Evaluating Flood Discharge and Bed Variation In The OTA River Floodway

Source: ICHE Conference Archive - https://mdi-de.baw.de/icheArchiv

Rigid-body fitting to atomic force microscopy images for inferring probe shape and biomolecular structure

Atomic force microscopy (AFM) can visualize functional biomolecules near the physiological condition, but the observed data are limited to the surface height of specimens. Since the AFM images highly depend on the probe tip shape, for successful inference of molecular structures from the measurement, the knowledge of the probe shape is required, but is often missing. Here, we developed a method of the rigid-body fitting to AFM images, which simultaneously finds the shape of the probe tip and the placement of the molecular structure via an exhaustive search. First, we examined four similarity scores via twin-experiments for four test proteins, finding that the cosine similarity score generally worked best, whereas the pixel-RMSD and the correlation coefficient were also useful. We then applied the method to two experimental high-speed-AFM images inferring the probe shape and the molecular placement. The results suggest that the appropriate similarity score can differ between target systems. For an actin filament image, the cosine similarity apparently worked best. For an image of the flagellar protein FlhAC, we found the correlation coefficient gave better results. This difference may partly be attributed to the flexibility in the target molecule, ignored in the rigid-body fitting. The inferred tip shape and placement results can be further refined by other methods, such as the flexible fitting molecular dynamics simulations. The developed software is publicly available

Molecular dynamics simulation of proton-transfer coupled rotations in ATP synthase FO motor

The FO motor in FOF1 ATP synthase rotates its rotor driven by the proton motive force. While earlier studies elucidated basic mechanisms therein, recent advances in high-resolution cryo-electron microscopy enabled to investigate proton-transfer coupled FO rotary dynamics at structural details. Here, taking a hybrid Monte Carlo/molecular dynamics simulation method, we studied reversible dynamics of a yeast mitochondrial FO. We obtained the 36°-stepwise rotations of FO per one proton transfer in the ATP synthesis mode and the proton pumping in the ATP hydrolysis mode. In both modes, the most prominent path alternatively sampled states with two and three deprotonated glutamates in c-ring, by which the c-ring rotates one step. The free energy transduction efficiency in the model FO motor reached ~ 90% in optimal conditions. Moreover, mutations in key glutamate and a highly conserved arginine increased proton leakage and markedly decreased the coupling, in harmony with previous experiments. This study provides a simple framework of simulations for chemical-reaction coupled molecular dynamics calling for further studies in ATP synthase and others

State-of-the-art of seismic response evaluation methods for metal roof spatial structures

[EN] The present paper is a result of a collaboration in IASS WG 8 for metal spatial structures to prepare state-ofthe-art reviews for earthquake response analysis methods and equivalent static seismic loads for metal spatial structures. It quotes mainly investigations from IASS symposia and related journals. First, the dynamic response characteristics of metal spatial structures are briefly explained. This is followed by a review of analytical methods for evaluating earthquake responses. Finally the equivalent seismic loads proposed for metal spatial structures are reviewed and some comments for future analysis of failure and fragility are provided.Nakazawa, S.; Kato, S.; Takeuchi, T.; Xue, S.; Lazaro, C. (2012). State-of-the-art of seismic response evaluation methods for metal roof spatial structures. Journal- International Association for Shell and Spatial Structures. 53(2):117-130. http://hdl.handle.net/10251/48932S11713053

Particle Filter Method to Integrate High-Speed Atomic Force Microscopy Measurements with Biomolecular Simulations

High-speed atomic force microscopy (HS-AFM) can be used to observe the structural dynamics of biomolecules at the single-molecule level in real time under near-physiological conditions; however, its spatiotemporal resolution is limited. Complementarily, molecular dynamics (MD) simulations have higher spatiotemporal resolutions, albeit with some artifacts. Here, to integrate HS-AFM data and coarse-grained molecular dynamics (CG-MD) simulations, we develop a particle filter method that implements a sequential Bayesian data assimilation approach. We test the method in a twin experiment. First, we generate a reference HS-AFM movie from the CG-MD trajectory of a test molecule, a nucleosome; this serves as the “experimental measurement”. Then, we perform a particle filter simulation with 512 particles, which captures the large-scale nucleosome structural dynamics compatible with the AFM movie. Comparing particle filter simulations with 8–8192 particles, we find that using greater numbers of particles consistently increases the likelihood of the whole AFM movie. By comparing the likelihoods for different ionic concentrations and time scale mappings, we find that the “true” concentration and time scale mapping can be inferred as the largest likelihood of the whole AFM movie but not that of each AFM image. The particle filter method provides a general approach for integrating HS-AFM data with MD simulations

Characteristic classes of Hilbert schemes of points via symmetric products

We obtain a formula for the generating series of (the push-forward under the Hilbert-Chow morphism of) the Hirzebruch homology characteristic classes of the Hilbert schemes of points for a smooth quasi-projective variety of arbitrary pure dimension. This result is based on a geometric construction of a motivic exponentiation generalizing the notion of motivic power structure, as well as on a formula for the generating series of the Hirzebruch homology characteristic classes of symmetric products. We apply the same methods for the calculation of generating series formulae for the Hirzebruch classes of the push-forwards of "virtual motives" of Hilbert schemes of a threefold. As corollaries, we obtain counterparts for the MacPherson (and Aluffi) Chern classes of Hilbert schemes of a smooth quasi-projective variety (resp. for threefolds). For a projective Calabi-Yau threefold, the latter yields a Chern class version of the dimension zero MNOP conjecture.Comment: comments are welcom

Cooperation among c-subunits of FoF1-ATP synthase in rotation-coupled proton translocation

In F₀F₁-ATP synthase, proton translocation through F₀ drives rotation of the c-subunit oligomeric ring relative to the a-subunit. Recent studies suggest that in each step of the rotation, key glutamic acid residues in different c-subunits contribute to proton release to and proton uptake from the a-subunit. However, no studies have demonstrated cooperativity among c-subunits toward F₀F₁-ATP synthase activity. Here, we addressed this using Bacillus PS3 ATP synthase harboring a c-ring with various combinations of wild-type and cE56D, enabled by genetically fused single-chain c-ring. ATP synthesis and proton pump activities were decreased by a single cE56D mutation and further decreased by double cE56D mutations. Moreover, activity further decreased as the two mutation sites were separated, indicating cooperation among c-subunits. Similar results were obtained for proton transfer-coupled molecular simulations. The simulations revealed that prolonged proton uptake in mutated c-subunits is shared between two c-subunits, explaining the cooperation observed in biochemical assays