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.     

Rapid separation and binding configuration prediction of the components in Danshen decoction to endothelin A receptor using affinity chromatography and molecular dynamics simulation

As a famous traditional Chinese formula, Danshen Decoction has the potential to relieve the pain of pulmonary arterial hypertension patients, however, the functional components remain unknown. Herein, we reported a method to screen the functional components in Danshen Decoction targeting endothelin receptor A, an accepted target for the treatment of the disease. The receptor was functionalized on the macroporous silica gel through an epidermal growth factor receptor fusion tag and its covalent inhibitor. Using the affinity gel as the stationary phase, the bioactive compound was identified as salvianolic acid B by mass spectrometry. The binding kinetic parameter (dissociation rate constants k_d) of salvianolic acid B with the receptor was determined via peak profiling. Using the specific ligands of the receptor as probes, the binding configuration prediction of salvianolic acid B with the receptor was performed by molecular dynamics simulation. Our results indicated that salvianolic acid B is a potential bioactive compound in Danshen Decoction targeting the receptor. This work showed that receptor chromatography in combination with molecular dynamics simulation is applicable to predicting the binding kinetics and configuration of a ligand to a receptor, providing crucial insight for the rational design of drugs that recognize functional proteins.     

铁脂质体/水分配系数测定及影响因素考察

基于PAF-301分子模型通过Li 掺杂或B取代等模式设计了几种新型多孔芳香骨架(PAFs)材料, 采用量子力学和分子力学方法对新材料的储氢性能进行研究. 由量子力学计算得到了不同分子片段与H₂之间的结合能, 并结合DDEC方法计算了各分子片段的原子电荷分布. 利用巨正则蒙特卡洛(GCMC)模拟方法计算了77和298 K下H₂在不同PAFs材料中的吸附平衡性质. 结果表明, H₂直接与苯环的结合能较低, 但掺杂Li 原子能够提高H₂与六元环的结合能, 同时Li 原子体现出较高的正电性质, B原子取代苯环中的两个C原子后, 使得原有C原子电负性增强; 77 K下PAF-301Li 具有最高的储氢性能, 而PAF-C₄B₂H₄-Li₂-Si 和PAF-C₄B₂H₄-Li₂-Ge体现出较好的常温储氢性能, 各种材料的常温储氢性能远低于其低温储氢性能. 通过77 K下H₂在PAFs材料中的等位能面分布和吸附平衡质心密度分布对H₂在PAFs 材料中的优先吸附位置进行分析, 发现在PAF-301 和PAF-301Li 骨架中, 由于中心能量较低的等位能区域范围较宽, H₂在其中存在四个明显的吸附高密度分布区域, 而其它三种PAFs晶胞中心能量较低的等位能区域范围较窄, 使得H₂在其中只存在两个明显的吸附高密度分布区域.     

分子动力学模拟研究[Bmim][PF6]+水+醇三元体系的微观结构和分子间相互作用

研究离子液体体系的微观结构和分子间相互作用具有重要意义. 本文对1-丁基-3-甲基咪唑六氟磷酸盐([Bmim][PF₆])+水+乙醇和[Bmim][PF₆]+水+异丙醇三元体系进行了分子模拟研究, 计算了径向分布函数和不同组成的水-醇混合溶剂与离子液体阴阳离子间的相互作用能, 并将其分解为库仑相互作用能和Lennard-Jones(LJ)势能. 在此基础上, 研究了溶液体系的微观结构、分子间相互作用和相行为. 结果表明, 水倾向于与离子液体阴离子和阳离子极性部分作用, 醇倾向于与阴离子和阳离子非极性部分作用; 库仑力主导阴离子-溶剂相互作用, 色散力主导阳离子-溶剂相互作用, 阴阳离子的缔合状态对色散力影响较小, 对库仑力的影响非常显著.