Computational Analysis Reveals a Critical Point Mutation in the N-Terminal Region of the Signaling Lymphocytic Activation Molecule Responsible for the Cross-Species Infection with Canine Distemper Virus

Infection of hosts by morbilliviruses is facilitated by the interaction between viral hemagglutinin (H-protein) and the signaling lymphocytic activation molecule (SLAM). Recently, the functional importance of the n-terminal region of human SLAM as a measles virus receptor was demonstrated. However, the functional roles of this region in the infection process by other morbilliviruses and host range determination remain unknown, partly because this region is highly flexible, which has hampered accurate structure determination of this region by X-ray crystallography. In this study, we analyzed the interaction between the H-protein from canine distemper virus (CDV-H) and SLAMs by a computational chemistry approach. Molecular dynamics simulations and fragment molecular orbital analysis demonstrated that the unique His28 in the N-terminal region of SLAM from Macaca is a key determinant that enables the formation of a stable interaction with CDV-H, providing a basis for CDV infection in Macaca. The computational chemistry approach presented should enable the determination of molecular interactions involving regions of proteins that are difficult to predict from crystal structures because of their high flexibility.     

Olive-Derived Triterpenes Suppress SARS COV-2 Main Protease: A Promising Scaffold for Future Therapeutics

SARS CoV-2 pandemic is still considered a global health disaster, and newly emerged variants keep growing. A number of promising vaccines have been recently developed as a protective measure; however, cost-effective treatments are also of great importance to support this critical situation. Previously, betulinic acid has shown promising antiviral activity against SARS CoV via targeting its main protease. Herein, we investigated the inhibitory potential of this compound together with three other triterpene congeners (i.e., ursolic acid, maslinic acid, and betulin) derived from olive leaves against the viral main protease (M^pro) of the currently widespread SARS CoV-2. Interestingly, betulinic, ursolic, and maslinic acids showed significant inhibitory activity (IC₅₀ = 3.22–14.55 µM), while betulin was far less active (IC₅₀ = 89.67 µM). A comprehensive in-silico analysis (i.e., ensemble docking, molecular dynamic simulation, and binding-free energy calculation) was then performed to describe the binding mode of these compounds with the enzyme catalytic active site and determine the main essential structural features required for their inhibitory activity. Results presented in this communication indicated that this class of compounds could be considered as a promising lead scaffold for developing cost-effective anti-SARS CoV-2 therapeutics.     

Performance evaluation of functionalized ordered mesoporous silica for VOCs adsorption by molecular dynamics simulation

Volatile organic compounds (VOCs) are growing pollutants now that cause the serious environmental pollution and threaten human health. The functionalized ordered mesoporous silica (FOMS) has attracted considerable attention in adsorbing VOCs. In this paper, the molecular dynamics simulation was used to simulate the adsorption performance of FOMS on VOCs (acetone, ethyl acetate and toluene). After simulating different pore sizes (2 nm, 3 nm and 4 nm) adsorption performances of ordered mesoporous silica (OMS) on VOCs, OMS with a pore size of 4 nm was selected to further study the influence of functional groups (vinyl, methyl, and phenyl). The following law was obtained: the saturated adsorption capacities of vinyl-functionalized OMS (V-FOMS) to acetone, ethyl acetate and toluene were 3.045 mmol.g^?1, 2.568 mmol.g^?1 and 1.976 mmol.g^?1 respectively; the saturated adsorption capacities of methyl-functionalized OMS (M-FOMS) to acetone, ethyl acetate and toluene were 2.798 mmol.g^?1, 2.312 mmol.g^?1 and 1.698 mmol.g^?1 respectively; the saturated adsorption capacities of phenyl-functionalized OMS (P-FOMS) to acetone, ethyl acetate and toluene were 2.124 mmol.g^?1, 1.941 mmol.g^?1 and 1.539 mmol.g^?1 respectively. These results show that the adsorption ability of FOMS for different adsorbates follows the sequence of acetone > ethyl acetate > toluene. Furthermore, the interaction between functional groups (vinyl, methyl and phenyl) in FOMS and VOCs was explored. It is found that the interaction between different functional groups and adsorbates is different (interaction energy effect). This interaction energy effect promotes FOMS to better adsorb VOCs. This work would provide fundamental understanding and guidance for the development of novel adsorption materials for the adsorption of VOCs.     

Application of DEM modified with enlarged particle model to simulation of bead motion in a bead mill

We applied the discrete element method （DEM） of simulation modified by an enlarged particle model to simulate bead motion in a large bead mill. The stainless-steel bead mill has inner diameter of 102 mm and mill length of 198 mm. The bead diameter and filling ratio were fixed respectively at 0.5 mm and 85%. The agitator rotational speed was changed from 1863 to 3261 rpm. The bead motion was monitored experimentally using a high-speed video camera through a transparent mill body. For the simulation, enlarged particle sizes were set as 3-6 mm in diameter. With the DEM modified by the enlarged particle model, the motion of enlarged particles in a mill was simulated.The velocity data of the simulated enlarged particles were compared with those obtained in the experiment. The simulated velocity of the enlarged particles depends on the virtual frictional coefficient in the DEM model. The optimized value of the virtual frictional coefficient can be determined by considering the accumulated mean value. Results show that the velocity of the enlarged particles simulated increases with an increase in the optimum virtual frictional coefficient, but the simulated velocity agrees well with that determined experimentally by optimizing the virtual frictional coefficient in the simulation. The computing time in the simulation decreases with increased particle size.     

Numerical analysis of the initial conditions in fractional systems

Fractional dynamics is a growing topic in theoretical and experimental scientific research. A classical problem is the initialization required by fractional operators. While the problem is clear from the mathematical point of view, it constitutes a challenge in applied sciences. This paper addresses the problem of initialization and its effect upon dynamical system simulation when adopting numerical approximations. The results are compatible with system dynamics and clarify the formulation of adequate values for the initial conditions in numerical simulations.     

电场下离子型聚合物复合囊泡结构变化的分子动力学模拟

利用粗粒化分子动力学模拟研究了电场作用下离子型聚合物复合囊泡形变与破裂的过程.定量分析了囊泡破裂过程中的结构变化,包括囊泡的形变程度、破裂速度、组分分布以及破裂后的结构.研究表明,电场强度较弱时,囊泡表面所吸附的聚电解质首先脱落,囊泡由球形结构转变为椭球结构.随着电场强度增大,离聚物的离子侧基发生重新排布,囊泡表面电荷的有序结构被破坏,导致囊泡的结构无法维持而破裂,囊泡塌缩,分裂形成离聚物团簇,并进一步破裂为小尺寸的离聚物聚集体,均匀分散于溶液中.本文利用分子动力学模拟明确了电场中离子型高分子复合囊泡破裂过程的分子机理,为药物释放技术的优化及发展提供了理论支持.     

Evidence for Multiple Binding Modes in the Initial Contact Between SARS-CoV-2 Spike S1 Protein and Cell Surface Glycans**

Infection of host cells by SARS-CoV-2 begins with recognition by the virus S (spike) protein of cell surface heparan sulfate (HS), tethering the virus to the extracellular matrix environment, and causing the subunit S1-RBD to undergo a conformational change into the ‘open’ conformation. These two events promote the binding of S1-RBD to the angiotensin converting enzyme 2 (ACE2) receptor, a preliminary step toward viral-cell membrane fusion. Combining ligand-based NMR spectroscopy with molecular dynamics, oligosaccharide analogues were used to explore the interactions between S1-RBD of SARS CoV-2 and HS, revealing several low-specificity binding modes and previously unidentified potential sites for the binding of extended HS polysaccharide chains. The evidence for multiple binding modes also suggest that highly specific inhibitors will not be optimal against protein S but, rather, diverse HS-based structures, characterized by high affinity and including multi-valent compounds, may be required.     

基于Aspen Plus耦合生命周期评价的科研案例在环境工程原理教学中的应用

将化工流程模拟Aspen Plus软件与环境影响评估领域常用的生命周期评价(LCA)进行集成应用,围绕环境工程原理教学中有关化工过程质量能量衡算与环境污染防治内容的协同应用与拓展,构建化工流程模拟-环境风险评估科研案例“苯酐生产流程模拟及环境风险研究”,并将其作为环境工程原理的综合教学案例。教学实践经验表明,通过引入工程相关综合教学案例,不仅使得抽象的理论知识更加生动具体,而且在深化学生对课程理论知识理解的同时,提高学生应用专业知识分析和解决化工生产环境污染工程问题的综合能力和素质,为学生将来步入相关领域工作奠定扎实的基础。     

Ion transmission in an electrospray ionization-mass spectrometry interface using an S-lens

We present the design and performance of an in-house built electrospray ionization-mass spectrometry (ESI-MS) interface equipped with an S-lens ion guide. The ion source was designed specifically for our ion beam experiments to investigate the chemical reactivity and deposition of the clusters and nanoparticles. It includes standard ESI-MS interface components, such as nanoelectrospray, ion transfer capillary, and the S-lens. A custom design enables systematic optimization of all relevant factors influencing ion formation and transfer through the interface. By varying the ESI voltage and flow rate, we determined the optimal operating conditions for selected silica emitters. A comparison of the pulled silica emitters with different tip inner diameters reveals that the total ion current is highest for the largest tip, whereas a tip with the smallest diameter exhibited the highest transmission efficiency through the ESI-MS interface. Ion transmission through the transfer capillary is strongly limited by its length, but the loss of ions can be reduced by increasing the capillary voltage and temperature. The S-lens was characterized over a wide range of RF frequencies and amplitudes. Maximum ion current was detected at RF amplitudes greater than 50 V peak-to-peak (p/p) and frequencies above 750 kHz, with a stable ion transmission region of about 20%. A factor of 2.6 increase in total ion current is observed for 650 kHz as RF amplitudes reach 400 V p/p. Higher RF amplitudes also focus the ions into a narrow beam, which mitigates their losses when passing through the ion guide.     

Study on gas adsorption and desorption characteristics on water injection coal

To study the desorption mechanism of methane in coal by H₂O injection and establish the Wiser molecular structure model of bituminous coal, the Grand Canonical Monte Carlo method was used to study the desorption behavior of CH₄ in coal with different amounts of H₂O injection at molecular scale. The results showed that at 293 K, the maximum adsorption capacity of H₂O was about 16 mmol/g, and that of CH₄ was about 8 mmol/g, which was about twice that of CH₄. This indicates that H₂O has a stronger adsorption capacity than CH₄. For methane-bearing coal, when the amount of water injected is 100, the average relative concentration of CH₄ is 0.5446, and the average relative concentration of CH₄ decreases by 33.77% compared to the water content of 20. Under the same time conditions, the root mean square displacement and diffusion coefficient of CH₄ decrease with the increase of H₂O injection quantity. With the increase of H₂O injection, the motion velocity of CH₄ in vacuum layer decreased. When water was injected, methane was trapped in the coal by water. The more H₂O injected, the more methane trapped in the coal, and the less methane desorption. This research lays a theoretical foundation for further research involving coal-water interaction.