[Movement of a fluvial particle under the influence of coherent structures]. / Bewegung eines Einzelkorns unter dem Einfluss kohärenter Strukturen.

In a fundamental study the influence of coherent structures on the incipient motion of single fluvial grain was experimentally investigated. To fully characterize coherent structures, the three-dimensional velocity field must be known with high temporal resolution. Using a tr-3D PTV system (tr = time-resolved, PTV = particle tracking velocimetry) this could be achieved. The influence of hairpin vortices and counter-rotating longitudinal vortices (VLSM) on sediment transport has been postulated in several studies, but due to the missing 3D information, evidence has been lacking. In the present "Rolling Stones test series", the incipient motion of a single grain was investigated for smooth and rough beds. It could be shown for the first time that both hairpin vortices and VLSM trigger particle entrainment. Hairpin vortices could also be detected on rough beds, contrary to common hypotheses, and triggered particle movement. The long-term study should also find practical applications in the coming years and increase the accuracy of sediment transport calculations in rivers.

[Experimental and numerical investigation of fluid-particle-interactions in water]. / Experimentelle und numerische Untersuchung von Fluid-Partikel-Interaktionen in Wasser.

For the development of improved sediment transport models, the basic understanding of the interaction between the solid particle and the moving fluid (water) is important. In this article, current developments in the field of fluid-particle interaction are presented based on two research articles by Gold et al. (2023) and Worf et al. (2022). One presented in this article uses state of the art measurement methods to investigate the flow around spheres of different densities that oscillate in initially resting body of water. For the spherical pendulum a similar vortex shedding characteristic was observed for all investigated fluid density ratios (m*=ρS/ρF=1.14,14.95, density ratio between solid and fluid). A new object tracking method (DOT) is also presented, which enables temporally and spatially resolved analysis of flow structures in the fluid field. The experimental results of Gold et al. (2023) show, that vortex shedding occurs during the first period. This vortex propagates downward and eventually dissipates. Furthermore, a damping optimum of the spherical pendulum in the range of m*=2.50 was observed. Additionally, an experiment with a cylindrical pendulum with m∗=4.98 was investigated numerically utilizing an immersed boundary method. The process of creation and separation up to the dissipation of a vortex ring was described. Furthermore, this investigation by Worf et al. (2022) described the creation of tip vortices. These were connected with the development of the three-dimensional flow and added mass coefficient.

Thermodynamic properties of the kinesin neck-region docking to the catalytic core.

Kinesin motors move on microtubules by a mechanism that involves a large, ATP-triggered conformational change in which a mechanical element called the neck linker docks onto the catalytic core, making contacts with the core throughout its length. Here, we investigate the thermodynamic properties of this conformational change using electron paramagnetic resonance (EPR) spectroscopy. We placed spin probes at several locations on the human kinesin neck linker and recorded EPR spectra in the presence of microtubules and either 5'-adenylylimidodiphosphate (AMPPNP) or ADP at temperatures of 4-30 degrees C. The free-energy change (DeltaG) associated with AMPPNP-induced docking of the neck linker onto the catalytic core is favorable but small, about 3 kJ/mol. In contrast, the favorable enthalpy change (DeltaH) and unfavorable entropy change (TDeltaS) are quite large, about 50 kJ/mol. A mutation in the neck linker, V331A/N332A, results in an unfavorable DeltaG for AMPPNP-induced zipping of the neck linker onto the core and causes motility defects. These results suggest that the kinesin neck linker folds onto the core from a more unstructured state, thereby paying a large entropic cost and gaining a large amount of enthalpy.

Effects of salt bridges on protein structure and design.

Theoretical calculations (Hendsch ZS & Tidor B, 1994, Protein Sci 3:211-226) and experiments (Waldburger CD et al., 1995, Nat Struct Biol 2:122-128; Wimley WC et al., 1996, Proc Natl Acad Sci USA 93:2985-2990) suggest that hydrophobic interactions are more stabilizing than salt bridges in protein folding. The lack of apparent stability benefit for many salt bridges requires an alternative explanation for their occurrence within proteins. To examine the effect of salt bridges on protein structure and stability in more detail, we have developed an energy function for simple cubic lattice polymers based on continuum electrostatic calculations of a representative selection of salt bridges found in known protein crystal structures. There are only three types of residues in the model, with charges of -1, 0, or + 1. We have exhaustively enumerated conformational space and significant regions of sequence space for three-dimensional cubic lattice polymers of length 16. The results demonstrate that, while the more highly charged sequences are less stable, the loss of stability is accompanied by a substantial reduction in the degeneracy of the lowest-energy state. Moreover, the reduction in degeneracy is greater due to charges that pair than for lone charges that remain relatively exposed to solvent. We have also explored and illustrated the use of ion-pairing strategies for rational structural design using model lattice studies.