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The reactor is an extreme environment of high temperature, high pressure, and high radiation dose. Damage accumulates in structural materials over service time. It will eventually lead to material failure, such as hardening, embrittlement, and swelling. The radiation damage accumulation is an inherent, complex, and multiscale process, which has been studied extensively with multiscale modeling and simulation methods. The rapid development of high-performance computing makes it possible to accurately operate multiscale simulation for the microstructure evolution of irradiated reactor materials. The European Union, the USA, and China have put great effort into this, and many related works have been carried out. This paper first outlines the basic application of multiscale modeling and simulation technology in understanding the effects of radiation on reactor structural materials. Then, some relevant projects carried out by the USA, the European Union, and China in recent years are summarized. Next, the paper focuses on three widely used simulation techniques at different scales: molecular dynamics, kinetic Monte Carlo, and cluster dynamics. For each method, some key developments in algorithms and computer implementations are reviewed. Finally, the comparison between them is discussed. [ABSTRACT FROM AUTHOR]

The scale of pig breeding in China is the largest in the world, and the pollution problem of breeding wastewater is serious. Supercritical water gasification (SCWG) process is a clean and efficient treatment technology for breeding wastewater. This paper involved constructing the molecular model of the primary organic components in pig breeding wastewater. The effects of time, temperature and mass concentration, and the interactions of different components on the SCWG characteristics of pig breeding wastewater were studied by molecular dynamics (MD) simulation, and the decomposition process of lignin and lipid molecules in the SCWG process were analyzed, and the possible intermediates were explored. The results showed that the effect of parameters on carbon gasification efficiency (CE) and H 2 production follows the order of temperature > time > mass concentration. During the gasification of lignin and lipid molecules, the C–O–C bond was broken first, and the gasification rate of lignin molecules was slow due to the benzene ring. Interactions among different organic decompositions hindered the gasification process. This paper will provide theoretical guidance for the selection of operation parameters and the control of products in the actual pig breeding wastewater treatment process. • The MD model of wastewater containing complex organics was established. • The effects of key parameters on SCWG of pig breeding wastewater were studied. • The detailed SCWG mechanisms of pig breeding wastewater were analyzed. • The intermediate products from SCWG of pig breeding wastewater were explored. • The interaction mechanisms of different organics during SCWG were analyzed. [ABSTRACT FROM AUTHOR]

Carbonate rocks are one of major geothermal reservoir types around the world. Understanding the thermal properties of carbonate rocks is of significance to the assessment and utilization of deep geothermal reservoirs. Different from conventional test methods, this paper introduced a new approach, molecular dynamics calculation (MDC), to studying the thermal properties of carbonate rocks. By means of MDC, the thermal properties including specific heat, thermal conductivity and thermal diffusivity of four types of carbonate rocks including calcite, dolomite, magnesite, and smithsonite were investigated. The intrinsic relationship among the Debye temperature, elastic and thermal properties of carbonate rocks was revealed. The variations of the thermal properties with the average atom weight and temperature (300–800K) were obtained and regressed as functional formulas for applications. Further, taking carbonate rock samples from North China as an example, the specific heat and thermal conductivity were tested and compared with the MDC results based on actual lattice parameters by using X-ray diffraction method (XRD). The results showed that there was a good agreement between the test and calculation results. Finally, the thermal properties of ferroan dolomite samples were predicted. The present method can provide a promising extension tool for analyzing other crystalline rocks for geothermal applications. [ABSTRACT FROM AUTHOR]

Shale oil in China is widely distributed and has enormous resource potential. The pores of shale are at the nanoscale, and traditional research methods encounter difficulty in accurately describing the fluid flow mechanism, which has become a bottleneck restricting the industrial development of shale oil in China. To clarify the distribution and migration laws of fluid microstructure in shale nanopores, we constructed a heterogeneous inorganic composite shale model and explored the fluid behavior in different regions of heterogeneous surfaces. The results revealed the adsorption capacity for alkanes in the quartz region was stronger than that in the illite region. When the aperture was small, solid–liquid interactions dominated; as the aperture increased, the bulk fluid achieved a more uniform and higher flow rate. Under conditions of small aperture/low temperature/low pressure gradient, the quartz region maintained a negative slip boundary. Illite was more hydrophilic than quartz; when the water content was low, water molecules formed a "liquid film" on the illite surface, and the oil flux percentages in the illite and quartz regions were 87% and 99%, respectively. At 50% water content, the adsorbed water in the illite region reached saturation, the quartz region remained unsaturated, and the difference in the oil flux percentage of the two regions decreased. At 70% water content, the adsorbed water in the two regions reached a fully saturated state, and a layered structure of "water–two-phase region–water" was formed in the heterogeneous nanopore. This study is of great significance for understanding the occurrence characteristics and flow mechanism of shale oil within inorganic nanopores. [ABSTRACT FROM AUTHOR]

The use of surfactants in oil recovery can effectively improve crude oil recovery rate. Due to the enhanced salt and temperature resistance of surfactant molecules by non-ionic chain segments, anionic groups have good emulsifying stability. Currently, there are many studies on anionic non-ionic surfactants for oil recovery in China, but there is relatively little systematic research on introducing EOs into hydrophobic alkyl chains, especially on their self-assembly behavior. This article proposes a simple and effective synthesis method, using 3-aminopropane sulfonic acid, fatty alcohol polyoxyethylene ether, and epichlorohydrin as raw materials, to insert EO into hydrophobic alkyl chains and synthesize a series of new anionic non-ionic Gemini surfactants (CnEO-5, n = 8, 12, 16). The surface activity, thermodynamic properties, and self-assembly behavior of these surfactants were systematically studied through surface tension, conductivity, steady-state fluorescence probes, transmission electron microscopy, and molecular dynamics simulations. The surface tension test results show that CnEO-5 has high surface activity and is higher than traditional single chain surfactants and structurally similar anionic non-ionic Gemini surfactants. Additionally, thermodynamic parameters (e.g., ΔG°mic ΔH°mic ΔS°mic et al. indicate that CnEO-5 molecules are exothermic and spontaneous during the micellization process. DLS, p-values, and TEM results indicate that anionic non-ionic Gemini surfactants with shorter hydrophobic chains (such as C8EO-5) tend to form larger vesicles in aqueous solutions, which are formed in a tail to tail and staggered manner; Negative non-ionic Gemini surfactants with longer hydrophobic chains (such as C12EO-5, C16EO-5) tend to form small micelles. The test results indicate that CnEO-5 anionic non-ionic Gemini surfactants have certain application prospects in improving crude oil recovery. [ABSTRACT FROM AUTHOR]

The novel coronavirus disease 19 (COVID-19) has resulted in an estimated 20 million excess deaths and the recent resurgence of COVID-19 in China is predicted to result in up to 1 million deaths over the next few months. With vaccines being ineffective in the case of immunocompromised patients, it is important to continue our quest for safe, effective and affordable drugs that will be available to all countries. Drug repurposing is one of the strategies being explored in this context. Recently, out of the 7817 drugs approved worldwide, 214 candidates were systematically down-selected using a combination of 11 filters including FDA/TGA approval status, assay data against SARS-CoV-2, pharmacokinetic, pharmacodynamic and toxicity profiles. These down-selected drugs were subjected in this study to virtual screening against various SARS-CoV-2 targets followed by molecular dynamics studies of the best scoring ligands against each target. The chosen molecular targets were spike receptor binding domain, nucleocapsid protein RNA binding domain and key nonstructural proteins 3, 5 and 12–14. Four drugs approved for other indications — alendronate, cromolyn, natamycin and treprostinil — look sufficiently promising from our in-silico studies to warrant further in-vitro and in-vivo investigations as appropriate to ascertain their extent of antiviral activities. The pandemic's death toll of more than 6.8 million deaths demand action. With vaccines that are inadequate for the immunocompromised, urgent focus shifts to safe treatment regimen. A rigorous study narrowed 214 repurposed drug candidates, identified alendronate, cromolyn, natamycin and treprostinil through virtual screening which needs to be evaluated in-vitro against COVID-19. [ABSTRACT FROM AUTHOR]

In the mudslide prone areas of western China, concrete piers were severely damaged by washing.In our previous research, the anti-abrasive UHPC prepared with saturated prewet high titanium heavy slag sand (ST-UHPC) is proposed to prevent such damage. And we studied the effect of grinding and erosion on the performance of ST-UHPC before, but the mechanism has not been studied in depth In order to study the microstructure evolution of ST-UHPC cement by the grinding and erosion, we use XRD, SEM, 27Al NMR, 29Si NMR test methods in this paper. By this way, we studied the effects of shock and salt erosion on hydration products composition, migration and transformation of Al-containing hydration products, hydration degree of cement and C-A-S-H gel microstructure. The results showed that the impact of bedload damaged the microstructure of UHPC. Then the damage of UHPC microstructure accelerates the transport of aggressive ions. Next, SO 4 2- erodes from the site of damage and produces expansive erosion products such as gypsum and calcareous vanadite. The erosion of SO 4 2- and Mg2+ resulted in the dealuminization and decalcification of C-A-S-H gel in UHPC cement and mechanical properties degradation. Thus, the expansion damage of UHPC and the impact damage of UHPC structure are aggravated. So the microstructure damage of UHPC was further aggravated. Under the action of impact, the water impacting material forms various chemical bonds with the C-A-S-H substrate. The chemical bonds results in the evolution of C-A-S-H microstructure. In conclusion, the structure of C-A-S-H substrate deteriorates obviously under the coupling effect of scouring and erosion. And the impact resistance of C-A-S-H substrate decreases significantly. • The anti-abrasive UHPC prepared with saturated prewet high titanium heavy slag sand was proposed. • XRD, SEM, 27Al NMR, 29Si NMR were used to study the microstructure evolution of ST-UHPC. • The microstructure evolution of UHPC was studied by molecular dynamics simulation. [ABSTRACT FROM AUTHOR]

Introduction: β-Glucosidase serves as the pivotal rate-limiting enzyme in the cellulose degradation process, facilitating the hydrolysis of cellobiose and cellooligosaccharides into glucose. However, the widespread application of numerous β-glucosidases is hindered by their limited thermostability and low glucose tolerance, particularly in elevated-temperature and high-glucose environments. Methods: This study presents an analysis of a β-glucosidase gene belonging to the GH1 family, denoted lqbg8, which was isolated from the metagenomic repository of Hehua hot spring located in Tengchong, China. Subsequently, the gene was cloned and heterologously expressed in Escherichia coli BL21(DE3). Post expression, the recombinant β-glucosidase (LQBG8) underwent purification through a Ni affinity chromatography column, thereby enabling the in-depth exploration of its enzymatic properties. Results: LQBG8 had an optimal temperature of 70°C and an optimum pH of 5.6. LQBG8 retained 100 and 70% of its maximum activity after 2-h incubation periods at 65°C and 70°C, respectively. Moreover, even following exposure to pH ranges of 3.0–10.0 for 24 h, LQBG8 retained approximately 80% of its initial activity. Notably, the enzymatic prowess of LQBG8 remained substantial at glucose concentrations of up to 3 M, with a retention of over 60% relative activity. The kinetic parameters of LQBG8 were characterized using cellobiose as substrate, with Km and Vmax values of 28 ± 1.9 mg/mL and 55 ± 3.2 μmol/min/mg, respectively. Furthermore, the introduction of LQBG8 (at a concentration of 0.03 mg/mL) into a conventional cellulase reaction system led to an impressive 43.7% augmentation in glucose yield from corn stover over a 24-h period. Molecular dynamics simulations offered valuable insights into LQBG8’s thermophilic nature, attributing its robust stability to reduced fluctuations, conformational changes, and heightened structural rigidity in comparison to mesophilic β-glucosidases. Discussion: In summation, its thermophilic, thermostable, and glucose-tolerant attributes, render LQBG8 ripe for potential applications across diverse domains encompassing food, feed, and the production of lignocellulosic ethanol. [ABSTRACT FROM AUTHOR]

The coal industry plays an essential role in China's economic development, and issues such as occupational health and environmental pollution caused by coal dust have attracted a great deal of attention. In accordance with the principles of environmental protection and waste management, this study used carboxymethyl ginkgo cellulose (CL) extracted and modified from Ginkgo biloba leaves as a matrix, and a graft copolymerized with sodium 3-allyloxy-1-hydroxy-1-propanesulfonate (AHPS) and N-isopropylacrylamide (NIPAM) monomers to prepare low-cost, environmentally friendly, and high-performance coal dust suppression (C-A-N). By optimizing fitting experimental data through three factors and two response surface analyses, the optimal dust suppression efficiency ratio was determined to be 4:8:5, and its swelling and water retention properties were analyzed. The microstructure, chemical reaction process, combustion performance and crusting property of the dust suppression gel were analyzed using Fourier-transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), thermogravimetry (TG), scanning electron microscopy (SEM), cone calorimetry, and consolidation layer strength tests. Relevant experiments show that the dust suppression gel prepared in this study has the characteristics of a strong wettability and minor impacts on the calorific value of coal, as well as green and environmental protection. When the wind speed is 10 m/s, the dust suppression effect reaches 93%, and the hardness of the solidified layer reaches 39.6 KPa. This study analyzed the migration and combination of functional groups in the interaction system using molecular dynamics simulation software. The microscopic effect and mechanism between dust suppression gel and coal are revealed from a molecular point of view. The feasibility and accuracy of the molecular dynamics simulation were verified by the consistency between simulation results and experimental data. Therefore, combining the utilization of waste resources with dust suppression can have important economic and social benefits. [ABSTRACT FROM AUTHOR]

The sulfur-containing compounds in China's crude oil mainly exist in the form of thiophene (TPs). More than 80% of TPs are composed of dibenzothiophene (DBT). The combustion of sulfur-containing fuel oil pollutes the air. Studies have shown that DES, as a new solvent similar to ionic liquids, has the advantages of simple preparation, easy availability of raw materials and high extraction rate. In this paper, experiments on DES synthesis were carried out to screen DES with the best extraction efficiency, and the effects of extraction operation temperature and initial sulfur concentration of raw oil on DES extraction and desulfurization were explored. The DES separation mechanism for DBT extraction from n-heptane-DBT was used as the simulated oil. Quantum chemistry was calculated for 9 commonly used DES, and the hydrogen bonding between DES-DET-n-heptane was analyzed by using the obtained σ-Profiles map information, and the selected DES was compared with the auxiliary experiment from the perspective of quantum chemistry. Then, the molecular dynamics (MD) simulation between different DES and raw oil was carried out, that is, the non-bond interaction energy, radial distribution function, spatial distribution function and mean square shift results of DBT-Heptane-DES calculated by molecular dynamics were used to deeply analyze the microscopic separation mechanism of DES extraction desulfurization. The results show that the DES composed of choline chloride/diethylene glycol can theoretically perform more efficient desulfurization operations, and this theoretical analysis method can provide a strong basis for the desulfurization of other types of DES and the separation of other systems. • Model oil extraction experiments to obtain optimal operating conditions for deep eutectic solvents. • Molecular dynamics (MD) simulations between different DES and feedstock oils were conducted. • In-depth analysis of the microscopic separation mechanism of extraction and desulfurization of DES. [ABSTRACT FROM AUTHOR]

Based on the thermodynamic stabilities and molecular simulation, two trimethyldibenzothiophene molecular indicators, that is, 2,4,6-/(1,4,6 + 1,4,8 + 3,4,6)-trimethyldibenzothiophene (TMDBT) and (2,4,7 + 2,4,8)-/(1,4,6 + 1,4,8 + 3,4,6)-TMDBT (the numbers indicate the position of methyl-substitute), were proposed to trace subsurface oil migration orientations and reservoir filling pathways. In this paper, we successfully applied the aforesaid parameters both in an Ordovician carbonate reservoir of the Tuoputai region of the Tarim Basin (NW China), and in an Eocene clastic lacustrine reservoir of the Fushan Depression in the Beibuwan Basin, South China Sea. Besides the migration fractionation is proven the main control factor for the relative contents of TMDBT isomers in corresponding oils, which indicates that the trimethyldibenzothiophene molecular parameters can serve as the effective oil migration tracer in an oil reservoir, especially in high to over mature and severely biodegraded oils. [ABSTRACT FROM AUTHOR]

The structural and dynamical properties of hydration water in aqueous solutions of trehalose are studied with molecular dynamics simulation. We simulate the systems in the supercooled region to investigate how the interaction with the trehalose molecules modifies the hydrogen bond network, the structural relaxation, and the diffusion properties of hydration water. The analysis is performed by considering the radial distribution functions, the residence time of water molecules in the hydration shell, the two body excess entropy, and the hydrogen bond water-water and water-trehalose correlations of the hydration water. The study of the two body excess entropy shows the presence of a fragile to strong crossover in supercooled hydration water also found in the relaxation time of the water-water hydrogen bond correlation function, and this is in agreement with predictions of the mode coupling theory and of previous studies of the oxygen-oxygen density correlators [A. Iorio et al., J. Mol. Liq. 282, 617 (2019); Sci. China: Phys., Mech. Astron. 62, 107011 (2019)]. The water-trehalose hydrogen bond correlation function instead evidences a strong to strong crossover in the relaxation time, and this crossover is related to a trehalose dynamical transition. This signals the role that the strong interplay between the soluted molecules and the surrounding solvent has in determining the dynamical transition common to both components of the system that happens upon cooling and that is similar to the well known protein dynamical transition. We connect our results with the cryoprotecting role of trehalose molecules. [ABSTRACT FROM AUTHOR]

[Display omitted] • The ReaxFF MD simulation and experiments of amoxicillin SCWG were conducted. • The decomposition of amoxicillin in supercritical water includes three stages. • The detailed process of amoxicillin decomposition in SCW was revealed. • The dual effect of OH radicals on the amoxicillin decomposition in SCW was found. • Reaction networks for nitrogen and sulfur conversion in SCW were obtained. The abuse of antibiotics in China has aroused widespread concern, and the resistance genes of antibiotics in the natural environment seriously threaten human health. The supercritical water gasification (SCWG) technology is a clean and efficient technology for the treatment of antibiotic wastewater. In this paper, amoxicillin is selected as the representative antibiotic in wastewater, and the detailed mechanisms of amoxicillin decomposition in supercritical water (SCW) are studied by ReaxFF reactive molecular dynamics (MD) simulation. The results show that the decomposition process of amoxicillin in SCW includes carbon ring opening, carbon chain breaking and small molecular compounds conversion. The molecular vibration leads to the breaking of C N and C S bonds. The OH radical is vital to the ring opening of benzene ring and the breaking of carbon chain. However, the yield of NO increases with increasing OH radical concentrations. The ReacNetGenerator tool is used for the first time to analyze the migration path of nitrogen and sulfur in the SCWG system. It shows that H 2 has a great effect on the transformation of sulfur, and OH radicals dominate the transformation of nitrogen. Decreasing the reaction time and the concentration of OH radicals result in inhibiting the NO production. This study will provide a theoretical guidance for understanding SCWG process of antibiotic-containing wastewater. [ABSTRACT FROM AUTHOR]

Simple description: The semi-coke water slurries (SCWSs) were prepared by mixing semi-coke powders, water and five anionic dispersants (NNO, SLS, SH, PCE and NNO/PCE).The effects of different anionic dispersants on the concentration, rheological behavior and static stability of SCWS were investigated. The adsorption capacity and adsorption kinetics of anionic dispersants on the surface of semi-coke particles were analyzed. The SEM-EDS, surface tension, contact angle, zeta potential measurement, and the E-DLVO calculations were also used to reveal the dispersion mechanism of anionic dispersants in SCWS. The improvement of the slurrying performance of SCWS by anionic dispersant is due to the comprehensive effect of van der Waals forces, electrostatic repulsion, and hydrophobic interactions between semi-coke particles. A model of the interaction mechanism of the anionic dispersants and semi-coke particles was proposed. [Display omitted] • SCWSs were prepared by mixing semi-coke powders, water and five dispersants. • The slurrying performance of SCWS added with NNO/PCE dispersant was the best. • The adsorption kinetics of the dispersants on semi-coke was quasi-second-order equation. • The interaction mechanism between the dispersants and semi-coke particles was proposed. It is essential to prepare the semi-coke water slurry (SCWS) using semi-coke powder in China. The preparation of SCWS can not only alleviate the oil demand, but can also provide a new way to utilize semi-coke powder. In this work, the effects of sodium methylene naphthalene sulfonate (NNO), sodium lignosulfonate (SLS), sodium humate (SH), polycarboxylate (PCE), and compound anion-anion (NNO/PCE), on the slurrying performance of semi-coke water slurry (SCWS) were studied. The results showed that the anionic dispersants increased the concentration of SCWSs, and the slurry exhibited the pseudoplastic rheological behavior of shear thinning. Adding PCE and NNO/PCE in the SCWS could improve its stability and fluidity. The absorbed capacity the microstructure of the particles, surface tension, contact angle, as well as Zeta potential of semi-coke powder were impacted by the addition of anionic dispersants in the SCWS. The results showed that anionic dispersants were adsorbed on the surface of semi-coke by a single-molecular layer. The developments of molecular dynamics simulation indicated that all dispersants should be spontaneously adsorbed on the surface of semi-coke, and the addition of anionic dispersants could reduce the contact angle and surface tension of the semi-char particle surface, increase the hydrophilicity and enhance the electronegativity. Finally, extended Derjaguin–Landau–Verwey –Overbeek (E-DLVO) theory calculations showed that adsorption of dispersants could significantly increase the total interaction energy between semi-coke particles. Finally, a model of the interaction mechanism of the anionic dispersants and semi-coke particles was proposed in this paper. [ABSTRACT FROM AUTHOR]

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Simulations are often used to investigate the flow structures and system dynamics of complex natural phenomena and systems, which are significantly harder to obtain from experiments or theoretical analyses. Surrogate models are employed to mimic the results of simulations by reducing computational costs. In order to reduce the amount of computational time consumed, a novel framework for building efficient surrogate models is proposed in this work. The novelty lies in that the new framework runs simulations using the different simulation time spans for different inputs and builds a comprehensive surrogate model through the fusion of non-homogeneous spatio-temporal data by integrating the temporal and spatial correlations in parametric space. This differs from the existing works in the literature, which only consider the situation of spatio-temporal data with a consistent time span during simulations under different inputs. Some simulation studies and real data analysis concerning the pollution of the river in the Sichuan Province of China are used to demonstrate the superior performance of the proposed methods. [ABSTRACT FROM AUTHOR]

Natural ester insulating oil not only has a biodegradation rate of almost 100% but also meets the carbon emission requirements of China’s “Carbon Peak and Carbon Neutrality” and the “European Green Deal” proposed by the European Union. It is considered to be a good substitute for mineral insulating oil. However, due to its higher kinematic viscosity than traditional mineral oil in low-temperature environments, it limits the safety promotion and application of transformers in cold regions. First, we design an experiment to test the kinematic viscosity and density of natural ester insulating oil. Under extremely harsh experimental conditions, we measure key experimental data such as kinematic viscosity. Second, the structure of the four main triglyceride molecules is optimized, and the molecular dynamics (MD) simulation technology is used to establish an MD model that can predict the kinematic viscosity of natural ester insulating oil (−20 °C to 20 °C). Finally, the model is further simplified by the free volume theory to better predict the kinematic viscosity of natural ester insulating oil. This study makes up for the lack of laboratory low-temperature testing of the kinematic viscosity of natural ester insulating oil and provides a convenient and reliable tool for predicting the kinematic viscosity of natural ester insulating oil. It can not only predict the natural ester insulating oil mixed in various proportions but also predict the kinematic viscosity of a certain natural ester molecule. Furthermore, it also provides a guiding direction for the improvement of low-temperature kinematic viscosity of natural ester insulating oil, as well as a strong reference for predicting other properties of other substances. [ABSTRACT FROM AUTHOR]

Background. Although Zuojin Pill (ZJP) is widely used in China as a traditional prescription to treat gastroesophageal reflux disease (GERD), its exact mechanism of action is still unknown. Therefore, we employed network pharmacology (NP), molecular docking (MD), and molecular dynamics simulation (MDS) to investigate the pharmacological mechanisms of ZJP against GERD. Methods. Active compounds and target genes corresponding to ZJP and target genes related to GERD were identified through analysis of publicly available datasets. Subsequently, the obtained data were subjected to further network pharmacological analysis to explore the potential key active compounds, core target genes, and biological processes (BPs) associated with the effect of ZJP against GERD. Finally, the prediction results of NP were validated by MD, and MDS of the optimal core protein-ligand for each component obtained by MD were performed using Gromacs 2020 software. Results. Twelve active components of ZJP were identified to act on 82 target genes associated with GERD, and ZJP might exert an anti-GERD effect through the regulation of BPs such as reactive oxygen species (ROS) metabolism, response to oxidative stress (OS), and ROS, as well as the activation of signaling pathways such as apoptosis, p53 signaling, chemical carcinogenesis-ROS, and HIF-1 signaling pathways. Furthermore, quercetin, kaempferol, and coptisine, the three key components of ZJP were shown to stably bond with the 14 core target genes, including AKT1, MMP2, TP53, EGFR, JUN, CASP3, CXCL8, HIF1α, IL-1β, MYC, PPARG, MMP9, PTGS2, and FOS. Results from MDS showed that PPARG-quercetin and MMP2-quercetin bound more stably. Conclusions. The findings suggest that ZJP alleviates the symptoms of GERD and improves the prognosis by regulating ROS metabolism, thereby reducing the secretion of proinflammatory cytokines like IL-1β, COX-2, CXCL8, and MMPs, regulating the expression of oncogenes such as JUN and FOS, and maintaining the normal expression of tumor suppressor genes such as TP53 and MYC. However, whether the effect of this modulation of ROS metabolism is positive or negative needs to be further verified by pharmacological experiments. [ABSTRACT FROM AUTHOR]

• The influence of different types of acid rain on the water stability of semi-flexible pavement is clarified. • The variation trend of water stability performance index of semi-flexible pavement under different acid rain types was obtained. • Based on molecular dynamics theory, a molecular dynamics model of acid rain corrosion of asphalt mixture was established. • Three different types of acid rain were first used for experimental simulation. • Based on experiments and supported by theory, the engineering problems are analyzed in detail. As is known to all, China is one of the countries with more acid rain in the world, and acid rain is mainly distributed in the southern humid climate area of China. However, the construction of semi-flexible asphalt pavement exposed to acid rain environment is a very realistic problem. In order to clarify the influence of different types of acid rain on the water stability of semi-flexible pavement, sulfuric acid type acid rain, nitric acid type acid rain and mixed type acid rain were prepared in this paper, and the semi-flexible specimens were soaked periodically. The water stability of semi-flexible pavement under different types of acid rain corrosion was evaluated macroscopically by standard Marshall test, immersion Marshall test, freeze-thaw splitting test and vacuum saturation test. It was concluded that the Marshall stability, immersion Marshall residual stability, freeze-thaw splitting strength ratio and vacuum saturation residual stability of semi-flexible pavement under different types of acid rain showed different degrees of decline. The reasons for the decline of water stability of semi-flexible pavement under different types of acid rain corrosion were analyzed by scanning electron microscopy and infrared spectroscopy. It was concluded that the acidification condition of rainwater was the main reason for the decrease of ductility, viscosity and plasticity of petroleum asphalt, which affected the binding force between petroleum asphalt and limestone aggregate, and ultimately led to the decline of water stability of semi-flexible pavement. Based on the molecular dynamics theory, the molecular dynamics model of acid rain corrosion asphalt mixture is established. According to the sensitivity of acid components to the main components of semi-flexible asphalt mixture, the asphalt, oil, resin and calcium carbonate with the most content in semi-flexible asphalt mixture are selected to simulate and study. The changes of bonding energy and diffusion coefficient of asphalt mixture under different types of acid rain are calculated and analyzed. It is concluded that sulfuric acid acid rain has the greatest influence on the water stability of semi-flexible specimens, followed by mixed acid rain, and the influence of nitric acid rain is relatively small. [ABSTRACT FROM AUTHOR]

A novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was identified as the cause of the COVID-19 pandemic that originated in China in December 2019. Although extensive research has been performed on SARS-CoV-2, the binding behavior of spike (S) protein and receptor binding domain (RBD) of SARS-CoV-2 at different environmental conditions have yet to be studied. The objective of this study is to investigate the effect of temperature, fatty acids, ions, and protein concentration on the binding behavior and rates of association and dissociation between the S protein and RBD of SARS-CoV-2 and the hydrophobic aminopropylsilane (APS) biosensors using biolayer interferometry (BLI) validated with molecular dynamics simulation. Our results suggest three conditions—high ionic concentration, presence of hydrophobic fatty acids, and low temperature—favor the attachment of S protein and RBD to hydrophobic surfaces. Increasing the temperature within an hour from 0 to 25 °C results in S protein detachment, suggesting that freezing can cause structural changes in the S protein, affecting its binding kinetics at higher temperature. At all the conditions, RBD exhibits lower dissociation capabilities than the full-length S trimer protein, indicating that the separated RBD formed stronger attachment to hydrophobic surfaces compared to when it was included in the S protein. [ABSTRACT FROM AUTHOR]

In shale reservoirs, the organic pores with various structures formed during the thermal evolution of organic matter are the main storage site for adsorbed methane. However, in the process of thermal evolution, the adsorption characteristics of methane in multi type and multi-scale organic matter pores have not been sufficiently studied. In this study, the molecular simulation method was used to study the adsorption characteristics of methane based on the geological conditions of Longmaxi Formation shale reservoir in Sichuan Basin, China. The results show that the characteristics of pore structure will affect the methane adsorption characteristics. The adsorption capacity of slit-pores for methane is much higher than that of cylindrical pores. The groove space inside the pore will change the density distribution of methane molecules in the pore, greatly improve the adsorption capacity of the pore, and increase the pressure sensitivity of the adsorption process. Although the variation of methane adsorption characteristics of different shapes is not consistent with pore size, all pores have the strongest methane adsorption capacity when the pore size is about 2 nm. In addition, the changes of temperature and pressure during the thermal evolution are also important factors to control the methane adsorption characteristics. The pore adsorption capacity first increases and then decreases with the increase of pressure, and increases with the increase of temperature. In the early stage of thermal evolution, pore adsorption capacity is strong and pressure sensitivity is weak; while in the late stage, it is on the contrary. [ABSTRACT FROM AUTHOR]

Objective. Chinese herbs play a positive role in the management of hepatocellular carcinoma (HCC) in China. However, it is not clear which of Chinese herbs are critical for the treatment of HCC. Besides, mechanisms of CCHs in the treatment of HCC remain unclear. Hence, our goal is to identify the core Chinese herbs (CCHs) for treating HCC and explore their antitumor mechanism. Methods. Firstly, clinical traditional Chinese medicine (TCM) prescriptions for HCC were collected from Chinese National Knowledge Infrastructure (CNKI) database, and then, data mining software was used to identify CCHs. After that, bioactive compounds and corresponding target genes of CCHs were obtained using three TCM databases, and target genes of HCC were acquired from MalaCards and OMIM. Subsequently, common target genes of CCHs and HCC were screened. Moreover, biological functions and pathways were analyzed, and Cytoscape plugin cytoHubba was used to identify hub genes. Finally, prognostic values of hub genes were verified by survival analysis, and the molecular docking approach was utilized to validate the interactions between targets and bioactive compounds of CCHs. Results. Eight CCHs were determined from 630 prescriptions, and 100 bioactive compounds (e.g., quercetin and luteolin) and 126 common target genes were screened. Furthermore, common target genes of CCHs and HCC were mainly enriched in cancer-associated pathways, and six hub genes with statistical significance in survival analysis were selected as key target genes for molecular docking. Additionally, molecular docking showed that the bioactive compounds docked well with the protein receptors of key target genes. Conclusion. By combining data mining, network pharmacology, molecular docking, and survival analysis methods, we found that CCHs may play a therapeutic role in HCC through regulating the target genes and pathways related to cancer occurrence and development, angiogenesis, metastasis, and prognosis. [ABSTRACT FROM AUTHOR]

High rates of esophageal cancer (EC) are found in people of the Henan Taihang Mountain, Fujian Minnan, and Chaoshan regions of China. Historical records describe great waves of populations migrating from north-central China (the Henan and Shanxi Hans) through coastal Fujian Province to the Chaoshan plain. Although these regions are geographically distant, we hypothesized that EC high-risk populations in these three areas could share a common ancestry. Accordingly, we used 16 East Asian-specific Y-chromosome biallelic markers (single nucleotide polymorphisms; Y-SNPs) and six Y-chromosome short tandem repeat (Y-STR) loci to infer the origin of the EC high-risk Chaoshan population (CSP) and the genetic relationship between the CSP and the EC high-risk Henan Taihang Mountain population (HTMP) and Fujian population (FJP). The predominant haplogroups in these three populations are O3*, O3e*, and O3e1, with no significant difference between the populations in the frequency of these genotypes. Frequency distribution and principal component analysis revealed that the CSP is closely related to the HTMP and FJP, even though the former is geographically nearer to other populations (Guangfu and Hakka clans). The FJP is between the CSP and HTMP in the principal component plot. The CSP, FJP and HTMP are more closely related to Chinese Hans than to minorities, except Manchu Chinese, and are descendants of Sino-Tibetans, not Baiyues. Correlation analysis, hierarchical clustering analysis, and phylogenetic analysis (neighbor-joining tree) all support close genetic relatedness among the CSP, FJP and HTMP. The network for haplogroup O3 (including O3*, O3e* and O3e1) showed that the HTMP have highest STR haplotype diversity, suggesting that the HTMP may be a progenitor population for the CSP and FJP. These findings support the potentially important role of shared ancestry in understanding more about the genetic susceptibility in EC etiology in high-risk populations and have implications for determining the molecular basis of this disease. [ABSTRACT FROM AUTHOR]

Deep marine shale gas reservoirs are extremely rich in the Sichuan basin in China. However, due to the in situ conditions with high temperature and high pressure (HTHP), in particular reservoir pressure being usually much higher than the test pressure, it is difficult to accurately clarify the adsorption behavior, as seepage theory plays an important role in shale gas reserves evaluation. Therefore, three kinds of sorbent, including illite, quartz and kerogen, and two simulation methods, containing the grand canonical ensemble Monte Carlo method and molecular dynamics method, are synthetically used to determine the methane adsorption behavior under HTHP. The results show that both absolute adsorption and excess adsorption decrease with the increase of temperature. When the pressure increases, the absolute adsorption increases quickly and then slowly, and the excess adsorption first increases and then decreases. The superposition of wall potential energy is strongest in a circular hole, second in a square hole, and weakest in a narrow slit. The effect of pore size increases with the decrease of the pore diameter. Under HTHP, multi-layer adsorption can occur in shale, but the timing and number of layers are related to the sorbent type. [ABSTRACT FROM AUTHOR]

Simple Summary: With the urgent necessity of potential treatment against novel coronavirus disease, we used several computational methods to search for active drugs from an extensive database. The results of our investigation suggested several established drugs that can be subjected to further analysis for the treatment of novel coronavirus disease. Various methods used in this study proved the effectiveness of the retrieved drugs. Therefore, our findings highly recommend the mentioned drugs to be scrutinized to discover drugs against novel coronavirus. Novel coronavirus disease (COVID-19) was identified from China in December 2019 and spread rapidly through human-to-human transmission, affecting so many people worldwide. Until now, there has been no specific treatment against the disease and repurposing of the drug. Our investigation aimed to screen potential inhibitors against coronavirus for the repurposing of drugs. Our study analyzed sequence comparison among SARS-CoV, SARS-CoV-2, and MERS-CoV to determine the identity matrix using discovery studio. SARS-CoV-2 Mpro was targeted to generate an E-pharmacophore hypothesis to screen drugs from the DrugBank database having similar features. Promising drugs were used for docking-based virtual screening at several precisions. Best hits from virtual screening were subjected to MM/GBSA analysis to evaluate binding free energy, followed by the analysis of binding interactions. Furthermore, the molecular dynamics simulation approaches were carried out to assess the docked complex's conformational stability. A total of 33 drug classes were found from virtual screening based on their docking scores. Among them, seven potential drugs with several anticancer, antibiotic, and immunometabolic categories were screened and showed promising MM/GBSA scores. During interaction analysis, these drugs exhibited different types of hydrogen and hydrophobic interactions with amino acid residue. Besides, 17 experimental drugs selected from virtual screening might be crucial for drug discovery against COVID-19. The RMSD, RMSF, SASA, Rg, and MM/PBSA descriptors from molecular dynamics simulation confirmed the complex's firm nature. Seven promising drugs for repurposing against SARS-CoV-2 main protease (Mpro), namely sapanisertib, ornidazole, napabucasin, lenalidomide, daniquidone, indoximod, and salicylamide, could be vital for the treatment of COVID-19. However, extensive in vivo and in vitro studies are required to evaluate the mentioned drug's activity. [ABSTRACT FROM AUTHOR]