Dynamic simulations of the late MIS 3 transgressions in the East China Sea and southern Yellow Sea,China

Abundant evidences of higher sea levels from Jiangsu and Fujian coasts have proved a marine transgression event during 30–40 ka BP, suggesting that there was a stage with high sea level and a warm climate when ice sheets shrank in the Northern Hemisphere. The duration of 30–40 ka BP spanned a period in the late Marine Isotope Stage 3（MIS 3） and was in nature an interstadial epoch during the Last Glacial period of the Quaternary. Different from the glacial period with a cold climate, this marine transgression considered as a penultimate higher sea level during the Quaternary remains a puzzle that why the evidence is contrary to the Quaternary glacial theory. It is important to understand sea level rise for these areas sensitively responding to the global changes in the future. To recognize the key issues on sea level changes, the eustatic sea level（H_S） was defined as the glaciation-climateforced sea levels, and the relative sea level change（H_R） was defined as that a sea level record was preserved in sediment that experienced multiple secondary actions of land and sea effects. On the basis as defined above, we constructed multi-level models of climate-driven glacio-eustatic changes and land-sea systems. By integrating data sets from eight borehole cores and prescribing the boundary conditions, we simulated the changes of HS and HR in the East China Sea and southern Yellow Sea areas in the late MIS 3. The marine transgression strata from the borehole core data was identified at ca. 30 m below present sea level as a result of the collective influence of ice melting water, neotectonic subsidence, sediment compaction and terrestrial sediment filling since ca. 35 ka ago,whereas the simulated relative sea-levels turned out to be –26.3––29.9 m a.s.l. The small error involved in the simulation results of ±（2.5–4.5） m demonstrated the credibility of the results. Our results indicated that sea level change in the late MIS 3 was dominated by glacial effects, in which the eustatic sea-level was between –19.2––22.1m a.s.l. The study sheds light on the nature of sea-level changes along the east coast of China in the late MIS 3 and contributes to understanding the characteristics of marine transgression under the effects of multiple complex land-sea interactions.

Inhibition Mechanism of Hydroxyproline-like Small Inhibitors to Disorder HIF-VHL Interaction by Molecular Dynamic Simulations and Binding Free Energy Calculations

Protein-protein interactions are vital for a wide range of biological processes.The interactions between the hypoxia-inducible factor and von Hippel Lindau(VHL)are attractive drug targets for ischemic heart disease.In order to disrupt this interaction,the strategy to target VHL binding site using a hydroxyproline-like(pro-like)small molecule has been reported.In this study,we focused on the inhibition mechanism between the pro-like inhibitors and the VHL protein,which were investigated via molecular dynamics simulations and binding free energy calculations.It was found that pro-like inhibitors showed a strong binding affinity toward VHL.Binding free energy calculations and free energy decompositions suggested that the modification of various regions of pro-like inhibitors may provide useful information for future drug design.

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.

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.

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.

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.

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.

Mean Residence Time of CO2 Molecules in Flexible ZIF-8 Cages Explored by Molecular Dynamics Simulations

The adsorption sites and diffusion mechanism of CO2 molecules in the flexible Zn（MeIM）2 （MeIM=2-methylimidazole） （ZIF-8） have been investigated by grand canonical Monte Carlo and molecular dynamics simulations. A reasonable time correlation function is for the first time constructed to explore the mean residence time of CO2 molecules in the ZIF-8 cages, suggesting that C02 molecules can remain in the same cage for up to several tens of picoseconds. Furthermore, we find that the mean residence time almost linearly increases with the increasing pressure （or loading） at 273 and 298 K.

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.

COMPUTATIONAL FLUID DYNAMICS(CFD) SIMULATIONS OF DRAG REDUCTION WITH PERIODIC MICRO-STRUCTURED WALL

Computational fluid dynamics（CFD） simulations are adopted to investigate rectangular microchannel flows with various periodic micro-structured wall by introducing velocity slip boundary condition at low Reynolds number. The purpose of the current study is to numerically find out the effects of periodic micro-structured wall on the flow resistance in rectangular microchannel with the different spacings between microridges ranging from 15 to 60 pm. The simulative results indicate that pressure drop with different spacing between microridges increases linearly with flow velocity and decreases monotonically with slip velocity; Pressure drop reduction also increases with the spacing between microridges at the same condition of slip velocity and flow velocity. The results of numerical simulation are compared with theoretical predictions and experimental results in the literatures. It is found that there is qualitative agreement between them.

Exploring the moderating role of financial development in environmental Kuznets curve for South Africa:fresh evidence from the novel dynamic ARDL simulations approach

The extant literature has produced mixed evidence on the relationship between finan-cial development and ecological sustainability.This work addresses this conundrum by investigating financial development’s direct and indirect consequences on ecologi-cal quality utilizing the environmental Kuznets curve(EKC)methodological approach.Our empirical analysis is based on the novel dynamic autoregressive distributed lag simulations approach for South Africa between 1960 and 2020.The results,which used five distinct financial development measures,demonstrate that financial develop-ment boosts ecological integrity and environmental sustainability over the long and short terms.In the instance of South Africa,we additionally confirm the validity of the EKC theory.More importantly,the outcomes of the indirect channels demonstrate that financial development increases energy usage’s role in causing pollution while attenuating the detrimental impacts of economic growth,trade openness,and foreign direct investment on ecological quality.Moreover,the presence of an inadequate financial system is a requirement for the basis of the pollution haven hypothesis(PHH),which we examine using trade openness and foreign direct investment variables.PHH for both of these variables disappears when financial development crosses specified thresholds.Finally,industrial value addition destroys ecological quality while tech-nological innovation enhances it.This research provides some crucial policy recom-mendations and fresh perspectives for South Africa as it develops national initiatives to support ecological sustainability and reach its net zero emissions goal.

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.

Dynamic Simulations of Post-stall Performance in Multistage Axial Compressors

In this contribution a quasi-one-dimensional tool for stationary and transient simulations of post-stall flows in multistage axial compressors is presented. An adapted version of the 1D Euler equations with additional source terms is discretized with a finite volume method and solved in time by a fourth-order Runge-Kutta scheme. The equations are discretized at midspan both inside the blade rows and the non-bladed regions. The source terms express the blade-flow interactions and are estimated by calculating the velocity triangles for each blade row. Loss and deviation correlations are implemented and compared to experimental data in normal flow, stalled flow and reversed flow regions. Transient simulations are carried out and a parameter study is presented to analyze the shape of the surge cycles and the frequency of the surge oscillations. At last, a bleeding control strategy is implemented to study the recoverability of the instabilities in a compression system.

Effects of tensile temperatures on phase transformations in zirconium by molecular dynamics simulations

The effects of tensile temperatures ranging from 100 K to 900 K on the phase transition of hexagonal close-packed(HCP)zirconium were investigated by molecular dynamics simulations,which were combined with experimental observation under high resolution transmission electron microscopy.The results show that externally applied loading first induced the HCP to body-centered cubic(BCC)phase transition in the Pitsch-Schrader(PS)orientation relationship(OR).Then,the face-centered cubic(FCC)structure transformed from the BCC phase in the Bain path.However,the HCP-to-BCC transition was incomplete at 100 K and 300 K,resulting in a prismatic-type OR between the FCC and original HCP phase.Additionally,at the temperature ranging from 100 K to 600 K,the inverse BCC-to-HCP transition occurred locally following other variants of the PS OR,resulting in a basal-type relation between the newly generated HCP and FCC phases.A higher tensile temperature promoted the amount of FCC phase transforming into the BCC phase when the strain exceeded 45%.Besides,the crystal stretched at lower temperatures exhibits relatively higher strength but by the compromise of plasticity.This study reveals the deformation mechanisms in HCP-Zr at different temperatures,which may provide a better understanding of the deformation mechanism of zirconium alloys under different application environments.

Understanding sequence effect in DNA bending elasticity by molecular dynamic simulations

Structural elasticity of double-strand DNAs is very important for their biological functions such as DNA-ligand binding and DNA-protein recognition.By all-atom molecular dynamics simulations,we investigated the bending elasticity of DNA with three typical sequences including poly(A)-poly(T)(AA-TT),poly(AT)-poly(TA)(AT-TA),and a generic sequence(GENE).Our calculations indicate that,AA-TT has an apparently larger bending persistence length(P~63 nm)than GENE(P~49 nm)and AT-TA(P~48 nm)while the persistence length of AT-TA is only very slightly smaller than that of GENE,which agrees well with those from existing works.Moreover,through extensive electrostatic calculations,we found that the sequence-dependent bending elasticity is attributed to the sequence-dependent electrostatic bending energy for AA-TT,AT-TA and GENE,which is coupled to their backbone structures.Particularly,the apparently stronger bending stiffness of AA-TT is attributed to its narrower minor groove.Interestingly,for the three DNAs,we predicted the non-electrostatic persistence length of~17 nm,thus electrostatic interaction makes the major contribution to DNA bending elasticity.The mechanism of electrostatic energy dominating sequence effect in DNA bending elasticity is furtherly illustrated through the electrostatic calculations for a grooved coarse-grained DNA model where minor groove width and other microscopic structural parameters can be artificially adjusted.

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.

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.