Prediction of Interaction Sites of PcRab7-VP28

White spot syndrome virus (WSSV) is one of the most important pathogens in the world. Since its outbreak in 1993, the virus has caused huge economic losses. Studies have confirmed that in the early stage of infection, VP28, the main envelope protein of WSSV, as a viral adhesion protein, binds to PcRab7 of Penaeus chinensis to help the virus enter the host cells. Understanding the mechanism of PcRab7-VP28 interaction is of great significance to understand the mechanism of WSSV infection and the development of antiviral drugs. In this research, the interaction interface and interaction sites were predicted by using the methods of molecular simulations. Results showed that VP28 binds to the second β-sheet (L73-D86) of PcRab7, which is consistent with the region detected in previous studies. Furthermore, we speculated the possible interaction sites in PcRab7 are E81, F77 and D76. These results may contribute to a deep understanding of the infection mechanism of WSSV on the host.

Dynamic soil-tunnel interaction in layered half-space for incident P-and SV-waves

The dynamic soil-tunnel interaction is studied by the model of a rigid tunnel embedded in layered half-space, which is simplified as a single soil layer on elastic bedrock to the excitation of P- and SV-waves. The indirect boundary element method is used, combined with the Green＇ s function of distributed loads acting on inclined lines. It is shown that the dynamic characteristics of soil-tunnel interaction in layered half-space are different much from that in homoge- neous half-space, and that the mechanism of soil-tunnel interaction is also different much from that of soil-founda- tion-superstructure interaction. For oblique incidence, the tunnel response for in-plane incident SV-waves is com- pletely different from that for incident SH-waves, while the tunnel response for vertically incident SV-wave is very similar to that of vertically incident SH-wave.

Time-dependent Diffusion Coefficient and Conventional Diffusion Constant of Nanoparticles in Polymer Melts by Mode-coupling Theory

Time-dependent diffusion coefficient and conventional diffusion constant are calculated and analyzed to study diffusion of nanoparticles in polymer melts. A generalized Langevin equa- tion is adopted to describe the diffusion dynamics. Mode-coupling theory is employed to calculate the memory kernel of friction. For simplicity, only microscopic terms arising from binary collision and coupling to the solvent density fluctuation are included in the formalism. The equilibrium structural information functions of the polymer nanocomposites required by mode-coupling theory are calculated on the basis of polymer reference interaction site model with Percus-Yevick closure. The effect of nanoparticle size and that of the polymer size are clarified explicitly. The structural functions, the friction kernel, as well as the diffusion coefficient show a rich variety with varying nanoparticle radius and polymer chain length. We find that for small nanoparticles or short chain polymers, the characteristic short time non-Markov diffusion dynamics becomes more prominent, and the diffusion coefficient takes longer time to approach asymptotically the conventional diffusion constant. This constant due to the microscopic contributions will decrease with the increase of nanoparticle size, while increase with polymer size. Furthermore, our result of diffusion constant from mode- coupling theory is compared with the value predicted from the Stokes-Einstein relation. It shows that the microscopic contributions to the diffusion constant are dominant for small nanoparticles or long chain polymers. Inversely, when nanonparticle is big, or polymer chain is short, the hydrodynamic contribution might play a significant role.

Influence of Zr, Ce, and La on Co_3O_4 catalyst for CO_2 methanation at low temperature

The Co3O4 and Zr-,Ce-,and La-Co3O4 catalysts were prepared,characterized,and applied to produce CH4 from CO2 catalytic hydrogenation in low temperature as 140–220℃.The results indicated that the addition of Zr,Ce,or La to the Co3O4 decreased the crystallite sizes of Co and the outer-shell electron density of Co^3＋,and increased the specific surface area,which would provide more active sites for the CO2 methanation.Especially,the addition of Zr also changed the reducing state of Co3O4 via an obvious change in the interaction between Co3O4 and ZrO2.Furthermore,Zr doped into the Co3O4 increased the basic intensity of the weak and medium basic sites,as well as the amount of Lewis acid sites,and Bronsted acid sites were also found on the Zr-Co3O4 surface.The introduction of Zr,Ce,or La favored the production of CH4,and the Zr-Co3O4catalyst exhibited the highest CO2 conversion（58.2%）and CH4 selectivity（100%）at 200℃,and 0.5 MPa with a gaseous hourly space velocity of 18,000 ml·g^-1（cat）·h^-1,and the catalytic activity of CO2methanation for the Zr-,Ce-,and La-Co3O4 exhibited more stable than Co3O4 in a 20-h reaction.

Numerical Analysis of PRISM-PY Calculations for Hard-and Soft-Core Generic Polymer Models

Generic polymer models capturing the chain connectivity and excluded-volume interactions between polymer segments can be classified, according to whether or not the 3D integral of the latter diverges, into hard- and soft-core models. Taking homogeneous systems of compressible homopolymer melts (or equivalently homopolymer solutions in an implicit, good solvent) in the continuum as an example, we recently compared the correlation effects on the structural and thermodynamic properties of the hard- and soft-core models given by the polymer reference interaction site model (PRISM) theory with the Percus-Yevick (PY) closure (Polymers 2023, 15, 1180). Here we analyzed in detail the numerical errors and behavior of the interchain pair correlation functions (PCFs) given by the PRISM-PY calculations of these models using an efficient numerical approach that we proposed. Our numerical approach has the least number of independent variables to be iteratively solved, analytically treats the discontinuities caused by the non-bonded pair potential (such as that of the hard spheres) and takes only the inverse Fourier transform of the interchain indirect PCF between polymer segments (which is continuous and decays towards 0 with increasing wavenumber much faster than both the interchain direct and total PCFs), and is essential for us to accurately solve the PRISM-PY theory for chain length N as large as 106. To capture the correlation-hole effect, the real-space cut-off in the PRISM calculations should be proportional to the square root of N.

Complexation process and binding parameters of curcumin and short amylose with V7-type helix structure

Pre-formed V7-type short amylose(SA)could interact with curcumin to form inclusion complex(IC)thereby to improve the stability of curcumin.However,the complexation mechanism of V7-type SA and curcumin is not clear,which limit the improvement of inclusion efficiency.To obtain a starch nanocarrier with high loading capacity,the encapsulation process and interaction parameters of V7-type SA-curcumin IC was studied.The analysis results demonstrated that stoichiometric ratio value of the SA-curcumin complex was around 1.V7-type SA performed excellently in the delivery of curcumin attributing to their high loading capacity(over 20%).It was found that curcumin could enter into the pre-formed helical cavity of SA to form an IC.The conformation change of SA caused the reduction in the interaction ratio in the last 20 ns of simulation.However,SA and curcumin always remained complexation status during the simulation.Hydrogen bonds(H-bonds)and hydrophobic interaction were the most critical acting forces involved in the formation and stability of V7-type SA-curcumin complex.Molecular docking presented that H-bonds interaction between curcumin ligand and V7-type SA chain(O3 at the 25th glucose unit,and O6 at the 17th and 20th glucose units)were found.Furthermore,the hydrophobic interactions were discovered between curcumin ligand and SA chain(18th,19th,21st,22nd and 23rd glucose units).