TY - JOUR A1 - Murib, Mohammed S. A1 - Tran, Anh Quang A1 - Ceuninck, Ward de A1 - Schöning, Michael Josef A1 - Nesladek, Milos A1 - Serpengüzel, Ali A1 - Wagner, Patrick T1 - Analysis of an optical biosensor based on elastic light scattering from diamond-, glass-, and sapphire microspheres JF - Physica Status Solidi A N2 - Deoxyribonucleic acid (DNA) and protein recognition are now standard tools in biology. In addition, the special optical properties of microsphere resonators expressed by the high quality factor (Q-factor) of whispering gallery modes (WGMs) or morphology dependent resonances (MDRs) have attracted the attention of the biophotonic community. Microsphere-based biosensors are considered as powerful candidates to achieve label-free recognition of single molecules due to the high sensitivity of their WGMs. When the microsphere surface is modified with biomolecules, the effective refractive index and the effective size of the microsphere change resulting in a resonant wavelength shift. The transverse electric (TE) and the transverse magnetic (TM) elastic light scattering intensity of electromagnetic waves at 600 and 1400 nm are numerically calculated for DNA and unspecific binding of proteins to the microsphere surface. The effect of changing the optical properties was studied for diamond (refractive index 2.34), glass (refractive index 1.50), and sapphire (refractive index 1.75) microspheres with a 50 µm radius. The mode spacing, the linewidth of WGMs, and the shift of resonant wavelength due to the change in radius and refractive index, were analyzed by numerical simulations. Preliminary results of unspecific binding of biomolecules are presented. The calculated shift in WGMs can be used for biomolecules detection. Y1 - 2012 U6 - https://doi.org/10.1002/pssa.201100795 SN - 1862-6319 N1 - Special Issue: "Fundamentals and Applications of Diamond" VL - 209 IS - 9 SP - 1804 EP - 1810 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Gutheil, Inge A1 - Berg, Tommy A1 - Grotendorst, Johannes T1 - Performance Analysis of Parallel Eigensolvers of two Libraries on BlueGene/P JF - Journal of Mathematics and Systems Science N2 - Many applications in computational science and engineering require the computation of eigenvalues and vectors of dense symmetric or Hermitian matrices. For example, in DFT (density functional theory) calculations on modern supercomputers 10% to 30% of the eigenvalues and eigenvectors of huge dense matrices have to be calculated. Therefore, performance and parallel scaling of the used eigensolvers is of upmost interest. In this article different routines of the linear algebra packages ScaLAPACK and Elemental for parallel solution of the symmetric eigenvalue problem are compared concerning their performance on the BlueGene/P supercomputer. Parameters for performance optimization are adjusted for the different data distribution methods used in the two libraries. It is found that for all test cases the new library Elemental which uses a two-dimensional element by element distribution of the matrices to the processors shows better performance than the old ScaLAPACK library which uses a block-cyclic distribution. KW - performance analysis KW - Elemental KW - ScaLAPACK KW - eigensolvers KW - Numerical linear algebra Y1 - 2012 U6 - https://doi.org/10.17265/2159-5291/2012.04.003 SN - 2159-5291 VL - 2 IS - 4 SP - 231 EP - 236 PB - David Publishing CY - Libertyville ER - TY - JOUR A1 - Grotendorst, Johannes T1 - IAS Winter School: Hierarchical Methods for Dynamics in Complex Molecular Systems JF - Innovatives Supercomputing in Deutschland : inSiDE. 10 (2012), H. 1 Y1 - 2012 SP - 104 PB - - ER - TY - JOUR A1 - Nomdedeu, Mar Monsonis A1 - Willen, Christine A1 - Schieffer, Andre A1 - Arndt, Hartmut T1 - Temperature-dependent ranges of coexistence in a model of a two-prey-one-predator microbial food web JF - Marine Biology N2 - The objective of our study was to analyze the effects of temperature on the population dynamics of a three-species food web consisting of two prey bacteria (Pedobacter sp. and Acinetobacter johnsonii) and a protozoan predator (Tetrahymena pyriformis) as model organisms. We assessed the effects of temperature on the growth rates of all three species with the objective of developing a model with four differential equations based on the experimental data. The following hypotheses were tested at a theoretical level: Firstly, temperature changes can affect the dynamic behavior of a system by temperature-dependent parameters and interactions and secondly, food web response to temperature cannot be derived from the single species temperature response. The main outcome of the study is that temperature changes affect the parameter range where coexistence is possible within all three species. This has significant consequences on our ideas regarding the evaluation of effects of global warming. Y1 - 2012 U6 - https://doi.org/10.1007/s00227-012-1966-x SN - 1432-1793 VL - 159 IS - 11 SP - 2423 EP - 2430 PB - Springer CY - Berlin ER - TY - JOUR A1 - Lustfeld, H. A1 - Pithan, C. A1 - Reißel, Martin T1 - Metallic electrolyte composites in the framework of the brick-layer model JF - Journal of the European Ceramic Society N2 - It is well known that the already large dielectric constants of some electrolytes like BaTiO₃ can be enhanced further by adding metallic (e.g. Ni, Cu or Ag) nanoparticles. The enhancement can be quite large, a factor of more than 1000 is possible. The consequences for the properties will be discussed in the present paper applying a brick-layer model (BLM) for calculating dc-resistivities of thin layers and a modified one (PBLM) that includes percolation for calculating dielectric properties of these materials. The PBLM results in an at least qualitative description and understanding of the physical phenomena: This model gives an explanation for the steep increase of the dielectric constant below the percolation threshold and why this increase is connected to a dramatic decrease of the breakdown voltage as well as the ability of storing electrical energy. We conclude that metallic electrolyte composites like BaTiO₃ are not appropriate for energy storage. Y1 - 2012 U6 - https://doi.org/10.1016/j.jeurceramsoc.2011.10.017 SN - 0955-2219 VL - 32 IS - 4 SP - 859 EP - 864 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Leurs, Ulrike A1 - Mezo, Gabor A1 - Öhlschläger, Peter A1 - Orban, Erika A1 - Marquard, Andrea A1 - Manea, Marilena T1 - Design, synthesis, in vitro stability and cytostatic effect of multifunctional anticancer drug-bioconjugates containing GnRH-III as a targeting moiety JF - Peptide Science N2 - Bioconjugates containing the GnRH-III hormone decapeptide as a targeting moiety are able to deliver chemotherapeutic agents specifically to cancer cells expressing GnRH receptors, thereby increasing their local efficacy while limiting the peripheral toxicity. However, the number of GnRH receptors on cancer cells is limited and they desensitize under continuous hormone treatment. A possible approach to increase the receptor mediated tumor targeting and consequently the cytostatic effect of the bioconjugates would be the attachment of more than one chemotherapeutic agent to one GnRH-III molecule. Here we report on the design, synthesis and biochemical characterization of multifunctional bioconjugates containing GnRH-III as a targeting moiety and daunorubicin as a chemotherapeutic agent. Two different drug design approaches were pursued. The first one was based on the bifunctional [4Lys]-GnRH-III (Glp-His-Trp-Lys-His-Asp-Trp-Lys-Pro-Gly-NH2) containing two lysine residues in positions 4 and 8, whose ϵ-amino groups were used for the coupling of daunorubicin. In the second drug design, the native GnRH-III (Glp-His-Trp-Ser-His-Asp-Trp-Lys-Pro-Gly-NH2) was used as a scaffold; an additional lysine residue was coupled to the ϵ-amino group of 8Lys in order to generate two free amino groups available for conjugation of daunorubicin. The in vitro stability/degradation of all synthesized compounds was investigated in human serum, as well as in the presence of rat liver lysosomal homogenate. Their cellular uptake was determined on human breast cancer cells and the cytostatic effect was evaluated on human breast, colon and prostate cancer cell lines. Compared with a monofunctional compound, both drug design approaches resulted in multifunctional bioconjugates with increased cytostatic effect. Y1 - 2012 U6 - https://doi.org/10.1002/bip.21640 SN - 1097-0282 VL - 98 IS - 1 SP - 1 EP - 10 PB - Wiley CY - New York, NY ER - TY - JOUR A1 - Grinsven, Bart van A1 - Bon, Natalie vanden A1 - Strauven, Hannelore A1 - Grieten, Lars A1 - Murib, Mohammed A1 - Jiménez Monroy, Kathia L. A1 - Janssens, Stoffel D. A1 - Haenen, Ken A1 - Schöning, Michael Josef A1 - Vermeeren, Veronique A1 - Ameloot, Marcel A1 - Michiels, Luc A1 - Thoelen, Ronald A1 - Ceuninck, Ward de A1 - Wagner, Patrick T1 - Heat-Transfer Resistance at Solid-Liquid Interfaces: A Tool for The Detection of Single Nucleotide Polymorphisms in DNA. JF - ACS Nano N2 - In this article, we report on the heat-transfer resistance at interfaces as a novel, denaturation-based method to detect single-nucleotide polymorphisms in DNA. We observed that a molecular brush of double-stranded DNA grafted onto synthetic diamond surfaces does not notably affect the heat-transfer resistance at the solid-to-liquid interface. In contrast to this, molecular brushes of single-stranded DNA cause, surprisingly, a substantially higher heat-transfer resistance and behave like a thermally insulating layer. This effect can be utilized to identify ds-DNA melting temperatures via the switching from low- to high heat-transfer resistance. The melting temperatures identified with this method for different DNA duplexes (29 base pairs without and with built-in mutations) correlate nicely with data calculated by modeling. The method is fast, label-free (without the need for fluorescent or radioactive markers), allows for repetitive measurements, and can also be extended toward array formats. Reference measurements by confocal fluorescence microscopy and impedance spectroscopy confirm that the switching of heat-transfer resistance upon denaturation is indeed related to the thermal on-chip denaturation of DNA. Y1 - 2012 U6 - https://doi.org/10.1021/nn300147e SN - 1936-086X VL - 6 IS - 3 SP - 2712 EP - 2721 PB - ACS Publications CY - Washington, DC ER - TY - JOUR A1 - Olaru, Alexandra Maria A1 - Kowalski, Julia A1 - Sethi, Vaishali A1 - Blümich, Bernhard T1 - Exchange relaxometry of flow at small Péclet numbers in a glass bead pack JF - Journal of Magnetic Resonance (JMR) N2 - In this paper we consider low Péclet number flow in bead packs. A series of relaxation exchange experiments has been conducted and evaluated by ILT analysis. In the resulting correlation maps, we observed a collapse of the signal and a translation towards smaller relaxation times with increasing flow rates, as well as a signal tilt with respect to the diagonal. In the discussion of the phenomena we present a mathematical theory for relaxation exchange experiments that considers both diffusive and advective transport. We perform simulations based on this theory and discuss them with respect to the conducted experiments. KW - NMR exchange relaxometry KW - Low-field NMR Y1 - 2012 U6 - https://doi.org/10.1016/j.jmr.2012.04.015 SN - 1096-0856 VL - 220 SP - 32 EP - 44 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Fischer, Jan-Thomas A1 - Kowalski, Julia A1 - Pudasaini, Shiva P. T1 - Topographic curvature effects in applied avalanche modelling JF - Cold Regions Science and Technology N2 - This paper describes the implementation of topographic curvature effects within the RApid Mass MovementS (RAMMS) snow avalanche simulation toolbox. RAMMS is based on a model similar to shallow water equations with a Coulomb friction relation and the velocity dependent Voellmy drag. It is used for snow avalanche risk assessment in Switzerland. The snow avalanche simulation relies on back calculation of observed avalanches. The calibration of the friction parameters depends on characteristics of the avalanche track. The topographic curvature terms are not yet included in the above mentioned classical model. Here, we fundamentally improve this model by mathematically and physically including the topographic curvature effects. By decomposing the velocity dependent friction into a topography dependent term that accounts for a curvature enhancement in the Coulomb friction, and a topography independent contribution similar to the classical Voellmy drag, we construct a general curvature dependent frictional resistance, and thus propose new extended model equations. With three site-specific examples, we compare the apparent frictional resistance of the new approach, which includes topographic curvature effects, to the classical one. Our simulation results demonstrate substantial effects of the curvature on the flow dynamics e.g., the dynamic pressure distribution along the slope. The comparison of resistance coefficients between the two models demonstrates that the physically based extension presents an improvement to the classical approach. Furthermore a practical example highlights its influence on the pressure outline in the run out zone of the avalanche. Snow avalanche dynamics modeling natural terrain curvature centrifugal force friction coefficients. KW - Snow KW - Avalanche Y1 - 2012 U6 - https://doi.org/10.1016/j.coldregions.2012.01.005 SN - 1872-7441 VL - 74-75 SP - 21 EP - 30 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Pieper, Martin A1 - Klein, Peter T1 - Application of simple, periodic homogenization techniques to non-linear heat conduction problems in non-periodic, porous media JF - Heat mass transfer N2 - Often, detailed simulations of heat conduction in complicated, porous media have large runtimes. Then homogenization is a powerful tool to speed up the calculations by preserving accurate solutions at the same time. Unfortunately real structures are generally non-periodic, which requires unpractical, complicated homogenization techniques. We demonstrate in this paper, that the application of simple, periodic techniques to realistic media, that are just close to periodic, gives accurate, approximative solutions. In order to obtain effective parameters for the homogenized heat equation, we have to solve a so called “cell problem”. In contrast to periodic structures it is not trivial to determine a suitable unit cell, which represents a non-periodic media. To overcome this problem, we give a rule of thumb on how to choose a good cell. Finally we demonstrate the efficiency of our method for virtually generated foams as well as real foams and compare these results to periodic structures. Y1 - 2012 U6 - https://doi.org/10.1007/s00231-011-0879-4 SN - 0947-7411 VL - 48 IS - 2 SP - 291 EP - 300 PB - Springer CY - Berlin ER -