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Institute
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Diffusion of finite-size particles in two-dimensional channels with random wall configurations
(2014)
Diffusion of chemicals or tracer molecules through complex systems containing irregularly shaped channels is important in many applications. Most theoretical studies based on the famed Fick-Jacobs equation focus on the idealised case of infinitely small particles and reflecting boundaries. In this study we use numerical simulations to consider the transport of finite-size particles through asymmetrical two-dimensional channels. Additionally, we examine transient binding of the molecules to the channel walls by applying sticky boundary conditions. We consider an ensemble of particles diffusing in independent channels, which are characterised by common structural parameters. We compare our results for the long-time effective diffusion coefficient with a recent theoretical formula obtained by Dagdug and Pineda
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 Forster 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) surfacefunctionalised 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 Forster theory, Forsterradii (R0) were found to be around 60 angstrom for organic dyes and around 105 angstrom for QDs. The FRET efficiency (Z) reached 80% and 25% for dye and QD acceptors, respectively. Physical donor-acceptor distances (r) have been determined in the range 45-60 angstrom for organic dye acceptors, while for acceptor QDs between 120 angstrom and 145 angstrom. 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.
Charge transport and structural dynamics in low molecular weight and polymerized 1-vinyl-3-pentylimidazolium bis(trifluoromethylsulfonyl) imide ionic liquids (ILs) are investigated by a combination of broadband dielectric spectroscopy, dynamic mechanical spectroscopy and differential scanning calorimetry. While the dc conductivity and fluidity exhibit practically identical temperature dependence for the non-polymerized IL, a significant decoupling of ionic conduction from structural dynamics is observed for the polymerized IL. In addition, the dc conductivity of the polymerized IL exceeds that of its molecular counterpart by four orders of magnitude at their respective calorimetric glass transition temperatures. This is attributed to the unusually high mobility of the anions especially at lower temperatures when the structural dynamics is significantly slowed down. A simple physical explanation of the possible origin of the remarkable decoupling of ionic conductivity from structural dynamics is proposed.
A feasible approach to construct multilayer films of sulfonated polyanilines - PMSA1 and PABMSA1 containing different ratios of aniline, 2-methoxyaniline-5-sulfonic acid (MAS) and 3-aminobenzoic acid (AB), with the entrapped redox enzyme pyrroloquinoline quinone-dependent glucose dehydrogenase (PQQ-GDH) on Au and ITO electrode surfaces, is described. The formation of layers has been followed and confirmed by electrochemical impedance spectroscopy (EIS), which demonstrates that the multilayer assembly can be achieved in a progressive and uniform manner. The gold and ITO electrodes subsequently modified with PMSA1:PQQ-GDH and PABMSA1 films are studied by cyclic voltammetry (CV) and UV-Vis spectroscopy which show a significant direct bioelectrocatalytical response to the oxidation of the substrate glucose without any additional mediator. This response correlates linearly with the number of deposited layers. Furthermore, the constructed polymer/enzyme multilayer system exhibits a rather good long-term stability, since the catalytic current response is maintained for more than 60% of the initial value even after two weeks of storage. This verifies that a productive interaction of the enzyme embedded in the film of substituted polyaniline can be used as a basis for the construction of bioelectronic units, which are useful as indicators for processes liberating glucose and allowing optical and electrochemical transduction.
Materials derived from renewable resources are highly desirable in view of more sustainable manufacturing. Among the available natural materials, wood is one of the key candidates, because of its excellent mechanical properties. However, wood and wood-based materials in engineering applications suffer from various restraints, such as dimensional instability upon humidity changes. Several wood modification treatments increase water repellence, but the insertion of hydrophobic polymers can result in a composite material which cannot be considered as renewable anymore. In this study, we report on the grafting of the fully biodegradable poly(epsilon-caprolactone) (PCL) inside the wood cell walls by Sn(Oct)(2) catalysed ring-opening polymerization (ROP). The presence of polyester chains within the wood cell wall structure is monitored by confocal Raman imaging and spectroscopy as well as scanning electron microscopy. Physical tests reveal that the modified wood is more hydrophobic due to the bulking of the cell wall structure with the polyester chains, which results in a novel fully biodegradable wood material with improved dimensional stability.
Hemocompatible materials are needed for internal and extracorporeal biomedical applications, which should be realizable by reducing protein and thrombocyte adhesion to such materials. Polyethers have been demonstrated to be highly efficient in this respect on smooth surfaces. Here, we investigate the grafting of oligo- and polyglycerols to rough poly(ether imide) membranes as a polymer relevant to biomedical applications and show the reduction of protein and thrombocyte adhesion as well as thrombocyte activation. It could be demonstrated that, by performing surface grafting with oligo-and polyglycerols of relatively high polydispersity (>1.5) and several reactive groups for surface anchoring, full surface shielding can be reached, which leads to reduced protein adsorption of albumin and fibrinogen. In addition, adherent thrombocytes were not activated. This could be clearly shown by immunostaining adherent proteins and analyzing the thrombocyte covered area. The presented work provides an important strategy for the development of application relevant hemocompatible 3D structured materials.
Photoinduced excitation energy transfer and accompanying charge separation are elucidated for a supramolecular system of a single fullerene covalently linked to six pyropheophorbide-a dye molecules. Molecular dynamics simulations are performed to gain an atomistic picture of the architecture and the surrounding solvent. Excitation energy transfer among the dye molecules and electron transfer from the excited dyes to the fullerene are described by a mixed quantum-classical version of the Forster rate and the semiclassical Marcus rate, respectively. The mean characteristic time of energy redistribution lies in the range of 10 ps, while electron transfer proceeds within 150 ps. In between, on a 20 to 50 ps time-scale, conformational changes take place in the system. This temporal hierarchy of processes guarantees efficient charge separation, if the structure is exposed to a solvent. The fast energy transfer can adopt the dye excitation to the actual conformation. In this sense, the probability to achieve charge separation is large enough since any dominance of unfavorable conformations that exhibit a large dye-fullerene distance is circumvented. And the slow electron transfer may realize an averaging with respect to different conformations. To confirm the reliability of our computations, ensemble measurements on the charge separation dynamics are simulated and a very good agreement with the experimental data is obtained.
The standard procedure in the lab for plasmid isolation usually involves a 2-mL, 16 h over-night cultivation in 15-mL bioreaction tubes in LB medium. This is time consuming, and not suitable for high-throughput applications. This study shows that it is possible to produce plasmid DNA (pDNA) in a 1.5-mL microcentrifuge tube with only 100 L cultivation volume in less than 7 h with a simple protocol. Compared with the standard LB cultivation for pDNA production reaching a final pDNA concentration range of 1.5-4 mu g mL(-1), a 6- to 10-fold increase in plasmid concentration (from 10 up to 25 mu g mL(-1) cultivation volume) is achieved using an optimized medium with an internal substrate delivery system (EnBase (R)). Different strains, plasmids, and the applicability of different inoculation tools (i.e. different starting ODs) were compared, demonstrating the robustness of the system. Additionally, dissolved oxygen was monitored in real time online, indicating that under optimized conditions oxygen limitation can be avoided. We developed a simple protocol with a significantly decreased procedure time, enabling simultaneous handling of more samples, while a consistent quality and a higher final pDNA concentration are ensured.
Recently, C K-edge Near Edge X-ray Absorption Fine Structure (NEXAFS) spectra of graphite (HOPG) surfaces have been measured for the pristine material, and for HOPG treated with either bromine or krypton plasmas (Lippitz et al., Surf. Sci., 2013, 611, L1). Changes of the NEXAFS spectra characteristic for physical (krypton) and/or chemical/physical modifications of the surface (bromine) upon plasma treatment were observed. Their molecular origin, however, remained elusive. In this work we study by density functional theory, the effects of selected point and line defects as well as chemical modifications on NEXAFS carbon K-edge spectra of single graphene layers. For Br-treated surfaces, also Br 3d X-ray Photoelectron Spectra (XPS) are simulated by a cluster approach, to identify possible chemical modifications. We observe that some of the defects related to plasma treatment lead to characteristic changes of NEXAFS spectra, similar to those in experiment. Theory provides possible microscopic origins for these changes.
Graphitic carbon nitride, g-C3N4, is a promising organic photo-catalyst for a variety of redox reactions. In order to improve its efficiency in a systematic manner, however, a fundamental understanding of the microscopic interaction between catalyst, reactants and products is crucial. Here we present a systematic study of water adsorption on g-C3N4 by means of density functional theory and the density functional based tight-binding method as a prerequisite for understanding photocatalytic water splitting. We then analyze this prototypical redox reaction on the basis of a thermodynamic model providing an estimate of the overpotential for both water oxidation and H+ reduction. While the latter is found to occur readily upon irradiation with visible light, we derive a prohibitive overpotential of 1.56 eV for the water oxidation half reaction, comparing well with the experimental finding that in contrast to H-2 production O-2 evolution is only possible in the presence of oxidation cocatalysts.
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 < x(2)(t) similar or equal to 2K(t)t with K(t) similar or equal to t(alpha-1) for 0 < 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.
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.
As a part of searching for fully aromatic chelate compounds, copper complexes of malondialdehyde as well as its sulfur and selenium derivatives were investigated using the DFT quantum chemical methods. Chelate complexes of both Cu(I) and Cu(II) ions wereconsidered. Aromaticity of the metal complexes studied were analyzed using NICS(0), NICS(1), PDI, I-ring, MCI, ICMCI and I-B aromaticity indices, and by TSNMRS visualizations of the spatial magnetic properties. It seems that partial aromaticityof studied chelates increases when oxygen atoms in malondialdehyde are replaced by sulfur and selenium.
The large-scale green synthesis of graphene-type two-dimensional materials is still challenging. Herein, we describe the ionothermal synthesis of carbon-based composites from fructose in the iron-containing ionic liquid 1-butyl-3-methylimidazolium tetrachloridoferrate(III), [Bmim][FeCl4] serving as solvent, catalyst, and template for product formation. The resulting composites consist of oligo-layer graphite nanoflakes and iron carbide particles. The mesoporosity, strong magnetic moment, and high specific surface area of the composites make them attractive for water purification with facile magnetic separation. Moreover, Fe3Cfree graphite can be obtained via acid etching, providing access to fairly large amounts of graphite material. The current approach is versatile and scalable, and thus opens the door to ionothermal synthesis towards the larger-scale synthesis of materials that are, although not made via a sustainable process, useful for water treatment such as the removal of organic molecules.
Polyglycolide (PGA) is a biodegradable polymer with multiple applications in the medical sector. Here the synthesis of high molecular weight polyglycolide by ring-opening polymerization of diglycolide is reported. For the first time stabilizer free supercritical carbon dioxide (scCO(2)) was used as a reaction medium. scCO(2) allowed for a reduction in reaction temperature compared to conventional processes. Together with the lowering of monomer concentration and consequently reduced heat generation compared to bulk reactions thermal decomposition of the product occurring already during polymerization is strongly reduced. The reaction temperatures and pressures were varied between 120 and 150 degrees C and 145 to 1400 bar. Tin(II) ethyl hexanoate and 1-dodecanol were used as catalyst and initiator, respectively. The highest number average molecular weight of 31 200 g mol(-1) was obtained in 5 hours from polymerization at 120 degrees C and 530 bar. In all cases the products were obtained as a dry white powder. Remarkably, independent of molecular weight the melting temperatures were always at (219 +/- 2)degrees C.
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.
For in vitro studies assessing the interaction of platelets with implant materials, common and standardized protocols for the preparation of platelet rich plasma (PRP) are lacking, which may lead to non-matching results due to the diversity of applied protocols. Particularly, the aging of platelets during prolonged preparation and storage times is discussed to lead to an underestimation of the material thrombogenicity. Here, we study the influence of whole blood-and PRP-storage times on changes in platelet morphology and function.
Whole blood PFA100 closure times increased after stimulation with collagen/ADP and collagen/epinephrine. Twenty four hours after blood collection, both parameters were prolonged pathologically above the upper limit of the reference range. Numbers of circulating platelets, measured in PRP, decreased after four hours, but no longer after twenty four hours. Mean platelet volumes (MPV) and platelet large cell ratios (P-LCR, 12 fL - 40 fL) decreased over time. Immediately after blood collection, no debris or platelet aggregates could be visualized microscopically. After four hours, first debris and very small aggregates occurred. After 24 hours, platelet aggregates and also debris progressively increased. In accordance to this, the CASY system revealed an increase of platelet aggregates (up to 90 mu m diameter)with increasing storage time.
The percentage of CD62P positive platelets and PF4 increased significantly with storage time in resting PRP. When soluble ADP was added to stored PRP samples, the number of activatable platelets decreased significantly over storage time. The present study reveals the importance of a consequent standardization in the preparation of WB and PRP. Platelet morphology and function, particularly platelet reactivity to adherent or soluble agonists in their surrounding milieu, changed rapidly outside the vascular system. This knowledge is of crucial interest, particularly in the field of biomaterial development for cardiovascular applications, and may help to define common standards in the in vitro hemocompatibility testing of biomaterials.
We report a 1,2,3-triazol fluoroionophore for detecting Na+ that shows in vitro enhancement in the Na+-induced fluorescence intensity and decay time. The Na+-selective molecule 1 was incorporated into a hydrogel as a part of a fiber optical sensor. This sensor allows the direct determination of Na+ in the range of 1-10 mM by measuring reversible fluorescence decay time changes.