@article{MetzlerJeonCherstvyetal.2014, author = {Metzler, Ralf and Jeon, Jae-Hyung and Cherstvy, Andrey G. and Barkai, Eli}, title = {Anomalous diffusion models and their properties}, series = {physical chemistry, chemical physics : PCCP}, volume = {2014}, journal = {physical chemistry, chemical physics : PCCP}, number = {16}, issn = {1463-9076}, doi = {10.1039/c4cp03465a}, pages = {24128 -- 24164}, year = {2014}, abstract = {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.}, language = {en} } @article{WessigGerngrossPapeetal.2014, author = {Wessig, Pablo and Gerngroß, Maik and Pape, Simon and Bruhns, Philipp and Weber, Jens}, title = {Novel porous materials based on oligospiroketals (OSK)}, series = {RSC Advances : an international journal to further the chemical sciences}, volume = {2014}, journal = {RSC Advances : an international journal to further the chemical sciences}, number = {4}, issn = {2046-2069}, doi = {10.1039/c4ra04437a}, pages = {31123 -- 31129}, year = {2014}, abstract = {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.}, language = {en} } @article{ZamponiPenfoldNachtegaaletal.2014, author = {Zamponi, Flavio and Penfold, Thomas J. and Nachtegaal, Maarten and L{\"u}bcke, Andrea and Rittmann, Jochen and Milne, Chris J. and Chergui, Majed and van Bokhoven, Jeroen A.}, title = {Probing the dynamics of plasmon-excited hexanethiol-capped gold nanoparticles by picosecond X-ray absorption spectroscopy}, series = {physical chemistry, chemical physics : PCCP}, volume = {2014}, journal = {physical chemistry, chemical physics : PCCP}, number = {16}, issn = {1463-9076}, doi = {10.1039/c4cp03301a}, pages = {23157 -- 23163}, year = {2014}, abstract = {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.}, language = {en} } @article{MeyerMatissekMuelleretal.2014, author = {Meyer, S{\"o}ren and Matissek, M. and M{\"u}ller, Sandra Marie and Taleshi, M. S. and Ebert, Franziska and Francesconi, Kevin A. and Schwerdtle, Tanja}, title = {In vitro toxicological characterisation of three arsenic-containing hydrocarbons}, series = {Metallomics}, volume = {2014}, journal = {Metallomics}, number = {6}, issn = {1756-591X}, doi = {10.1039/c4mt00061g}, pages = {1023 -- 1033}, year = {2014}, abstract = {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.}, language = {en} } @article{UnterbergLeffersHuebneretal.2014, author = {Unterberg, Marlies and Leffers, Larissa and H{\"u}bner, Florian and Humpf, Hans-Ulrich and Lepikhov, Konstantin and Walter, J{\"o}rn and Ebert, Franziska and Schwerdtle, Tanja}, title = {Toxicity of arsenite and thio-DMAV after long-term (21 days) incubation of human urothelial cells: cytotoxicity, genotoxicity and epigenetics}, series = {Toxicology Research}, volume = {3}, journal = {Toxicology Research}, number = {6}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {2045-4538}, pages = {456 -- 464}, year = {2014}, abstract = {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.}, language = {en} } @article{GhoshCherstvyMetzler2014, author = {Ghosh, Surya K. and Cherstvy, Andrey G. and Metzler, Ralf}, title = {Non-universal tracer diffusion in crowded media of non-inert obstacles}, series = {Physical Chemistry Chemical Physics}, volume = {3}, journal = {Physical Chemistry Chemical Physics}, number = {17}, editor = {Metzler, Ralf}, publisher = {The Royal Society of Chemistry}, address = {Cambridge}, issn = {1463-9076}, pages = {1847 -- 1858}, year = {2014}, abstract = {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.}, language = {en} } @article{ShinCherstvyMetzler2014, author = {Shin, Jaeoh and Cherstvy, Andrey G. and Metzler, Ralf}, title = {Kinetics of polymer looping with macromolecular crowding: effects of volume fraction and crowder size}, series = {Soft Matter}, journal = {Soft Matter}, editor = {Metzler, Ralf}, publisher = {The Royal Society of Chemistry}, address = {Cambridge}, issn = {1744-683X}, pages = {472 -- 488}, year = {2014}, abstract = {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.}, language = {en} } @article{PereiraNascimentoMagalhaesetal.2014, author = {Pereira, Fernanda S. and Nascimento, Heliara D. L. and Magalhaes, Alvicler and Peter, Martin G. and Bataglion, Giovana Anceski and Eberlin, Marcos N. and Gonzalez, Eduardo R. P.}, title = {ESI(+)-MS and GC-MS study of the hydrolysis of N-azobenzyl derivatives of chitosan}, series = {Molecules}, volume = {19}, journal = {Molecules}, number = {11}, publisher = {MDPI}, address = {Basel}, issn = {1420-3049}, doi = {10.3390/molecules191117604}, pages = {17604 -- 17618}, year = {2014}, abstract = {New N-p-chloro-, N-p-bromo-, and N-p-nitrophenylazobenzylchitosan derivatives, as well as the corresponding azophenyl and azophenyl-p-sulfonic acids, were synthesized by coupling N-benzylvchitosan with aryl diazonium salts. The synthesized molecules were analyzed by UV-Vis, FT-IR, H-1-NMR and N-15-NMR spectroscopy. The capacity of copper chelation by these materials was studied by AAS. Chitosan and the derivatives were subjected to hydrolysis and the products were analyzed by ESI(+)-MS and GC-MS, confirming the formation of N-benzyl chitosan. Furthermore, the MS results indicate that a nucleophilic aromatic substitution (SnAr) reaction occurs under hydrolysis conditions, yielding chloroaniline from N-p-bromo-, and N-p-nitrophenylazo-benzylchitosan as well as bromoaniline from N-p-chloro-, and N-p-nitrophenylazobenzyl-chitosan.}, language = {en} } @article{YuAstYuetal.2014, author = {Yu, Mingfeng and Ast, Sandra and Yu, Qun and Lo, Anthony T. S. and Flehr, Roman and Todd, Matthew H. and Rutledge, Peter J.}, title = {Incorporating a piperidinyl group in the fluorophore extends the fluorescence lifetime of click-derived cyclam-naphthalimide conjugates}, series = {PLoS one}, volume = {9}, journal = {PLoS one}, number = {7}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0100761}, pages = {12}, year = {2014}, abstract = {Ligands incorporating a tetraazamacrocycle receptor, a 'click'-derived triazole and a 1,8-naphthalimide fluorophore have proven utility as probes for metal ions. Three new cyclam-based molecular probes are reported, in which a piperidinyl group has been introduced at the 4-position of the naphthalimide fluorophore. These compounds have been synthesized using the copper(I)-catalyzed azide-alkyne Huisgen cycloaddition and their photophysical properties studied in detail. The alkylamino group induces the expected red-shift in absorption and emission spectra relative to the simple naphthalimide derivatives and gives rise to extended fluorescence lifetimes in aqueous buffer. The photophysical properties of these systems are shown to be highly solvent-dependent. Screening the fluorescence responses of the new conjugates to a wide variety of metal ions reveals significant and selective fluorescence quenching in the presence of copper(II), yet no fluorescence enhancement with zinc(II) as observed previously for the simple naphthalimide derivatives. Reasons for this different behaviour are proposed. Cytotoxicity testing shows that these new cyclam-triazole-dye conjugates display little or no toxicity against either DLD-1 colon carcinoma cells or MDA-MB-231 breast carcinoma cells, suggesting a potential role for these and related systems in biological sensing applications.}, language = {en} } @article{OrtmannAhrensMilewskietal.2014, author = {Ortmann, Thomas and Ahrens, Heiko and Milewski, Sven and Lawrenz, Frank and Groening, Andreas and Laschewsky, Andr{\´e} and Garnier, Sebastien and Helm, Christiane A.}, title = {Lipid monolayers with adsorbed oppositely charged polyelectrolytes: Influence of reduced charge densities}, series = {Polymers}, volume = {6}, journal = {Polymers}, number = {7}, publisher = {MDPI}, address = {Basel}, issn = {2073-4360}, doi = {10.3390/polym6071999}, pages = {1999 -- 2017}, year = {2014}, abstract = {Polyelectrolytes in dilute solutions (0.01 mmol/L) adsorb in a two-dimensional lamellar phase to oppositely charged lipid monolayers at the air/water interface. The interchain separation is monitored by Grazing Incidence X-ray Diffraction. On monolayer compression, the interchain separation decreases to a factor of two. To investigate the influence of the electrostatic interaction, either the line charge density of the polymer is reduced (a statistic copolymer with 90\% and 50\% charged monomers) or mixtures between charged and uncharged lipids are used (dipalmitoylphosphatidylcholine (DPPC)/dioctadecyldimethylammonium bromide (DODAB)) On decrease of the surface charge density, the interchain separation increases, while on decrease of the linear charge density, the interchain separation decreases. The ratio between charged monomers and charged lipid molecules is fairly constant; it decreases up to 30\% when the lipids are in the fluid phase. With decreasing surface charge or linear charge density, the correlation length of the lamellar order decreases.}, language = {en} }