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Salts and proteins comprise two of the basic molecular components of biological materials. Kosmotropic/chaotropic co-solvation and matching ion water affinities explain basic ionic effects on protein aggregation observed in simple solutions. However, it is unclear how these theories apply to proteins in complex biological environments and what the underlying ionic binding patterns are. Using the positive ion Ca2+ and the negatively charged membrane protein SNAP25, we studied ion effects on protein oligomerization in solution, in native membranes and in molecular dynamics (MD) simulations. We find that concentration-dependent ion-induced protein oligomerization is a fundamental chemico-physical principle applying not only to soluble but also to membrane-anchored proteins in their native environment. Oligomerization is driven by the interaction of Ca2+ ions with the carboxylate groups of aspartate and glutamate. From low up to middle concentrations, salt bridges between Ca2+ ions and two or more protein residues lead to increasingly larger oligomers, while at high concentrations oligomers disperse due to overcharging effects. The insights provide a conceptual framework at the interface of physics, chemistry and biology to explain binding of ions to charged protein surfaces on an atomistic scale, as occurring during protein solubilisation, aggregation and oligomerization both in simple solutions and membrane systems.
SpMV Runtime Improvements with Program Optimization Techniques on Different Abstraction Levels
(2016)
The multiplication of a sparse matrix with a dense vector is a performance critical computational kernel in many applications, especially in natural and engineering sciences. To speed up this operation, many optimization techniques have been developed in the past, mainly focusing on the data layout for the sparse matrix. Strongly related to the data layout is the program code for the multiplication. But even for a fixed data layout with an accommodated kernel, there are several alternatives for program optimizations. This paper discusses a spectrum of program optimization techniques on different abstraction layers for six different sparse matrix data format and kernels. At the one end of the spectrum, compiler options can be used that hide from the programmer all optimizations done by the compiler internally. On the other end of the spectrum, a multiplication kernel can be programmed that use highly sophisticated intrinsics on an assembler level that ask for a programmer with a deep understanding of processor architectures. These special instructions can be used to efficiently utilize hardware features in processors like vector units that have the potential to speed up sparse matrix computations. The paper compares the programming effort and required knowledge level for certain program optimizations in relation to the gained runtime improvements.
Digitale Gemeingüter
(2016)
Die Klausur: VWL
(2016)
Zweiseitige Märkte
(2016)
Die Klausur: VWL
(2016)
Currently, there are a lot of research activities dealing with gamma titanium aluminide (γ-TiAl) alloys as new materials for low pressure turbine (LPT) blades. Even though the scatter in mechanical properties of such intermetallic alloys is more distinctive as in conventional metallic alloys, stochastic investigations on γ -TiAl alloys are very rare. For this reason, we analyzed the scatter in static and dynamic mechanical properties of the cast alloy Ti-48Al-2Cr-2Nb. It was found that this alloy shows a size effect in strength which is less pronounced than the size effect of brittle materials. A weakest-link approach is enhanced for describing a scalable size effect under multiaxial stress states and implemented in a post processing tool for reliability analysis of real components. The presented approach is a first applicable reliability model for semi-brittle materials. The developed reliability tool was integrated into a multidisciplinary optimization of the geometry of a LPT blade. Some processes of the optimization were distributed in a wide area network, so that specialized tools for each discipline could be employed. The optimization results show that it is possible to increase the aerodynamic efficiency and the structural mechanics reliability at the same time, while ensuring the blade can be manufactured in an investment casting process.
Brentuximab vedotin (SGN-35) is an antibody–drug conjugate with a high selectivity against CD30+ cell lines and more than 300-fold less activity against antigen-negative cells. In the last years, the results of many in vitro and in vivo studies have led to the fast approval of this drug to treat lymphoma patients. Another innovative method to treat tumor cells including lymphoma cells is the use cytokine-induced killer (CIK) cells, which have also been approved and proven to be a safe treatment with only minor adverse events. In this study, a possible additive effect when combining SGN-35 with CIK cells was investigated. The combinational treatment showed that it reduces the viability of CD30+ cell lines significantly in vitro. Additionally, the amount of lymphoma cells was significantly reduced when exposed to CIK cells as well as when exposed to SGN-35. A significant negative effect of SGN-35 on the function of CIK cells could be excluded. These results lead to the assumption that SGN-35 and CIK cells in combination might achieve better results in an in vitro setting compared to the single use of SGN-35 and CIK cells. Further investigations in in vivo models must be conducted to obtain a better understanding of the exact mechanisms of both treatments when applied in combination.
IT-Controlling
(2016)