本文在分子动力学模拟基础上采用了考虑黏附作用的JKR理论取代传统Hertz理论作为颗粒间作用力,并吸取了DEM中滑动摩擦、滚动摩擦和扭动摩擦的思想建立一种细颗粒碰撞和团聚过程的多时间尺度粒子动力学模拟方法.成功地实现了颗粒在纤维...本文在分子动力学模拟基础上采用了考虑黏附作用的JKR理论取代传统Hertz理论作为颗粒间作用力,并吸取了DEM中滑动摩擦、滚动摩擦和扭动摩擦的思想建立一种细颗粒碰撞和团聚过程的多时间尺度粒子动力学模拟方法.成功地实现了颗粒在纤维上沉积过程的模拟,结果表明微米颗粒的Van der Waals力量纲约是曳力2～10倍,中心流线附近颗粒更易于在纤维上沉积,初始沉积的颗粒则会在纤维上形成"遮挡"效应。展开更多
Molecular dynamics simulation is carried out to study the nanometric machining of single crystal Nickel(Ni). Through an investigation of atomic displacement and the variation of cutting force, it is found that the lat...Molecular dynamics simulation is carried out to study the nanometric machining of single crystal Nickel(Ni). Through an investigation of atomic displacement and the variation of cutting force, it is found that the latter is in accordance with the number variation of elastic displaced atoms in the workpiece. It is further found that the generation of complex stacking faults is the predominant cause of cutting force fluctuation, and the stacking faults with complex structures lead to work-hardening. The temperature of the cutting tool and workpiece is studied during the machining process. It is concluded that the selection of averaging steps has a significant influence on the system temperature distribution. Thus, the time-spatial averaging method, which has a high accuracy and consistency in temperature distribution, is proposed.展开更多
This article presents a multiscale simulation approach starting at the molecular level for the adsorption process development. A grand canonical Monte Carlo method is used for the prediction of adsorption isotherms of...This article presents a multiscale simulation approach starting at the molecular level for the adsorption process development. A grand canonical Monte Carlo method is used for the prediction of adsorption isotherms of methanol on an activated carbon at the molecular level. The adsorption isotherms obtained in the linear region （or adsorption constant） are exploited as a model parameter required for the adsorption process simulation. The adsorption process model described by a set of partial differential equations （PDEs） is solved by using the conservation element and solution element method, which produces a fast and an accurate numerical solution to PDEs. The simulation results obtained from the adsorption constant estimated at the molecular level are in good agreement with the experimental results of the pulse response. The systematical multiscale simulation approach addressed in this study may be useful to accelerate the adsorption process development by reducing the number of experiments.展开更多
Molecular dynamics simulation is a powerful tool in the study of polymeric systems.Among various simulation methods,coarse-grained(CG)model is particularly impactful because it effectively reduces the computational co...Molecular dynamics simulation is a powerful tool in the study of polymeric systems.Among various simulation methods,coarse-grained(CG)model is particularly impactful because it effectively reduces the computational complexity and enables the simulation of large-scale polymer systems.In this review,we briefly summarize recent progresses in our group on the development of CG simulation methods,models,as well as in the software development.By compiling the CG models and various simulation methods,we have successfully developed a GPU-accelerated large-scale molecular simulation toolkit(GALAMOST),which provides an efficient platform for polymer simulations.We further developed the new-generation PyGAMD(Python GPU-Accelerated MD Software,website:)software based on the Python platform,which makes the polymer simulation more powerful,flexible and user-friendly.In addition,some recent application cases in different polymer systems are also introduced.The aspiration of this review is to assist researchers in understanding the role of molecular simulations in the design and development of advanced polymer materials not only for academic researches,but also for possible industrial applications.展开更多
The insulin-degrading enzyme(IDE)plays a significant role in the degradation of the amyloid beta(Aβ),a peptide found in the brain regions of the patients with early Alzheimer’s disease.Adenosine triphosphate(ATP)all...The insulin-degrading enzyme(IDE)plays a significant role in the degradation of the amyloid beta(Aβ),a peptide found in the brain regions of the patients with early Alzheimer’s disease.Adenosine triphosphate(ATP)allosterically regulates the Aβ-degrading activity of IDE.The present study investigates the electrostatic interactions between ATP-IDE at the allosteric site of IDE,including thermostabilities/flexibilities of IDE residues,which have not yet been explored systematically.This study applies the quantum mechanics/molecular mechanics(QM/MM)to the proposed computational model for exploring electrostatic interactions between ATP and IDE.Molecular dynamic(MD)simulations are performed at different temperatures for identifying flexible and thermostable residues of IDE.The proposed computational model predicts QM/MM energy-minimised structures providing the IDE residues(Lys530 and Asp385)with high binding affinities.Considering root mean square fluctuation values during the MD simulations at 300.00 K including heat-shock temperatures(321.15 K and 315.15 K)indicates that Lys530 and Asp385 are also the thermostable residues of IDE,whereas Ser576 and Lys858 have high flexibilities with compromised thermostabilities.The present study sheds light on the phenomenon of biological recognition and interactions at the ATP-binding domain,which may have important implications for pharmacological drug design.The proposed computational model may facilitate the development of allosteric IDE activators/inhibitors,which mimic ATP interactions.展开更多
文摘本文在分子动力学模拟基础上采用了考虑黏附作用的JKR理论取代传统Hertz理论作为颗粒间作用力,并吸取了DEM中滑动摩擦、滚动摩擦和扭动摩擦的思想建立一种细颗粒碰撞和团聚过程的多时间尺度粒子动力学模拟方法.成功地实现了颗粒在纤维上沉积过程的模拟,结果表明微米颗粒的Van der Waals力量纲约是曳力2～10倍,中心流线附近颗粒更易于在纤维上沉积,初始沉积的颗粒则会在纤维上形成"遮挡"效应。
基金supported by the National Natural Science Foundation of China(Grant No.51375082)
文摘Molecular dynamics simulation is carried out to study the nanometric machining of single crystal Nickel(Ni). Through an investigation of atomic displacement and the variation of cutting force, it is found that the latter is in accordance with the number variation of elastic displaced atoms in the workpiece. It is further found that the generation of complex stacking faults is the predominant cause of cutting force fluctuation, and the stacking faults with complex structures lead to work-hardening. The temperature of the cutting tool and workpiece is studied during the machining process. It is concluded that the selection of averaging steps has a significant influence on the system temperature distribution. Thus, the time-spatial averaging method, which has a high accuracy and consistency in temperature distribution, is proposed.
基金the Basic Research Program of the Korea Science & Engineering Foundation (KoSEF, No. R01-2006-000-10786-0).
文摘This article presents a multiscale simulation approach starting at the molecular level for the adsorption process development. A grand canonical Monte Carlo method is used for the prediction of adsorption isotherms of methanol on an activated carbon at the molecular level. The adsorption isotherms obtained in the linear region （or adsorption constant） are exploited as a model parameter required for the adsorption process simulation. The adsorption process model described by a set of partial differential equations （PDEs） is solved by using the conservation element and solution element method, which produces a fast and an accurate numerical solution to PDEs. The simulation results obtained from the adsorption constant estimated at the molecular level are in good agreement with the experimental results of the pulse response. The systematical multiscale simulation approach addressed in this study may be useful to accelerate the adsorption process development by reducing the number of experiments.
基金supported by the National Key Research and Development Program of China(2022YFB3707300)the National Natural Science Foundation of China(22133002,22273031 and 22003019).
文摘Molecular dynamics simulation is a powerful tool in the study of polymeric systems.Among various simulation methods,coarse-grained(CG)model is particularly impactful because it effectively reduces the computational complexity and enables the simulation of large-scale polymer systems.In this review,we briefly summarize recent progresses in our group on the development of CG simulation methods,models,as well as in the software development.By compiling the CG models and various simulation methods,we have successfully developed a GPU-accelerated large-scale molecular simulation toolkit(GALAMOST),which provides an efficient platform for polymer simulations.We further developed the new-generation PyGAMD(Python GPU-Accelerated MD Software,website:)software based on the Python platform,which makes the polymer simulation more powerful,flexible and user-friendly.In addition,some recent application cases in different polymer systems are also introduced.The aspiration of this review is to assist researchers in understanding the role of molecular simulations in the design and development of advanced polymer materials not only for academic researches,but also for possible industrial applications.
文摘The insulin-degrading enzyme(IDE)plays a significant role in the degradation of the amyloid beta(Aβ),a peptide found in the brain regions of the patients with early Alzheimer’s disease.Adenosine triphosphate(ATP)allosterically regulates the Aβ-degrading activity of IDE.The present study investigates the electrostatic interactions between ATP-IDE at the allosteric site of IDE,including thermostabilities/flexibilities of IDE residues,which have not yet been explored systematically.This study applies the quantum mechanics/molecular mechanics(QM/MM)to the proposed computational model for exploring electrostatic interactions between ATP and IDE.Molecular dynamic(MD)simulations are performed at different temperatures for identifying flexible and thermostable residues of IDE.The proposed computational model predicts QM/MM energy-minimised structures providing the IDE residues(Lys530 and Asp385)with high binding affinities.Considering root mean square fluctuation values during the MD simulations at 300.00 K including heat-shock temperatures(321.15 K and 315.15 K)indicates that Lys530 and Asp385 are also the thermostable residues of IDE,whereas Ser576 and Lys858 have high flexibilities with compromised thermostabilities.The present study sheds light on the phenomenon of biological recognition and interactions at the ATP-binding domain,which may have important implications for pharmacological drug design.The proposed computational model may facilitate the development of allosteric IDE activators/inhibitors,which mimic ATP interactions.
