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 bendin...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.展开更多
The lubrication characteristics of liquid crystal(LC) molecules sheared between two crystalline surfaces obtained from molecular dynamics(MD) simulations are reported in this article.We consider a coarse-grained rigid...The lubrication characteristics of liquid crystal(LC) molecules sheared between two crystalline surfaces obtained from molecular dynamics(MD) simulations are reported in this article.We consider a coarse-grained rigid bead-necklace model of the LC molecules confined between two atomic surfaces subject to different shearing velocities.A systematic study shows that the slip length of LC lubrication changes significantly as a function of the LC-surface interaction energy,which can be well described though a theoretical curve.The slip length increases as shear rate increases at high LC-surface interaction energy.However,this trend can not be observed for low interaction energy.The orientation of the LC molecules near the surface is found to be guided by the atomics surfaces.The influence of temperature on the lubrication characteristics is also discussed in this article.展开更多
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...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.展开更多
Compared to the well-studied two-dimensional(2D)ferroelectricity,the appearance of 2D antiferroelectricity is much rarer,where local dipoles from the nonequivalent sublattices within 2D monolayers are oppositely orien...Compared to the well-studied two-dimensional(2D)ferroelectricity,the appearance of 2D antiferroelectricity is much rarer,where local dipoles from the nonequivalent sublattices within 2D monolayers are oppositely oriented.Using NbOCl_(2) monolayer with competing ferroelectric(FE)and antiferroelectric(AFE)phases as a 2D material platform,we demonstrate the emergence of intrinsic antiferroelectricity in NbOCl_(2) monolayer under experimentally accessible shear strain,along with new functionality associated with electric field-induced AFE-to-FE phase transition.Specifically,the complex configuration space accommodating FE and AFE phases,polarization switching kinetics,and finite temperature thermodynamic properties of 2D NbOCl_(2) are all accurately predicted by large-scale molecular dynamics simulations based on deep learning interatomic potential model.Moreover,room temperature stable antiferroelectricity with low polarization switching barrier and one-dimensional collinear polarization arrangement is predicted in shear-deformed NbOCl_(2) monolayer.The transition from AFE to FE phase in 2D NbOCl_(2) can be triggered by a low critical electric field,leading to a double polarization–electric(P–E)loop with small hysteresis.A new type of optoelectronic device composed of AFE-NbOCl_(2) is proposed,enabling electric“writing”and nonlinear optical“reading”logical operation with fast operation speed and low power consumption.展开更多
Vitrimers belong to a class of polymeric materials capable of bond exchange reactions,showing great promise for environmental protection and sustainable development.However,studies on the coupling mechanism between th...Vitrimers belong to a class of polymeric materials capable of bond exchange reactions,showing great promise for environmental protection and sustainable development.However,studies on the coupling mechanism between the bond exchange kinetics and segmental dynamics near the glass transition temperature(T_(g))remain scarce.Herein,we employed molecular dynamics simulations to investigate the dynamic heterogeneity of the segment motion and bond exchange in vitrimers.The simulation results revealed that the bond exchange energy barrier exerts a much stronger influence on the bond exchange kinetics than on the segmental dynamics.At lower temperatures,slower segmental relaxation further constraind the bond exchange rate.Additionally,increasing the bond exchange energy barrier markedly enhanced the dynamic heterogeneity of segment motion.A close correlation was observed between heterogeneity and bond exchange.This study elucidated the coupling mechanism between bond exchange and segmental dynamics at the molecular scale,thereby providing a theoretical basis for designing vitrimer materials with tunable dynamic properties.展开更多
The structural changes in the CaO-SiO_(2)-Al_(2)O_(3)-MgO slag system with varying CaO contents were investigated through molecular dynamics(MD)simulations,and its effect on the dissolution behavior of alumina inclusi...The structural changes in the CaO-SiO_(2)-Al_(2)O_(3)-MgO slag system with varying CaO contents were investigated through molecular dynamics(MD)simulations,and its effect on the dissolution behavior of alumina inclusions was characterized by the Kullback-Leibler(KL)divergence.The slag structure analysis revealed that the[AlO]tetrahedral structure was the primary network structure in the slag.With increasing the CaO content,the non-bridge oxygen(NBO)content in the slag structure increases,and the bridge oxygen(BO)content decreases,thereby reducing the complexity of the slag network structure.Raman spectroscopy detection verifies the results of the MD simulations.The results indicated that the dissolution rate of alumina inclusions accelerates with increasing the CaO content in the slag,owing to the reduced complexity of the slag network structure and the enhanced interatomic interactions.The simulation results for the dissolution of alumina inclusions were consistent with theoretical calculations based on the slag inclusion capacity and the dimensionless dissolution rate of inclusions.Radial distribution function analysis demonstrated that the interaction between atoms in the slag system and alumina inclusions strengthens,increasing the dissolution rate of alumina inclusions.The[AlO_(6)]octahedral structure of the alumina inclusions is disrupted,forming BO structures,which in turn enhances the complexity of the slag network structure,slowing the dissolution rate of alumina inclusions.In contrast,the slag system with a higher CaO content has a relatively simpler network structure,promoting faster alumina inclusion dissolution.展开更多
The migration mechanisms of ore-forming fluids have long been a focus in the field of ore deposit studies.Calcite is ubiquitously present in various types of rocks in the lithosphere,and the underlying mechanisms of i...The migration mechanisms of ore-forming fluids have long been a focus in the field of ore deposit studies.Calcite is ubiquitously present in various types of rocks in the lithosphere,and the underlying mechanisms of its influence on fluid migration are of crucial importance.While previous studies have revealed that salinity changes can modulate fluid migration,the underlying mechanisms remain poorly understood.We employ molecular dynamics simulations to elucidate how salinity variations in ore-forming fluids modulate the adsorption onto calcite nanopore walls,thereby revealing the microscopic mechanisms governing ore fluid transport through calcite nano-fractures.The results show that the adsorption energy Eint of the solution on the calcite surface increased from -14,948.84±182.48 kcal/mol to -12,144.08±118.2 kcal/mol as salinity increased,which is conducive to the long-range transport of the fluid in the calcite nanopore.展开更多
This study investigates the influence of hydrogen concentration at grain boundaries on the sensitivity of polycrystalline iron to hydrogen embrittlement using molecular dynamics simulations.These simulations reveal th...This study investigates the influence of hydrogen concentration at grain boundaries on the sensitivity of polycrystalline iron to hydrogen embrittlement using molecular dynamics simulations.These simulations reveal the diffusion behavior of hydrogen atoms at grain boundaries and their consequential impact on the hydrogen embrittlement sensitivity of iron alloys.The findings indicate that as the hydrogen concentration increases,both the yield strength and ultimate tensile strength of Fe-H alloys exhibit a declining trend.Moreover,the capture of hydrogen atoms at the grain boundaries significantly influences the fracture toughness of the material and promotes the formation and propagation of cracks.This study provides a novel theoretical basis for understanding and predicting the hydrogen embrittlement behavior of iron-based materials in hydrogen-rich environments,offering valuable insights for the design and development of Fe alloys with enhanced resistance to hydrogen embrittlement.展开更多
This study uses all-atom molecular dynamics simulations to investigate the dislocation propagation, stress transmission, and mechanical properties in poly(p-phenylene terephthalamide) fibers under uniaxial tension. Th...This study uses all-atom molecular dynamics simulations to investigate the dislocation propagation, stress transmission, and mechanical properties in poly(p-phenylene terephthalamide) fibers under uniaxial tension. The results indicate that the dislocation propagates and the stress transfers not only along the fiber axis but also between adjacent molecular chains through hydrogen bonds, demonstrating their influence on the yield behavior. As the degree of polymerization increases, breakage of covalent bonds and interchain slippage contribute to the yield of fibers together. This work provides theoretical guidance for the design and manufacturing of high-performance fibers.展开更多
Eutectic high entropy alloys are noted for their excellent castability and comprehensive mechanical properties.The excellent mechanical properties are closely related to the activation and evolution of deformation mec...Eutectic high entropy alloys are noted for their excellent castability and comprehensive mechanical properties.The excellent mechanical properties are closely related to the activation and evolution of deformation mechanisms at the atomic scale.In this work,AlCoCrFeNi2.1 alloy is taken as the research object.The mechanical behaviors and deformation mechanisms of the FCC and B2 single crystals with different orientations and the FCC/B2 composites with K-S orientation relationship during nanoindentation processes are systematically studied by molecular dynamics simulations.The results show that the mechanical behaviors of FCC single crystals are significantly orientation-dependent,meanwhile,the indentation force of[110]single crystal is the lowest at the elastic-plastic transition point,and that for[100]single crystal is the lowest in plastic deformation stage.Compared with FCC,the stress for B2 single crystals at the elastic-plastic transition point is higher.However,more deformation systems such as stacking faults,twins and dislocation loops are activated in FCC single crystal during the plastic deformation process,resulting in higher indentation force.For composites,the flow stress increases with the increase of B2 phase thickness during the initial stage of deformation.When indenter penetrates heterogeneous interface,the significantly increased deformation system in FCC phase leads to a significant increase in indentation force.The mechanical behaviors and deformation mechanisms depend on the component single crystal.When the thickness of the component layer is less than 15 nm,the heterogeneous interfaces fail to prevent the dislocation slip and improve the indentation force.The results will enrich the plastic deformation mechanisms of multi-principal eutectic alloys and provide guidance for the design of nanocrystalline metallic materials.展开更多
Recent advancements in nanotechnology have spotlighted the catalytic potential of nanozymes, particularly single-atom nanozymes(SANs), which are pivotal for innovations in biosensing and medical diagnostics. Among oth...Recent advancements in nanotechnology have spotlighted the catalytic potential of nanozymes, particularly single-atom nanozymes(SANs), which are pivotal for innovations in biosensing and medical diagnostics. Among others, DNA stands out as an ideal biological regulator. Its inherent programmability and interaction capabilities allow it to significantly modulate nanozyme activity. This study delves into the dynamic interplay between DNA and molybdenum-zinc single-atom nanozymes(Mo-Zn SANs). Using molecular dynamics simulations, we uncover how DNA influences the peroxidase-like activities of Mo-Zn SANs, providing a foundational understanding that broadens the application scope of SANs in biosensing.With these insights as a foundation, we developed and demonstrated a model aptasensor for point-ofcare testing(POCT), utilizing a label-free colorimetric approach that leverages DNA-nanozyme interactions to achieve high-sensitivity detection of lysozyme. Our work elucidates the nuanced control DNA exerts over nanozyme functionality and illustrates the application of this molecular mechanism through a smartphone-assisted biosensing platform. This study not only underscores the practical implications of DNA-regulated Mo-Zn SANs in enhancing biosensing platforms, but also highlights the potential of single-atom nanozyme technology to revolutionize diagnostic tools through its inherent versatility and sensitivity.展开更多
The kinetic properties of Mg alloy melts are crucial for determining the forming quality of castings,as they directly affect crystal nucleation and dendritic growth.However,accurately assessing the kinetic properties ...The kinetic properties of Mg alloy melts are crucial for determining the forming quality of castings,as they directly affect crystal nucleation and dendritic growth.However,accurately assessing the kinetic properties of molten Mg alloys remains challenging due to the difficulties in experimentally character-izing the high-temperature melts.Herein,we propose that molecular dynamics(MD)simulations driven by deep learning based interatomic potentials(DPs),referred to as DPMD,are a promising strategy to tackle this challenge.We develop MgAl-DP,MgSi-DP,MgCa-DP,and MgZn-DP to assess the kinetic prop-erties of Mg-Al,Mg-Si,Mg-Ca,and Mg-Zn alloy melts.The reliability of our DPs is rigorously evaluated by comparing the DPMD results with those from ab initio MD(AIMD)simulations,as well as available ex-perimental results.Our theoretically evaluated viscosity of Mg-Al melts shows excellent agreement with experimental results over a wide temperature range.Additionally,we found that the solute elements Ca and Zn exhibit sluggish kinetics in the studied melts,which supporting the promising glass-forming abil-ity of the Mg-Zn-Ca alloy system.The computational efficiency of DPMD simulations is several orders of magnitude higher than that of AIMD simulations,while maintaining ab initio-level accuracy.This makes DPMD a highly feasible protocol for building a comprehensive and reliable database of kinetic properties of Mg alloy melts.展开更多
Uranium–molybdenum(U–Mo) alloys are critical for nuclear power generation and propulsion because of their superior thermal conductivity, irradiation stability, and anti-swelling properties. This study explores the p...Uranium–molybdenum(U–Mo) alloys are critical for nuclear power generation and propulsion because of their superior thermal conductivity, irradiation stability, and anti-swelling properties. This study explores the plastic deformation mechanisms of γ-phase U–Mo alloys using molecular dynamics(MD) simulations. In the slip model, the generalized stacking fault energy(GSFE) and the modified Peierls–Nabarro(P–N) model are used to determine the competitive relationships among different slip systems. In the twinning model, the generalized plane fault energy(GPFE) is assessed to evaluate the competition between slip and twinning. The findings reveal that among the three slip systems, the {110}<111>slip system is preferentially activated, while in the {112}<111> system, twinning is favored over slip, as confirmed by MD tensile simulations conducted in various directions. Additionally, the impact of Mo content on deformation behavior is emphasized. Insights are provided for optimizing process conditions to avoid γ → α′′ transitions, thereby maintaining a higher proportion of γ-phase U–Mo alloys for practical applications.展开更多
The experiment explored the Fe_(2)O_(3) reduction process with H_(2)/CO mixed gas and confirmed a promoting effect from CO when its volume proportion in mixed gas is 20% at 850℃.The ReaxFF molecular dynamics(MD)simul...The experiment explored the Fe_(2)O_(3) reduction process with H_(2)/CO mixed gas and confirmed a promoting effect from CO when its volume proportion in mixed gas is 20% at 850℃.The ReaxFF molecular dynamics(MD)simulation method was used to observe the reduction process and provide an atomic-level explanation.The accuracy of the parameters used in the simulation was verified by the density functional theory(DFT)calculation.The simulation shows that the initial reduction rate of H_(2) is much faster than that of CO(from 800 to 950℃).As the reduction proceeds,cementite,obtained after CO participates in the reduction at 850℃,will appear on the iron surface.Due to the active properties of C atoms in cementite,they are easy to further react with the O atoms in Fe_(2)O_(3).The generation of internal CO may destroy the dense structure of the surface layer,thereby affecting the overall reduction swelling of Fe_(2)O_(3).However,excess CO is detrimental to the reaction rate,mainly because of the poor thermodynamic conditions of CO in the temperature range and the molecular diffusion capacity is not as good as that of H_(2).Furthermore,the surface structures obtained after H_(2) and CO reduction have been compared,and it was found that the structure obtained by CO reduction has a larger surface area,thus promoting the sub sequent reaction of H_(2).展开更多
The hybrid CO_(2) thermal technique has achieved considerable success globally in extracting residual heavy oil from reserves following a long-term steam stimulation process.Using microscopic visualization experiments...The hybrid CO_(2) thermal technique has achieved considerable success globally in extracting residual heavy oil from reserves following a long-term steam stimulation process.Using microscopic visualization experiments and molecular dynamics(MD)simulations,this study investigates the microscopic enhanced oil recovery(EOR)mechanisms underlying residual oil removal using hybrid CO_(2) thermal systems.Based on the experimental models for the occurrence of heavy oil,this study evaluates the performance of hybrid CO_(2) thermal systems under various conditions using MD simulations.The results demonstrate that introducing CO_(2) molecules into heavy oil can effectively penetrate and decompose dense aggregates that are originally formed on hydrophobic surfaces.A stable miscible hybrid CO_(2) thermal system,with a high effective distribution ratio of CO_(2),proficiently reduces the interaction energies between heavy oil and rock surfaces,as well as within heavy oil.A visualization analysis of the interactions reveals that strong van der Waals(vdW)attractions occur between CO_(2) and heavy oil molecules,effectively promoting the decomposition and swelling of heavy oil.This unlocks the residual oil on the hydrophobic surfaces.Considering the impacts of temperature and CO_(2) concentration,an optimal gas-to-steam injection ratio(here,the CO_(2):steam ratio)ranging between 1:6 and 1:9 is recommended.This study examines the microscopic mechanisms underlying the hybrid CO_(2) thermal technique at a molecular scale,providing a significant theoretical guide for its expanded application in EOR.展开更多
The multi-scale modeling combined with the cohesive zone model(CZM)and the molecular dynamics(MD)method were preformed to simulate the crack propagation in NiTi shape memory alloys(SMAs).The metallographic microscope ...The multi-scale modeling combined with the cohesive zone model(CZM)and the molecular dynamics(MD)method were preformed to simulate the crack propagation in NiTi shape memory alloys(SMAs).The metallographic microscope and image processing technology were employed to achieve a quantitative grain size distribution of NiTi alloys so as to provide experimental data for molecular dynamics modeling at the atomic scale.Considering the size effect of molecular dynamics model on material properties,a reasonable modeling size was provided by taking into account three characteristic dimensions from the perspective of macro,meso,and micro scales according to the Buckinghamπtheorem.Then,the corresponding MD simulation on deformation and fracture behavior was investigated to derive a parameterized traction-separation(T-S)law,and then it was embedded into cohesive elements of finite element software.Thus,the crack propagation behavior in NiTi alloys was reproduced by the finite element method(FEM).The experimental results show that the predicted initiation fracture toughness is in good agreement with experimental data.In addition,it is found that the dynamics initiation fracture toughness increases with decreasing grain size and increasing loading velocity.展开更多
Using molecular dynamics methods,simulations of collision cascades in polycrystalline tungsten(W)have been conducted in this study,including different primary-knock-on atom(PKA)directions,grain sizes,and PKA energies ...Using molecular dynamics methods,simulations of collision cascades in polycrystalline tungsten(W)have been conducted in this study,including different primary-knock-on atom(PKA)directions,grain sizes,and PKA energies between 1 keV and 150 keV.The results indicate that a smaller grain size leads to more defects forming in grain boundary regions during cascade processes.The impact of high-energy PKA may cause a certain degree of distortion of the grain boundaries,which has a higher probability in systems with smaller grain sizes and becomes more pronounced as the PKA energy increases.The direction of PKA can affect the formation and diffusion pathways of defects.When the PKA direction is perpendicular to the grain boundary,defects preferentially form near the grain boundary regions;by contrast,defects are more inclined to form in the interior of the grains.These results are of great significance for comprehending the changes in the performance of polycrystalline W under the high-energy fusion environments and can provide theoretical guidance for further optimization and application of W-based plasma materials.展开更多
The formation of donut-shaped penetration pore upon membrane fusion in a closed lipid membrane system is of biological significance,since such the structures extensively exist in living body with various functions.How...The formation of donut-shaped penetration pore upon membrane fusion in a closed lipid membrane system is of biological significance,since such the structures extensively exist in living body with various functions.However,the related formation dynamics is unclear because of the limitation of experimental techniques.This work developed a new model of intra-vesicular fusion to elaborate the formation and stabilization of penetration pores by employing molecular dynamics simulations,based on simplified spherical lipid vesicle system,and investigated the regulation of membrane lipid composition.Results showed that penetration pore could be successfully formed based on the strategy of membrane fusion.The ease of intra-vesicular fusion and penetration pore formation was closely correlated with the lipid curvature properties,where negative spontaneous curvature of lipids seemed to be unfavorable for intra-vesicle fusion.Furthermore,the inner membrane tension around the pore was much larger than other regions,which governed the penetration pore size and stability.This work provided basic understanding for vesicle penetration pore formation and stabilization mechanisms.展开更多
The effects of temperature and Re content on the mechanical properties,dislocation morphology,and deformation mechanism of γ-γ′phases nickel-based single crystal superalloys are investigated by using the molecular ...The effects of temperature and Re content on the mechanical properties,dislocation morphology,and deformation mechanism of γ-γ′phases nickel-based single crystal superalloys are investigated by using the molecular dynamics method through the model of γ-γ′phases containing hole defect.The addition of Re makes the dislocation distribution tend towards the γ phase.The higher the Re content,the earlier theγphase yields,while the γ′phase yields later.Dislocation bends under the combined action of the applied force and the resistance of the Re atoms to form a bend point.The Re atoms are located at the bend points and strengthen the alloy by fixing the dislocation and preventing it from cutting the γ′phase.Dislocations nucleate first in the γ phase,causing theγphase to deform plastically before the γ′phase.As the strain increases,the dislocation length first remains unchanged,then increases rapidly,and finally fluctuates and changes.The dislocation lengths in the γ phase are larger than those in the γ′phase at different temperatures.The dislocation length shows a decreasing tendency with the increase of the temperature.Temperature can affect movement of the dislocation,and superalloys have different plastic deformation mechanisms at low,medium and high temperatures.展开更多
OSCA/TMEM63 protein families are recognized as typical mechanosensitive(MS)ion channels in both plants and animals.Resolved OSCA and TMEM63 structures have revealed that these channels are forming dimer and monomer,re...OSCA/TMEM63 protein families are recognized as typical mechanosensitive(MS)ion channels in both plants and animals.Resolved OSCA and TMEM63 structures have revealed that these channels are forming dimer and monomer,respectively.Despite the distinguished architectures,OSCA and TMEM63 serve similar functions in multiple physiological processes.Recently,human TMEM63A(hTMEM63A)structure was identified,allowing for investigation into the activation mechanism of hTMEM63A through molecular dynamics(MD)simulations.In this study,we performed multiscale MD simulations toward hTMEM63A,aiming to reveal how lipid binding regulates hTMEM63A activation.Our results identified two regions on the surface of hTMEM63A,exhibiting a preference for lysophosphatidylcholine(LPC)lipids.Further conformation analyses clarified the activation mechanism of hTMEM63A induced by LPC insertion.These simulation results provide detailed insights into the hTMEM63A–lipid interaction and significant conformational changes associated with hTMEM63A gating,thereby shed lights on the MS ion channel activation mechanism driven by lipid plugging.展开更多
基金supported by grants from the National Science Foundation of China(Grant Nos.11774272,and 12075171)。
文摘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.
基金Supported by the National Natural Science Foundation of China under Grant Nos.11504384 and 11121403computational resources provided by Supercomputing Center of Chinese Academy of Sciences(SCCAS)
文摘The lubrication characteristics of liquid crystal(LC) molecules sheared between two crystalline surfaces obtained from molecular dynamics(MD) simulations are reported in this article.We consider a coarse-grained rigid bead-necklace model of the LC molecules confined between two atomic surfaces subject to different shearing velocities.A systematic study shows that the slip length of LC lubrication changes significantly as a function of the LC-surface interaction energy,which can be well described though a theoretical curve.The slip length increases as shear rate increases at high LC-surface interaction energy.However,this trend can not be observed for low interaction energy.The orientation of the LC molecules near the surface is found to be guided by the atomics surfaces.The influence of temperature on the lubrication characteristics is also discussed in this article.
基金supported by the National Natural Science Foundation of China(No.21973064)the Post-Doctor Research Project,West China Hospital,Sichuan University(No.2021HXBH017)。
文摘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.
基金supported by the National Natural Science Foundation of China (Grant No.11574244 for G.Y.G.)the XJTU Research Fund for AI Science (Grant No.2025YXYC011 for G.Y.G.)the Hong Kong Global STEM Professorship Scheme (for X.C.Z.)。
文摘Compared to the well-studied two-dimensional(2D)ferroelectricity,the appearance of 2D antiferroelectricity is much rarer,where local dipoles from the nonequivalent sublattices within 2D monolayers are oppositely oriented.Using NbOCl_(2) monolayer with competing ferroelectric(FE)and antiferroelectric(AFE)phases as a 2D material platform,we demonstrate the emergence of intrinsic antiferroelectricity in NbOCl_(2) monolayer under experimentally accessible shear strain,along with new functionality associated with electric field-induced AFE-to-FE phase transition.Specifically,the complex configuration space accommodating FE and AFE phases,polarization switching kinetics,and finite temperature thermodynamic properties of 2D NbOCl_(2) are all accurately predicted by large-scale molecular dynamics simulations based on deep learning interatomic potential model.Moreover,room temperature stable antiferroelectricity with low polarization switching barrier and one-dimensional collinear polarization arrangement is predicted in shear-deformed NbOCl_(2) monolayer.The transition from AFE to FE phase in 2D NbOCl_(2) can be triggered by a low critical electric field,leading to a double polarization–electric(P–E)loop with small hysteresis.A new type of optoelectronic device composed of AFE-NbOCl_(2) is proposed,enabling electric“writing”and nonlinear optical“reading”logical operation with fast operation speed and low power consumption.
基金financially supported by the National Natural Science Foundation of China(Nos.52173020 and 52573023)。
文摘Vitrimers belong to a class of polymeric materials capable of bond exchange reactions,showing great promise for environmental protection and sustainable development.However,studies on the coupling mechanism between the bond exchange kinetics and segmental dynamics near the glass transition temperature(T_(g))remain scarce.Herein,we employed molecular dynamics simulations to investigate the dynamic heterogeneity of the segment motion and bond exchange in vitrimers.The simulation results revealed that the bond exchange energy barrier exerts a much stronger influence on the bond exchange kinetics than on the segmental dynamics.At lower temperatures,slower segmental relaxation further constraind the bond exchange rate.Additionally,increasing the bond exchange energy barrier markedly enhanced the dynamic heterogeneity of segment motion.A close correlation was observed between heterogeneity and bond exchange.This study elucidated the coupling mechanism between bond exchange and segmental dynamics at the molecular scale,thereby providing a theoretical basis for designing vitrimer materials with tunable dynamic properties.
基金supported by Special Funding Projects for Local Science and Technology Development guided by the Central Committee(No.YDZJSX2022C028)the Fundamental Research Program of Shanxi Province(Nos.20210302123218 and 202203021211187)+4 种基金Innovation and Entrepreneurship Training Program for College Students in Shanxi Province(202210109006)the National Natural Science Foundation(52474367)the Key Research and Development for University-Local Government Collaboration of Lvliang City(2024XDHZ01)the Scientific and Technological Innovation Programs of Higher Education Institutions in Shanxi(2025Q022)the Foundation of State Key Laboratory of Advanced Metallurgy,USTB(K22-10).
文摘The structural changes in the CaO-SiO_(2)-Al_(2)O_(3)-MgO slag system with varying CaO contents were investigated through molecular dynamics(MD)simulations,and its effect on the dissolution behavior of alumina inclusions was characterized by the Kullback-Leibler(KL)divergence.The slag structure analysis revealed that the[AlO]tetrahedral structure was the primary network structure in the slag.With increasing the CaO content,the non-bridge oxygen(NBO)content in the slag structure increases,and the bridge oxygen(BO)content decreases,thereby reducing the complexity of the slag network structure.Raman spectroscopy detection verifies the results of the MD simulations.The results indicated that the dissolution rate of alumina inclusions accelerates with increasing the CaO content in the slag,owing to the reduced complexity of the slag network structure and the enhanced interatomic interactions.The simulation results for the dissolution of alumina inclusions were consistent with theoretical calculations based on the slag inclusion capacity and the dimensionless dissolution rate of inclusions.Radial distribution function analysis demonstrated that the interaction between atoms in the slag system and alumina inclusions strengthens,increasing the dissolution rate of alumina inclusions.The[AlO_(6)]octahedral structure of the alumina inclusions is disrupted,forming BO structures,which in turn enhances the complexity of the slag network structure,slowing the dissolution rate of alumina inclusions.In contrast,the slag system with a higher CaO content has a relatively simpler network structure,promoting faster alumina inclusion dissolution.
基金financed jointly by the National Major Science and Technology Special Project on Deep Earth Exploration(2024ZD1001701-5)the National Natural Science Foundation of China(42472127,42172086)+2 种基金the Yunnan Major Project of Basic Research(202401BN070001-002)Yunnan Mineral Resources Prediction and Evaluation Engineering Research Center(2011)Innovation Team Program of Kunming University of Science and Technology,Yunnan Province。
文摘The migration mechanisms of ore-forming fluids have long been a focus in the field of ore deposit studies.Calcite is ubiquitously present in various types of rocks in the lithosphere,and the underlying mechanisms of its influence on fluid migration are of crucial importance.While previous studies have revealed that salinity changes can modulate fluid migration,the underlying mechanisms remain poorly understood.We employ molecular dynamics simulations to elucidate how salinity variations in ore-forming fluids modulate the adsorption onto calcite nanopore walls,thereby revealing the microscopic mechanisms governing ore fluid transport through calcite nano-fractures.The results show that the adsorption energy Eint of the solution on the calcite surface increased from -14,948.84±182.48 kcal/mol to -12,144.08±118.2 kcal/mol as salinity increased,which is conducive to the long-range transport of the fluid in the calcite nanopore.
基金supported by the National Science Fund for Distinguished Young Scholars(No.52425404).
文摘This study investigates the influence of hydrogen concentration at grain boundaries on the sensitivity of polycrystalline iron to hydrogen embrittlement using molecular dynamics simulations.These simulations reveal the diffusion behavior of hydrogen atoms at grain boundaries and their consequential impact on the hydrogen embrittlement sensitivity of iron alloys.The findings indicate that as the hydrogen concentration increases,both the yield strength and ultimate tensile strength of Fe-H alloys exhibit a declining trend.Moreover,the capture of hydrogen atoms at the grain boundaries significantly influences the fracture toughness of the material and promotes the formation and propagation of cracks.This study provides a novel theoretical basis for understanding and predicting the hydrogen embrittlement behavior of iron-based materials in hydrogen-rich environments,offering valuable insights for the design and development of Fe alloys with enhanced resistance to hydrogen embrittlement.
基金financially supported by the National Natural Science Foundation of China(Nos.22473105 and 22341302).
文摘This study uses all-atom molecular dynamics simulations to investigate the dislocation propagation, stress transmission, and mechanical properties in poly(p-phenylene terephthalamide) fibers under uniaxial tension. The results indicate that the dislocation propagates and the stress transfers not only along the fiber axis but also between adjacent molecular chains through hydrogen bonds, demonstrating their influence on the yield behavior. As the degree of polymerization increases, breakage of covalent bonds and interchain slippage contribute to the yield of fibers together. This work provides theoretical guidance for the design and manufacturing of high-performance fibers.
基金supported by the Natural Science Foundation of Hebei Province(E2024209052)the Youth Scholars Promotion Plan of North China University of Science and Technology(QNTJ202307).
文摘Eutectic high entropy alloys are noted for their excellent castability and comprehensive mechanical properties.The excellent mechanical properties are closely related to the activation and evolution of deformation mechanisms at the atomic scale.In this work,AlCoCrFeNi2.1 alloy is taken as the research object.The mechanical behaviors and deformation mechanisms of the FCC and B2 single crystals with different orientations and the FCC/B2 composites with K-S orientation relationship during nanoindentation processes are systematically studied by molecular dynamics simulations.The results show that the mechanical behaviors of FCC single crystals are significantly orientation-dependent,meanwhile,the indentation force of[110]single crystal is the lowest at the elastic-plastic transition point,and that for[100]single crystal is the lowest in plastic deformation stage.Compared with FCC,the stress for B2 single crystals at the elastic-plastic transition point is higher.However,more deformation systems such as stacking faults,twins and dislocation loops are activated in FCC single crystal during the plastic deformation process,resulting in higher indentation force.For composites,the flow stress increases with the increase of B2 phase thickness during the initial stage of deformation.When indenter penetrates heterogeneous interface,the significantly increased deformation system in FCC phase leads to a significant increase in indentation force.The mechanical behaviors and deformation mechanisms depend on the component single crystal.When the thickness of the component layer is less than 15 nm,the heterogeneous interfaces fail to prevent the dislocation slip and improve the indentation force.The results will enrich the plastic deformation mechanisms of multi-principal eutectic alloys and provide guidance for the design of nanocrystalline metallic materials.
基金supported by the Science and Technology Research Project from Education Department of Jilin Province (No. JJKH20231296KJ)the Natural Science Foundation of Science and Technology Department of Jilin Province (Joint Fund Project) (No. YDZJ202201ZYTS340)+9 种基金the Fundamental Research Funds for the Central Universities (No. 2412022ZD013)the Science and Technology Development Plan Project of Jilin Province (Nos. SKL202302030, SKL202402017, 20210204126YY, 20230204113YY, 20240602003RC, 20210402059GH)the National Natural Science Foundation of China (Nos. 22174137, 22322410, 92372102 and 22073094)the Cooperation Funding of Changchun with Chinese Academy of Sciences (No. 22SH13)the Capital Construction Fund Projects within the Budget of Jilin Province (No. 2023C042–5)the University Level Scientific Research Projects of Ordinary Universities in Xinjiang Uygur Autonomous Region (No. 2022YQSN002)the State Key Laboratory of Molecular Engineering of Polymers (Fudan University) (No. K2024–11)the Program for Young Scholars in Regional Development of CASthe essential support of the Network and Computing Center, CIAC, CASthe Computing Center of Jilin Province。
文摘Recent advancements in nanotechnology have spotlighted the catalytic potential of nanozymes, particularly single-atom nanozymes(SANs), which are pivotal for innovations in biosensing and medical diagnostics. Among others, DNA stands out as an ideal biological regulator. Its inherent programmability and interaction capabilities allow it to significantly modulate nanozyme activity. This study delves into the dynamic interplay between DNA and molybdenum-zinc single-atom nanozymes(Mo-Zn SANs). Using molecular dynamics simulations, we uncover how DNA influences the peroxidase-like activities of Mo-Zn SANs, providing a foundational understanding that broadens the application scope of SANs in biosensing.With these insights as a foundation, we developed and demonstrated a model aptasensor for point-ofcare testing(POCT), utilizing a label-free colorimetric approach that leverages DNA-nanozyme interactions to achieve high-sensitivity detection of lysozyme. Our work elucidates the nuanced control DNA exerts over nanozyme functionality and illustrates the application of this molecular mechanism through a smartphone-assisted biosensing platform. This study not only underscores the practical implications of DNA-regulated Mo-Zn SANs in enhancing biosensing platforms, but also highlights the potential of single-atom nanozyme technology to revolutionize diagnostic tools through its inherent versatility and sensitivity.
基金Financial support from the National Natural Science Founda-tion of China(Nos.52222409 and52074132)the National Key Research and Development Program(No.2022YFE0122000)+1 种基金Partial financial support comes from the Science and Technology Development Program of Jilin Province(No.20210301025GX)the Fundamental Research Funds for the Central Universities,JLU.
文摘The kinetic properties of Mg alloy melts are crucial for determining the forming quality of castings,as they directly affect crystal nucleation and dendritic growth.However,accurately assessing the kinetic properties of molten Mg alloys remains challenging due to the difficulties in experimentally character-izing the high-temperature melts.Herein,we propose that molecular dynamics(MD)simulations driven by deep learning based interatomic potentials(DPs),referred to as DPMD,are a promising strategy to tackle this challenge.We develop MgAl-DP,MgSi-DP,MgCa-DP,and MgZn-DP to assess the kinetic prop-erties of Mg-Al,Mg-Si,Mg-Ca,and Mg-Zn alloy melts.The reliability of our DPs is rigorously evaluated by comparing the DPMD results with those from ab initio MD(AIMD)simulations,as well as available ex-perimental results.Our theoretically evaluated viscosity of Mg-Al melts shows excellent agreement with experimental results over a wide temperature range.Additionally,we found that the solute elements Ca and Zn exhibit sluggish kinetics in the studied melts,which supporting the promising glass-forming abil-ity of the Mg-Zn-Ca alloy system.The computational efficiency of DPMD simulations is several orders of magnitude higher than that of AIMD simulations,while maintaining ab initio-level accuracy.This makes DPMD a highly feasible protocol for building a comprehensive and reliable database of kinetic properties of Mg alloy melts.
基金Project supported by the National Natural Science Foundation of China (Grant No. 52271105)。
文摘Uranium–molybdenum(U–Mo) alloys are critical for nuclear power generation and propulsion because of their superior thermal conductivity, irradiation stability, and anti-swelling properties. This study explores the plastic deformation mechanisms of γ-phase U–Mo alloys using molecular dynamics(MD) simulations. In the slip model, the generalized stacking fault energy(GSFE) and the modified Peierls–Nabarro(P–N) model are used to determine the competitive relationships among different slip systems. In the twinning model, the generalized plane fault energy(GPFE) is assessed to evaluate the competition between slip and twinning. The findings reveal that among the three slip systems, the {110}<111>slip system is preferentially activated, while in the {112}<111> system, twinning is favored over slip, as confirmed by MD tensile simulations conducted in various directions. Additionally, the impact of Mo content on deformation behavior is emphasized. Insights are provided for optimizing process conditions to avoid γ → α′′ transitions, thereby maintaining a higher proportion of γ-phase U–Mo alloys for practical applications.
基金financial support from the National Natural Science Foundation of China(Nos.52204335 and 52374319)the National Nature Science Foundation of China(No.52174291)the Central Universities Foundation of China(No.06500170)。
文摘The experiment explored the Fe_(2)O_(3) reduction process with H_(2)/CO mixed gas and confirmed a promoting effect from CO when its volume proportion in mixed gas is 20% at 850℃.The ReaxFF molecular dynamics(MD)simulation method was used to observe the reduction process and provide an atomic-level explanation.The accuracy of the parameters used in the simulation was verified by the density functional theory(DFT)calculation.The simulation shows that the initial reduction rate of H_(2) is much faster than that of CO(from 800 to 950℃).As the reduction proceeds,cementite,obtained after CO participates in the reduction at 850℃,will appear on the iron surface.Due to the active properties of C atoms in cementite,they are easy to further react with the O atoms in Fe_(2)O_(3).The generation of internal CO may destroy the dense structure of the surface layer,thereby affecting the overall reduction swelling of Fe_(2)O_(3).However,excess CO is detrimental to the reaction rate,mainly because of the poor thermodynamic conditions of CO in the temperature range and the molecular diffusion capacity is not as good as that of H_(2).Furthermore,the surface structures obtained after H_(2) and CO reduction have been compared,and it was found that the structure obtained by CO reduction has a larger surface area,thus promoting the sub sequent reaction of H_(2).
基金financially supported by the National Natural Science Foundation of China(No.U20B6003)the China Scholarship Council(No.202306440015)a project of the China Petroleum&Chemical Corporation(No.P22174)。
文摘The hybrid CO_(2) thermal technique has achieved considerable success globally in extracting residual heavy oil from reserves following a long-term steam stimulation process.Using microscopic visualization experiments and molecular dynamics(MD)simulations,this study investigates the microscopic enhanced oil recovery(EOR)mechanisms underlying residual oil removal using hybrid CO_(2) thermal systems.Based on the experimental models for the occurrence of heavy oil,this study evaluates the performance of hybrid CO_(2) thermal systems under various conditions using MD simulations.The results demonstrate that introducing CO_(2) molecules into heavy oil can effectively penetrate and decompose dense aggregates that are originally formed on hydrophobic surfaces.A stable miscible hybrid CO_(2) thermal system,with a high effective distribution ratio of CO_(2),proficiently reduces the interaction energies between heavy oil and rock surfaces,as well as within heavy oil.A visualization analysis of the interactions reveals that strong van der Waals(vdW)attractions occur between CO_(2) and heavy oil molecules,effectively promoting the decomposition and swelling of heavy oil.This unlocks the residual oil on the hydrophobic surfaces.Considering the impacts of temperature and CO_(2) concentration,an optimal gas-to-steam injection ratio(here,the CO_(2):steam ratio)ranging between 1:6 and 1:9 is recommended.This study examines the microscopic mechanisms underlying the hybrid CO_(2) thermal technique at a molecular scale,providing a significant theoretical guide for its expanded application in EOR.
基金Funded by the National Natural Science Foundation of China Academy of Engineering Physics and Jointly Setup"NSAF"Joint Fund(No.U1430119)。
文摘The multi-scale modeling combined with the cohesive zone model(CZM)and the molecular dynamics(MD)method were preformed to simulate the crack propagation in NiTi shape memory alloys(SMAs).The metallographic microscope and image processing technology were employed to achieve a quantitative grain size distribution of NiTi alloys so as to provide experimental data for molecular dynamics modeling at the atomic scale.Considering the size effect of molecular dynamics model on material properties,a reasonable modeling size was provided by taking into account three characteristic dimensions from the perspective of macro,meso,and micro scales according to the Buckinghamπtheorem.Then,the corresponding MD simulation on deformation and fracture behavior was investigated to derive a parameterized traction-separation(T-S)law,and then it was embedded into cohesive elements of finite element software.Thus,the crack propagation behavior in NiTi alloys was reproduced by the finite element method(FEM).The experimental results show that the predicted initiation fracture toughness is in good agreement with experimental data.In addition,it is found that the dynamics initiation fracture toughness increases with decreasing grain size and increasing loading velocity.
基金Project supported by the National MCF Energy Research and Development Program of China(Grant No.2018YFE0308101)the National Key Research and Development Program of China(Grant No.2018YFB0704000)+1 种基金the Suqian Science and Technology Program(Grant No.K202337)the Natural Science Foundation of the Jiangsu Higher Education Institutions of China(Grant No.23KJD490001).
文摘Using molecular dynamics methods,simulations of collision cascades in polycrystalline tungsten(W)have been conducted in this study,including different primary-knock-on atom(PKA)directions,grain sizes,and PKA energies between 1 keV and 150 keV.The results indicate that a smaller grain size leads to more defects forming in grain boundary regions during cascade processes.The impact of high-energy PKA may cause a certain degree of distortion of the grain boundaries,which has a higher probability in systems with smaller grain sizes and becomes more pronounced as the PKA energy increases.The direction of PKA can affect the formation and diffusion pathways of defects.When the PKA direction is perpendicular to the grain boundary,defects preferentially form near the grain boundary regions;by contrast,defects are more inclined to form in the interior of the grains.These results are of great significance for comprehending the changes in the performance of polycrystalline W under the high-energy fusion environments and can provide theoretical guidance for further optimization and application of W-based plasma materials.
基金supported by the National Natural Science Foundation of China(Grants Nos.T2394512,32130061,and 12172366)the Scientific Instrument Developing Project of the Chinese Academy of Sciences(Grant No.GJJSTD20220002).
文摘The formation of donut-shaped penetration pore upon membrane fusion in a closed lipid membrane system is of biological significance,since such the structures extensively exist in living body with various functions.However,the related formation dynamics is unclear because of the limitation of experimental techniques.This work developed a new model of intra-vesicular fusion to elaborate the formation and stabilization of penetration pores by employing molecular dynamics simulations,based on simplified spherical lipid vesicle system,and investigated the regulation of membrane lipid composition.Results showed that penetration pore could be successfully formed based on the strategy of membrane fusion.The ease of intra-vesicular fusion and penetration pore formation was closely correlated with the lipid curvature properties,where negative spontaneous curvature of lipids seemed to be unfavorable for intra-vesicle fusion.Furthermore,the inner membrane tension around the pore was much larger than other regions,which governed the penetration pore size and stability.This work provided basic understanding for vesicle penetration pore formation and stabilization mechanisms.
基金Project supported by the Xi’an Science and Technology Plan Project of Shaanxi Province of China(Grant No.23GXFW0086).
文摘The effects of temperature and Re content on the mechanical properties,dislocation morphology,and deformation mechanism of γ-γ′phases nickel-based single crystal superalloys are investigated by using the molecular dynamics method through the model of γ-γ′phases containing hole defect.The addition of Re makes the dislocation distribution tend towards the γ phase.The higher the Re content,the earlier theγphase yields,while the γ′phase yields later.Dislocation bends under the combined action of the applied force and the resistance of the Re atoms to form a bend point.The Re atoms are located at the bend points and strengthen the alloy by fixing the dislocation and preventing it from cutting the γ′phase.Dislocations nucleate first in the γ phase,causing theγphase to deform plastically before the γ′phase.As the strain increases,the dislocation length first remains unchanged,then increases rapidly,and finally fluctuates and changes.The dislocation lengths in the γ phase are larger than those in the γ′phase at different temperatures.The dislocation length shows a decreasing tendency with the increase of the temperature.Temperature can affect movement of the dislocation,and superalloys have different plastic deformation mechanisms at low,medium and high temperatures.
基金supported by the Natural Science Foundation of Shandong Province(Grant Nos.ZR2024QC388 and ZR2023MH101)Science and Technology Support Plan for Youth Innovation of Colleges and Universities of Shandong Province(Grant No.2020KJK006)。
文摘OSCA/TMEM63 protein families are recognized as typical mechanosensitive(MS)ion channels in both plants and animals.Resolved OSCA and TMEM63 structures have revealed that these channels are forming dimer and monomer,respectively.Despite the distinguished architectures,OSCA and TMEM63 serve similar functions in multiple physiological processes.Recently,human TMEM63A(hTMEM63A)structure was identified,allowing for investigation into the activation mechanism of hTMEM63A through molecular dynamics(MD)simulations.In this study,we performed multiscale MD simulations toward hTMEM63A,aiming to reveal how lipid binding regulates hTMEM63A activation.Our results identified two regions on the surface of hTMEM63A,exhibiting a preference for lysophosphatidylcholine(LPC)lipids.Further conformation analyses clarified the activation mechanism of hTMEM63A induced by LPC insertion.These simulation results provide detailed insights into the hTMEM63A–lipid interaction and significant conformational changes associated with hTMEM63A gating,thereby shed lights on the MS ion channel activation mechanism driven by lipid plugging.
