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

Experimental Simulation of High Temperature Plasma Transport Using Almost Dimensionally Similar Cold Plasmas in the Compact Helical System

In the Compact Helical System (CHS), experimental simulation of high temperature plasma transport is attempted by using cold plasma having similar dimensionless parameters such as electron-ion collision frequency normalized by bounce frequency v*ei, averaged toroidal beta value βt and the normalized gyro radius ρs*. The cold plasma is produced by 2.45 GHz electron cyclotron waves at very low toroidal field less than 0.1 T, and has v*ei ~ 0.05?1, βt < 0.02 % and ρs* ~ 0.02?0.05. The radial profiles of fluctuation amplitude have similarity to those in a high temperature plasma. In the cold plasma with low v*ei < 0.1, internal transport barrier is clearly formed in electron density and temperature profiles when the radial electric field rapidly evolves to positive value

Hyperosmolarity Attenuates the Contraction of Rat Trachea Through the Inhibition of Phosphatidylinositol Response

Although hyperosmolarity associated with diabetes is known to attenuate contractile response of airway smooth muscle, intracellular mechanisms involved are not fully understood. We examined the effects of hyperosmolarity on carbachol (CCh)- and aluminum fluoride (AF)-induced contractile and phosphatidylinositol (PI) responses of rat trachea. In vitro measurements of isometric tension and [3H] inositol monophosphate (IP1) formed were conducted by using rat tracheal rings and slices. Hyperosmolarity solutions of 350, 450 and 600 mOsm were made with dissolving glucose in Krebs-Henseleit (K-H) solution. Hyperosmolarity attenuated dose-dependently CCh-induced contraction of rat trachea (1.86 ± 0.13 g at 300 mOsm, 1.85 ± 0.16 g at 350 mOsm, 1.37 ± 0.07 g at 450 mOsm and 0.50 ± 0.04 g at 600 mOsm, respectively), and also attenuated CCh- induced IP1 accumulation (5.77 ± 0.33 Bq at 300 mOsm, 3.38 ± 0.26 Bq at 350 mOsm, 2.08 ± 0.30 Bq at 450 mOsm and 1.71 ± 0.40 Bq at 600 mOsm, respectively), and AF-induced IP1 accumulation (3.93 ± 0.22 Bq at 300 mOsm, 1.63 ± 0.14 Bq at 450 mOsm and 1.02 ± 0.14 Bq at 600 mOsm, respectively). The results suggest that hyperosmolarity would inhibit G-protein-coupled phospholipase C, resulting in attenuation of CCh-induced airway smooth muscle contraction

Impact of Energetic Ion Driven Global Modes on Toroidal Plasma Confinements

Excitation of energetic-ion-driven Alfv6n eigenmodes (AEs) and their impact on energetic ion confinement are widely and intensively studied in helical devices such as CHS and LHD as well as major tokamaks. The excitation of AEs sensitively depends on the parameter space defined by the averaged beam beta and the velocity ratio V6nlV6 (V611 : injected beam ion velocity, Va: Alfv6n velocity). In LHD, these two relevant parameters are widely scanned without suffering from current disruptions. So far, toroidicity induced AE (TAE), global AE (GAE) and energetic particle mode (EPM) or resonant TAE (R-TAE) were identified during tangential neutral beam injection (NBI) in CHS and LHD. Moreover, a new coherent mode with the frequency by about 8 times higher than the TAE frequency was observed in NBI heated plasmas of LHD at low magnetic field (<0.6T). This mode may be induced by helical field components of the confinement field. Nonlinear phenomena of bursting amplitude modulation and fast frequency chirping are clearly seen for TAEs and EPMs in CHS and LHD. EPMs in CHS and bursting TAEs in LHD enhance radial transport of energetic ions in certain plasma conditions