In-situ TEM observation was conducted during Ni^(+)&He^(+)dual-beam irradiation to monitor the evolution of dislocation loops accompanied by He bubbles in the Ni-based alloy GH3535.Two distinct evolutions of dislo...In-situ TEM observation was conducted during Ni^(+)&He^(+)dual-beam irradiation to monitor the evolution of dislocation loops accompanied by He bubbles in the Ni-based alloy GH3535.Two distinct evolutions of dislocation loops,driven by residual stresses,were observed within the monitored grains.Hence,molec-ular dynamics(MD)simulations were employed to reveal the effects of stress magnitude and direction on loop evolution,including size,number density,type and variation.The simulations revealed that the presence of compressive stress reduced the formation energy of perfect dislocation loops,thus promoting their formation.Stress state was found to influence the preferential orientation of the loops,and com-pressive stress resulted in a decreased number density of dislocation loops but an increase in their size.This establishes a clear relationship between stress state and magnitude and the evolution of dislocation loops during ion beam irradiation.Additionally,the nature and characteristics of dislocation loops were quantified to explore the effects of He concentrations on their evolution.The higher He concentration not only promotes the nucleation of dislocation loops,leading to their higher number density,but also facil-itates the unfaulting evolution by increasing the stacking fault energy(SFE).Moreover,the accumulation of He in the lower-He-concentration sample led to the growth of dislocation loops in multiple stages,explaining their nearly identical average sizes when compared to the higher-He-concentration sample.展开更多
The binding of Endonuclease colicin 9 (E9) by Immunity protein 9 (Im9) was found to involve some hotspots from helix III of Im9 on protein-protein interface that contribute the dominant binding energy to the complex.I...The binding of Endonuclease colicin 9 (E9) by Immunity protein 9 (Im9) was found to involve some hotspots from helix III of Im9 on protein-protein interface that contribute the dominant binding energy to the complex.In the current work,MD simulations of the WT and three hotspot mutants (D51A,Y54A and Y55A of Im9) of the E9-Im9 complexes were carried out to investigate specific interaction mechanisms of these three hotspot residues.The changes of binding energy between the WT and mutants of the complex were computed by the MM/PBSA method using a polarized force field and were in excellent agreement with experiment values,verifying that these three residues were indeed hotspots of the binding complex.Energy decomposition analysis revealed that binding by D51 to E9 was dominated by electrostatic interaction due to the presence of the carboxyl group of Asp51 which hydrogen bonds to K89.For binding by hotspots Y54 and Y55,van der Waals interaction from the aromatic side chain of tyrosine provided the dominant interaction.For comparison,calculation by using the standard (nonpolarizable) AMBER99SB force field produced binding energy changes from these mutations in opposite direction to the experimental observation.Dynamic hydrogen bond analysis showed that conformations sampled from MD simulation in the standard AMBER force field were distorted from the native state and they disrupted the inter-protein hydrogen bond network of the protein-protein complex.The current work further demonstrated that electrostatic polarization plays a critical role in modulating protein-protein binding.展开更多
HDAC8 is an important target for the treatment of many cancers and other diseases. To develop potent and selective HDAC8 inhibitors, molecular docking and molecular dynamics(MD) simulations were employed for investiga...HDAC8 is an important target for the treatment of many cancers and other diseases. To develop potent and selective HDAC8 inhibitors, molecular docking and molecular dynamics(MD) simulations were employed for investigation of the mechanism of HDAC8 inhibitions containing hydroxamic acid group. Compound 1 with high activity and compound 2 with low activity were selected for comparative study. Compound 1 formed a stronger chelation with Zn ion and was more stable in the HDAC8 pocket than compound 2. Residues HIS-180, ASP-178, ASP-267, and GLY-140 played a critical role in securing the position of compound 1. Both the head and tail of compound 1 formed strong hydrogen bonds with ASP-178, facilitating the ZBG of compound 1 close to the Zn ion so that they formed permanent chelation during the simulation period. The Cap group of the compounds with branch and long chains was advantageous to form interaction with active pocket opening. What’s more, based on the results of this study, three innovative recommendations for the design of highly active HDAC8 inhibitors were presented, which will be useful for the development of new HDAC8 inhibitors.展开更多
LiNO_(3) is known to significantly enhance the reversibility of lithium metal batteries;however,the modification of solvation structures in various solvents and its further impact on the interface have not been fully ...LiNO_(3) is known to significantly enhance the reversibility of lithium metal batteries;however,the modification of solvation structures in various solvents and its further impact on the interface have not been fully revealed.Herein,we systematically studied the evolution of solvation structures with increasing LiNO_(3) concentration in both carbonate and ether electrolytes.The results from molecular dynamics simulations unveil that the Li^(+)solvation structure is less affected in carbonate electrolytes,while in ether electrolytes,there is a significant decrease of solvent molecules in Li^(+)coordination,and a larger average size of Li^(+)solvation structure emerges as LiNO_(3) concentration increases.Notably,the formation of large ion aggregates with size of several nanometers(nano-clusters),is observed in ether-based electrolytes at conventional Li^(+)concentration(1 M)with higher NO_(3)^(-) ratio,which is further proved by infrared spectroscopy and small-angle X-ray scattering experiments.The nano-clusters with abundant anions are endowed with a narrow energy gap of molecular orbitals,contributing to the formation of an inorganic rich electrode/electrolyte interphase that enhances the reversibility of lithium stripping/plating with Coulombic efficiency up to 99.71%.The discovery of nano-clusters elucidates the underlying mechanism linking ions/solvent aggregation states of electrolytes to interfacial stability in advanced battery systems.展开更多
The identification and optimization of mutations in nanobodies are crucial for enhancing their thera-peutic potential in disease prevention and control.However,this process is often complex and time-consuming,which li...The identification and optimization of mutations in nanobodies are crucial for enhancing their thera-peutic potential in disease prevention and control.However,this process is often complex and time-consuming,which limit its widespread application in practice.In this study,we developed a work-flow,named Evolutionary-Nanobody(EvoNB),to predict key mutation sites of nanobodies by combining protein language models(PLMs)and molecular dynamic(MD)simulations.By fine-tuning the ESM2 model on a large-scale nanobody dataset,the ability of EvoNB to capture specific sequence features of nanobodies was significantly enhanced.The fine-tuned EvoNB model demonstrated higher predictive accuracy in the conserved framework and highly variable complementarity-determining regions of nanobodies.Additionally,we selected four widely representative nanobodyeantigen complexes to verify the predicted effects of mutations.MD simulations analyzed the energy changes caused by these mu-tations to predict their impact on binding affinity to the targets.The results showed that multiple mu-tations screened by EvoNB significantly enhanced the binding affinity between nanobody and its target,further validating the potential of this workflow for designing and optimizing nanobody mutations.Additionally,sequence-based predictions are generally less dependent on structural absence,allowing them to be more easily integrated with tools for structural predictions,such as AlphaFold 3.Through mutation prediction and systematic analysis of key sites,we can quickly predict the most promising variants for experimental validation without relying on traditional evolutionary or selection processes.The EvoNB workflow provides an effective tool for the rapid optimization of nanobodies and facilitates the application of PLMs in the biomedical field.展开更多
Magnesium(Mg)based alloys are promising candidates for many applications,but their untreated surfaces usually have low strength and hardness.In this study,a single point diamond turning(SPDT)technique was applied to r...Magnesium(Mg)based alloys are promising candidates for many applications,but their untreated surfaces usually have low strength and hardness.In this study,a single point diamond turning(SPDT)technique was applied to refine the grain size and improve the mechanical properties of the surface layers of Mg-Li alloys.By refining grains in the topmost layer to the nanometer scale(~60 nm),the surface hardness was found to be enhanced by approximately 60%.The atomic plastic deformation process during the SPDT was then studied by the real-time atomistic molecular dynamics(MD)simulations.A series of MD simulations with different combinations of parameters,including rake angle,cutting speed and cutting depth,were conducted to understand their influences on the microstructural evolution and associated plastic deformation mechanisms on the surface layer of the workpieces.The MD simulation results suggest that using increased rake angle,cutting speed and cutting depth can help to achieve better grain refinement.These simulation results,which provide atomic-level details of the deformation mechanism,can assist the parameter design for the SPDT techniques to achieve the high-performance heterogeneous nanostructured materials.展开更多
Heavy metal-contaminated sites are primarily treated via solidification and adsorption.Calcium silicate hydrate(C-S-H)is generated during the soil stabilization process and contributes significantly to the strength an...Heavy metal-contaminated sites are primarily treated via solidification and adsorption.Calcium silicate hydrate(C-S-H)is generated during the soil stabilization process and contributes significantly to the strength and durability of the stabilized soil.To understand how the soil moisture content and heavy metal concentration affect the transport of heavy metals and the tensile strength of C-S-H,this study performed molecular dynamics(MD)simulations under different moisture and concentration levels.The results showed that Pb2+presented the highest adsorption to the surface of C-S-H due to its strong electrostatic interaction energy.The adsorption density peaks of Pb2+were 1.5–5 times greater than those of Cd2+and Zn2+.Zn2+and Cd2+ions were more likely to be adsorbed onto water molecules and form a larger hydrated radius than Pb2+.The adsorption of heavy metals onto C-S-H initially increased as the metal concentration increased and then decreased because of the limited sorption sites on C-S-H.The diffusion coefficients of the multicomponent metals in C-S-H showed no consistent trends.The maximum tensile strength of C-S-H decreased with increasing soil moisture and heavy metal concentrations.The tensile stress increased approximately linearly with strain until it reached a peak,after which it gradually declined but remained above zero,indicating good ductility and toughness under unsaturated conditions.These findings offer valuable molecular insights into the interactions between C-S-H and heavy metals and soil moisture,thereby advancing our understanding of their combined effects on soil stabilization.展开更多
Objective:Prostate cancer(PCA)is the second most widespread cancer among men globally,with a rising mortality rate.Enzyme-responsive lipid nanoparticles(ERLNs)are promising vectors for the selective delivery of antica...Objective:Prostate cancer(PCA)is the second most widespread cancer among men globally,with a rising mortality rate.Enzyme-responsive lipid nanoparticles(ERLNs)are promising vectors for the selective delivery of anticancer agents to tumor cells.The goal of this study is to fabricate ERLNs for dual delivery of gefitinib(GF)and simvastatin(SV)to PCA cells.Methods:ERLNs loaded with GF and SV(ERLNGFSV)were assembled using bottomup and top-down techniques.Subsequently,these ERLN cargoes were coated with triacylglycerol,and phospholipids and capped with chitosan(CS).The ERLNGFSV,and CS engineered ERLNGFSV(CERLNGFSV)formulations were characterized for particle size(PS),zeta potential(ZP),and polydispersity index(PDI).The biocompatibility,and cytotoxicity of the plain and GF plus SV-loaded ERLN cargoes were assessed using erythrocytes and PC-3 cell line.Additionally,molecular docking simulations(MDS)were conducted to examine the influence of GF and SV on succinate dehydrogenase(SDH),glutathione peroxidase-4(GPX-4),and 5α-reductase(5α-RD).Results:These results showed that plain,ERLNGFSV,and CERLNGFSV cargoes have a nanoscale size and homogeneous appearance.Moreover,ERLNGFSV and CERLNGFSV were biocompatible,with no detrimental effects on erythrocytes.Treatment with GF,SV,GF plus SV,ERLNGFSV,and CERLNGFSV significantly reduced the viability of PC-3 cells compared to control cells.Particularly,the blend of GF and SV,as well as ERLNGFSV and CERLNGFSV augmented PC-3 cell death.Also,treating PC-3 cells with free drugs,their combination,ERLNGFSV,and CERLNGFSV formulations elevated the percentage of apoptotic cells.MDS studies demonstrated that GF and SV interact with the active sites of SDH,GPX-4,and 5α-reductase.Conclusions:This study concludes that SVGF combination and ERLNs loading induce particular delivery,and synergism on PC-3 death through action on multiple pathways involved in cell proliferation,and apoptosis,besides the interaction with SDH,GPX-4,and 5α-RD.Therefore,GFSV-loaded ERLN cargoes are a promising strategy for PCA treatment.In vivo studies are necessary to confirm these findings for clinical applications.展开更多
The bioactive constituents found in natural products(NPs)are crucial in protein-ligand interactions and drug discovery.However,it is difficult to identify ligand molecules from complex NPs that specifically bind to ta...The bioactive constituents found in natural products(NPs)are crucial in protein-ligand interactions and drug discovery.However,it is difficult to identify ligand molecules from complex NPs that specifically bind to target protein,which often requires time-consuming and labor-intensive processes such as isolation and enrichment.To address this issue,in this study we developed a method that combines ultra-high performance liquid chromatography-electrospray ionization-mass spectrometry(UHPLCESI-MS)with molecular dynamics(MD)simulation to identify and observe,rapidly and efficiently,the bioactive components in NPs that bind to specific protein target.In this method,a specific protein target was introduced online using a three-way valve to form a protein-ligand complex.The complex was then detected in real time using high-resolution MS to identify potential ligands.Based on our method,only 10 molecules from green tea(a representative natural product),including the commonly reported epigallocatechin gallate(EGCG)and epicatechin gallate(ECG),as well as the previously unreported eepicatechin(4β→8)-epigallocatechin 3-O-gallate(EC-EGCG)and eepiafzelechin 3-O-gallate-(4β→8)-epigallocatechin 3-O-gallate(EFG-EGCG),were screened out,which could form complexes with Aβ_(1-42)(a representative protein target),and could be potential ligands of Aβ_(1-42).Among of them,EC-EGCG demonstrated the highest binding free energy with Aβ_(1-42)(−68.54±3.82 kcal/mol).On the other side,even though the caffeine had the highest signal among green tea extracts,it was not observed to form a complex with Aβ_(1-42).Compared to other methods such as affinity selection mass spectrometry(ASMS)and native MS,our method is easy to operate and interpret the data.Undoubtedly,it provides a new methodology for potential drug discovery in NPs,and will accelerate the research on screening ligands for specific proteins from complex NPs.展开更多
The continuous reduction in sulfur content of fuels would lead to diesel fuel with poor lubricity which could re- sult in engine pump failure. In the present work, fatty acids were adopted as lubricity additives to lo...The continuous reduction in sulfur content of fuels would lead to diesel fuel with poor lubricity which could re- sult in engine pump failure. In the present work, fatty acids were adopted as lubricity additives to low-sulfur diesel fuel. It was attempted to correlate the molecular structures of fatty acids, such as carbon chain length, degree of saturation and hy- droxylation, to their lubricity enhancement, which was evaluated by the High-Frequency Reciprocating Rig （HFRR） meth- od. The efficiency order was supported by the density functional theory （DFT） calculations and the molecular dynamics （MD） simulations. The lubricity enhancing properties of fatty acids are mainly determined by the cohesive energy of adsorbed films furmed on iron surface. The greater the cohesive energy, the more efficiently the fatty acid would enhance the lubricity of low-sulfur diesel fuel.展开更多
The effect of sodium lignosulfonate(SL)as additive on the preparation of low-rank coal-water slurry(LCWS)was studied by experiments and molecular dynamics(MD)simulation s.The experimental results show that the appropr...The effect of sodium lignosulfonate(SL)as additive on the preparation of low-rank coal-water slurry(LCWS)was studied by experiments and molecular dynamics(MD)simulation s.The experimental results show that the appropriate amount of additives is beneficial to reduce the viscosity of LCWS and increase the slurry concentration.Adsorption isotherm studies showed that SL conforms to single-layer adsorption on the coal surface,andΔG_(ads)^(0) was negative,proving that the reaction was spontaneous.Zeta potential measurements showed that SL increased the negative charge on coal.FTIR scanning and XPS wide-range scanning were performed on the coal before and after adsorption,and it was found that the content of oxygen functional groups on coal increased after adsorption.Simulation results show that when a large number of SL molecules exist in the solution,some SL molecules will bind to hydrophobic hydrocarbon groups on coal.The rest of the SL molecule s,their hydrophobic alkyl tails,come into contact with each other and aggregate in solution.The agglomeration of SL molecules and the surface of coal with static electricity will also produce electrostatic interaction,which is conducive to the even dispersion of coal particles.The results of mean square displacement(MSD)and self-diffusion coefficient(D)show that the addition of SL reduces the diffusion rate of water molecules.Simulation results correspond to experimental results,indicating that MD simulation is accurate and feasible.展开更多
In this work,fatty acid and its derivatives were adopted as lubricity additives for low sulfur diesel.Tribological evaluation obtained from the High-Frequency Reciprocating Rig(HFRR)apparatus showed that the lubricati...In this work,fatty acid and its derivatives were adopted as lubricity additives for low sulfur diesel.Tribological evaluation obtained from the High-Frequency Reciprocating Rig(HFRR)apparatus showed that the lubricating performance of the additives increased in the following order:stearic acid>glycol monopalmitate>stearyl alcohol>ethyl palmitate>cetyl ethyl ether.The adsorption behavior of the additives on Fe(110)surface and Fe2O3(001)surface was investigated by molecular dynamics(MD)simulations to verify their lubricity performance.The results suggested that adsorption energies of the additives on Fe(110)surface are determined by the van der Waals forces,while adsorptions on Fe2O3(001)surface are significantly attributed to the electrostatic attractive forces.Higher values of adsorption energy of the additives on Fe2O3(001)surface indicate that the additive has more efficient lubricity enhancing properties.展开更多
Control of ion transport and fluid flow through nanofluidic devices is of primary importance for energy storage and conversion, drug delivery and a wide range of biological processes. Recent development of nanotechnol...Control of ion transport and fluid flow through nanofluidic devices is of primary importance for energy storage and conversion, drug delivery and a wide range of biological processes. Recent development of nanotechnology, synthesis techniques, purification technologies, and experiment have led to rapid advances in simulation and modeling studies on ion transport properties. In this review, the applications of Poisson-Nernst-Plank （PNP） equations in analyzing transport properties are presented. The molecular dynamics （MD） studies of transport properties of ion and fluidic flow through nanofluidic devices are reported as well.展开更多
All-atom molecular dynamics （MD） simulations and chemical shifts were used to study interactions and structures in the glycine-water system. Radial distribution functions and the hydrogen-bond network were applied i...All-atom molecular dynamics （MD） simulations and chemical shifts were used to study interactions and structures in the glycine-water system. Radial distribution functions and the hydrogen-bond network were applied in MD simulations. Aggregates in the aqueous glycine solution could be classified into different regions by analysis of the hydrogen-bonding network. Temperature-dependent NMR spectra and the viscosity of glycine in aqueous solutions were measured to compare with the results of MD simulations. The variation tendencies of the hydrogen atom chemical shifts and viscosity with concentration of glycine agree with the statistical results of hydrogen bonds in the MD simulations.展开更多
2,6-bis(picrylamino)-3,5-dinitropyridine(PYX)has excellent thermostability,which makes its thermal decomposition mechanism receive much attention.In this paper,the mechanism of PYX thermal decomposition was investigat...2,6-bis(picrylamino)-3,5-dinitropyridine(PYX)has excellent thermostability,which makes its thermal decomposition mechanism receive much attention.In this paper,the mechanism of PYX thermal decomposition was investigated thoroughly by the ReaxFF-lg force field combined with DFT-B3LYP(6-311++G)method.The detailed decomposition mechanism,small-molecule product evolution,and cluster evolution of PYX were mainly analyzed.In the initial stage of decomposition,the intramolecular hydrogen transfer reaction and the formation of dimerized clusters are earlier than the denitration reaction.With the progress of the reaction,one side of the bitter amino group is removed from the pyridine ring,and then the pyridine ring is cleaved.The final products produced in the thermal decomposition process are CO_(2),H_(2)O,N_(2),and H_(2).Among them,H_(2)O has the earliest generation time,and the reaction rate constant(k_(3))is the largest.Many clusters are formed during the decomposition of PYX,and the formation,aggregation,and decomposition of these clusters are strongly affected by temperature.At low temperatures(2500 K-2750 K),many clusters are formed.At high temperatures(2750 K-3250 K),the clusters aggregate to form larger clusters.At 3500 K,the large clusters decompose and become small.In the late stage of the reaction,H and N in the clusters escaped almost entirely,but more O was trapped in the clusters,which affected the auto-oxidation process of PYX.PYX's initial decomposition activation energy(E_(a))was calculated to be 126.58 kJ/mol.This work contributes to a theoretical understanding of PYX's entire thermal decomposition process.展开更多
The nanoscale confinement is of great important for the industrial applications of molecular sieve,desalination,and also essential in bio-logical transport systems.Massive efforts have been devoted to the influence of...The nanoscale confinement is of great important for the industrial applications of molecular sieve,desalination,and also essential in bio-logical transport systems.Massive efforts have been devoted to the influence of restricted spaces on the properties of confined fluids.However,the situation of channel-wall is crucial but attracts less attention and remains unknown.To fundamentally understand the mechanism of channel-walls in nanoconfinement,we investigated the interaction between the counter-force of the liquid and interlamellar spacing of nanochannel walls by considering the effect of both spatial confinement and surface wettability.The results reveal that the nanochannel stables at only a few discrete spacing states when its confinement is within 1.4 nm.The quantized interlayer spacing is attributed to water molecules becoming laminated structures,and the stable states are corresponding to the monolayer,bilayer and trilayer water configurations,respectively.The results can potentially help to understand the characterized interlayers spacing of graphene oxide membrane in water.Our findings are hold great promise in design of ion filtration membrane and artificial water/ion channels.展开更多
SiCp/Al composites are used in aerospace and deep-space exploration equipment because of their extremely high strength and thrust-to-weight ratios;however,the differences in the properties of the reinforcement and mat...SiCp/Al composites are used in aerospace and deep-space exploration equipment because of their extremely high strength and thrust-to-weight ratios;however,the differences in the properties of the reinforcement and matrix materials in this type of composites have restricted their applications.The ultrahigh-frequency vibration characteristics of ultrasonic vibration processing technology can effectively solve the above bottlenecks,but the effect of high-frequency vibration on the interfacial properties of SiCp/Al composites is still unclear.The effects of ultrasonic vibration on the interface strength of composites were analyzed from a microscale perspective by means of single particle push-out Molecular Dynamics(MD)simulations and tests under different conditions.The results show that the interface strength is negatively correlated with particle size but positively correlated with ultrasonic amplitude,with a maximum increase of about 51%relative to no ultrasound.Brittle-plastic transition was observed on the surface of particles with high interface strength,and lateral microcracks due to stress concentration were present on the surface of particles with low interface strength.Higher strains and grain refinement were obtained for larger amplitudes,and stacking faults and tangle dislocations appeared on the side of the interface layer close to the Al matrix.The results provide potential insights to improve the micromechanical and mechanical properties of SiCp/Al composites,enhance the longevity of the materials,and realize the sustainable use of resources by expanding the efficient,precise,and clean machining of such materials.展开更多
Grain boundaries(GBs)play a crucial role on the structural stability and mechanical properties of Cu and its alloys.In this work,molecular dynamics(MD)simulations are employed to study the effects of Fe solutes on the...Grain boundaries(GBs)play a crucial role on the structural stability and mechanical properties of Cu and its alloys.In this work,molecular dynamics(MD)simulations are employed to study the effects of Fe solutes on the formation energy,excess volume,dislocations and melting behaviors of GBs in CuFe alloys.It is illustrated that Fe solute affects the structural stability of Cu GBs substantially,the formation energy of GBs is reduced,but the thickness and melting point of GBs are increased,that is,the structural stability of Cu GBs is significantly improved owing to the Fe solutes.A strong scaling law exists between the formation energy,excess volume,thickness and melting point of GBs.Therefore,Fe solid solute plays an important role in the characteristics of GBs in bi-crystal Cu.展开更多
Understanding how supercoiled DNA releases intramolecular stress is essential for its functional realization.However,the molecular mechanism underlying the relaxation process remains insufficiently explored.Here we em...Understanding how supercoiled DNA releases intramolecular stress is essential for its functional realization.However,the molecular mechanism underlying the relaxation process remains insufficiently explored.Here we employed MD simulations based on the oxDNA2 model to investigate the relaxation process of a 336-base pair supercoiled minicircular DNA under double-strand breaks with two fixed endpoints.Our simulations show that the conformational changes in the DNA occur continuously,with intramolecular stress release happening abruptly only when the DNA chain traverses the breakage site.The relaxation process is influenced not only by the separation distance between the fixed ends but also their angle.Importantly,we observe an inhibitory effect on the relaxation characterized by small angles,where short terminal loops impede DNA conformational adjustments,preserving the supercoiled structure.These findings elucidate the intricate interplay between DNA conformational change,DNA motion and intramolecular stress release,shedding light on the mechanisms governing the relaxation of supercoiled DNA at the molecular level.展开更多
At present,there are few studies on the phase transition during the thermocompression plastic deformation of magnesium alloy.In this study,the evolution model of thermal compression plastic of AZ31 magnesium alloy was...At present,there are few studies on the phase transition during the thermocompression plastic deformation of magnesium alloy.In this study,the evolution model of thermal compression plastic of AZ31 magnesium alloy was constructed by molecular dynamics,and the phase transition relationship between HCP and FCC at different thermal compression rates was studied.By combining GLEEBLE thermal compression experiment with transmission electron microscopy experiment,high-resolution transmission electron microscopy images were taken to analyze the transition rules between HCP and FCC during plastic deformation at different thermal compression rates,and the accuracy of molecular dynamics analysis was verified.It is found that the slip of Shockley’s incomplete dislocation produces obvious HCP→FCC phase transition at low strain rate and base plane dislocation at high strain rate,which makes the amorphous phase transition of HCP→OTHER more obvious,which provides theoretical guidance for the formulation of forming mechanism and preparation process of magnesium alloy.展开更多
基金supported by the National Natural Science Foundation of China(Nos.U2341261 and 12375280)the Young Potential Program of Shanghai Institute of Applied Physics,Chinese Academy of Sciences(No.YXJH-2022002)the National MCF Energy R&D Program(No.2022YFE03110000).
文摘In-situ TEM observation was conducted during Ni^(+)&He^(+)dual-beam irradiation to monitor the evolution of dislocation loops accompanied by He bubbles in the Ni-based alloy GH3535.Two distinct evolutions of dislocation loops,driven by residual stresses,were observed within the monitored grains.Hence,molec-ular dynamics(MD)simulations were employed to reveal the effects of stress magnitude and direction on loop evolution,including size,number density,type and variation.The simulations revealed that the presence of compressive stress reduced the formation energy of perfect dislocation loops,thus promoting their formation.Stress state was found to influence the preferential orientation of the loops,and com-pressive stress resulted in a decreased number density of dislocation loops but an increase in their size.This establishes a clear relationship between stress state and magnitude and the evolution of dislocation loops during ion beam irradiation.Additionally,the nature and characteristics of dislocation loops were quantified to explore the effects of He concentrations on their evolution.The higher He concentration not only promotes the nucleation of dislocation loops,leading to their higher number density,but also facil-itates the unfaulting evolution by increasing the stacking fault energy(SFE).Moreover,the accumulation of He in the lower-He-concentration sample led to the growth of dislocation loops in multiple stages,explaining their nearly identical average sizes when compared to the higher-He-concentration sample.
基金the National Natural Science Foundation of China(21003048,10974054,and 20933002)Shanghai PuJiang Program (09PJ1404000) for financial support XXY is also supported by "Scientific Research Foundation for Agricultural Machinery Bureau of Jiangsu Province (gxz10008)"CGJ is also supported by "the Fundamental Research Funds for the Central Universities"
文摘The binding of Endonuclease colicin 9 (E9) by Immunity protein 9 (Im9) was found to involve some hotspots from helix III of Im9 on protein-protein interface that contribute the dominant binding energy to the complex.In the current work,MD simulations of the WT and three hotspot mutants (D51A,Y54A and Y55A of Im9) of the E9-Im9 complexes were carried out to investigate specific interaction mechanisms of these three hotspot residues.The changes of binding energy between the WT and mutants of the complex were computed by the MM/PBSA method using a polarized force field and were in excellent agreement with experiment values,verifying that these three residues were indeed hotspots of the binding complex.Energy decomposition analysis revealed that binding by D51 to E9 was dominated by electrostatic interaction due to the presence of the carboxyl group of Asp51 which hydrogen bonds to K89.For binding by hotspots Y54 and Y55,van der Waals interaction from the aromatic side chain of tyrosine provided the dominant interaction.For comparison,calculation by using the standard (nonpolarizable) AMBER99SB force field produced binding energy changes from these mutations in opposite direction to the experimental observation.Dynamic hydrogen bond analysis showed that conformations sampled from MD simulation in the standard AMBER force field were distorted from the native state and they disrupted the inter-protein hydrogen bond network of the protein-protein complex.The current work further demonstrated that electrostatic polarization plays a critical role in modulating protein-protein binding.
基金Talents Introduction Foundation for Universities of Guangdong Province(GD 2011)the Science and Technology Planning Project of Guangzhou(No.2013J4100071)。
文摘HDAC8 is an important target for the treatment of many cancers and other diseases. To develop potent and selective HDAC8 inhibitors, molecular docking and molecular dynamics(MD) simulations were employed for investigation of the mechanism of HDAC8 inhibitions containing hydroxamic acid group. Compound 1 with high activity and compound 2 with low activity were selected for comparative study. Compound 1 formed a stronger chelation with Zn ion and was more stable in the HDAC8 pocket than compound 2. Residues HIS-180, ASP-178, ASP-267, and GLY-140 played a critical role in securing the position of compound 1. Both the head and tail of compound 1 formed strong hydrogen bonds with ASP-178, facilitating the ZBG of compound 1 close to the Zn ion so that they formed permanent chelation during the simulation period. The Cap group of the compounds with branch and long chains was advantageous to form interaction with active pocket opening. What’s more, based on the results of this study, three innovative recommendations for the design of highly active HDAC8 inhibitors were presented, which will be useful for the development of new HDAC8 inhibitors.
基金supported by the National Natural Science Foundation of China(No.22372083,52201259)the National Key R&D Program of China(2021YFB2500300)+2 种基金the Fundamental Research Funds for the Central Universities:Nankai University(63241607)the Natural Science Foundation of Tianjin(No.22JCZDJC00380)the Young Elite Scientist Sponsorship Program by CAST.
文摘LiNO_(3) is known to significantly enhance the reversibility of lithium metal batteries;however,the modification of solvation structures in various solvents and its further impact on the interface have not been fully revealed.Herein,we systematically studied the evolution of solvation structures with increasing LiNO_(3) concentration in both carbonate and ether electrolytes.The results from molecular dynamics simulations unveil that the Li^(+)solvation structure is less affected in carbonate electrolytes,while in ether electrolytes,there is a significant decrease of solvent molecules in Li^(+)coordination,and a larger average size of Li^(+)solvation structure emerges as LiNO_(3) concentration increases.Notably,the formation of large ion aggregates with size of several nanometers(nano-clusters),is observed in ether-based electrolytes at conventional Li^(+)concentration(1 M)with higher NO_(3)^(-) ratio,which is further proved by infrared spectroscopy and small-angle X-ray scattering experiments.The nano-clusters with abundant anions are endowed with a narrow energy gap of molecular orbitals,contributing to the formation of an inorganic rich electrode/electrolyte interphase that enhances the reversibility of lithium stripping/plating with Coulombic efficiency up to 99.71%.The discovery of nano-clusters elucidates the underlying mechanism linking ions/solvent aggregation states of electrolytes to interfacial stability in advanced battery systems.
基金supported by the National Natural Science Foundation of China(Grant Nos.:92477103,22273023,12474285 and 22373116)the National Key R&D Program of China(Grant No.:2019YFA0905200)+5 种基金Shanghai Municipal Natural Science Foundation(Grant No.:23ZR1418200)Natural Science Foundation of Chongqing,China(Grant No.:CSTB2023NSCQ-MSX0616)Shanghai Frontiers Science Center of Molecule Intelligent SynthesesShanghai Future Discipline Program(Quantum Science and Tech-nology)Shanghai Municipal Education Commission’s“Artificial Intelligence-Driven Research Paradigm Reform and Discipline Advancement Program”the Fundamental Research Funds for the Central Universities.
文摘The identification and optimization of mutations in nanobodies are crucial for enhancing their thera-peutic potential in disease prevention and control.However,this process is often complex and time-consuming,which limit its widespread application in practice.In this study,we developed a work-flow,named Evolutionary-Nanobody(EvoNB),to predict key mutation sites of nanobodies by combining protein language models(PLMs)and molecular dynamic(MD)simulations.By fine-tuning the ESM2 model on a large-scale nanobody dataset,the ability of EvoNB to capture specific sequence features of nanobodies was significantly enhanced.The fine-tuned EvoNB model demonstrated higher predictive accuracy in the conserved framework and highly variable complementarity-determining regions of nanobodies.Additionally,we selected four widely representative nanobodyeantigen complexes to verify the predicted effects of mutations.MD simulations analyzed the energy changes caused by these mu-tations to predict their impact on binding affinity to the targets.The results showed that multiple mu-tations screened by EvoNB significantly enhanced the binding affinity between nanobody and its target,further validating the potential of this workflow for designing and optimizing nanobody mutations.Additionally,sequence-based predictions are generally less dependent on structural absence,allowing them to be more easily integrated with tools for structural predictions,such as AlphaFold 3.Through mutation prediction and systematic analysis of key sites,we can quickly predict the most promising variants for experimental validation without relying on traditional evolutionary or selection processes.The EvoNB workflow provides an effective tool for the rapid optimization of nanobodies and facilitates the application of PLMs in the biomedical field.
基金the National Key Research and Development Program of China(2018YFE0124900)the National Natural Science Foundation of China(51861165204/51778370/51701171/51971187)+2 种基金the Natural Science Foundation of Guangdong(2017B030311004)the Shenzhen Science and Technology Project(GJHZ20180928155819738)the Partner State Key Laboratories in Hong Kong from the Innovation and Technology Commission(ITC)(Project Code:1-BBXA)。
文摘Magnesium(Mg)based alloys are promising candidates for many applications,but their untreated surfaces usually have low strength and hardness.In this study,a single point diamond turning(SPDT)technique was applied to refine the grain size and improve the mechanical properties of the surface layers of Mg-Li alloys.By refining grains in the topmost layer to the nanometer scale(~60 nm),the surface hardness was found to be enhanced by approximately 60%.The atomic plastic deformation process during the SPDT was then studied by the real-time atomistic molecular dynamics(MD)simulations.A series of MD simulations with different combinations of parameters,including rake angle,cutting speed and cutting depth,were conducted to understand their influences on the microstructural evolution and associated plastic deformation mechanisms on the surface layer of the workpieces.The MD simulation results suggest that using increased rake angle,cutting speed and cutting depth can help to achieve better grain refinement.These simulation results,which provide atomic-level details of the deformation mechanism,can assist the parameter design for the SPDT techniques to achieve the high-performance heterogeneous nanostructured materials.
基金supported by the National Natural Science Foundation of China(Grant Nos.42030710 and 52308345)the National Key Research and Development Program of China(Grant No.2023YFC3707903).
文摘Heavy metal-contaminated sites are primarily treated via solidification and adsorption.Calcium silicate hydrate(C-S-H)is generated during the soil stabilization process and contributes significantly to the strength and durability of the stabilized soil.To understand how the soil moisture content and heavy metal concentration affect the transport of heavy metals and the tensile strength of C-S-H,this study performed molecular dynamics(MD)simulations under different moisture and concentration levels.The results showed that Pb2+presented the highest adsorption to the surface of C-S-H due to its strong electrostatic interaction energy.The adsorption density peaks of Pb2+were 1.5–5 times greater than those of Cd2+and Zn2+.Zn2+and Cd2+ions were more likely to be adsorbed onto water molecules and form a larger hydrated radius than Pb2+.The adsorption of heavy metals onto C-S-H initially increased as the metal concentration increased and then decreased because of the limited sorption sites on C-S-H.The diffusion coefficients of the multicomponent metals in C-S-H showed no consistent trends.The maximum tensile strength of C-S-H decreased with increasing soil moisture and heavy metal concentrations.The tensile stress increased approximately linearly with strain until it reached a peak,after which it gradually declined but remained above zero,indicating good ductility and toughness under unsaturated conditions.These findings offer valuable molecular insights into the interactions between C-S-H and heavy metals and soil moisture,thereby advancing our understanding of their combined effects on soil stabilization.
文摘Objective:Prostate cancer(PCA)is the second most widespread cancer among men globally,with a rising mortality rate.Enzyme-responsive lipid nanoparticles(ERLNs)are promising vectors for the selective delivery of anticancer agents to tumor cells.The goal of this study is to fabricate ERLNs for dual delivery of gefitinib(GF)and simvastatin(SV)to PCA cells.Methods:ERLNs loaded with GF and SV(ERLNGFSV)were assembled using bottomup and top-down techniques.Subsequently,these ERLN cargoes were coated with triacylglycerol,and phospholipids and capped with chitosan(CS).The ERLNGFSV,and CS engineered ERLNGFSV(CERLNGFSV)formulations were characterized for particle size(PS),zeta potential(ZP),and polydispersity index(PDI).The biocompatibility,and cytotoxicity of the plain and GF plus SV-loaded ERLN cargoes were assessed using erythrocytes and PC-3 cell line.Additionally,molecular docking simulations(MDS)were conducted to examine the influence of GF and SV on succinate dehydrogenase(SDH),glutathione peroxidase-4(GPX-4),and 5α-reductase(5α-RD).Results:These results showed that plain,ERLNGFSV,and CERLNGFSV cargoes have a nanoscale size and homogeneous appearance.Moreover,ERLNGFSV and CERLNGFSV were biocompatible,with no detrimental effects on erythrocytes.Treatment with GF,SV,GF plus SV,ERLNGFSV,and CERLNGFSV significantly reduced the viability of PC-3 cells compared to control cells.Particularly,the blend of GF and SV,as well as ERLNGFSV and CERLNGFSV augmented PC-3 cell death.Also,treating PC-3 cells with free drugs,their combination,ERLNGFSV,and CERLNGFSV formulations elevated the percentage of apoptotic cells.MDS studies demonstrated that GF and SV interact with the active sites of SDH,GPX-4,and 5α-reductase.Conclusions:This study concludes that SVGF combination and ERLNs loading induce particular delivery,and synergism on PC-3 death through action on multiple pathways involved in cell proliferation,and apoptosis,besides the interaction with SDH,GPX-4,and 5α-RD.Therefore,GFSV-loaded ERLN cargoes are a promising strategy for PCA treatment.In vivo studies are necessary to confirm these findings for clinical applications.
基金supported by the National Key R&D Program of China(No.2018YFA0800900).
文摘The bioactive constituents found in natural products(NPs)are crucial in protein-ligand interactions and drug discovery.However,it is difficult to identify ligand molecules from complex NPs that specifically bind to target protein,which often requires time-consuming and labor-intensive processes such as isolation and enrichment.To address this issue,in this study we developed a method that combines ultra-high performance liquid chromatography-electrospray ionization-mass spectrometry(UHPLCESI-MS)with molecular dynamics(MD)simulation to identify and observe,rapidly and efficiently,the bioactive components in NPs that bind to specific protein target.In this method,a specific protein target was introduced online using a three-way valve to form a protein-ligand complex.The complex was then detected in real time using high-resolution MS to identify potential ligands.Based on our method,only 10 molecules from green tea(a representative natural product),including the commonly reported epigallocatechin gallate(EGCG)and epicatechin gallate(ECG),as well as the previously unreported eepicatechin(4β→8)-epigallocatechin 3-O-gallate(EC-EGCG)and eepiafzelechin 3-O-gallate-(4β→8)-epigallocatechin 3-O-gallate(EFG-EGCG),were screened out,which could form complexes with Aβ_(1-42)(a representative protein target),and could be potential ligands of Aβ_(1-42).Among of them,EC-EGCG demonstrated the highest binding free energy with Aβ_(1-42)(−68.54±3.82 kcal/mol).On the other side,even though the caffeine had the highest signal among green tea extracts,it was not observed to form a complex with Aβ_(1-42).Compared to other methods such as affinity selection mass spectrometry(ASMS)and native MS,our method is easy to operate and interpret the data.Undoubtedly,it provides a new methodology for potential drug discovery in NPs,and will accelerate the research on screening ligands for specific proteins from complex NPs.
基金supported by the Fundamental Research Funds for the Central Universities of China(11CX06036A)
文摘The continuous reduction in sulfur content of fuels would lead to diesel fuel with poor lubricity which could re- sult in engine pump failure. In the present work, fatty acids were adopted as lubricity additives to low-sulfur diesel fuel. It was attempted to correlate the molecular structures of fatty acids, such as carbon chain length, degree of saturation and hy- droxylation, to their lubricity enhancement, which was evaluated by the High-Frequency Reciprocating Rig （HFRR） meth- od. The efficiency order was supported by the density functional theory （DFT） calculations and the molecular dynamics （MD） simulations. The lubricity enhancing properties of fatty acids are mainly determined by the cohesive energy of adsorbed films furmed on iron surface. The greater the cohesive energy, the more efficiently the fatty acid would enhance the lubricity of low-sulfur diesel fuel.
基金supported by SDUST Research Fund(Grant No.2018TDJH101)Key Research and Development Project of Shandong(Grant No.2019GGX103035)+2 种基金National Natural Science Foundation of China(Grant Nos.51904174,52074175)Young Science and Technology Innovation Program of Shandong Province(Grant No.2020KJD001)Project of Shandong Province Higher Educational Young Innovative Talent Introduction and Cultivation Team。
文摘The effect of sodium lignosulfonate(SL)as additive on the preparation of low-rank coal-water slurry(LCWS)was studied by experiments and molecular dynamics(MD)simulation s.The experimental results show that the appropriate amount of additives is beneficial to reduce the viscosity of LCWS and increase the slurry concentration.Adsorption isotherm studies showed that SL conforms to single-layer adsorption on the coal surface,andΔG_(ads)^(0) was negative,proving that the reaction was spontaneous.Zeta potential measurements showed that SL increased the negative charge on coal.FTIR scanning and XPS wide-range scanning were performed on the coal before and after adsorption,and it was found that the content of oxygen functional groups on coal increased after adsorption.Simulation results show that when a large number of SL molecules exist in the solution,some SL molecules will bind to hydrophobic hydrocarbon groups on coal.The rest of the SL molecule s,their hydrophobic alkyl tails,come into contact with each other and aggregate in solution.The agglomeration of SL molecules and the surface of coal with static electricity will also produce electrostatic interaction,which is conducive to the even dispersion of coal particles.The results of mean square displacement(MSD)and self-diffusion coefficient(D)show that the addition of SL reduces the diffusion rate of water molecules.Simulation results correspond to experimental results,indicating that MD simulation is accurate and feasible.
基金financially supported by "the Fundamental Research Funds for the Central Universities,China"(11CX06036A)
文摘In this work,fatty acid and its derivatives were adopted as lubricity additives for low sulfur diesel.Tribological evaluation obtained from the High-Frequency Reciprocating Rig(HFRR)apparatus showed that the lubricating performance of the additives increased in the following order:stearic acid>glycol monopalmitate>stearyl alcohol>ethyl palmitate>cetyl ethyl ether.The adsorption behavior of the additives on Fe(110)surface and Fe2O3(001)surface was investigated by molecular dynamics(MD)simulations to verify their lubricity performance.The results suggested that adsorption energies of the additives on Fe(110)surface are determined by the van der Waals forces,while adsorptions on Fe2O3(001)surface are significantly attributed to the electrostatic attractive forces.Higher values of adsorption energy of the additives on Fe2O3(001)surface indicate that the additive has more efficient lubricity enhancing properties.
基金Project supported by the National Natural Science Foundation of China(Grant Nos.11374243 and 11574256)
文摘Control of ion transport and fluid flow through nanofluidic devices is of primary importance for energy storage and conversion, drug delivery and a wide range of biological processes. Recent development of nanotechnology, synthesis techniques, purification technologies, and experiment have led to rapid advances in simulation and modeling studies on ion transport properties. In this review, the applications of Poisson-Nernst-Plank （PNP） equations in analyzing transport properties are presented. The molecular dynamics （MD） studies of transport properties of ion and fluidic flow through nanofluidic devices are reported as well.
基金Supported by the National Natural Science Foundation of China(No.20903026)the Talents Introduction Foundation for Universities of Guangdong Province(2011)Scientific Research Foundation of the Natural Science Foundation of Guangdong Province(No.S2011010002483)
文摘All-atom molecular dynamics （MD） simulations and chemical shifts were used to study interactions and structures in the glycine-water system. Radial distribution functions and the hydrogen-bond network were applied in MD simulations. Aggregates in the aqueous glycine solution could be classified into different regions by analysis of the hydrogen-bonding network. Temperature-dependent NMR spectra and the viscosity of glycine in aqueous solutions were measured to compare with the results of MD simulations. The variation tendencies of the hydrogen atom chemical shifts and viscosity with concentration of glycine agree with the statistical results of hydrogen bonds in the MD simulations.
基金funded by the National Natural Science Foundation of China(Grant No.21975024)。
文摘2,6-bis(picrylamino)-3,5-dinitropyridine(PYX)has excellent thermostability,which makes its thermal decomposition mechanism receive much attention.In this paper,the mechanism of PYX thermal decomposition was investigated thoroughly by the ReaxFF-lg force field combined with DFT-B3LYP(6-311++G)method.The detailed decomposition mechanism,small-molecule product evolution,and cluster evolution of PYX were mainly analyzed.In the initial stage of decomposition,the intramolecular hydrogen transfer reaction and the formation of dimerized clusters are earlier than the denitration reaction.With the progress of the reaction,one side of the bitter amino group is removed from the pyridine ring,and then the pyridine ring is cleaved.The final products produced in the thermal decomposition process are CO_(2),H_(2)O,N_(2),and H_(2).Among them,H_(2)O has the earliest generation time,and the reaction rate constant(k_(3))is the largest.Many clusters are formed during the decomposition of PYX,and the formation,aggregation,and decomposition of these clusters are strongly affected by temperature.At low temperatures(2500 K-2750 K),many clusters are formed.At high temperatures(2750 K-3250 K),the clusters aggregate to form larger clusters.At 3500 K,the large clusters decompose and become small.In the late stage of the reaction,H and N in the clusters escaped almost entirely,but more O was trapped in the clusters,which affected the auto-oxidation process of PYX.PYX's initial decomposition activation energy(E_(a))was calculated to be 126.58 kJ/mol.This work contributes to a theoretical understanding of PYX's entire thermal decomposition process.
基金support from the National Natural Science Foundation of China(Grant Nos.12372327,12372109,11972171)National Key R&D Program of China(Grant No.2023YFB4605101).
文摘The nanoscale confinement is of great important for the industrial applications of molecular sieve,desalination,and also essential in bio-logical transport systems.Massive efforts have been devoted to the influence of restricted spaces on the properties of confined fluids.However,the situation of channel-wall is crucial but attracts less attention and remains unknown.To fundamentally understand the mechanism of channel-walls in nanoconfinement,we investigated the interaction between the counter-force of the liquid and interlamellar spacing of nanochannel walls by considering the effect of both spatial confinement and surface wettability.The results reveal that the nanochannel stables at only a few discrete spacing states when its confinement is within 1.4 nm.The quantized interlayer spacing is attributed to water molecules becoming laminated structures,and the stable states are corresponding to the monolayer,bilayer and trilayer water configurations,respectively.The results can potentially help to understand the characterized interlayers spacing of graphene oxide membrane in water.Our findings are hold great promise in design of ion filtration membrane and artificial water/ion channels.
基金supported by the National Natural Science Foundation of China(Nos.52475448,51975188)the Henan Provincial Science and Technology Research Project,China(No.222102220005).
文摘SiCp/Al composites are used in aerospace and deep-space exploration equipment because of their extremely high strength and thrust-to-weight ratios;however,the differences in the properties of the reinforcement and matrix materials in this type of composites have restricted their applications.The ultrahigh-frequency vibration characteristics of ultrasonic vibration processing technology can effectively solve the above bottlenecks,but the effect of high-frequency vibration on the interfacial properties of SiCp/Al composites is still unclear.The effects of ultrasonic vibration on the interface strength of composites were analyzed from a microscale perspective by means of single particle push-out Molecular Dynamics(MD)simulations and tests under different conditions.The results show that the interface strength is negatively correlated with particle size but positively correlated with ultrasonic amplitude,with a maximum increase of about 51%relative to no ultrasound.Brittle-plastic transition was observed on the surface of particles with high interface strength,and lateral microcracks due to stress concentration were present on the surface of particles with low interface strength.Higher strains and grain refinement were obtained for larger amplitudes,and stacking faults and tangle dislocations appeared on the side of the interface layer close to the Al matrix.The results provide potential insights to improve the micromechanical and mechanical properties of SiCp/Al composites,enhance the longevity of the materials,and realize the sustainable use of resources by expanding the efficient,precise,and clean machining of such materials.
基金supported by National Key Research and Development Program of China(No.2021YFB3400800)National Natural Science Foundation of China(Grant No.52271136,51901177)Natural Science Foundation of Shaanxi Province(No.2021JC-06,2019TD-020).
文摘Grain boundaries(GBs)play a crucial role on the structural stability and mechanical properties of Cu and its alloys.In this work,molecular dynamics(MD)simulations are employed to study the effects of Fe solutes on the formation energy,excess volume,dislocations and melting behaviors of GBs in CuFe alloys.It is illustrated that Fe solute affects the structural stability of Cu GBs substantially,the formation energy of GBs is reduced,but the thickness and melting point of GBs are increased,that is,the structural stability of Cu GBs is significantly improved owing to the Fe solutes.A strong scaling law exists between the formation energy,excess volume,thickness and melting point of GBs.Therefore,Fe solid solute plays an important role in the characteristics of GBs in bi-crystal Cu.
基金supported by the National Natural Science Foundation of China(Nos.12274212,12347102 and 12174184).
文摘Understanding how supercoiled DNA releases intramolecular stress is essential for its functional realization.However,the molecular mechanism underlying the relaxation process remains insufficiently explored.Here we employed MD simulations based on the oxDNA2 model to investigate the relaxation process of a 336-base pair supercoiled minicircular DNA under double-strand breaks with two fixed endpoints.Our simulations show that the conformational changes in the DNA occur continuously,with intramolecular stress release happening abruptly only when the DNA chain traverses the breakage site.The relaxation process is influenced not only by the separation distance between the fixed ends but also their angle.Importantly,we observe an inhibitory effect on the relaxation characterized by small angles,where short terminal loops impede DNA conformational adjustments,preserving the supercoiled structure.These findings elucidate the intricate interplay between DNA conformational change,DNA motion and intramolecular stress release,shedding light on the mechanisms governing the relaxation of supercoiled DNA at the molecular level.
基金supported by the National Key Research and Development Project(No.2018YFB1307902)the National Natural Science Foundation of China(No.52175353,51905366 and 52275382)+5 种基金Shanxi young top tal-ent project,Shanxi Province Science Foundation for Youths(No.201901D211312)Excellent young academic leaders in Shanxi colleges and universities(No.2019045)Excellent Achievements Cultivation Project of Shanxi Higher Education Institutions(No.2019KJ028)Key Research and Development Projects of Shanxi Province(No.201903D121043)Key Research and Development Plan of Shanxi Province(No.202102150401002)Innovative projects in graduate education(NO.XCX211001).
文摘At present,there are few studies on the phase transition during the thermocompression plastic deformation of magnesium alloy.In this study,the evolution model of thermal compression plastic of AZ31 magnesium alloy was constructed by molecular dynamics,and the phase transition relationship between HCP and FCC at different thermal compression rates was studied.By combining GLEEBLE thermal compression experiment with transmission electron microscopy experiment,high-resolution transmission electron microscopy images were taken to analyze the transition rules between HCP and FCC during plastic deformation at different thermal compression rates,and the accuracy of molecular dynamics analysis was verified.It is found that the slip of Shockley’s incomplete dislocation produces obvious HCP→FCC phase transition at low strain rate and base plane dislocation at high strain rate,which makes the amorphous phase transition of HCP→OTHER more obvious,which provides theoretical guidance for the formulation of forming mechanism and preparation process of magnesium alloy.
