Institut für Physik und Astronomie
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Importance of polar solvation for cross-reactivity of antibody and its variants with steroids
(2011)
Understanding the factors determining the binding of ligands to receptors in detail is essential for rational drug design. Here, the free energies of binding of the steroids progesterone (PRG) and 5 beta-androstane-3,17-dione (SAD) to the Diels-Alderase antibody 1E9, as well as the Leu(H47)Trp/Arg(H100)Trp 1E9 double mutant (1E9dm) and the corresponding single mutants, have been estimated and decomposed using the molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) method. Also the difference in binding free energies between the PRG-1E9dm complex and the complex of PRG with the antiprogesterone antibody DB3 have been evaluated and decomposed. The steroids bind less strongly to 1E9 than to DB3, but the mutations tend to improve the steroid affinity, in quantitative agreement with experimental data. Although the complexes formed by PRG or SAD with 1E9dm and by PRG with DB3 have similar affinity, the binding mechanisms are different. Reduced Waals for SAD-1E9dm versus PRG-1E9dm or for PRG-1E9dm versus PRG-DB3 are energetically compensated by an increased solvation of polar groups, partly contrasting previous conclusions based on structural inspection. Our study illustrates that deducing binding mechanisms from structural models alone can be misleading. Therefore, taking into account solvation effects as in MM-PBSA calculations is essential to elucidate molecular recognition.
Characterization and calibration of piezoelectric polymers in situ measurements of body vibrations
(2011)
Piezoelectric polymers are known for their flexibility in applications, mainly due to their bending ability, robustness, and variable sensor geometry. It is an optimal material for minimal-invasive investigations in vibrational systems, e.g., for wood, where acoustical impedance matches particularly well. Many applications may be imagined, e. g., monitoring of buildings, vehicles, machinery, alarm systems, such that our investigations may have a large impact on technology. Longitudinal piezoelectricity converts mechanical vibrations normal to the polymer-film plane into an electrical signal, and the respective piezoelectric coefficient needs to be carefully determined in dependence on the relevant material parameters. In order to evaluate efficiency and durability for piezopolymers, we use polyvinylidene fluoride and measure the piezoelectric coefficient with respect to static pressure, amplitude of the dynamically applied force, and long-term stability. A known problem is the slow relaxation of the material towards equilibrium, if the external pressure changes; here, we demonstrate how to counter this problem with careful calibration. Since our focus is on acoustical measurements, we determine accurately the frequency response curve - for acoustics probably the most important characteristic. Eventually, we show that our piezopolymer transducers can be used as a calibrated acoustical sensors for body vibration measurements on a wooden musical instrument, where it is important to perform minimal-invasive measurements. A comparison with the simultaneously recorded airborne sound yields important insight of the mechanism of sound radiation in comparison with the sound propagating in the material. This is especially important for transient signals, where not only the long-living eigenmodes contribute to the sound radiation. Our analyses support that piezopolymer sensors can be employed as a general tool for the determination of the internal dynamics of vibrating systems.
Organic thin film transistors (TFT) are an attractive option for low cost electronic applications and may be used for active matrix displays and for RFID applications. To extend the range of applications there is a need to develop and optimise the performance of non-volatile memory devices that are compatible with the solution-processing fabrication procedures used in plastic electronics. A possible candidate is an organic TFT incorporating the ferroelectric co-polymer poly(vinylidenefluoride-trifluoroethylene)(P(VDF-TrFE)) as the gate insulator. Dielectric measurements have been carried out on all-organic metal-insulator-semiconductor structures with the ferroelectric polymer poly(vinylidenefluoride-trifluoroethylene) (P(VDF-TrFE)) as the gate insu-lator. The capacitance spectra of MIS devices, were measured under different biases, showing the effect of charge accumulation and depletion on the Maxwell-Wagner peak. The position and height of this peak clearly indicates the lack of stable depletion behavior and the decrease of mobility when increasing the depletion zone width, i.e. upon moving into the P3HT bulk. The lack of stable depletion was further investigated with capacitance-voltage (C-V) measurements. When the structure was driven into depletion, C-V plots showed a positive flat-band voltage shift, arising from the change in polarization state of the ferroelectric insulator. When biased into accumulation, the polarization was reversed. It is shown that the two polarization states are stable i.e. no depolarization occurs below the coercive field. However, negative charge trapped at the semiconductor-insulator interface during the depletion cycle masks the negative shift in flat-band voltage expected during the sweep to accumulation voltages. The measured output characteristics of the studied ferroelectric-field-effect transistors confirmed the results of the C-V plots. Furthermore, the results indicated a trapping of electrons at the positively charged surfaces of the ferroelectrically polarized P(VDF-TrFE) crystallites near the insulator/semiconductor in-terface during the first poling cycles. The study of the MIS structure by means of thermally stimulated current (TSC) revealed further evidence for the stability of the polarization under depletion voltages. It was shown, that the lack of stable depletion behavior is caused by the compensation of the orientational polarization by fixed electrons at the interface and not by the depolarization of the insulator, as proposed in several publications. The above results suggest a performance improvement of non-volatile memory devices by the optimization of the interface.
Dielectric measurements have been carried out on all-organic metal-insulator-semiconductor structures with the ferroelectric polymer poly(vinylidenefluoride-trifluoroethylene) as the gate insulator. It is shown that the polarization states remain stable after poling with accumulation and depletion voltage. However, negative charge trapped at the semiconductor-insulator interface during the depletion cycle masks the negative shift in flatband voltage expected during the sweep to accumulation voltages.
Analysis of the operating characteristics of a dielectric elastomer actuator (DEA) submount for the high-precision positioning of optical components in one dimension is presented. Precise alignment of a single-mode fiber is demonstrated and variation of the sensitivity of the submount motion by changing the bias voltage is confirmed. A comparison of the performance of the DEA submount with a piezoelectric alignment stage is made, which demonstrates that DEAs could present a very attractive, low-cost alternative to currently used manual technologies in overcoming the hurdle of expensive packaging of single-mode optical components.
We present Hubble Space Telescope Observations of (596) Scheila during its recent dust outburst. The nucleus remained point-like with absolute magnitude H(V) = 8.85 +/- 0.02 in our data, equal to the pre-outburst value, with no secondary fragments of diameter >= 100m (for assumed albedos 0.04). We find a coma having a peak scattering cross section similar to 2.2x10(4) km(2), corresponding to a mass in micron-sized particles of similar to 4x10(7) kg. The particles are deflected by solar radiation pressure on projected spatial scales similar to 2x10(4) km, in the sunward direction, and swept from the vicinity of the nucleus on timescales of weeks. The coma fades by similar to 30% between observations on UT 2010 December 27 and 2011 January 4. The observed mass loss is inconsistent with an origin either by rotational instability of the nucleus or by electrostatic ejection of regolith charged by sunlight. Dust ejection could be caused by the sudden but unexplained exposure of buried ice. However, the data are most simply explained by the impact, at similar to 5 km s(-1), of a previously unknown asteroid similar to 35m in diameter.
The outcomes of measurements on entangled quantum systems can be nonlocally correlated. However, while it is easy to write down toy theories allowing arbitrary nonlocal correlations, those allowed in quantum mechanics are limited. Quantum correlations cannot, for example, violate a principle known as macroscopic locality, which implies that they cannot violate Tsirelson's bound. This paper shows that there is a connection between the strength of nonlocal correlations in a physical theory and the structure of the state spaces of individual systems. This is illustrated by a family of models in which local state spaces are regular polygons, where a natural analogue of a maximally entangled state of two systems exists. We characterize the nonlocal correlations obtainable from such states. The family allows us to study the transition between classical, quantum and super-quantum correlations by varying only the local state space. We show that the strength of nonlocal correlations-in particular whether the maximally entangled state violates Tsirelson's bound or not-depends crucially on a simple geometric property of the local state space, known as strong self-duality. This result is seen to be a special case of a general theorem, which states that a broad class of entangled states in probabilistic theories-including, by extension, all bipartite classical and quantum states-cannot violate macroscopic locality. Finally, our results show that models exist that are locally almost indistinguishable from quantum mechanics, but can nevertheless generate maximally nonlocal correlations.
Photo-induced deformations in azobenzene-containing polymers (azo-polymers) are central to a number of applications, such as optical storage and fabrication of diffractive elements. The microscopic nature of the underlying opto-mechanical coupling is yet not clear. In this study, we address the experimental finding that the scenario of the effects depends on molecular architecture of the used azo-polymer. Typically, opposite deformations in respect to the direction of light polarization are observed for liquid crystalline and amorphous azo-polymers. In this study, we undertake molecular dynamics simulations of two different models that mimic these two types of azo-polymers. We employ hybrid force field modeling and consider only trans-isomers of azobenzene, represented as Gay-Berne sites. The effect of illumination on the orientation of the chromophores is considered on the level of orientational hole burning and emphasis is given to the resulting deformation of the polymer matrix. We reproduce deformations of opposite sign for the two models being considered here and discuss the relevant microscopic mechanisms in both cases.
We present applications of the renormalization algorithm with graph enhancement (RAGE). This analysis extends the algorithms and applications given for approaches based on matrix product states introduced in [Phys. Rev. A 79, 022317 (2009)] to other tensor-network states such as the tensor tree states (TTS) and projected entangled pair states. We investigate the suitability of the bare TTS to describe ground states, showing that the description of certain graph states and condensed-matter models improves. We investigate graph-enhanced tensor-network states, demonstrating that in some cases (disturbed graph states and for certain quantum circuits) the combination of weighted graph states with TTS can greatly improve the accuracy of the description of ground states and time-evolved states. We comment on delineating the boundary of the classically efficiently simulatable states of quantum many-body systems.
Active Galactic Nuclei (AGN) are powered by gas accretion onto supermassive Black Holes (BH). The luminosity of AGN can exceed the integrated luminosity of their host galaxies by orders of magnitude, which are then classified as Quasi-Stellar Objects (QSOs). Some mechanisms are needed to trigger the nuclear activity in galaxies and to feed the nuclei with gas. Among several possibilities, such as gravitational interactions, bar instabilities, and smooth gas accretion from the environment, the dominant process has yet to be identified. Feedback from AGN may be important an important ingredient of the evolution of galaxies. However, the details of this coupling between AGN and their host galaxies remain unclear. In this work we aim to investigate the connection between the AGN and their host galaxies by studying the properties of the extendend ionised gas around AGN. Our study is based on observations of ~50 luminous, low-redshift (z<0.3) QSOs using the novel technique of integral field spectroscopy that combines imaging and spectroscopy. After spatially separating the emission of AGN-ionised gas from HII regions, ionised solely by recently formed massive stars, we demonstrate that the specific star formation rates in several disc-dominated AGN hosts are consistent with those of normal star forming galaxies, while others display no detectable star formation activity. Whether the star formation has been actively suppressed in those particular host galaxies by the AGN, or their gas content is intrinsically low, remains an open question. By studying the kinematics of the ionised gas, we find evidence for non-gravitational motions and outflows on kpc scales only in a few objects. The gas kinematics in the majority of objects however indicate a gravitational origin. It suggests that the importance of AGN feedback may have been overrated in theoretical works, at least at low redshifts. The [OIII] line is the strongest optical emission line for AGN-ionised gas, which can be extended over several kpc scales, usually called the Narrow-Line Region (NLR). We perform a systematic investigation of the NLR size and determine a NLR size-luminosity relation that is consistent with the scenario of a constant ionisation parameter throughout the NLR. We show that previous narrow-band imaging with the Hubble Space Telescope underestimated the NLR size by a factor of >2 and that the continuum AGN luminosity is better correlated with the NLR size than the [OIII] luminosity. These affects may account for the different NLR size-luminosity relations reported in previous studies. On the other hand, we do not detect extended NLRs around all QSOs, and demonstrate that the detection of extended NLRs goes along with radio emission. We employ emission line ratios as a diagnostic for the abundance of heavy elements in the gas, i.e. its metallicity, and find that the radial metallicity gradients are always flatter than in inactive disc-dominated galaxies. This can be interpreted as evidence for radial gas flows from the outskirts of these galaxies to the nucleus. Recent or ongoing galaxy interactions are likely responsible for this effect and may turn out to be a common prerequisite for QSO activity. The metallicity of bulge-dominated hosts are systematically lower than their disc-dominated counterparts, which we interpret as evidence for minor mergers, supported by our detailed study of the bulge-dominated host of the luminous QSO HE 1029-1401, or smooth gas accretion from the environment. In this line another new discovery is that HE 2158-0107 at z=0.218 is the most metal poor luminous QSO ever observed. Together with a large (30kpc) extended structure of low metallicity ionised gas, we propose smooth cold gas accretion as the most likely scenario. Theoretical studies suggested that this process is much more important at earlier epochs of the universe, so that HE 2158-0107 might be an ideal laboratory to study this mechanism of galaxy and BH growth at low redshift more detailed in the furture.
Intrinsically disordered proteins (IDPs) constitute a substantial part of cellular proteomes. late embryogenesis abundant (LEA) proteins are mostly predicted to be IDPs associated with dehydration tolerance in many plant, animal and bacterial species. Their functions, however, are largely unexplored and also their structure and interactions with potential target molecules have only recently been experimentally investigated in a small number of proteins. Here, we report on the structure and interactions with membranes of the Pfam LEA_1 protein LEA18 from the higher plant Arabidopsis thaliana. This functionally uncharacterized positively charged protein specifically aggregated and destabilized negatively charged liposomes. Isothermal titration calorimetry showed binding of the protein to both charged and uncharged membranes. LEA18 alone was largely unstructured in solution. While uncharged membranes had no influence on the secondary structure of LEA18, the protein partially folded into beta-sheet structure in the presence of negatively charged liposomes. These data suggest that LEA18 does not function as a membrane stabilizing protein, as suggested for other LEA proteins. Instead, a possible function of LEA18 could be the composition-dependent modulation of membrane stability, e.g., during signaling or vesicle-mediated transport.
The star zeta Ophiuchi is one of the brightest massive stars in the northern hemisphere and was intensively studied in various wavelength domains. The currently available observational material suggests that certain observed phenomena are related to the presence of a magnetic field. We acquired spectropolarimetric observations of zeta Oph with FORS 1 mounted on the 8-m Kueyen telescope of the VLT to investigate if a magnetic field is indeed present in this star. Using all available absorption lines, we detect a mean longitudinal magnetic field < B(z)>(all) = 141 +/- 45 G, confirming the magnetic nature of this star. We review the X-ray properties of zeta Oph with the aim to understand whether the X-ray emission of zeta Oph is dominated by magnetic or by wind instability processes.
In this paper, we study the complete synchronization of a class of time-varying delayed coupled chaotic systems using feedback control. In terms of Linear Matrix Inequalities, a sufficient condition is obtained through using a Lyapunov-Krasovskii functional and differential equation in equalities. The conditions can be easily verified and implemented. We present two simulation examples to illustrate the effectiveness of the proposed method.
Prerequisite for the rational design of functional organic materials with tailor-made electronic properties is the knowledge of the structure-property relationship for the specific class of molecules under consideration. This encouraged us to systematically study the influence of the molecular structure and substitution pattern of aromatically substituted 1,3,4-oxadiazoles on the electronic properties and packing motifs of these molecules and on the interplay of these factors. For this purpose, seven diphenyl-oxadiazoles equipped with methyl substituents in the ortho- and meta-position(s) were synthesized and characterized. Absorption and fluorescence spectra in solution served here as tools to monitor substitution-induced changes in the electronic properties of the individual molecules whereas X-ray and optical measurements in the solid state provided information on the interplay of electronic and packing effects. In solution, the spectral position of the absorption maximum, the size of Stokes shift, and the fluorescence quantum yield are considerably affected by ortho-substitution in three or four ortho-positions. This results in blue shifted absorption bands, increased Stokes shifts, and reduced fluorescence quantum yields whereas the spectral position and vibrational structure of the emission bands remain more or less unaffected. In the crystalline state, however, the spectral position and shape of the emission bands display a strong dependence on the molecular structure and/or packing motifs that seem to control the amount of dye-dye-interactions. These observations reveal the limited value of commonly reported absorption and fluorescence measurements in solution for a straightforward comparison of spectroscopic results with single X-ray crystallography. This underlines the importance of solid state spectroscopic studies for a better understanding of the interplay of electronic effects and molecular order.
The Arctic is a particularly sensitive area with respect to climate change due to the high surface albedo of snow and ice and the extreme radiative conditions. Clouds and aerosols as parts of the Arctic atmosphere play an important role in the radiation budget, which is, as yet, poorly quantified and understood. The LIDAR (Light Detection And Ranging) measurements presented in this PhD thesis contribute with continuous altitude resolved aerosol profiles to the understanding of occurrence and characteristics of aerosol layers above Ny-Ålesund, Spitsbergen. The attention was turned to the analysis of periods with high aerosol load. As the Arctic spring troposphere exhibits maximum aerosol optical depths (AODs) each year, March and April of both the years 2007 and 2009 were analyzed. Furthermore, stratospheric aerosol layers of volcanic origin were analyzed for several months, subsequently to the eruptions of the Kasatochi and Sarychev volcanoes in summer 2008 and 2009, respectively. The Koldewey Aerosol Raman LIDAR (KARL) is an instrument for the active remote sensing of atmospheric parameters using pulsed laser radiation. It is operated at the AWIPEV research base and was fundamentally upgraded within the framework of this PhD project. It is now equipped with a new telescope mirror and new detection optics, which facilitate atmospheric profiling from 450m above sea level up to the mid-stratosphere. KARL provides highly resolved profiles of the scattering characteristics of aerosol and cloud particles (backscattering, extinction and depolarization) as well as water vapor profiles within the lower troposphere. Combination of KARL data with data from other instruments on site, namely radiosondes, sun photometer, Micro Pulse LIDAR, and tethersonde system, resulted in a comprehensive data set of scattering phenomena in the Arctic atmosphere. The two spring periods March and April 2007 and 2009 were at first analyzed based on meteorological parameters, like local temperature and relative humidity profiles as well as large scale pressure patterns and air mass origin regions. Here, it was not possible to find a clear correlation between enhanced AOD and air mass origin. However, in a comparison of two cloud free periods in March 2007 and April 2009, large AOD values in 2009 coincided with air mass transport through the central Arctic. This suggests the occurrence of aerosol transformation processes during the aerosol transport to Ny-Ålesund. Measurements on 4 April 2009 revealed maximum AOD values of up to 0.12 and aerosol size distributions changing with altitude. This and other performed case studies suggest the differentiation between three aerosol event types and their origin: Vertically limited aerosol layers in dry air, highly variable hygroscopic boundary layer aerosols and enhanced aerosol load across wide portions of the troposphere. For the spring period 2007, the available KARL data were statistically analyzed using a characterization scheme, which is based on optical characteristics of the scattering particles. The scheme was validated using several case studies. Volcanic eruptions in the northern hemisphere in August 2008 and June 2009 arose the opportunity to analyze volcanic aerosol layers within the stratosphere. The rate of stratospheric AOD change was similar within both years with maximum values above 0.1 about three to five weeks after the respective eruption. In both years, the stratospheric AOD persisted at higher rates than usual until the measurements were stopped in late September due to technical reasons. In 2008, up to three aerosol layers were detected, the layer structure in 2009 was characterized by up to six distinct and thin layers which smeared out to one broad layer after about two months. The lowermost aerosol layer was continuously detected at the tropopause altitude. Three case studies were performed, all revealed rather large indices of refraction of m = (1.53–1.55) - 0.02i, suggesting the presence of an absorbing carbonaceous component. The particle radius, derived with inversion calculations, was also similar in both years with values ranging from 0.16 to 0.19 μm. However, in 2009, a second mode in the size distribution was detected at about 0.5 μm. The long term measurements with the Koldewey Aerosol Raman LIDAR in Ny-Ålesund provide the opportunity to study Arctic aerosols in the troposphere and the stratosphere not only in case studies but on longer time scales. In this PhD thesis, both, tropospheric aerosols in the Arctic spring and stratospheric aerosols following volcanic eruptions have been described qualitatively and quantitatively. Case studies and comparative studies with data of other instruments on site allowed for the analysis of microphysical aerosol characteristics and their temporal evolution.
Quantum correlations exhibit behaviour that cannot be resolved with a local hidden variable picture of the world. In quantum information, they are also used as resources for information processing tasks, such as measurement-based quantum computation (MQC). In MQC, universal quantum computation can be achieved via adaptive measurements on a suitable entangled resource state. In this paper, we look at a version of MQC in which we remove the adaptivity of measurements and aim to understand what computational abilities remain in the resource. We show that there are explicit connections between this model of computation and the question of non-classicality in quantum correlations. We demonstrate this by focusing on deterministic computation of Boolean functions, in which natural generalizations of the Greenberger-Horne-Zeilinger paradox emerge; we then explore probabilistic computation via, which multipartite Bell inequalities can be defined. We use this correspondence to define families of multi-party Bell inequalities, which we show to have a number of interesting contrasting properties.
Synchrotron based combined in situ x-ray diffractometry and reflectometry is used to investigate the role of vacancies for the relaxation of residual stress in thin metallic Pt films. From the experimentally determined relative changes of the lattice parameter a and of the film thickness L the modification of vacancy concentration and residual strain was derived as a function of annealing time at 130 degrees C. The results indicate that relaxation of strain resulting from compressive stress is accompanied by the creation of vacancies at the free film surface. This proves experimentally the postulated dominant role of vacancies for stress relaxation in thin metal films close to room temperature.
Aims. We study an evolving bipolar active region that exhibits flux cancellation at the internal polarity inversion line, the formation of a soft X-ray sigmoid along the inversion line and a coronal mass ejection. The aim is to investigate the quantity of flux cancellation that is involved in flux rope formation in the time period leading up to the eruption.
Methods. The active region is studied using its extreme ultraviolet and soft X-ray emissions as it evolves from a sheared arcade to flux rope configuration. The evolution of the photospheric magnetic field is described and used to estimate how much flux is reconnected into the flux rope.
Results. About one third of the active region flux cancels at the internal polarity inversion line in the 2.5 days leading up to the eruption. In this period, the coronal structure evolves from a weakly to a highly sheared arcade and then to a sigmoid that crosses the inversion line in the inverse direction. These properties suggest that a flux rope has formed prior to the eruption. The amount of cancellation implies that up to 60% of the active region flux could be in the body of the flux rope. We point out that only part of the cancellation contributes to the flux in the rope if the arcade is only weakly sheared, as in the first part of the evolution. This reduces the estimated flux in the rope to similar to 30% or less of the active region flux. We suggest that the remaining discrepancy between our estimate and the limiting value of similar to 10% of the active region flux, obtained previously by the flux rope insertion method, results from the incomplete coherence of the flux rope, due to nonuniform cancellation along the polarity inversion line. A hot linear feature is observed in the active region which rises as part of the eruption and then likely traces out the field lines close to the axis of the flux rope. The flux cancellation and changing magnetic connections at one end of this feature suggest that the flux rope reaches coherence by reconnection immediately before and early in the impulsive phase of the associated flare. The sigmoid is destroyed in the eruption but reforms quickly, with the amount of cancellation involved being much smaller than in the course of its original formation.
Within the Schwinger-Keldysh formalism we derive a Ginzburg-Landau theory for the Bose-Hubbard model which describes the real-time dynamics of the complex order parameter field. Analyzing the excitations in the vicinity of the quantum phase transitions it turns out that particle/hole dispersions in the Mott phase map continuously onto corresponding amplitude/phase excitations in the superfluid phase. Furthermore, in the superfluid phase we find a sound mode, which is in accordance with recent Bragg spectroscopy measurements in the Bogoliubov regime, as well as an additional gapped mode, which seems to have been detected via lattice modulation.
We establish a link between unitary relaxation dynamics after a quench in closed many-body systems and the entanglement in the energy eigenbasis. We find that even if reduced states equilibrate, they can have memory on the initial conditions even in certain models that are far from integrable. We show that in such situations the equilibrium states are still described by a maximum entropy or generalized Gibbs ensemble, regardless of whether a model is integrable or not, thereby contributing to a recent debate. In addition, we discuss individual aspects of the thermalization process, comment on the role of Anderson localization, and collect and compare different notions of integrability.