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.

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.

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.

In situ TEM observations and molecular dynamics simulations of deformation defect activities in Mg via nanoindentation

In this work, we performed in situ nanoindentation in TEM to capture the real-time dislocation and twinning activities in pure Mg during loading and unloading. We demonstrated that the screw component of dislocations glides continuously, while the edge components rapidly become sessile during loading. The twin tip propagation is intermittent, whereas the twin boundary migration is more continuous. During unloading, we observed the elastic strain relaxation causes both dislocation retraction and detwinning. Moreover,we note that the plastic zone comprised of dislocations in Mg is well-defined, which contrasts with the diffused plastic zones observed in face-centered cubic metals under the nanoindentation impressions. Additionally, molecular dynamics simulations were performed to study the formation and evolution of deformation-induced crystallographic defects at the early stages of indentation. We observed that,in addition to dislocations, the I1stacking fault bounded with a <1/2c+p> Frank loop can be generated from the plastic zone ahead of the indenter, and potentially serve as a nucleation source for abundant dislocations observed experimentally. These new findings are anticipated to provide new knowledge on the deformation mechanisms of Mg, which are difficult to obtain through conventional ex situ approaches. These observations may serve as a baseline for simulation work that investigate the dynamics of dislocation slip and twinning in Mg and alloys.

Understanding the interfacial behaviors of benzene alkylation with butene using chloroaluminate ionic liquid catalyst: A molecular dynamics simulation

To better understand the benzene alkylation with chloroaluminate ionic liquids(ILs) as catalyst, the interfacial properties between the benzene/butene binary reactants and chloroaluminate ILs with varying cation alkyl chain length and different anions were investigated using molecular dynamics(MD) simulations. The results indicate that ILs can obviously improve the interfacial width, solubility and diffusion of reactants compared to H_(2)SO_(4). The longer alkyl chains of cations present a density enrichment at the interface and protrude into the binary reactants phase. Furthermore, the ILs consisting of 1-octyl-3-methylimidazolium cations([Omim]^(+)) and the stronger acidity heptachlorodialuminate anions([Al_(2)Cl_(7)]^(-)) are more beneficial to promote the interfacial width and facilitate the dissolution and diffusion of benzene in both the IL bulk and the interfacial region in comparison to the ones with shorter alkyl chains cations and weaker acidity anions. The information gives us a better guideline for the design of ILs for benzene alkylation.

Molecular Dynamics Simulation of Interface Properties between Water-Based Inorganic Zinc Silicate Coating Modified by Organosilicone and Iron Substrate

The interface properties of Fe(101)/zinc silicate modified by organo-siloxane(KH-570)was studied by using the method of molecular dynamics simulation.By calculating the temperature and energy fluctuation of equilibrium state,equilibrium concentration distribution,MSD of layer and different groups,and interaction energy of two interface models,the influencing mechanism on the interface properties of adding organosiloxane into coating system was studied at the atomic scale.It shows that the temperature and energy of interface oscillated in a small range and it was exited in a state of dynamic equilibrium within the initial simulation stage(t<20 ps).It can be seen from the multiple peak states of concentration distribution that the iron substrate,organo-siloxane and zinc silicate are distributed in the form of a concentration gradient in the real environment.The rapid diffusion of free zinc powder in zinc silicate coating was the essential reason that affected the comprehensive properties of coating.The interface thickness decreased from 7.45 to 6.82Å,the MSD of free zinc powder was effectively reduced,and the interfacial energy was increased from 104.667 to 347.158 kcal/mol after being modified by organo-siloxane.

Molecular Dynamics Simulation of Hydrate Decomposition Under Action of Alcohol Inhibitors

The molecular dynamics method is used to investigate decomposition of methane hydrate at different temperatures,pressures and concentrations of inhibitor.By analyzing the parameters of system conformation,mean square displacement and radial distribution function,the decomposition of hydrate in the presence of alcohol inhibitors ethylene glycol and glycerol is explored.The results show that the hydroxyl groups in alcohol molecules can destroy the cage structure of hydrate,and form hydrogen bonds with nearby water molecules to effectively prevent the reformation of hydrate.Therefore,ethylene glycol and glycerol serve as inhibitors of methane hydrate,furthermore,in terms of inhibition effect,glycerol is better than ethylene glycol by comparing rate of hydrate decomposition.

Elucidating the molecular targets of Curcuma longa for breast cancer treatment using network pharmacology,molecular docking and molecular dynamics simulation

Background:To elucidate the molecular mechanisms of Curcuma longa(C.longa)in breast cancer treatment.Methods:Phytocompounds of C.longa were obtained from Dr.Duke’s Phytochemical and Ethnobotanical Database.Potential active targets were retrieved from Bindingdb,SEA and Swiss Target Prediction databases.Breast cancer targets were retrieved from the Therapeutic Target Database.Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were done using DAVID and KOBAS3.0 databases respectively.The Cytoscape software was used to construct the phytocompound-target-pathway network.The PyRx and Desmond software were utilized for molecular docking and molecular dynamics simulation respectively.Results:Out of one hundred and fifty-six phytocompounds,fifty-four modulated proteins involved in breast cancer.Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated C.longa exerts its therapeutic effect through regulating several key pathways.Molecular docking analysis revealed that most phytocompounds of C.longa had a good affinity with the key targets.Molecular dynamics simulation showed that ethinylestradiol formed stable ligand-protein complexes.Conclusion:The results of this study will enhance our understanding of the potential molecular mechanisms by which C.longa inhibits breast cancer and lay a foundation for future experimental studies.

Exploring unbinding mechanism of drugs from SERT via molecular dynamics simulation and its implication in antidepressants

The human serotonin transporter(SERT)terminates neurotransmission by removing serotonin from the synaptic cleft,which is an essential process that plays an important role in depression.In addition to natural substrate serotonin,SERT is also the target of the abused drug cocaine and,clinically used antidepressants,escitalopram,and paroxetine.To date,few studies have attempted to investigate the unbinding mechanism underlying the orthosteric and allosteric modulation of SERT.In this article,the conserved property of the orthosteric and allosteric sites(S1 and S2)of SERT was revealed by combining the high resolutions of x-ray crystal structures and molecular dynamics(MD)simulations.The residues Tyr95 and Ser438 located within the S1 site,and Arg104 located within the S2 site in SERT illustrate conserved interactions(hydrogen bonds and hydrophobic interactions),as responses to selective serotonin reuptake inhibitors.Van der Waals interactions were keys to designing effective drugs inhibiting SERT and further,electrostatic interactions highlighted escitalopram as a potent antidepressant.We found that cocaine,escitalopram,and paroxetine,whether the S1 site or the S2 site,were more competitive.According to this potential of mean force(PMF)simulations,the new insights reveal the principles of competitive inhibitors that lengths of trails from central SERT to an opening were~18A for serotonin and~22 A for the above-mentioned three drugs.Furthermore,the distance between the natural substrate serotonin and cocaine(or escitalopram)at the allosteric site was~3A.Thus,it can be inferred that the potent antidepressants tended to bind at deeper positions of the S1 or the S2 site of SERT in comparison to the substrate.Continuing exploring the processes of unbinding four ligands against the two target pockets of SERT,this study observed a broad pathway in which serotonin,cocaine,escitalopram(at the S1 site),and paroxetine all were pulled out to an opening between MT1b and MT6a,which may be helpful to understand the dissociation mechanism of antidepressants.

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.

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.

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.

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.

Molecular Dynamics Simulations of the Interactions between Konjac Glucomannan and Carrageenan

The interactions between konjac glucomannan and carrageenan were studied with the method of molecular dynamics simulation. Part representative structure segments of KGM and two unit structures of κ-carrageenan （Fig. 2） were used as mode, and the force-field was AMBER2. The stability and sites of konjac glucomannan/carrageenan interactions in water were researched at 373 K with the following results： the potential energy （EPOT） of the mixed gel was dropped, while those of single-konjac glucomannan gel and single carrageenan were increased. The surface area （SA） of KGM in the mixed system was decreased to 1002.2A^°^2, and that of carrageenan to 800.9 A^°^2. The variations of two parameters showed that the stability of compound gel konjac glucomannan/carrageenan was improved, which is consistent with the previous studies. The sites of interactions in the mixed gel were the -OH groups on C（2）, C（4） and C（6）, the acetyl group in KGM mannose, and the -OH group on C（6） in carrageenan. 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 dynamics simulation of peeling a DNA molecule on substrate

Molecular dynamics （MD） simulations are performed to study adhesion and peeling of a short fragment of single strand DNA （ssDNA） molecule from a graphite surface. The critical peel-off force is found to depend on both the peeling angle and the elasticity of ssDNA. For the short ssDNA strand under investigation, we show that the simulation results can be explained by a continuum model of an adhesive elastic band on substrate. The analysis suggests that it is often the peak value, rather than the mean value, of adhesion energy which determines the peeling of a nanoscale material.

Swelling of K＋, Na＋ and Ca2＋-montmorillonites and hydration of interlayer cations： a molecular dynamics simulation

This paper performs molecular dynamics simulations to investigate the role of the monovalent cations K, Na and the divalent cation Ca on the stability and swelling of montmorillonite. The recently developed CLAYFF force field is used to predict the basal spacing as a function of the water content in the interlayer. The simulations reproduced the swelling pattern of these montmorillonites, suggesting a mechanism of their hydration different （K＋ 〈 Na＋ 〈 Ca2＋） from that of K＋-, Na＋-, and Ca2＋-montmorillonites. In particular, these results indicate that the valence of the cations has the larger impact on the behaviour of clay water systems. It also finds that the differences in size and hydration energy of K＋, Na＋ and Ca2＋ ions have strong implications for the structure of interlayer. This leads to the differences in the layer spacings of the simulated K＋-, Na＋-, and Ca2＋-montmorillonites. Furthermore, these simulations show that the K cations interact strongly with the clay sheets for the dehydrated clay sheets, but for the hydrated clays the Ca cations interact clearly strongly with the clay sheets.

Protein conformation and electric attraction adsorption mechanisms on anodized magnesium alloy by molecular dynamics simulations

Protein adsorption preferentially occurs and significantly affects the physicochemical reactions once the biodegradable magnesium alloys as bone replacements have been implanted. To date, interactions mechanisms between Mg implants and proteins remain unclear at a molecular level. Thereby, a combination of molecular dynamic(MD) simulations and experimental exploration is used to investigate the adsorption behavior and conformational change of bovine serum albumin(BSA), a representative protein of blood plasma, upon the surface of microarc oxidation(MAO) coated Mg alloy AZ31. The influences of absorbed proteins on the cytocompatibility of MAO coating are evaluated by virtue of cytotoxicity assay. Results indicate that the negatively charged O atoms(BSA) exhibit strong interaction with Mg^(2+) ions of Mg(OH)_(2), revealing that BSA molecules are ionically adsorbed on the AZ31 surface. Interestingly, MD simulation reveals that MAO coating demonstrates superior ability to capture BSA molecules during the process of adsorption owing to strong electric attraction between the negatively charged O atoms in BSA molecules with Mg atoms of MgO in MAO coating. Moreover, the α-helix part of absorbed BSA molecules on AZ31 substrate and MAO coating markedly decreases with an increase in β-sheet, β-turn and unordered contents, which is attributed to the reduction in the number of hydrogen bonds in BSA molecules. Furthermore, the adsorbed BSA molecules improve the cytocompatibility of MAO coating since the positively charged-NH_(3)^(+) group and β-sheet content of absorbed BSA molecules mediate the cell adhesion by interacting with the negatively charged cell membrane.