Unravelling biotoxicity of graphdiyne:Molecular dynamics simulation of the interaction between villin headpiece protein and graphdiyne

Recently,there has been a growing prevalence in the utilization of graphdiyne(GDY)in the field of biomedicine,attributed to its distinctive physical structure and chemical properties.Additionally,its biocompatibility has garnered increasing attention.However,there is a lack of research on the biological effects and physical mechanisms of GDYprotein interactions at the molecular scale.In this study,the villin headpiece subdomain(HP35)served as a representative protein model.Molecular dynamics simulations were employed to investigate the interaction process between the HP35 protein and GDY,as well as the structural evolution of the protein.The data presented in our study demonstrate that GDY can rapidly adsorb HP35 protein and induce denaturation to one of the a-helix structures of HP35 protein.This implies a potential cytotoxicity concern of GDY for biological systems.Compared to graphene,GDY induced less disruption to HP35 protein.This can be attributed to the presence of natural triangular vacancies in GDY,which prevents p–p stacking action and the limited interaction of GDY with HP35 protein is not conducive to the expansion of protein structures.These findings unveil the biological effects of GDY at the molecular level and provide valuable insights for the application of GDY in biomedicine.

Molecular dynamics simulation of the flow mechanism of shear-thinning fluids in a microchannel

Shear-thinning fluids have been widely used in microfluidic systems,but their internal flow mechanism is still unclear.Therefore,in this paper,molecular dynamics simulations are used to study the laminar flow of shear-thinning fluid in a microchannel.We validated the feasibility of our simulation method by evaluating the mean square displacement and Reynolds number of the solution layers.The results show that the change rule of the fluid system's velocity profile and interaction energy can reflect the shear-thinning characteristics of the fluids.The velocity profile resembles a top-hat shape,intensifying as the fluid's power law index decreases.The interaction energy between the wall and the fluid decreases gradually with increasing velocity,and a high concentration of non-Newtonian fluid reaches a plateau sooner.Moreover,the velocity profile of the fluid is related to the molecule number density distribution and their values are inversely proportional.By analyzing the radial distribution function,we found that the hydrogen bonds between solute and water molecules weaken with the increase in velocity.This observation offers an explanation for the shear-thinning phenomenon of the non-Newtonian flow from a micro perspective.

Temperature effect on nanotwinned Ni under nanoindentation using molecular dynamic simulation

Temperature effect on atomic deformation of nanotwinned Ni (nt-Ni) under localized nanoindentation is investigated in comparison with nanocrystalline Ni (nc-Ni) through molecular simulation.The nt-Ni exhibits enhanced critical load and hardness compared to nc-Ni,where perfect,stair-rod and Shockley dislocations are activated at (111),(111) and (111) slip planes in nt-Ni compared to only SSockley dislocation nucleation at (111) and (111) slip planes of nc-Ni.The nt-Ni exhibits a less significant indentation size effect in comparison with nc-Ni due to the dislocation slips hindrance of the twin boundary.The atomic deformation associated with the indentation size effect is investigated during dislocation transmission.Different from the decreasing partial slips parallel to the indenter surface in nc-Ni with increasing temperature,the temperaturedependent atomic deformation of nt-Ni is closely related to the twin boundary:from the partial slips parallel to the twin boundary (~10 K),to increased confined layer slips and decreased twin migration(300 K–600 K),to decreased confined layer slips and increased dislocation interaction of dislocation pinning and dissociation (900 K–1200 K).Dislocation density and atomic structure types through quantitative analysis are implemented to further reveal the above-mentioned dislocation motion and atomic structure alteration.Our study is helpful for understanding the temperature-dependent plasticity of twin boundary in nanotwinned materials.

Investigation of Projectile Impact Behaviors of Graphene Aerogel Using Molecular Dynamics Simulations

Graphene aerogel(GA),as a novel solid material,has shown great potential in engineering applications due to its unique mechanical properties.In this study,the mechanical performance of GA under high-velocity projectile impacts is thoroughly investigated using full-atomic molecular dynamics(MD)simulations.The study results show that the porous structure and density are key factors determining the mechanical response of GA under impact loading.Specifically,the impact-induced penetration of the projectile leads to the collapse of the pore structure,causing stretching and subsequent rupture of covalent bonds in graphene sheets.Moreover,the effects of temperature on the mechanical performance of GA have been proven to be minimal,thereby highlighting the mechanical stability of GA over a wide range of temperatures.Finally,the energy absorption density(EAD)and energy absorption efficiency(EAE)metrics are adopted to assess the energy absorption capacity of GA during projectile penetration.The research findings of this work demonstrate the significant potential of GA for energy absorption applications.

Temperature-Induced Unfolding Pathway of Staphylococcal Enterotoxin B:Insights from Circular Dichroism and Molecular Dynamics Simulation

In this study,circular dichroism(CD)and molecular dynamics(MD)simulation were used to investigate the thermal unfolding pathway of staphylococcal enterotoxin B(SEB)at temperatures of 298–371 and 298–500 K,and the relationship between the experimental and simulation results were explored.Our computational findings on the secondary structure of SEB showed that at room temperature,the CD spectroscopic results were highly consistent with the MD results.Moreover,under heating conditions,the changing trends of helix,sheet and random coil obtained by CD spectral fitting were highly consistent with those obtained by MD.In order to gain a deeper understanding of the thermal stability mechanism of SEB,the MD trajectories were analyzed in terms of root mean square deviation(RMSD),secondary structure assignment(SSA),radius of gyration(R_(g)),free energy surfaces(FES),solvent-accessible surface area(SASA),hydrogen bonds and salt bridges.The results showed that at low heating temperature,domain Ⅰ without loops(omitting the mobile loop region)mainly relied on hydrophobic interaction to maintain its thermal stability,whereas the thermal stability of domain Ⅱ was mainly controlled by salt bridges and hydrogen bonds.Under high heating temperature conditions,the hydrophobic interactions in domain Ⅰ without loops were destroyed and the secondary structure was almost completely lost,while domain Ⅱ could still rely on salt bridges as molecular staples to barely maintain the stability of the secondary structure.These results help us to understand the thermodynamic and kinetic mechanisms that maintain the thermal stability of SEB at the molecular level,and provide a direction for establishing safer and more effective food sterilization processes.

Study of the Relationship Between New Ionic Interaction Parameters and Salt Solubility in Electrolyte Solutions Based on Molecular Dynamics Simulation

Studying the relationship between ionic interactions and salt solubility in seawater has implications for seawater desalination and mineral extraction.In this paper,a new method of expressing ion-to-ion interaction is proposed by using molecular dynamics simulation,and the relationship between ion-to-ion interaction and salt solubility in a simulated seawater water-salt system is investigated.By analyzing the variation of distance and contact time between ions in an electrolyte solution,from both spatial and temporal perspectives,new parameters were proposed to describe the interaction between ions:interaction distance(ID),and interaction time ratio(ITR).The best correlation between characteristic time ratio and solubility was found for a molar ratio of salt-to-water of 10:100 with a correlation coefficient of 0.96.For the same salt,a positive correlation was found between CTR and the molar ratio of salt and water.For type 1-1,type 2-1,type 1-2,and type 2-2 salts,the correlation coefficients between CTR and solubility were 0.93,0.96,0.92,and 0.98 for a salt-to-water molar ratio of 10:100,respectively.The solubility of multiple salts was predicted by simulations and compared with experimental values,yielding an average relative deviation of 12.4%.The new ion-interaction parameters offer significant advantages in describing strongly correlated and strongly hydrated electrolyte solutions.

Molecular Dynamics Simulation of Shock Response of CL-20 Co-crystals Containing Void Defects

To investigate the effect of void defects on the shock response of hexanitrohexaazaisowurtzitane(CL-20)co-crystals,shock responses of CL-20 co-crystals with energetic materials ligands trinitrotoluene(TNT),1,3-dinitrobenzene(DNB),solvents ligands dimethyl carbonate(DMC) and gamma-butyrolactone(GBL)with void were simulated,using molecular dynamics method and reactive force field.It is found that the CL-20 co-crystals with void defects will form hot spots when impacted,significantly affecting the decomposition of molecules around the void.The degree of molecular fragmentation is relatively low under the reflection velocity of 2 km/s,and the main reactions are the formation of dimer and the shedding of nitro groups.The existence of voids reduces the safety of CL-20 co-crystals,which induced the sensitivity of energetic co-crystals CL-20/TNT and CL-20/DNB to increase more significantly.Detonation has occurred under the reflection velocity of 4 km/s,energetic co-crystals are easier to polymerize than solvent co-crystals,and are not obviously affected by voids.The results show that the energy of the wave decreases after sweeping over the void,which reduces the chemical reaction frequency downstream of the void and affects the detonation performance,especially the solvent co-crystals.

Ab initio molecular dynamics simulation reveals the influence of entropy effect on Co@BEA zeolite-catalyzed dehydrogenation of ethane

The C–H bond activation in alkane dehydrogenation reactions is a key step in determining the reaction rate.To understand the impact of entropy,we performed ab initio static and molecular dynamics free energy simulations of ethane dehydrogenation over Co@BEA zeolite at different temperatures.AIMD simulations showed that a sharp decrease in free energy barrier as temperature increased.Our analysis of the temperature dependence of activation free energies uncovered an unusual entropic effect accompanying the reaction.The unique spatial structures around the Co active site at different temperatures influenced both the extent of charge transfer in the transition state and the arrangement of 3d orbital energy levels.We provided explanations consistent with the principles of thermodynamics and statistical physics.The insights gained at the atomic level have offered a fresh interpretation of the intricate long-range interplay between local chemical reactions and extensive chemical environments.

Molecular dynamics simulation study of nitrogen vacancy color centers prepared by carbon ion implantation into diamond

Nitrogen vacancy(NV)color centers in diamond have useful applications in quantum sensing andfluorescent marking.They can be gen-erated experimentally by ion implantation,femtosecond lasers,and chemical vapor deposition.However,there is a lack of studies of the yield of NV color centers at the atomic scale.In the molecular dynamics simulations described in this paper,NV color centers are pre-pared by ion implantation in diamond with pre-doped nitrogen and subsequent annealing.The differences between the yields of NV color centers produced by implantation of carbon(C)and nitrogen(N)ions,respectively,are investigated.It is found that C-ion implantation gives a greater yield of NV color centers and superior location accuracy.The effects of different pre-doping concentrations(400–1500 ppm)and implantation energies(1.0–3.0 keV)on the NV color center yield are analyzed,and it is shown that a pre-doping concentra-tion of 1000 ppm with 2 keV C-ion implantation can produce a 13%yield of NV color centers after 1600 K annealing for 7.4 ns.Finally,a brief comparison of the NV color center identification methods is presented,and it is found that the error rate of an analysis utiliz-ing the identify diamond structure coordination analysis method is reduced by about 7%compared with conventional identification+methods.

Molecular Dynamics Numerical Simulation of Adsorption Characteristics and Exploitation Limits in Shale Oil Microscopic Pore Spaces

Microscopic pore structure in continental shale oil reservoirs is characterized by small pore throats and complex micro-structures.The adsorption behavior of hydrocarbons on the pore walls exhibits unique physical and chemical properties.Therefore,studying the adsorption morphology of hydrocarbon components in nanometer-sized pores and clarifying the exploitation limits of shale oil at the microscopic level are of great practical significance for the efficient development of continental shale oil.In this study,molecular dynamics simulations were employed to investigate the adsorption characteristics of various single-component shale oils in inorganic quartz fissures,and the influence of pore size and shale oil hydrocarbon composition on the adsorption properties in the pores was analyzed.The results show that different molecules have different adsorption capacities in shale oil pores,with lighter hydrocarbon components(C6H14)exhibiting stronger adsorption abilities.For the same adsorbed molecule,the adsorption amount linearly increases with the increase in pore diameter,but larger pores contribute more to shale oil adsorption.In shale pores,the thickness of the adsorption layer formed by shale oil molecules ranges from 0.4 to 0.5 nm,which is similar to the width of alkane molecules.Shale oil in the adsorbed state that is difficult to be exploited is mainly concentrated in the first adsorption layer.Among them,the volume fraction of adsorbed shale oil in 6 nm shale pores is 40.8%,while the volume fraction of shale oil that is difficult to be exploited is 16.2%.

A Unique Modelling Strategy to Dynamically Simulate the Performance of a Lobe Pump for Industrial Applications

The performance of a newly designed tri-lobe industrial lobe pump of high capacity is simulated by using commercial CFD solver Ansys Fluent. A combination of user-defined-functions and meshing strategies is employed to capture the rotation of the lobes. The numerical model is validated by comparing the simulated results with the literature values. The processes of suction, displacement, compression and exhaust are accurately captured in the transient simulation. The fluid pressure value remains in the range of inlet pressure value till the processes of suction and displacement are over. The instantaneous process of compression is accurately captured in the simulation. The movement of a particular working chamber is traced along the gradual degree of lobe’s rotation. At five different degrees of lobe’s rotation, pressure contour plots are reported which clearly shows the pressure values inside the working chamber. Each pressure value inside the working chamber conforms to the particular process in which the working chamber is operating. Finally, the power requirement at the shaft of rotation is estimated from the simulated values. The estimated value of power requirement is 3.61 BHP FHP whereas the same calculated theoretically is 3 BHP FHP. The discrepancy is attributed to the assumption of symmetry of blower along the thickness.

Exploring the molecular mechanism of action of curcumin for the treatment of diabetic retinopathy,using network pharmacology,molecular docking,and molecular dynamics simulation

Background:Based on network pharmacology and molecular docking,the present study investigated the mechanism of curcumin(CUR)in diabetic retinopathy treatment.Methods:Based on the DisGeNET,Swiss TargetPrediction,GeneCards,Online Mendelian Inheritance in Man,Gene Expression Omnibus,and Comparative Toxicogenomics Database,the intersection core targets of CUR and diabetic retinopathy were identified.The intersection target was imported into the STRING database to obtain the protein-protein interaction map.According to the Database for Annotation,Visualization and Integrated Discovery database,the intersected targets were enriched in Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes pathways.Then Cytoscape 3.9.1 is used to make the drug-target-disease-pathway network.The mechanism of CUR and diabetic retinopathy was further verified by molecular docking and molecular dynamics simulation.Results:There were 203 intersecting targets of CUR and diabetic retinopathy identified.1320 GO entries were enriched for GO functions,which were primarily involved in the composition of cells such as identical protein binding,protein binding,enzyme binding,etc.It was found that 175 pathways were enriched using Kyoto Encyclopedia of Genes and Genomes pathway enrichment methods,which were mainly included in the lipid and atherosclerosis,AGE-RAGE signaling pathway in diabetic complications,pathways in cancer,etc.In the molecular docking analysis,CUR was found to have a good ability to bind to the core targets of albumin,IL-1B,and IL-6.The binding of albumin to CUR was further verified by molecular dynamics simulation.Conclusion:As a result of this study,CUR may exert a role in the treatment of diabetic retinopathy through multi-target and multi-pathway regulation,which indicates a possible direction of future research.

Refinement of Adaptive Dynamical Simulation of Quantum Mechanical Double Slit Interference Phenomenon

We applied adaptive dynamics to double slit interference phenomenon using particle model and obtained partial successful results in our previous report. The patterns qualitatively corresponded well with experiments. Several properties such as concave single slit pattern and large influence of slight displacement of the emission position were different from the experimental results. In this study we tried other slit conditions and obtained consistent patterns with experiments. We do not claim that the adaptive dynamics is the principle of quantum mechanics, but the present results support the probability of adaptive dynamics as the candidate of the basis of quantum mechanics. We discuss the advantages of the adaptive dynamical view for foundations of quantum mechanics.

基于FDS的风扇舱双油池火温度变化特征

航空发动机燃油泄漏形成的油池火威胁发动机运行和飞机安全,为描述风扇舱内油池火复杂的物理传播过程,开展双油池火温度变化特征的研究。首先,基于火灾动力学模拟软件(FDS)建立CFM56-7B发动机风扇舱物理计算模型;然后,比较Trent 800发动机风扇舱单油池火温度计算值与试验值,验证网格独立性;最后,借助探测器和切片分析舱内双油池火的发展过程和温度变化特征。结果表明:双油池火温度在舱内环向上经历增加和振荡准稳态2个变化阶段,其变化幅度与探测器和油池的间距相关;油池火向左偏斜现象导致左半边温度较高;火焰在轴向上经历火羽流上浮、火焰开始融合、融合扩大和完全融合等阶段。

基于FDS的管廊电缆火灾动态风险评估研究

为解决管廊或管沟内的电缆敷设密度较大,发生火灾极易形成电力系统的连锁事故等问题,采用FDS仿真软件,综合考虑传感器、喷淋系统、通风系统和防火门等安全屏障不同响应情况构建管廊电缆火灾动态风险评估模型,并应用Arrhenius公式将数值仿真结果指标映射为电缆火灾风险值,进而绘制时变的电缆火灾风险曲线,探究火灾情景下管廊电缆风险动态评估及应急决策优化方案。研究结果表明:喷淋系统是管廊电缆火灾风险的最关键影响因素,喷淋系统的安装位置以及动作状态在很大程度上影响管廊电缆火灾风险。研究结果可为地下管廊电缆线路典型事故的预防、处理和恢复提供应用价值。

基于FDS的甲醇罐区池火灾事故后果模拟研究

大容量的甲醇罐区在化工生产项目中往往以危险化学品重大危险源的形式存在,是防灭火的重点目标。为了有效选取最佳灭火位置、科学应急处置,通过池火灾模型分析与计算,确定在常年风向一定时,无风、平均风速、中等风速和最大风速四种情况下甲醇储罐区池火灾热辐射强度和范围。文章以徐州某化工厂甲醇罐区为例,利用FDS软件构建火灾模型,分析不同热辐射强度对周围设施的破坏情况,完成热辐射演化三维仿真效果,为最佳灭火位置设置提供建议。

Dynamic analysis of axle box bearings on the high-speed train caused by wheel-rail excitation

To explore the impact of wheel-rail excitation on the dynamic performance of axle box bearings,a dynamic model of the high-speed train including axle box bearings is developed.Subsequently,the dynamic response characteristics of the axle box bearing are examined.The investigation focuses on the acceleration characteristics of bearing vibration under excitation of track irregularities and wheel flats.In addition,experiments on both normal and faulty bearings are conducted separately,and the correctness of the model and some conclusions are verified.According to the research,track irregularity is unfavorable for bearing fault detection based on resonance demodulation.Under the same speed conditions,the acceleration peak of bearing is inversely proportional to the length of the wheel flat and directly proportional to its depth.The paper will contribute to a deeper understanding of the dynamic performance of axle box bearings.

Electronic effects on radiation damage inα-iron:A molecular dynamics study

Iron(Fe)-based alloys,which have been widely used as structural materials in nuclear reactors,can significantly change their microstructure properties and macroscopic properties under high flux neutron irradiation during operation,thus,the problems associated with the safe operation of nuclear reactors have been put forward naturally.In this work,a molecular dynamics simulation approach combined with electronic effects is developed for investigating the primary radiation damage process inα-Fe.Specifically,the influence of electronic effects on the collision cascade in Fe is systematically evaluated based on two commonly used interatomic potentials for Fe.The simulation results reveal that both electronic stopping(ES)and electron-phonon coupling(EPC)can contribute to the decrease of the number of defects in the thermal spike phase.The application of ES reduces the number of residual defects after the cascade evolution,whereas EPC has a reverse effect.The introduction of electronic effects promotes the formation of the dispersive subcascade:ES significantly changes the geometry of the damaged region in the thermal spike phase,whereas EPC mainly reduces the extent of the damaged region.Furthermore,the incorporation of electronic effects effectively mitigates discrepancies in simulation outcomes when using different interatomic potentials.

The Effect of Key Nodes on theMalware Dynamics in the Industrial Control Network

As industrialization and informatization becomemore deeply intertwined,industrial control networks have entered an era of intelligence.The connection between industrial control networks and the external internet is becoming increasingly close,which leads to frequent security accidents.This paper proposes a model for the industrial control network.It includes a malware containment strategy that integrates intrusion detection,quarantine,and monitoring.Basedonthismodel,the role of keynodes in the spreadofmalware is studied,a comparisonexperiment is conducted to validate the impact of the containment strategy.In addition,the dynamic behavior of the model is analyzed,the basic reproduction number is computed,and the disease-free and endemic equilibrium of the model is also obtained by the basic reproduction number.Moreover,through simulation experiments,the effectiveness of the containment strategy is validated,the influence of the relevant parameters is analyzed,and the containment strategy is optimized.In otherwords,selective immunity to key nodes can effectively suppress the spread ofmalware andmaintain the stability of industrial control systems.The earlier the immunization of key nodes,the better.Once the time exceeds the threshold,immunizing key nodes is almost ineffective.The analysis provides a better way to contain the malware in the industrial control network.

Micro defects formation and dynamic response analysis of steel plate of quasi-cracking area subjected to explosive load

As the protective component,steel plate had attracted extensive attention because of frequently threats of explosive loads.In this paper,the evolution of microstructure and the mechanism of damage in the quasi-cracking area of steel plate subjected to explosive load were discussed and the relationships between micro defects and dynamic mechanical response were revealed.After the explosion experiment,five observation points were selected equidistant from the quasi-cracking area of the section of the steel plate along the thickness direction,and the characteristics of micro defects at the observation points were analyzed by optical microscope(OM),scanning electron microscope(SEM) and electron backscattered diffraction(EBSD).The observation result shows that many slip bands(SBs) appeared,and the grain orientation changed obviously in the steel plate,the two were the main damage types of micro defects.In addition,cracks,peeling pits,grooves and other lager micro defects were appeared in the lower area of the plate.The stress parameters of the observation points were obtained through an effective numerical model.The mechanism of damage generation and crack propagation in the quasicracking area were clarified by comparing the specific impulse of each observation point with the corresponding micro defects.The result shows that the generation and expansion of micro defects are related to the stress area(i.e.the upper compression area,the neutral plane area,and the lower tension area).The micro defects gather and expand at the grain boundary,and will become macroscopic damage under the continuous action of tensile stress.Besides,the micro defects at the midpoint of the section of the steel plate in the direction away from the explosion center(i.e.the horizontal direction) were also studied.It was found that the specific impulse at these positions were much smaller than that in the thickness direction,the micro defects were only SBs and a few micro cracks,and the those decreased with the increase of the distance from the explosion center.