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.

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.

Molecular dynamics simulations for the growth of CH_4-CO_2 mixed hydrate

Molecular dynamics simulations are performed to study the growth mechanism of CH4-CO2 mixed hydrate in xco2 = 75%, xco2 = 50%, and zco2 = 25% systems at T = 250 K, 255 K and 260 K, respectively. Our simulation results show that the growth rate of CH4-CO2 mixed hydrate increases as the CO2 concentration in the initial solution phase increases and the temperature decreases. Via hydrate formation, the composition of CO2 in hydrate phase is higher than that in initial solution phase and the encaging capacity of CO2 in hydrates increases with the decrease in temperature. By analysis of the cage occupancy ratio of CH4 molecules and CO2 molecules in large cages to small cages, we find that CO2 molecules are preferably encaged into the large cages of the hydrate crystal as compared with CH4 molecules. Interestingly, CH4 molecules and CO2 molecules frequently replace with each other in some particular cage sites adjacent to hydrate/solution interface during the crystal growth process. These two species of guest molecules eventually act to stabilize the newly formed hydrates, with CO2 molecules occupying large cages and CH4 molecules occupying small cages in hydrate.

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.

MOLECULAR DYNAMICS SIMULATIONS OF FILLED AND EMPTY CAGE-LIKE WATER CLUSTERS IN LIQUID WATER AND THEIR SIGNIFICANCE TO GAS HYDRATE FORMATION MECHANISMS

Molecular dynamics simulations are performed to observe the evolutions of 512 and 51262 cage-like water clusters filled with or without a methane molecule immersed in bulk liquid water at 250 K and 230 K. The lifetimes of these clusters are calculated according to their Lindemann index δ (t) using the criteria of δ≥0.07. For both the filled and empty clusters, we find the dynamics of bulk water determines the lifetimes of cage-like water clusters, and that the lifetime of 512 62 cage-like cluster is the same as that of 512 cage-like cluster. Although the methane molecule indeed makes the filled cage-like cluster more stable than the empty one, the empty cage-like cluster still has chance to be long-lived compared with the filled clusters. These observations support the labile cluster hypothesis on the formation mechanisms of gas hydrates.

Molecular dynamics simulations of the effects of sodium dodecyl sulfate on lipid bilayer

Molecular dynamics simulations have been performed on the fully hydrated lipid bilayer with different concentrations of sodium dodecyl sulfate （SDS）. SDS can readily penetrate into the membrane. The insertion of SDS causes a decrease in the bilayer area and increases in the bilayer thickness and lipid tail order, when the fraction of SDS is less than 28%. Through calculating the binding energy, we confirm that the presence of SDS strengthens the interactions among the DPPC lipids, while SDS molecules act as intermedia. Both the strong hydrophilic interactions between sulfate and phosphocholine groups and the hydrophobic interactions between SDS and DPPC hydrocarbon chains contribute to the tight packing and ordered alignment of the lipids. These results are in good agreement with the experimental observations and provide atomic level information that complements the experiments.

Molecular dynamics simulations of displacement cascades in Fe-10%Cr systems

Molecular dynamics simulations of the displacement cascades in Fe 10%Cr systems are used to sinmlate the primary knocked-on atom events of the irradiation damage at temperatures 300, 600, and 750 K with primary knockedon atom energies between 1 and 15 keV. The results indicate that the vacancies produced by the cascade are all in the central region of the displacement cascade. During the cascade, all recoil Fe and Cr atoms combine with each other to form Fe Cr or Fe Fe interstitial dumbbells as well as interstitial clusters. The number and the size of interstitial clusters increase with the energy of the primary knocked-on atom and the temperature. A few large clusters consist of a large number of lee interstitials with a few Cr atoms, the rest are lee Cr clusters with small and medium sizes. The interstitial dumbbells of Fe lee and Fe-Cr are in the （111）and （110） series directions, respectively.

Multi-scale molecular dynamics simulations and applications on mechanosensitive proteins of integrins

Molecular dynamics simulation(MDS)is a powerful technology for investigating evolution dynamics of target proteins,and it is used widely in various fields from materials to biology.This mini-review introduced the principles,main preforming procedures,and advances of MDS,as well as its applications on the studies of conformational and allosteric dynamics of proteins especially on that of the mechanosensitive integrins.Future perspectives were also proposed.This review could provide clues in understanding the potentiality of MD simulations in structure–function relationship investigation of biological proteins.

Molecular dynamics simulations of A-DNA in bivalent metal ions salt solution

A-form DNA is one of the biologically active double helical structure.The study of A-DNA structure has an extensive application for developing the field of DNA packaging in biotechnology.In aqueous solution,the A-DNA structure will have a free transformation,the A-DNA structure will be translated into B-form structure with the evolution of time,and eventually stabilized in the B-DNA structure.To explore the stability function of the bivalent metal ions on the A-DNA structure,a series of molecular dynamics simulations have been performed on the A-DNA of sequence(CCCGGCCGGG).The results show that bivalent metal ions(Mg^(2+),Zn^(2+),Ca^(2+))generate a great effect on the structural stability of A-DNA in the environment of high concentration.As the interaction between metal ions and electronegative DNA chains,the stability of A-DNA in solution is gradually improved with the increasing solution concentration of ions.In metal salt solution with high concentration,metal ions can be easily distributed in the solvation shells around the phosphate groups and further lead to the formation of shorter and more compact DNA structure.Also,under the condition of the same concentration and valency of the metal ions,the stability of A-DNA structure is different.The calculations indicate that the structure of A-DNA in CaCl_(2)solution is less stable than in MgCl_(2)and ZnCl_(2)solution.

Identification of key residues in protein functional movements by using molecular dynamics simulations combined with a perturbation-response scanning method

The realization of protein functional movement is usually accompanied by specific conformational changes,and there exist some key residues that mediate and control the functional motions of proteins in the allosteric process.In the present work,the perturbation-response scanning method developed by our group was combined with the molecular dynamics(MD)simulation to identify the key residues controlling the functional movement of proteins.In our method,a physical quantity that is directly related to protein specific function was introduced,and then based on the MD simulation trajectories,the perturbation-response scanning method was used to identify the key residues for functional motions,in which the residues that highly correlated with the fluctuation of the function-related quantity were identified as the key residues controlling the specific functional motions of the protein.Two protein systems,i.e.,the heat shock protein 70 and glutamine binding protein,were selected as case studies to validate the effectiveness of our method.Our calculated results are in good agreement with the experimental results.The location of the key residues in the two proteins are similar,indicating the similar mechanisms behind the performance of their biological functions.

Molecular dynamics simulations on the wet/dry self-latching and electric fields triggered wet/dry transitions between nanosheets:A non-volatile memory nanostructure

We design a nanostructure composing of two nanoscale graphene sheets parallelly immersed in water.Using molecular dynamics simulations,we demonstrate that the wet/dry state between the graphene sheets can be self-latched;moreover,the wet→dry/dry→wet transition takes place when applying an external electric field perpendicular/parallel to the graphene sheets(E;/E;).This structure works like a flash memory device(a non-volatile memory):the stored information(wet and dry states)of the system can be kept spontaneously,and can also be rewritten by external electric fields.On the one hand,when the distance between the two nanosheets is close to a certain distance,the free energy barriers for the transitions dry→wet and wet→dry can be quite large.As a result,the wet and dry states are self-latched.On the other hand,an E;and an E;will respectively increase and decrease the free energy of the water located in-between the two nanosheets.Consequently,the wet→dry and dry→wet transitions are observed.Our results may be useful for designing novel information memory devices.

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 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.

Quantitative prediction and ranking of the shock sensitivity ofexplosives via reactive molecular dynamics simulations

A deep understanding of explosive sensitivities and their factors is important for safe and reliable applications.However,quantitative prediction of the sensitivities is difficult.Here,reactive molecular dynamics simulation models for high-speed piston impacts on explosive supercells were established.Simulations were also performed to investigate shock-induced reactions of various high-energy explosives.The fraction of reacted explosive molecules in an initial supercell changed linearly with the propagation distance of the shock-wave front.The corresponding slope could be used as a reaction rate for a specific shock-loading velocity.Reaction rates that varied with the shock-loading pressure exhibited two-stage linearities with different slopes.The two inflection points corresponded to the initial and accelerated reactions,which respectively correlated to the thresholds of shock-induced ignition and detonation.Therefore,the ignition and detonation critical pressures could be determined.The sensitivity could then be a quantitative prediction of the critical pressure.The accuracies of the quantitative shock sensitivity predictions were verified by comparing the impact and shock sensitivities of common explosives and the characteristics of anisotropic shock-induced reactions.Molecular dynamics simulations quantitatively predict and rank shock sensitivities by using only crystal structures of the explosives.Overall,this method will enable the design and safe use of explosives.

MOLECULAR DYNAMICS SIMULATIONS OF DFZ

Dislocation emission from the crack tip in copper under mode II loading is simulated with molecular dynamics method. After 26 partial dislocations are emitted and then relaxed to reach the equilibrium under the constant displacement, the double pile-ups (including an inverse pile-up and a pile-up) are formed. i.e., the first dislocation is piled up before the obstruction, and the last dislocation is piled up ahead of the crack tip. These results conform to the TEM observations.

Molecular dynamics simulations on the dynamics of two-dimensional rounded squares

The collective motion of rounded squares with different comer-roundness ζ is studied by molecular dynamlcs （MD） simulation in this work. Three types of translational collective motion pattern are observed, including＇, gliding, hopping and a mixture of gliding and hopping. Quantitatively, the dynamics of each observed ordered phase is characterized by both mean square displacement and van Hove functions for both translation and rotation. The effect of corner-roundness on the dynamics is further studied by comparing the dynamics of the rhombic crystal phases folmed by different comer-.rounded particles at a same surface fraction. The results show that as ζ increases from 0.286 to 0.667, the translational collective motion of particles changes from a gliding-dominant pattern to a hopping-dominant patte;n, whereas the rotational motion pattern is hopping-like and does not change in its type, but the rotational hopping becomes much more frequent as increases （i.e., as particles become more rounded）. A simple geometrical model is proposed to explain the trend of gliding motion observed in MD simulations.

Processes of DNA condensation induced by multivalent cations: Approximate annealing experiments and molecular dynamics simulations

The condensation of DNA induced by spermine is studied by atomic force microscopy （AFM） and molecular dynamics （MD） simulation in this paper. In our experiments, an equivalent amount of multivalent cations is added to the DNA solutions in different numbers of steps, and we find that the process of DNA condensation strongly depends on the speed of adding cations. That is, the slower the spermine cations are added, the slower the DNA aggregates. The MD and steered molecular dynamics （SMD） simulation results agree well with the experimental results, and the simulation data also show that the more steps of adding multivalent cations there are, the more compact the condensed DNA structure will be. This investigation can help us to control DNA condensation and understand the complicated structures of DNA--cation complexes.

Molecular dynamics simulations of La_2O_3 thin films on SiO_2

Classical molecular dynamics is used to investigate the equilibrium state of the surface region and interface of heteroepitaxial La2O3 thin films.Due to the lattice mismatch,heteroepitaxial thin films are subject to very large stress.For this reason the behavior of La2O3 thin films at SiO2interface becomes an important concern.Our result indicates that La2O3 can uniformly wet SiO2 surface.The properties of the simulated films are analyzed and the lack of any discernible crystalline phase in epitaxial La2O3 on SiO2 indicates that the lattice mismatch between SiO2 and La2O3 is sufficiently large to prevent the formation of even short-range orders in La2O3 film.

Crystallization of amorphous Ni-Zr alloys during heating with molecular dynamics simulations

The heating processes of amorphous NixZr100-x(x=10, 16.7, 33.3) alloys were investigated with molecular dynamics simu- lations. The simulation results show that the crystallization of amorphous alloys during heating is controlled by the heating rate and the alloy’s composition. The slower heating rate depresses the crystallizing temperatures and the melting temperatures of the amor- phous alloys. Crystallization can be eliminated at rapid heating rates, the critical value of which decreases with increasing Ni content of the studied amorphous Ni-Zr alloys. Different crystalline structures formed during crystallizing depend on the heating rate, and the transition between crystalline structures was observed in the heating processes.

Decondensation behavior of DNA chains induced by multivalent cations at high salt concentrations:Molecular dynamics simulations and experiments

Using molecular dynamics simulations and atomic force microscopy （AFM）, we study the decondensation process of DNA chains induced by multivalent cations at high salt concentrations in the presence of short cationic chains in solutions. The typical simulation conformations of DNA chains with varying salt concentrations for multivalent cations imply that the concentration of salt cations and the valence of multivalent cations have a strong influence on the process of DNA decondensation. The DNA chains are condensed in the absence of salt or at low salt concentrations, and the compacted conformations of DNA chains become loose when a number of cations and anions are added into the solution. It is explicitly demonstrated that cations can overcompensate the bare charge of the DNA chains and weaken the attraction interactions between the DNA chains and short cationic chains at high salt concentrations. The condensation-decondensation transi- tions of DNA are also experimentally observed in mixing spermidine with X-phage DNA at different concentrations of NaCl/MgCl2 solutions.