In Silico Study of Pacific oyster Antiviral Polypeptides as Potential Inhibitory Compounds for SARS-CoV-2 Main Protease

Background: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel pathogen that has triggered a pneumonia outbreak, and despite the measures, the pandemic still continues to occur. Objectives: The molecular docking analysis was used to test whether the human immunodeficiency virus 1 (HIV-1) protease inhibitory peptides. These marine polypeptides were isolated from the hydrolysate of Pacific oyster. Methods: Molecular docking process was performed using Molegro Virtual Docker software. The protein data bank file of the crystal structure of COVID-19 main protease in complex with an inhibitor N3 (ID 6LU7) was obtained from the PubChem data source. After preparing protein and removing water and internal ligand, the major cavity was selected for the next step, the docking procedure. Afterward, the MolDock score, Rerank score, Total interaction energy (between energy), and HBond item were calculated. The Remdesivir was used as a positive control in the docking project. Results: The results of the docking step were evaluated based on several bioinformatics docking scores, including MolDock score, Rerank score, Total interaction energy (between energy), and HBond. The hydrogen bond of remdesivir was -6.03673, and Leu-Leu-Glu-Tyr-Ser-Ileu polypeptide was -6.44185. The Rerank score of remdesivir was -98.9254 and for Leu-Leu-Glu-Tyr-Ser-Ileu polypeptide was -107.821. Of the two screened Pacific oyster polypeptides, the score of Leu-Leu-Glu-Tyr-Ser-Ileu ligand was higher than remdesivir. Conclusions: This study demonstrated that Pacific oyster compounds may have the potency to be evolved as an anti-COVID-19 main protease drug to fight against the novel coronavirus; however, preclinical and clinical trials are needed for further experimental and/or clinical scientific validation.

The use of nanotechnology to prevent and mitigate fine migration: a comprehensive review

Fine migration is a serious problem in petroleum reservoir that causes damage to the reservoir and production equipment. One of the methods to solve this problem is using nanotechnology. Nanoparticles can reduce fine migration by various mechanisms such as reducing the zeta potential, changing the total interaction energy between surfaces, pH, and roughness of the particle’s surfaces. This study presents a review of the methods such as sand pack test, core flood test, and proppant test that study the nanoparticles’ influence on fine migration. Also, there are two different scenarios for the use of nanoparticles to mitigate fine migration. One of these scenarios is the co-injection of nanoparticles and particles suspended fluid, and another scenario is the initial injection of nanoparticles into the porous media (pre-flush). The results of the studies have shown that pre-flush of nanoparticles has a better effect on the control of fine migration.

Quantitative Analysis of Membrane Fouling Mechanisms Involved in Microfiltration of Humic Acid–Protein Mixtures at Different Solution Conditions

A systematical quantitative understanding of different mechanisms, though of fundamental importance for better fouling control, is still unavailable for the microfiltration (MF) of humic acid (HA) and protein mixtures. Based on extended Derjaguin–Landau–Verwey–Overbeek (xDLVO) theory, the major fouling mechanisms, i.e., Lifshitz–van der Waals (LW), electrostatic (EL), and acid–base (AB) interactions, were for the first time quantitatively analyzed for model HA–bovine serum albumin (BSA) mixtures at different solution conditions. Results indicated that the pH, ionic strength, and calcium ion concentration of the solution significantly affected the physicochemical properties and the interaction energy between the polyethersulfone (PES) membrane and HA–BSA mixtures. The free energy of cohesion of the HA–BSA mixtures was minimum at pH = 3.0, ionic strength = 100 mM, and c(Ca2+) = 1.0 mM. The AB interaction energy was a key contributor to the total interaction energy when the separation distance between the membrane surface and HA–BSA mixtures was less than 3 nm, while the influence of EL interaction energy was of less importance to the total interaction energy. The attractive interaction energies of membrane–foulant and foulant–foulant increased at low pH, high ionic strength, and calcium ion concentration, thus aggravating membrane fouling, which was supported by the fouling experimental results. The obtained findings would provide valuable insights for the quantitative understanding of membrane fouling mechanisms of mixed organics during MF.

A quantum chemistry investigation of a potential inhibitory drug against the dengue virus

The total interaction energy of the inhibitor Bz-nKRR-H bound to a serine protease of the dengue virus is mainly due to the action of Asn152, Met49, Tyr161, Asp129 and Gly151 (Met84, Met75, Asp81, Asp79 and Asp80) residues at the NS3 (NS2B) subunit.

The Mechanism of Activated Sludge Flocculation under Al3+ Dosin

The mechanism governing activated sludge flocculation under Al3+ dosing was studied in this paper. Activated sludge was cultivated in sequencing batch reactors (SBR) at 22°C. Batch dosages of Al3+ were 0.00, 0.125, 0.5, 1 and 1.5meq/L respectively, and continuous dosage was 0.1meq/L. As batch dosage increased, the total interaction energy, zeta potential and turbidity tended to decline, which suggested that batch dosing promoted sludge flocculation. Under the equivalent dose, the zeta potential of continuous dosing was higher, while the LB-EPS content showed the opposite tendency and turbidity reduction was similar. Both batch and continuous dosing promoted flocculation performance: in terms of interaction energy, batch dosing was more effective; while in terms of EPS, it was on the contrary.

Zeta-Potential Investigation and Experimental Study of Nanoparticles Deposited on Rock Surface To Reduce Fines Migration

Summary Fines migration is a noticeable problem in petroleum-production engineering. Plugging of throats in porous media occurs because of detachment of fine particles from sand surfaces. Thus, the study of interactions between fines and pore surfaces and the investigation of governing forces are important factors to consider when describing the mechanism of the fines-release process. The main types of these forces are electric double-layer repulsion (DLR) and London–van der Waals attraction (LVA). It may be possible to alter these forces with nanoparticles (NPs) as surface coatings. In comparison with repulsion forces, NPs increase the effect of attraction forces. In this paper, we present new experiments and simple modeling to observe such properties of NPs. For this purpose, the surfaces of pores were coated with different types of NPs: magnesium oxide (MgO), silicon dioxide (SiO2), and aluminum oxide (Al2O3). A zeta-potential test was used to examine changes in the potential of the pore surfaces. Total interaction energy was then mathematically calculated to compare different states. Total interaction energy is a fitting criterion that gives proper information about the effect of different NPs on surface properties. Consequently, total interaction plots are found to be suitable tools for selecting the best coating material. On the basis of experimental results, the magnitude of change in zeta potential for the MgO NP was 45 mV. Our model demonstrated that the magnitude of the electric DLR in comparison with the LVA of the probe and plate surface was considerably diminished when MgO NPs were used to coat the surface of the plate, which agrees completely with our experimental observation.

SIGNIFICANCE OF MANY-BODY CONTRIBUTIONS TO CASIMIR ENERGIES

Irreducible many-body contributions to Green's functions and Casimir energies are defined. We show that the irreducible three-body contribution to Casimir energies are significant and can be more than twenty percent of the total interaction energy. Irreducible three-body contribution for three parallel semitransparent plates in the limit when two plates overlap is obtained in terms of irreducible two-body contributions and shown to be finite and well defined in this limit.