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The synthesis of two novel types of π-expanded coumarins has been developed. Modified Knoevenagel bis-condensation afforded 3,9-dioxa-perylene-2,8-diones. Subsequent oxidative aromatic coupling or light driven electrocyclization reaction led to dibenzo-1,7-dioxacoronene-2,8-dione. Unparalleled synthetic simplicity, straightforward purification and superb optical properties have the potential to bring these perylene and coronene analogs towards various applications.
Two-photon polymerization of hydrogels – versatile solutions to fabricate well-defined 3D structures
(2014)
Hydrogels are cross-linked water-containing polymer networks that are formed by physical, ionic or covalent interactions. In recent years, they have attracted significant attention because of their unique physical properties, which make them promising materials for numerous applications in food and cosmetic processing, as well as in drug delivery and tissue engineering. Hydrogels are highly water-swellable materials, which can considerably increase in volume without losing cohesion, are biocompatible and possess excellent tissue-like physical properties, which can mimic in vivo conditions. When combined with highly precise manufacturing technologies, such as two-photon polymerization (2PP), well-defined three-dimensional structures can be obtained. These structures can become scaffolds for selective cell-entrapping, cell/drug delivery, sensing and prosthetic implants in regenerative medicine. 2PP has been distinguished from other rapid prototyping methods because it is a non-invasive and efficient approach for hydrogel cross-linking. This review discusses the 2PP-based fabrication of 3D hydrogel structures and their potential applications in biotechnology. A brief overview regarding the 2PP methodology and hydrogel properties relevant to biomedical applications is given together with a review of the most important recent achievements in the field.
Cywiński, Piotr J. ; Nono, Katia Nchimi ; Charbonnière, Loïc J. ; Hammann, Tommy ; Löhmannsröben, Hans-Gerd
A new functional luminescent lanthanide complex (LLC) has been synthesized with terbium as a central lanthanide ion and biotin as a functional moiety. Unlike in typical lanthanide complexes assembled via carboxylic moieties, in the presented complex, four phosphate groups are chelating the central lanthanide ion. This special chemical assembly enhances the complex stability in phosphate buffers conventionally used in biochemistry. The complex synthesis strategy and photophysical properties are described as well as the performance in time-resolved Förster Resonance Energy Transfer (FRET) assays. In those assays, this biotin-LLC transferred energy either to acceptor organic dyes (Cy5 or AF680) labelled on streptavidin or to quantum dots (QD655 or QD705) surface-functionalised with streptavidins. The permanent spatial donor–acceptor proximity is assured through strong and stable biotin–streptavidin binding. The energy transfer is evidenced from the quenching observed in donor emission and from a decrease in donor luminescence decay, both associated with simultaneous increase in acceptor intensity and in the decay time. The dye-based assays are realised in TRIS and in PBS, whereas QD-based systems are studied in borate buffer. The delayed emission analysis allows for quantifying the recognition process and for auto-fluorescence-free detection, which is particularly relevant for application in bioanalysis. In accordance with Förster theory, Förster-radii (R0) were found to be around 60 Å for organic dyes and around 105 Å for QDs. The FRET efficiency (η) reached 80% and 25% for dye and QD acceptors, respectively. Physical donor–acceptor distances (r) have been determined in the range 45–60 Å for organic dye acceptors, while for acceptor QDs between 120 Å and 145 Å. This newly synthesised biotin-LLC extends the class of highly sensitive analytical tools to be applied in the bioanalytical methods such as time-resolved fluoroimmunoassays (TR-FIA), luminescent imaging and biosensing.
This book presents an agile and model-driven approach to manage scientific workflows. The approach is based on the Extreme Model Driven Design (XMDD) paradigm and aims at simplifying and automating the complex data analysis processes carried out by scientists in their day-to-day work. Besides documenting the impact the workflow modeling might have on the work of natural scientists, this book serves three major purposes: 1. It acts as a primer for practitioners who are interested to learn how to think in terms of services and workflows when facing domain-specific scientific processes. 2. It provides interesting material for readers already familiar with this kind of tools, because it introduces systematically both the technologies used in each case study and the basic concepts behind them. 3. As the addressed thematic field becomes increasingly relevant for lectures in both computer science and experimental sciences, it also provides helpful material for teachers that plan similar courses.
Potentiality of nanosized materials has been largely proved but a closer look shows that a significant percentage of this research is related to oxides and metals, while the number drastically drops for metallic ceramics, namely transition metal nitrides and metal carbides. The lack of related publications do not reflect their potential but rather the difficulties related to their synthesis as dense and defect-free structures, fundamental prerequisites for advanced mechanical applications.
The present habilitation work aims to close the gap between preparation and processing, indicating novel synthetic pathways for a simpler and sustainable synthesis of transition metal nitride (MN) and carbide (MC) based nanostructures and easier processing thereafter. In spite of simplicity and reliability, the designed synthetic processes allow the production of functional materials, with the demanded size and morphology.
The goal was achieved exploiting classical and less-classical precursors, ranging from common metal salts and molecules (e.g. urea, gelatin, agar, etc), to more exotic materials, such as leafs, filter paper and even wood. It was found that the choice of precursors and reaction conditions makes it possible to control chemical composition (going for instance from metal oxides to metal oxy-nitrides to metal nitrides, or from metal nitrides to metal carbides, up to quaternary systems), size (from 5 to 50 nm) and morphology (going from mere spherical nanoparticles to rod-like shapes, fibers, layers, meso-porous and hierarchical structures, etc). The nature of the mixed precursors also allows the preparation of metal nitrides/carbides based nanocomposites, thus leading to multifunctional materials (e.g. MN/MC@C, MN/MC@PILs, etc) but also allowing dispersion in liquid media. Control over composition, size and morphology is obtained with simple adjustment of the main route, but also coupling it with processes such as electrospin, aerosol spray, bio-templating, etc. Last but not least, the nature of the precursor materials also allows easy processing, including printing, coating, casting, film and thin layers preparation, etc).
The designed routes are, concept-wise, similar and they all start by building up a secondary metal ion-N/C precursor network, which converts, upon heat treatment, into an intermediate “glass”. This glass stabilizes the nascent nanoparticles during their nucleation and impairs their uncontrolled growth during the heat treatment (scheme 1). This way, one of the main problems related to the synthesis of MN/MC, i.e. the need of very high temperature, could also be overcome (from up to 2000°C, for classical synthesis, down to 700°C in the present cases). The designed synthetic pathways are also conceived to allow usage of non-toxic compounds and to minimize (or even avoid) post-synthesis purification, still bringing to phase pure and well-defined (crystalline) nanoparticles.
This research aids to simplify the preparation of MN/MC, making these systems now readily available in suitable amounts both for fundamental and applied science. The prepared systems have been tested (in some cases for the first time) in many different fields, e.g. battery (MnN0.43@C shown a capacity stabilized at a value of 230 mAh/g, with coulombic efficiencies close to 100%), as alternative magnetic materials (Fe3C nanoparticles were prepared with different size and therefore different magnetic behavior, superparamagnetic or ferromagnetic, showing a saturation magnetization value up to 130 emu/g, i.e. similar to the value expected for the bulk material), as filters and for the degradation of organic dyes (outmatching the performance of carbon), as catalysts (both as active phase but also as active support, leading to high turnover rate and, more interesting, to tunable selectivity). Furthermore, with this route, it was possible to prepare for the first time, to the best of our knowledge, well-defined and crystalline MnN0.43, Fe3C and Zn1.7GeN1.8O nanoparticles via bottom-up approaches.
Once the synthesis of these materials can be made straightforward, any further modification, combination, manipulation, is in principle possible and new systems can be purposely conceived (e.g. hybrids, nanocomposites, ferrofluids, etc).
The atmosphere over the Arctic Ocean is strongly influenced by the distribution of sea ice and open water. Leads in the sea ice produce strong convective fluxes of sensible and latent heat and release aerosol particles into the atmosphere. They increase the occurrence of clouds and modify the structure and characteristics of the atmospheric boundary layer (ABL) and thereby influence the Arctic climate.
In the course of this study aircraft measurements were performed over the western Arctic Ocean as part of the campaign PAMARCMIP 2012 of the Alfred Wegener Institute for Polar and Marine Research (AWI). Backscatter from aerosols and clouds within the lower troposphere and the ABL were measured with the nadir pointing Airborne Mobile Aerosol Lidar (AMALi) and dropsondes were launched to obtain profiles of meteorological variables. Furthermore, in situ measurements of aerosol properties, meteorological variables and turbulence were part of the campaign. The measurements covered a broad range of atmospheric and sea ice conditions.
In this thesis, properties of the ABL over Arctic sea ice with a focus on the influence of open leads are studied based on the data from the PAMARCMIP campaign. The height of the ABL is determined by different methods that are applied to dropsonde and AMALi backscatter profiles. ABL heights are compared for different flights representing different conditions of the atmosphere and of sea ice and open water influence. The different criteria for ABL height that are applied show large variation in terms of agreement among each other, depending on the characteristics of the ABL and its history. It is shown that ABL height determination from lidar backscatter by methods commonly used under mid-latitude conditions is applicable to the Arctic ABL only under certain conditions. Aerosol or clouds within the ABL are needed as a tracer for ABL height detection from backscatter. Hence an aerosol source close to the surface is necessary, that is typically found under the present influence of open water and therefore convective conditions. However it is not always possible to distinguish residual layers from the actual ABL. Stable boundary layers are generally difficult to detect.
To illustrate the complexity of the Arctic ABL and processes therein, four case studies are analyzed each of which represents a snapshot of the interplay between atmosphere and underlying sea ice or water surface. Influences of leads and open water on the aerosol and clouds within the ABL are identified and discussed. Leads are observed to cause the formation of fog and cloud layers within the ABL by humidity emission. Furthermore they decrease the stability and increase the height of the ABL and consequently facilitate entrainment of air and aerosol layers from the free troposphere.
Cyanobacteria produce about 40 percent of the world’s primary biomass, but also a variety of often toxic peptides such as microcystin. Mass developments, so called blooms, can pose a real threat to the drinking water supply in many parts of the world. This study aimed at characterizing the biological function of microcystin production in one of the most common bloom-forming cyanobacterium Microcystis aeruginosa.
In a first attempt, the effect of elevated light intensity on microcystin production and its binding to cellular proteins was studied. Therefore, conventional microcystin quantification techniques were combined with protein-biochemical methods. RubisCO, the key enzyme for primary carbon fixation was a major microcystin interaction partner. High light exposition strongly stimulated microcystin-protein interactions. Up to 60 percent of the total cellular microcystin was detected bound to proteins, i.e. inaccessible for standard quantification procedures. Underestimation of total microcystin contents when neglecting the protein fraction was also demonstrated in field samples. Finally, an immuno-fluorescence based method was developed to identify microcystin producing cyanobacteria in mixed populations.
The high light induced microcystin interaction with proteins suggested an impact of the secondary metabolite on the primary metabolism of Microcystis by e.g. modulating the activity of enzymes. For addressing that question, a comprehensive GC/MS-based approach was conducted to compare the accumulation of metabolites in the wild-type of Microcystis aeruginosa PCC 7806 and the microcystin deficient ΔmcyB mutant. From all 501 detected non-redundant metabolites 85 (17 percent) accumulated significantly different in either of both genotypes upon high light exposition. Accumulation of compatible solutes in the ΔmcyB mutant suggests a role of microcystin in fine-tuning the metabolic flow to prevent stress related to excess light, high oxygen concentration and carbon limitation.
Co-analysis of the widely used model cyanobacterium Synechocystis PCC 6803 revealed profound metabolic differences between species of cyanobacteria. Whereas Microcystis channeled more resources towards carbohydrate synthesis, Synechocystis invested more in amino acids. These findings were supported by electron microscopy of high light treated cells and the quantification of storage compounds. While Microcystis accumulated mainly glycogen to about 8.5 percent of its fresh weight within three hours, Synechocystis produced higher amounts of cyanophycin. The results showed that the characterization of species-specific metabolic features should gain more attention with regard to the biotechnological use of cyanobacteria.
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.
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.
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.
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.
Zamponi, Flavio ; Penfold, Thomas J. ; Nachtegaal, Maarten ; Lübcke, Andrea ; Rittmann, Jochen ; Milne, Chris J. ; Chergui, Majed ; van Bokhoven, Jeroen A.
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.
Zamponi, Flavio ; Penfold, Thomas J. ; Nachtegaal, Maarten ; Lübcke, Andrea ; Rittmann, Jochen ; Milne, Chris J. ; Chergui, Majed ; van Bokhoven, Jeroen A.
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.
We study the thermal Markovian diffusion of tracer particles in a 2D medium with spatially varying diffusivity D(r), mimicking recently measured, heterogeneous maps of the apparent diffusion coefficient in biological cells. For this heterogeneous diffusion process (HDP) we analyse the mean squared displacement (MSD) of the tracer particles, the time averaged MSD, the spatial probability density function, and the first passage time dynamics from the cell boundary to the nucleus. Moreover we examine the non-ergodic properties of this process which are important for the correct physical interpretation of time averages of observables obtained from single particle tracking experiments. From extensive computer simulations of the 2D stochastic Langevin equation we present an in-depth study of this HDP. In particular, we find that the MSDs along the radial and azimuthal directions in a circular domain obey anomalous and Brownian scaling, respectively. We demonstrate that the time averaged MSD stays linear as a function of the lag time and the system thus reveals a weak ergodicity breaking. Our results will enable one to rationalise the diffusive motion of larger tracer particles such as viruses or submicron beads in biological cells.
We study the thermal Markovian diffusion of tracer particles in a 2D medium with spatially varying diffusivity D(r), mimicking recently measured, heterogeneous maps of the apparent diffusion coefficient in biological cells. For this heterogeneous diffusion process (HDP) we analyse the mean squared displacement (MSD) of the tracer particles, the time averaged MSD, the spatial probability density function, and the first passage time dynamics from the cell boundary to the nucleus. Moreover we examine the non-ergodic properties of this process which are important for the correct physical interpretation of time averages of observables obtained from single particle tracking experiments. From extensive computer simulations of the 2D stochastic Langevin equation we present an in-depth study of this HDP. In particular, we find that the MSDs along the radial and azimuthal directions in a circular domain obey anomalous and Brownian scaling, respectively. We demonstrate that the time averaged MSD stays linear as a function of the lag time and the system thus reveals a weak ergodicity breaking. Our results will enable one to rationalise the diffusive motion of larger tracer particles such as viruses or submicron beads in biological cells.
Meyer, Sören ; Matissek, M. ; Müller, Sandra Marie ; Taleshi, M. S. ; Ebert, Franziska ; Francesconi, Kevin A. ; Schwerdtle, Tanja
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.
Meyer, Sören ; Matissek, M. ; Müller, Sandra Marie ; Taleshi, M. S. ; Ebert, Franziska ; Francesconi, Kevin A. ; Schwerdtle, Tanja
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.
Unterberg, Marlies ; Leffers, Larissa ; Hübner, Florian ; Humpf, Hans-Ulrich ; Lepikhov, Konstantin ; Walter, Jörn ; Ebert, Franziska ; Schwerdtle, Tanja
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.
Unterberg, Marlies ; Leffers, Larissa ; Hübner, Florian ; Humpf, Hans-Ulrich ; Lepikhov, Konstantin ; Walter, Jörn ; Ebert, Franziska ; Schwerdtle, Tanja
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.
Probably no other field of statistical physics at the borderline of soft matter and biological physics has caused such a flurry of papers as polymer translocation since the 1994 landmark paper by Bezrukov, Vodyanoy, and Parsegian and the study of Kasianowicz in 1996. Experiments, simulations, and theoretical approaches are still contributing novel insights to date, while no universal consensus on the statistical understanding of polymer translocation has been reached. We here collect the published results, in particular, the famous–infamous debate on the scaling exponents governing the translocation process. We put these results into perspective and discuss where the field is going. In particular, we argue that the phenomenon of polymer translocation is non-universal and highly sensitive to the exact specifications of the models and experiments used towards its analysis.
Probably no other field of statistical physics at the borderline of soft matter and biological physics has caused such a flurry of papers as polymer translocation since the 1994 landmark paper by Bezrukov, Vodyanoy, and Parsegian and the study of Kasianowicz in 1996. Experiments, simulations, and theoretical approaches are still contributing novel insights to date, while no universal consensus on the statistical understanding of polymer translocation has been reached. We here collect the published results, in particular, the famous–infamous debate on the scaling exponents governing the translocation process. We put these results into perspective and discuss where the field is going. In particular, we argue that the phenomenon of polymer translocation is non-universal and highly sensitive to the exact specifications of the models and experiments used towards its analysis.
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.
Geocoder accuracy ranking
(2014)
Finding an address on a map is sometimes tricky: the chosen map application may be unfamiliar with the enclosed region. There are several geocoders on the market, they have different databases and algorithms to compute the query. Consequently, the geocoding results differ in their quality. Fortunately the geocoders provide a rich set of metadata. The workflow described in this paper compares this metadata with the aim to find out which geocoder is offering the best-fitting coordinate for a given address.
Geometric generalization is a fundamental concept in the digital mapping process. An increasing amount of spatial data is provided on the web as well as a range of tools to process it. This jABC workflow is used for the automatic testing of web-based generalization services like mapshaper.org by executing its functionality, overlaying both datasets before and after the transformation and displaying them visually in a .tif file. Mostly Web Services and command line tools are used to build an environment where ESRI shapefiles can be uploaded, processed through a chosen generalization service and finally visualized in Irfanview.
In the geoinformatics field, remote sensing data is often used for analyzing the characteristics of the current investigation area. This includes DEMs, which are simple raster grids containing grey scales representing the respective elevation values. The project CREADED that is presented in this paper aims at making these monochrome raster images more significant and more intuitively interpretable. For this purpose, an executable interactive model for creating a colored and relief-shaded Digital Elevation Model (DEM) has been designed using the jABC framework. The process is based on standard jABC-SIBs and SIBs that provide specific GIS functions, which are available as Web services, command line tools and scripts.
This paper describes the implementation of a workflow model for service-oriented computing of potential areas for wind turbines in jABC. By implementing a re-executable model the manual effort of a multi-criteria site analysis can be reduced. The aim is to determine the shift of typical geoprocessing tools of geographic information systems (GIS) from the desktop to the web. The analysis is based on a vector data set and mainly uses web services of the “Center for Spatial Information Science and Systems” (CSISS). This paper discusses effort, benefits and problems associated with the use of the web services.
Location analyses are among the most common tasks while working with spatial data and geographic information systems. Automating the most frequently used procedures is therefore an important aspect of improving their usability. In this context, this project aims to design and implement a workflow, providing some basic tools for a location analysis. For the implementation with jABC, the workflow was applied to the problem of finding a suitable location for placing an artificial reef. For this analysis three parameters (bathymetry, slope and grain size of the ground material) were taken into account, processed, and visualized with the The Generic Mapping Tools (GMT), which were integrated into the workflow as jETI-SIBs. The implemented workflow thereby showed that the approach to combine jABC with GMT resulted in an user-centric yet user-friendly tool with high-quality cartographic outputs.
Creation of topographic maps
(2014)
Location analyses are among the most common tasks while working with spatial data and geographic information systems. Automating the most frequently used procedures is therefore an important aspect of improving their usability. In this context, this project aims to design and implement a workflow, providing some basic tools for a location analysis. For the implementation with jABC, the workflow was applied to the problem of finding a suitable location for placing an artificial reef. For this analysis three parameters (bathymetry, slope and grain size of the ground material) were taken into account, processed, and visualized with the The Generic Mapping Tools (GMT), which were integrated into the workflow as jETI-SIBs. The implemented workflow thereby showed that the approach to combine jABC with GMT resulted in an user-centric yet user-friendly tool with high-quality cartographic outputs.
GraffDok is an application helping to maintain an overview over sprayed images somewhere in a city. At the time of writing it aims at vandalism rather than at beautiful photographic graffiti in an underpass. Looking at hundreds of tags and scribbles on monuments, house walls, etc. it would be interesting to not only record them in writing but even make them accessible electronically, including images.
GraffDok’s workflow is simple and only requires an EXIF-GPS-tagged photograph of a graffito. It automatically determines its location by using reverse geocoding with the given GPS-coordinates and the Gisgraphy WebService. While asking the user for some more meta data, GraffDok analyses the image in parallel with this and tries to detect fore- and background – before extracting the drawing lines and make them stand alone. The command line based tool ImageMagick is used here as well as for accessing EXIF data.
Any meta data is written to csv-files, which will stay easily accessible and can be integrated in TeX-files as well. The latter ones are converted to PDF at the end of the workflow, containing a table about all graffiti and a summary for each – including the generated characteristic graffiti pattern image.
The protein classification workflow described in this report enables users to get information about a novel protein sequence automatically. The information is derived by different bioinformatic analysis tools which calculate or predict features of a protein sequence. Also, databases are used to compare the novel sequence with known proteins.
Analyses of metagenomes in life sciences present new opportunities as well as challenges to the scientific community and call for advanced computational methods and workflows. The large amount of data collected from samples via next-generation sequencing (NGS) technologies render manual approaches to sequence comparison and annotation unsuitable. Rather, fast and efficient computational pipelines are needed to provide comprehensive statistics and summaries and enable the researcher to choose appropriate tools for more specific analyses. The workflow presented here builds upon previous pipelines designed for automated clustering and annotation of raw sequence reads obtained from next-generation sequencing technologies such as 454 and Illumina. Employing specialized algorithms, the sequence reads are processed at three different levels. First, raw reads are clustered at high similarity cutoff to yield clusters which can be exported as multifasta files for further analyses. Independently, open reading frames (ORFs) are predicted from raw reads and clustered at two strictness levels to yield sets of non-redundant sequences and ORF families. Furthermore, single ORFs are annotated by performing searches against the Pfam database
Exploratory Data Analysis
(2014)
In bioinformatics the term exploratory data analysis refers to different methods to get an overview of large biological data sets. Hence, it helps to create a framework for further analysis and hypothesis testing. The workflow facilitates this first important step of the data analysis created by high-throughput technologies. The results are different plots showing the structure of the measurements. The goal of the workflow is the automatization of the exploratory data analysis, but also the flexibility should be guaranteed. The basic tool is the free software R.
With the jABC it is possible to realize workflows for numerous questions in different fields. The goal of this project was to create a workflow for the identification of differentially expressed genes. This is of special interest in biology, for it gives the opportunity to get a better insight in cellular changes due to exogenous stress, diseases and so on. With the knowledge that can be derived from the differentially expressed genes in diseased tissues, it becomes possible to find new targets for treatment.
A workflow for visualizing server connections using the Google Maps API was built in the jABC. It makes use of three basic services: An XML-based IP address geolocation web service, a command line tool and the Static Maps API. The result of the workflow is an URL leading to an image file of a map, showing server connections between a client and a target host.
Spotlocator is a game wherein people have to guess the spots of where photos were taken. The photos of a defined area for each game are from panoramio.com. They are published at http://spotlocator. drupalgardens.com with an ID. Everyone can guess the photo spots by sending a special tweet via Twitter that contains the hashtag #spotlocator, the guessed coordinates and the ID of the photo. An evaluation is published for all tweets. The players are informed about the distance to the real photo spots and the positions are shown on a map.
Through the use of next generation sequencing (NGS) technology, a lot of newly sequenced organisms are now available. Annotating those genes is one of the most challenging tasks in sequence biology. Here, we present an automated workflow to find homologue proteins, annotate sequences according to function and create a three-dimensional model.
In this project I constructed a workflow that takes a DNA sequence as input and provides a phylogenetic tree, consisting of the input sequence and other sequences which were found during a database search. In this phylogenetic tree the sequences are arranged depending on similarities. In bioinformatics, constructing phylogenetic trees is often used to explore the evolutionary relationships of genes or organisms and to understand the mechanisms of evolution itself.
Civil society is either considered as a motor of democratization or stabilizer of authoritarian rule. This dichotomy is partly due to the dominance of domains-based definitions of the concept that reduce civil society to a small range of formally organized, independent and democratically oriented NGOs. Additionally, research often treats civil society as a ‘black box’ without differentiating between potential variations in impact of different types of civil society actors on existing regime structures. In this thesis, I present an alternative conceptualization of civil society based on the interactions of societal actors to arrive at a more inclusive understanding of the term which is more suited for analysis in non-democratic settings. The operationalization of the action-based approach I develop allows for an empirical assessment of a large range of societal activities that can accordingly be categorized from little to very civil society-like depending on their specific modes of interactions within four dimensions. I employ this operationalization in a qualitative case study including different actors in the authoritarian monarchy of Jordan which suggests that Jordanian societal actors mostly exhibit tolerant and democratically oriented modes of interaction and do not reproduce authoritarian patterns. However, even democratically oriented actors do not necessarily take on an oppositional positions vis-à-vis the authoritarian regime. Thus, the Jordanian civil society might not feature a high potential to challenge existing power structures in the country.
In March 2010, the project CoCoCo (incipient COntinent-COntinent COllision) recorded a 650 km long amphibian N-S wide-angle seismic profile, extending from the Eratosthenes Seamount (ESM) across Cyprus and southern Turkey to the Anatolian plateau. The aim of the project is to reveal the impact of the transition from subduction to continent-continent collision of the African plate with the Cyprus-Anatolian plate. A visual quality check, frequency analysis and filtering were applied to the seismic data and reveal a good data quality. Subsequent first break picking, finite-differences ray tracing and inversion of the offshore wide-angle data leads to a first-arrival tomographic model. This model reveals (1) P-wave velocities lower than 6.5 km/s in the crust, (2) a variable crustal thickness of about 28 - 37 km and (3) an upper crustal reflection at 5 km depth beneath the ESM. Two land shots on Turkey, also recorded on Cyprus, airgun shots south of Cyprus and geological and previous seismic investigations provide the information to derive a layered velocity model beneath the Anatolian plateau and for the ophiolite complex on Cyprus. The analysis of the reflections provides evidence for a north-dipping plate subducting beneath Cyprus. The main features of this layered velocity model are (1) an upper and lower crust with large lateral changes of the velocity structure and thickness, (2) a Moho depth of about 38 - 45 km beneath the Anatolian plateau, (3) a shallow north-dipping subducting plate below Cyprus with an increasing dip and (4) a typical ophiolite sequence on Cyprus with a total thickness of about 12 km. The offshore-onshore seismic data complete and improve the information about the velocity structure beneath Cyprus and the deeper part of the offshore tomographic model. Thus, the wide-angle seismic data provide detailed insights into the 2-D geometry and velocity structures of the uplifted and overriding Cyprus-Anatolian plate. Subsequent gravity modelling confirms and extends the crustal P-wave velocity model. The deeper part of the subducting plate is constrained by the gravity data and has a dip angle of ~ 28°. Finally, an integrated analysis of the geophysical and geological information allows a comprehensive interpretation of the crustal structure related to the collision process.