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.

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.

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.

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.

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.

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.

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.

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.

Dynamics simulation of tertiary amines adsorbing on kaolinite(001) plane

The collecting power of tertiary amines（DRN,DEN and DPN） on kaolinite follows the order of DENDPNDRN.After reacting with DRN,DEN and DPN,the surface potentials of kaolinite increase remarkably,and the recruitments caused by collectors also follow the order of DENDPNDRN.The results of dynamics simulation show that the geometries of substituent groups bonding to N are deflected and twisted,and some of bond angles are changed when tertiary amines cations adsorb on kaolinite（001） surface.Based on the results of dynamics simulations and quantum chemistry calculations,the electrostatic forces between three tertiary amines cations and 4×4×3（001） plane of kaolinite are 1.38×10？7 N（DRN12H＋）,1.44×10-6 N（DEN12H＋）,1.383×10-6 N（DPN12H＋）,respectively.

Molecular dynamics simulation of relationship between local structure and dynamics during glass transition of Mg_7Zn_3 alloy

The rapid solidification process of Mg7Zn3 alloy was simulated by the molecular dynamics method. The relationship between the local structure and the dynamics during the liquid-glass transition was deeply investigated. It was found that the Mg-centered FK polyhedron and the Zn-centered icosahedron play a critical role in the formation of Mg7Zn3 metallic glass. The self-diffusion coefficients of Mg and Zn atoms deviate from the Arrhenius law near the melting temperature and then satisfy the power law. According to the time correlation functions of mean-square displacement, incoherent intermediate scattering function and non-Gaussian parameter, it was found that the β-relaxation in Mg7Zn3 supercooled liquid becomes more and more evident with decreasing temperature, and the α-relaxation time rapidly increases in the VFT law. Moreover, the smaller Zn atom has a faster relaxation behavior than the Mg atom. Some local atomic structures with short-range order have lower mobility, and they play a critical role in the appearance of cage effect in theβ-relaxation regime. The dynamics deviates from the Arrhenius law just at the temperature as the number of local atomic structures begins to rapidly increase. The dynamic glass transition temperature （Tc） is close to the glass transition point in structure （TgStr）.

Molecular dynamics simulation of ion transportation through graphene nanochannels

The model of ion transportation through graphene nanochannels is established by the molecular dynamics simulation method. Statistics of the electric potential and charge distribution are made, respectively, on both sides of graphene nanopore with various diameters. Then, their changing relationship with respect to the nanopore diameter is determined. When applying a uniform electric field, polar water molecules are rearranged so that the corresponding relationship between the polarized degree of these molecules and the nanopore diameter can be created. Based on the theoretical model of ion transportation through nanochannels,the changing relationship between the concentration of anions/cations in nanochannels and bulk solution concentration is quantitatively analyzed. The results show that the increase of potential drop and charge accumulation, as well as a more obvious water polarization, will occur with the decrease of nanopore diameter. In addition, hydrogen ion concentration has a large proportion in nanochannels with a sodium chloride（NaCl） solution at a relative low concentration. As the NaCl concentration increases, the concentration appreciation of sodium ions tends to be far greater than the concentration drop of chloride ions. Therefore, sodium ion concentration makes more contribution to ionic conductance.

Local structure of calcium silicate melts from classical molecular dynamics simulation and a newly constructed thermodynamic model

The distributions of local structural units of calcium silicate melts were quantified by means of classical molecular dynamics simulation and a newly constructed structural thermodynamic model. The distribution of five kinds of Si-O tetrahedra Qi from these two methods was compared with each other and also with the experimental Raman spectra, an excellent agreement was achieved. These not only displayed the panorama distribution of microstructural units in the whole composition range, but also proved that the thermodynamic model is suitable for the utilization as the subsequent application model of spectral experiments for the thermodynamic calculation. Meanwhile, the five refined regions mastered by different disproportionating reactions were obtained. Finally, the distributions of two kinds of connections between Qi were obtained, denoted as Qi-Ca-Qj and Qi-[Ob]-Qj, from the thermodynamic model, and a theoretical verification was given that the dominant connections for any composition are equivalent connections.

Molecular Dynamics Simulations for Melting Temperatures of SrF2 and BaF2

The shell-model molecular dynamics method was applied to simulate the melting temper- atures of SrF2 and BaF2 at elevated temperatures and high pressures. The same method was used to calculate the equations of state for SrF2 and BaF2 over the pressure range of 0.1 MPa-3 GPa and 0.1 MPa-7 GPa. Compared with previous results for equations of state, the maximum errors are 0.3% and 2.2%, respectively. Considering the pre-melting in the fluorite-type crystals, we made the necessary corrections for the simulated melting temper- atures of SrF2 and BaF2. Consequently, the melting temperatures of SrF2 and BaF2 were obtained for high pressures. The melting temperatures of SrF2 and BaF2 that were obtained by the simulation are in good agreement with available experimental data.

Melting Behaviour of Shell-symmetric Aluminum Nanoparticles： Molecular Dynamics Simulation

Molecular dynamics simulations with embedded atom method potential were carried out for A1 nanoparticles of 561 atoms in three structures： icosahedron, decahedron, and truncated octahedron. The total potential energy and specific heat capacity were calculated to estimate the melting temperatures. The melting point is 540＋10 K for the icosahedral structure, 500±10 K for the decahedral structure, and 520±10 K for the truncated octahedral structure. With the results of mean square displacement, the bond order parameters and radius of gyration are consistent with the variation of total potential energy and specific heat capacity. The relaxation time and stretching parameters in the Kohlraush-William-Watts relaxation law were obtained by fitting the mean square displacement. The results show that the relationship between the relaxation time and the temperatures is in agreement with standard Arrhenius relation in the high temperature range.

High density gas state at water/graphite interface studied by molecular dynamics simulation

In this paper molecular dynamics simulations are performed to study the accumulation behaviour of N2 and H2 at water/graphite interface under ambient temperature and pressure. It finds that both N2 and H2 molecules can accumulate at the interface and form one of two states according to the ratio of gas molecules number to square of graphite surface from our simulation results： gas films （pancake-like） for a larger ratio and nanobubbles for a smaller ratio. In addition, we discuss the stabilities of nanobubbles at different environment temperatures. Surprisingly, it is found that the density of both kinds of gas states can be greatly increased, even comparable with that of the liquid N2 and liquid H2. The present results are expected to be helpful for the understanding of the stable existence of gas film （pancake-like） and nanobubbles.

Insight into the topology effect on the diffusion of ethene and propene in zeolites: A molecular dynamics simulation study

Selectivity control is a difficult scientific and industrial challenge in methanol-to-olefins(MTO)conversion.It has been experimentally established that the topology of zeolite catalysts influenced the distribution of products.Besides the topology effect on reaction kinetics,the topology influences the diffusion of reactants and products in catalysts as well.In this work,by using COMPASS force-field molecular dynamics method,we investigated the intracrystalline diffusion of ethene and propene in four different zeolites,CHA,MFI,BEA and FAU,at different temperatures.The self-diffusion coefficients and diffusion activation barriers were calculated.A strong restriction on the diffusion of propene in CHA was observed because the self-diffusion coefficient ratio of ethene to propene is larger than 18 and the diffusion activation barrier of propene is more than 20 kJ/mol in CHA.This ratio decreases with the increase of temperature in the four investigated zeolites.The shape selectivity on products from diffusion perspective can provide some implications on the understanding of the selectivity difference between HSAPO-34 and HZSM-5 catalysts for the MTO conversion.

Molecular Dynamics Simulations of the Interactions Between Konjac Glucomannan and Soy Protein Isolate

The interactions between konjac glucomannan（KGM） and soy protein isolate （SPI） were studied with the method of molecular dynamics simulation. Part representative structures segments of KGM and SPI were used as mode, and the force-field was FF03. The stability and sites of KGM/SPI interactions in water were researched at 363 K with the following results： the potential energy （EPOT） of the mixed gel dropped, while that of single KGM gel increased. The surface area （SA） of KGM in the mixed system was decreased to 401.41 from 1 267.54 Az, and that of SPI to 484.94 from 1 943.28 A2. The sum potential energy of KGM and soy protein in the mixed system was decreased to -13 402.41 from -5 768.56 kcal mol^-1. The variations of two parameters showed that the stability of compound gel KGM/SPI was improved, which was consistent with the previous studies. The sites of interactions in the mixed gel were the -OH groups on C（2） in KGM mannose and glucose, and the amide linkage group on Histidine, Asparagine and Leucine in SPI. The hydrogen bond was formed directly or indirectly by the bridge of waters.

A possible therapeutic potential of quercetin through inhibition of μ-calpain in hypoxia induced neuronal injury:a molecular dynamics simulation study

The neuroprotective property of quercetin is well reported against hypoxia and ischemia in past studies.This property of quercetin lies in its antioxidant property with blood-brain barrier permeability and anti-inflammatory capabilities.μ-Calpain,a calcium ion activated intracellular cysteine protease causes serious cellular insult,leading to cell death in various pathological conditions including hypoxia and ischemic stroke.Hence,it may be considered as a potential drug target for the treatment of hypoxia induced neuronal injury.As the inhibitory property of μ-calpain is yet to be explored in details,hence,in the present study,we investigated the interaction of quercetin with μ-calpain through a molecular dynamics simulation study as a tool through clarifying the molecular mechanism of such inhibition and determining the probable sites and modes of quercetin interaction with the μ-calpain catalytic domain.In addition,we also investigated the structure-activity relationship of quercetin with μ-calpain.Affinity binding of quercetin with μ-calpain had a value of –28.73 k J/mol and a Ki value of 35.87 μM that may be a probable reason to lead to altered functioning of μ-calpain.Hence,quercetin was found to be an inhibitor of μ-calpain which might have a possible therapeutic role in hypoxic injury.

Molecular mechanics and dynamics simulation of hydrogen diffusion in aluminum melt

The main impurities in aluminum melt are hydrogen and Al_2O_3,which can deteriorate melt quality and materials performance.However,the diffusion process of H atoms in aluminum melt and the interactions among Al atoms,Al_2O_3 and hydrogen have been studied rarely.Molecular mechanics and dynamics simulations are employed to study the diffusion behaviors of different types of hydrogen,such as free H atoms,H atoms in H_2 and H^+ions in H_2O using COMPASS force field.Correspondingly,force field types h,h1h and h1o are used to describe different types of hydrogen which are labeled as H_h,H_(h1h) and H_(h1o).The results show that the adsorption areas are maximum for H_(h1o),followed by H_(h1h) and H_h.The diffusion ability of H_(h1o) is the strongest whereas H_h is hard to diffuse in aluminum melt because of the differences in radius and potential well depth of various types of hydrogen.Al_2O_3 cluster makes the Al atoms array disordered,creating the energy conditions for hydrogen diffusion in aluminum melt.Al_2O_3 improves the diffusion of H_h and H_(h1o),and constrains H_(h1h) which accumulates around it and forms gas porosities in aluminum.H_(h1o) is the most dispersive in aluminum melt,moreover,the distance of Al-H_(h1o) is shorter than that of Al-H_(h1h),both of which are detrimental to the removal of H_(h1o).The simulation results indicate that the gas porosities can be eliminated by the removal of Al_2O_3 inclusions,and the dispersive hydrogen can be removed by adsorption function of gas bubbles or molten fluxes.