GalaxyTongDock: Symmetric and asymmetric ab initio protein–protein docking web server with improved energy parameters

Protein–protein docking methods are spotlighted for their roles in providing insights into protein–protein interactions in the absence of full structural information by experiment. GalaxyTongDock is an ab initio protein–protein docking web server that performs rigid-body docking just like ZDOCK but with improved energy parameters. The energy parameters were trained by iterative docking and parameter search so that more native-like structures are selected as top rankers. GalaxyTongDock performs asymmetric docking of two different proteins (GalaxyTongDock_A) and symmetric docking of homo-oligomeric proteins with C_n and D_n symmetries (GalaxyTongDock_C and GalaxyTongDock_D). Performance tests on an unbound docking benchmark set for asymmetric docking and a model docking benchmark set for symmetric docking showed that GalaxyTongDock is better or comparable to other state-of-the-art methods. Experimental and/or evolutionary information on binding interfaces can be easily incorporated by using block and interface options. GalaxyTongDock web server is freely available at http://galaxy.seoklab.org/tongdock . © 2019 Wiley Periodicals, Inc.     

Approximate MPA-based method for performing incremental dynamic analysis

In performance based earthquake engineering, it is important to accurately predict the seismic demand and capacities of structures. One recent estimation method is incremental dynamic analysis (IDA), which requires a series of nonlinear response history analyses (RHA) of the structure under various ground motions, each scaled to multiple levels of intensity, selected to cover entire range of structural response from elasticity, to yield and finally global dynamic instability. The implementation of IDA requires intensive computation and detailed knowledge of the nonlinear RHA of structures. In response to the complexity of IDA, an approximate method based on modal pushover analysis (MPA-based IDA) was developed. In MPA-based IDA, seismic demands are computed using the nonlinear RHA of the equivalent SDF systems instead of using nonlinear RHA of MDF systems. The objective of this study is to develop a simpler MPA-based IDA procedure that can avoid nonlinear RHA of equivalent SDF systems. For this purpose, MPA-based IDA employs the empirical equation of the inelastic displacement ratio (C _R ), defined as the ratio of peak displacement of the inelastic SDF system to that of the corresponding elastic SDF system given the strength ratio R, and that of the collapse strength ratio (R _c), which is the ratio of collapse intensity to yield strength. The proposed procedure is verified by comparing the seismic demands and capacities of 6-, 9-, and 20-story steel moment frames as determined by the proposed method and exact IDA.     

Growth behavior of Bi2Te3 and Sb2Te3 thin films on graphene substrate grown by plasma‐enhanced chemical vapor deposition

A comparative study of the substrate effect on the growth mechanism of chalcogenide Bi₂Te₃ and Sb₂Te₃ thin films was carried out. Obvious microstructural discrepancy in both the as‐deposited Bi₂Te₃ and Sb₂Te₃ thin films was observed when grown on graphene or SiO₂/Si substrate. Bi₂Te₃ and Sb₂Te₃ thin films deposited on the graphene substrate were observed to be grown epitaxially along c‐axis and show very smooth surface compared to that on SiO₂/Si substrate. Based on the experimental results of this study, the initial adsorption sites on graphene substrate during deposition process, which had been discussed theoretically, could be demonstrated empirically.     

Using intravoxel incoherent motion (IVIM) MR imaging to predict lipiodol uptake in patients with hepatocellular carcinoma following transcatheter arterial chemoembolization: A preliminary result

Purpose

To assess the usefulness of intravoxel incoherent motion diffusion weighted imaging (IVIM-DWI) for predicting lipiodol uptake in patients with hepatocellular carcinoma (HCC) after transcatheter arterial chemoembolization (TACE).

Materials and methods

The institutional review board approved this study. 44 HCC patients underwent IVIM-DWI and Gd-EOB-DTPA-enhanced MRI prior to TACE. Using post-TACE CT as a reference standard, each HCC was classified into either lipiodol good uptake (LGU) or poor uptake (LPU) group. Apparent diffusion coefficient (ADC), true diffusion coefficient (D), perfusion coefficient (D*), and perfusion fraction (f) in HCC were calculated. Arterial enhancement ratio (AER) and IVIM parameters were compared between those two groups using the Mann-Whitney U test.

Results

Of the 51 HCCs, 37 (72.5%) were LGU group and 14 (27.5%) were LPU group. AER of HCC was significantly higher in LGU than LPU (0.99 ± 0.54 and 0.67 ± 0.45; P = .034). ADC, D, and f values were not significantly different (P = .073, .059, and .196, respectively) between these two groups. D* was significantly elevated in LGU than LPU (48.10 ± 15.33 and 26.75 ± 9.55; P = .001).

Conclusion

Both AER derived from contrast enhanced MRI and D* values derived from IVIM-DWI for HCC were significantly higher in LGU than in LPU. These parameters would be helpful for predicting the lipiodol uptake.     

The electronic structure and magnetism of GdSi2 by first-principles study

We have investigated electronic and magnetic properties of hexagonal, tetragonal, and orthorhombic GdSi₂, using the full-potential linearized augmented plane-wave method based on general gradient approximation for exchange-correlation potential. Antiferromagnetic (AFM) states of the GdSi₂ are found from total energy calculations to be energetically more stable, compared to ferromagnetic (FM) states in all of the considered present crystal structures. It is in good agreement with an experimental result. The calculated magnetic moments of valence electrons of the Gd atoms are 0.16, 0.14, and 0.14 μ_B for hexagonal, tetragonal, and orthorhombic crystal structures in AFM states, respectively, and the Si atoms are coupled antiferromagnetically to the Gd atoms irrespective of crystal structure even though their magnitudes are negligible.     

Optical encryption of gray-level image using on-axis and 2-f digital holography with two-step phase-shifting method

In this paper we propose an encryption/decryption technique of gray-level image information using an on-axis 2-f digital holographic optical encrypting system with two-step phase-shifting method. This technique reduces the number of holograms in phase-shifting digital holography and minimizes the setup of the encryption system more than multistep phase-shifting technique. We are able to get the complete decrypted image by controlling the K-ratio which is defined as the reference beam intensity versus the object beam intensity. We remove the DC-term of the phase-shifting digital hologram to reconstruct and decrypt the original image information. Simulation results show that the proposed method can be used for encryption and decryption of a 256 gray-level image. Also, the result shows some errors of the decrypted image according to K-ratio.     

Fabrication and characterization of suspended single-walled carbon nanotubes

Suspended single-walled carbon nanotubes (SWCNTs) between SiO₂ pillars via a direct lithographic route using a simple mixture of catalyst precursor [Co(III) acetylacetonate, Co(acac)₃] and conventional electron beam resist (ma-N2403) were fabricated. The catalytic electron beam resist (Cat-ER) layer plays dual roles as a catalyst and a resist layer for the growth and alignment of CNTs, respectively. The structure of the grown nanotube was characterized by Raman spectroscopy (633 nm laser excitation). Nanotubes grown from Cat-ER with Co(acac)₃ show the typical Raman spectra of SWCNTs which are characterized by the strong tangential bands near to 1590 cm⁻¹ and radial breathing modes (RBMs) in the low frequency region (<300 cm⁻¹). The calculated diameter of the probed nanotubes individually corresponds to the range 0.86-1.77 nm.     

Nonlinear diffusive-dispersive limits for scalar multidimensional conservation laws

We consider a class of multidimensional conservation laws with vanishing nonlinear diffusion and dispersion terms. Under a condition on the relative size of the diffusion and dispersion coefficients, we show that the approximate solutions converge in a strong topology to the entropy solution of a scalar conservation law. Our proof is based on methodology developed in [S. Hwang, A.E. Tzavaras, Kinetic decomposition of approximate solutions to conservation laws: Applications to relaxation and diffusion-dispersion approximations, Comm. Partial Differential Equations 27 (2002) 1229-1254] which uses the averaging lemma.