Hydration and its Hydrogen Bonding State on a Protein Surface in the Crystalline State as Revealed by Molecular Dynamics Simulation

Protein hydration is crucial for the stability and molecular recognition of a protein. Water molecules form a hydration water network on a protein surface via hydrogen bonds. This study examined the hydration structure and hydrogen bonding state of a protein, staphylococcal nuclease, at various hydration levels in its crystalline state by all-atom molecular dynamics (MD) simulation. Hydrophilic residues were more hydrated than hydrophobic residues. As the water content increases, both types of residues were uniformly more hydrated. The number of hydrogen bonds per single water asymptotically approaches 4, the same as bulk water. The distances and angles of hydrogen bonds in hydration water in the protein crystal were almost the same as those in the tetrahedral structure of bulk water regardless of the hydration level. The hydrogen bond structure of hydration water observed by MD simulations of the protein crystalline state was compared to the Hydrogen and Hydration Database for Biomolecule from experimental protein crystals.

Ultrasonic Assessment of Thickness and Bonding Quality of Coating Layer Based on Short-Time Fourier Transform and Convolutional Neural Networks

Ultrasonic non-destructive analysis is a promising and effective method for the inspection of protective coating materials. Offshore coating exhibits a high attenuation rate of ultrasonic energy due to the absorption and ultrasonic pulse echo testing becomes difficult due to the small amplitude of the second echo from the back wall of the coating layer. In order to address these problems, an advanced ultrasonic signal analysis has been proposed. An ultrasonic delay line was applied due to the high attenuation of the coating layer. A short-time Fourier transform (STFT) of the waveform was implemented to measure the thickness and state of bonding of coating materials. The thickness of the coating material was estimated by the projection of the STFT into the time-domain. The bonding and debonding of the coating layers were distinguished using the ratio of the STFT magnitude peaks of the two subsequent wave echoes. In addition, the advantage of the STFT-based approach is that it can accurately and quickly estimate the time of flight (TOF) of a signal even at low signal-to-noise ratios. Finally, a convolutional neural network (CNN) was applied to automatically determine the bonding state of the coatings. The time–frequency representation of the waveform was used as the input to the CNN. The experimental results demonstrated that the proposed method automatically determines the bonding state of the coatings with high accuracy. The present approach is more efficient compared to the method of estimating bonding state using attenuation.

Monitoring Carbon in Electron and Ion Beam Deposition within FIB-SEM

It is well known that carbon present in scanning electron microscopes (SEM), Focused ion beam (FIB) systems and FIB-SEMs, causes imaging artefacts and influences the quality of TEM lamellae or structures fabricated in FIB-SEMs. The severity of such effects depends not only on the quantity of carbon present but also on its bonding state. Despite this, the presence of carbon and its bonding state is not regularly monitored in FIB-SEMs. Here we demonstrated that Secondary Electron Hyperspectral Imaging (SEHI) can be implemented in different FIB-SEMs (ThermoFisher Helios G4-CXe PFIB and Helios Nanolab G3 UC) and used to observe carbon built up/removal and bonding changes resulting from electron/ion beam exposure. As well as the ability to monitor, this study also showed the capability of Plasma FIB Xe exposure to remove carbon contamination from the surface of a Ti6246 alloy without the requirement of chemical surface treatments.