric technique. By appropriate thickness optimization, the zero-dispersion wavelength is tuned over a large spectral range in single-and multicladding waveguides with small refractive index contrast (3%). A flat dispersion profile with +/- 3.2 ps/nm/km variation over 500 nm is obtained in a multicladding waveguide fabricated with a refractive index contrast of 37%. Finally, we generate a nearly three-octave supercontinuum in this dispersion flattened multicladding SiXNY waveguide. (C) 2014 Optical Society of America Y1 - 2014 U6 - https://doi.org/10.1364/JOSAB.31.002846 SN - 0740-3224 SN - 1520-8540 VL - 31 IS - 11 SP - 2846 EP - 2857 PB - Optical Society of America CY - Washington ER - TY - JOUR A1 - Metzler, Ralf A1 - Jeon, Jae-Hyung A1 - Cherstvy, Andrey G. A1 - Barkai, Eli T1 - Anomalous diffusion models and their properties BT - non-stationarity, non-ergodicity, and ageing at the centenary of single particle tracking JF - physical chemistry, chemical physics : PCCP N2 - Modern microscopic techniques following the stochastic motion of labelled tracer particles have uncovered significant deviations from the laws of Brownian motion in a variety of animate and inanimate systems. Such anomalous diffusion can have different physical origins, which can be identified from careful data analysis. In particular, single particle tracking provides the entire trajectory of the traced particle, which allows one to evaluate different observables to quantify the dynamics of the system under observation. We here provide an extensive overview over different popular anomalous diffusion models and their properties. We pay special attention to their ergodic properties, highlighting the fact that in several of these models the long time averaged mean squared displacement shows a distinct disparity to the regular, ensemble averaged mean squared displacement. In these cases, data obtained from time averages cannot be interpreted by the standard theoretical results for the ensemble averages. Here we therefore provide a comparison of the main properties of the time averaged mean squared displacement and its statistical behaviour in terms of the scatter of the amplitudes between the time averages obtained from different trajectories. We especially demonstrate how anomalous dynamics may be identified for systems, which, on first sight, appear to be Brownian. Moreover, we discuss the ergodicity breaking parameters for the different anomalous stochastic processes and showcase the physical origins for the various behaviours. This Perspective is intended as a guidebook for both experimentalists and theorists working on systems, which exhibit anomalous diffusion. KW - intermittent chaotic systems KW - Fokker-Planck equations KW - time random-walks KW - fluorescence photobleaching recovery KW - fluctuation-dissipation theorem KW - fractional dynamics approach KW - photon-counting statistics KW - weak ergodicity breaking KW - flight search patterns KW - levy flights Y1 - 2014 U6 - https://doi.org/10.1039/c4cp03465a SN - 1463-9076 SN - 1463-9084 VL - 2014 IS - 16 SP - 24128 EP - 24164 ER - TY - JOUR A1 - Wessig, Pablo A1 - Gerngroß, Maik A1 - Pape, Simon A1 - Bruhns, Philipp A1 - Weber, Jens T1 - Novel porous materials based on oligospiroketals (OSK) JF - RSC Advances : an international journal to further the chemical sciences N2 - New porous materials based on covalently connected monomers are presented. The key step of the synthesis is an acetalisation reaction. In previous years we used acetalisation reactions extensively to build up various molecular rods. Based on this approach, investigations towards porous polymeric materials were conducted by us. Here we wish to present the results of these studies in the synthesis of 1D polyacetals and porous 3D polyacetals. By scrambling experiments with 1D acetals we could prove that exchange reactions occur between different building blocks (evidenced by MALDI-TOF mass spectrometry). Based on these results we synthesized porous 3D polyacetals under the same mild conditions. KW - microporous organic polymers KW - molecular rods KW - construction KW - frameworks KW - membranes KW - sorption KW - models Y1 - 2014 U6 - https://doi.org/10.1039/c4ra04437a SN - 2046-2069 VL - 2014 IS - 4 SP - 31123 EP - 31129 ER - TY - JOUR A1 - Zamponi, Flavio A1 - Penfold, Thomas J. A1 - Nachtegaal, Maarten A1 - Lübcke, Andrea A1 - Rittmann, Jochen A1 - Milne, Chris J. A1 - Chergui, Majed A1 - van Bokhoven, Jeroen A. T1 - Probing the dynamics of plasmon-excited hexanethiol-capped gold nanoparticles by picosecond X-ray absorption spectroscopy JF - physical chemistry, chemical physics : PCCP N2 - Picosecond X-ray absorption spectroscopy (XAS) is used to investigate the electronic and structural dynamics initiated by plasmon excitation of 1.8 nm diameter Au nanoparticles (NPs) functionalised with 1-hexanethiol. We show that 100 ps after photoexcitation the transient XAS spectrum is consistent with an 8% expansion of the Au–Au bond length and a large increase in disorder associated with melting of the NPs. Recovery of the ground state occurs with a time constant of ∼1.8 ns, arising from thermalisation with the environment. Simulations reveal that the transient spectrum exhibits no signature of charge separation at 100 ps and allows us to estimate an upper limit for the quantum yield (QY) of this process to be <0.1. KW - TiO2 nanoparticles KW - diimine-complexes KW - electron-transfer KW - supported gold KW - visible-light KW - water KW - surface KW - reactivity KW - nanoclusters KW - excitation Y1 - 2014 U6 - https://doi.org/10.1039/c4cp03301a SN - 1463-9076 SN - 1463-9084 VL - 2014 IS - 16 SP - 23157 EP - 23163 ER - TY - JOUR A1 - Meyer, Sören A1 - Matissek, M. A1 - Müller, Sandra Marie A1 - Taleshi, M. S. A1 - Ebert, Franziska A1 - Francesconi, Kevin A. A1 - Schwerdtle, Tanja T1 - In vitro toxicological characterisation of three arsenic-containing hydrocarbons JF - Metallomics N2 - Arsenic-containing hydrocarbons are one group of fat-soluble organic arsenic compounds (arsenolipids) found in marine fish and other seafood. A risk assessment of arsenolipids is urgently needed, but has not been possible because of the total lack of toxicological data. In this study the cellular toxicity of three arsenic-containing hydrocarbons was investigated in cultured human bladder (UROtsa) and liver (HepG2) cells. Cytotoxicity of the arsenic-containing hydrocarbons was comparable to that of arsenite, which was applied as the toxic reference arsenical. A large cellular accumulation of arsenic, as measured by ICP-MS/MS, was observed after incubation of both cell lines with the arsenolipids. Moreover, the toxic mode of action shown by the three arsenic-containing hydrocarbons seemed to differ from that observed for arsenite. Evidence suggests that the high cytotoxic potential of the lipophilic arsenicals results from a decrease in the cellular energy level. This first in vitro based risk assessment cannot exclude a risk to human health related to the presence of arsenolipids in seafood, and indicates the urgent need for further toxicity studies in experimental animals to fully assess this possible risk. KW - cod-liver KW - human-cells KW - arsenolipids present KW - excision-repair KW - fatty-acids KW - marine oils KW - RP-HPLC KW - metabolites KW - identification KW - trivalent Y1 - 2014 U6 - https://doi.org/10.1039/c4mt00061g SN - 1756-591X SN - 1756-5901 VL - 2014 IS - 6 SP - 1023 EP - 1033 ER - TY - JOUR A1 - Unterberg, Marlies A1 - Leffers, Larissa A1 - Hübner, Florian A1 - Humpf, Hans-Ulrich A1 - Lepikhov, Konstantin A1 - Walter, Jörn A1 - Ebert, Franziska A1 - Schwerdtle, Tanja T1 - Toxicity of arsenite and thio-DMAV after long-term (21 days) incubation of human urothelial cells: cytotoxicity, genotoxicity and epigenetics JF - Toxicology Research N2 - This study aims to further mechanistically understand toxic modes of action after chronic inorganic arsenic exposure. Therefore long-term incubation studies in cultured cells were carried out, to display chronically attained changes, which cannot be observed in the generally applied in vitro short-term incubation studies. Particularly, the cytotoxic, genotoxic and epigenetic effects of an up to 21 days incubation of human urothelial (UROtsa) cells with pico- to nanomolar concentrations of iAsIII and its metabolite thio-DMAV were compared. After 21 days of incubation, cytotoxic effects were strongly enhanced in the case of iAsIII and might partly be due to glutathione depletion and genotoxic effects on the chromosomal level. These results are in strong contrast to cells exposed to thio-DMAV. Thus, cells seemed to be able to adapt to this arsenical, as indicated among others by an increase in the cellular glutathione level. Most interestingly, picomolar concentrations of both iAsIII and thio-DMAV caused global DNA hypomethylation in UROtsa cells, which was quantified in parallel by 5-medC immunostaining and a newly established, reliable, high resolution mass spectrometry (HRMS)-based test system. This is the first time that epigenetic effects are reported for thio-DMAV; iAsIII induced epigenetic effects occur in at least 8000 fold lower concentrations as reported in vitro before. The fact that both arsenicals cause DNA hypomethylation at really low, exposure-relevant concentrations in human urothelial cells suggests that this epigenetic effect might contribute to inorganic arsenic induced carcinogenicity, which for sure has to be further investigated in future studies. KW - induced malignant-transformation KW - genomic dna methylation KW - vitro toxicological characterization KW - thio-dimethylarsinic acid KW - bladder-cancer KW - methyltransferases dnmt3a KW - cytosine methylation KW - carcinogen exposure KW - mass-spectrometry KW - gene-expression Y1 - 2014 SN - 2045-4538 SN - 2045-452X VL - 3 IS - 6 SP - 456 EP - 464 PB - Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Ghosh, Surya K. A1 - Cherstvy, Andrey G. A1 - Metzler, Ralf ED - Metzler, Ralf T1 - Non-universal tracer diffusion in crowded media of non-inert obstacles JF - Physical Chemistry Chemical Physics N2 - We study the diffusion of a tracer particle, which moves in continuum space between a lattice of excluded volume, immobile non-inert obstacles. In particular, we analyse how the strength of the tracer–obstacle interactions and the volume occupancy of the crowders alter the diffusive motion of the tracer. From the details of partitioning of the tracer diffusion modes between trapping states when bound to obstacles and bulk diffusion, we examine the degree of localisation of the tracer in the lattice of crowders. We study the properties of the tracer diffusion in terms of the ensemble and time averaged mean squared displacements, the trapping time distributions, the amplitude variation of the time averaged mean squared displacements, and the non-Gaussianity parameter of the diffusing tracer. We conclude that tracer–obstacle adsorption and binding triggers a transient anomalous diffusion. From a very narrow spread of recorded individual time averaged trajectories we exclude continuous type random walk processes as the underlying physical model of the tracer diffusion in our system. For moderate tracer–crowder attraction the motion is found to be fully ergodic, while at stronger attraction strength a transient disparity between ensemble and time averaged mean squared displacements occurs. We also put our results into perspective with findings from experimental single-particle tracking and simulations of the diffusion of tagged tracers in dense crowded suspensions. Our results have implications for the diffusion, transport, and spreading of chemical components in highly crowded environments inside living cells and other structured liquids. KW - fluorescence correlation spectroscopy KW - single-particle tracking KW - anomalous diffusion KW - living cells KW - physiological consequences KW - langevin equation KW - infection pathway KW - excluded volume KW - brownian-motion KW - random-walks Y1 - 2014 SN - 1463-9076 VL - 3 IS - 17 SP - 1847 EP - 1858 PB - The Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Shin, Jaeoh A1 - Cherstvy, Andrey G. A1 - Metzler, Ralf ED - Metzler, Ralf T1 - Kinetics of polymer looping with macromolecular crowding: effects of volume fraction and crowder size JF - Soft Matter N2 - The looping of polymers such as DNA is a fundamental process in the molecular biology of living cells, whose interior is characterised by a high degree of molecular crowding. We here investigate in detail the looping dynamics of flexible polymer chains in the presence of different degrees of crowding. From the analysis of the looping–unlooping rates and the looping probabilities of the chain ends we show that the presence of small crowders typically slows down the chain dynamics but larger crowders may in fact facilitate the looping. We rationalise these non-trivial and often counterintuitive effects of the crowder size on the looping kinetics in terms of an effective solution viscosity and standard excluded volume. It is shown that for small crowders the effect of an increased viscosity dominates, while for big crowders we argue that confinement effects (caging) prevail. The tradeoff between both trends can thus result in the impediment or facilitation of polymer looping, depending on the crowder size. We also examine how the crowding volume fraction, chain length, and the attraction strength of the contact groups of the polymer chain affect the looping kinetics and hairpin formation dynamics. Our results are relevant for DNA looping in the absence and presence of protein mediation, DNA hairpin formation, RNA folding, and the folding of polypeptide chains under biologically relevant high-crowding conditions. KW - gene-regulation kinetics KW - physiological consequences KW - spatial-organization KW - anomalous diffusion KW - folding kinetics KW - living cells KW - dna coiling KW - in-vitro KW - dynamics KW - mixtures Y1 - 2014 SN - 1744-683X SP - 472 EP - 488 PB - The Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Schmidt, Joachim A1 - Bechmann, Wolfgang T1 - Zur Anwendung des Skalarprodukts von Kraft und Weg auf reversible Prozesse (Druck-Volumen-Änderung, Dehnung, Elektrostatische Wechselwirkung, Hub) T1 - To the application of the scalar product of force and displacement to reversible processes (pressure-volume change, elongation, electrostatic interaction, raising) BT - die Verwendung äußerer oder systemimmanenter Kräfte BT - the use of external or system-immanent forces N2 - Wir schlagen einen allgemein anwendbaren Algorithmus vor, der unter Verwendung des Skalarprodukts von Kraft und Weg zum richtigen Vorzeichen in den Gleichungen für die Arbeit und die Potentielle Energie bei reversiblen Prozessen (Druck-Volumen-Änderung, Dehnung, Elektrostatische Wechselwirkung, Hub)führt. Wir zeigen, dass es dabei möglich ist, systemimmanente oder externe Kräfte zu benutzen. Wir zeigen, dass bei Verwendung von systemimmanenten Kräften das Skalarprodukt mit negativem Vorzeichen anzusetzen ist. Zudem ist es sehr wichtig, nötige Vorzeichenwechsel bei den einzelnen Schritten zu beachten. Wir betonen dies, weil gelegentlich übersehen wird, dass ein Vorzeichenwechsel nötig ist, wenn das Wegdifferential ds durch das Höhendifferential dh beziehungsweise durch das Abstandsdifferential dx oder dr ersetzt werden muss. KW - Skalarprodukt von Kraft und Weg KW - systemimmanente Kräfte KW - Druck-Volumen-Änderung KW - Dehnung KW - Elektrostatische Wechselwirkung KW - Gravitation KW - scalar product of force and displacement KW - system-immanent forces KW - pressure-volume change KW - elongation KW - electrostatic interaction KW - gravitation Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-69732 ER - TY - JOUR A1 - Omosa, Leonidah K. A1 - Amugune, Beatrice A1 - Ndunda, Beth A1 - Milugo, Trizah K. A1 - Heydenreich, Matthias A1 - Yenesew, Abiy A1 - Midiwo, Jacob O. T1 - Antimicrobial flavonoids and diterpenoids from Dodonaea angustifolia JF - South African journal of botany : an international interdisciplinary journal for botanical sciences KW - Dodonaea angustifolia KW - Surface exudates KW - Flavone KW - Flavanone KW - Diterpenoid KW - Antimicrobial activities Y1 - 2014 U6 - https://doi.org/10.1016/j.sajb.2013.11.012 SN - 0254-6299 SN - 1727-9321 VL - 91 SP - 58 EP - 62 PB - Elsevier CY - Amsterdam ER -