Like-charge pairing is a physical manifestation of the unique solvation properties of certain ion pairs in water.Water's high dielectric constant and related charge screening capability significantly influence the...Like-charge pairing is a physical manifestation of the unique solvation properties of certain ion pairs in water.Water's high dielectric constant and related charge screening capability significantly influence the interaction between like-charged ions,with the possibility to transform it-in exceptional cases when noncovalent interactions are involved-from repulsion to attraction.Guanidinium cations(Gdm^(+))represent a quintessential example of such like-charge pairing due to their specific geometry and electronic structure.In this work,we present experimental validation and quantification of Gdm^(+)-Gdm contact ion pairing in water utilizing nuclear magnetic resonance(NMR)spectroscopy complemented by molecular dynamics(MD)simulations and density functional theory(DFT)calculations.The observed Gdm^(+)-Gdm^(+)interaction is attractive albeit weak-about 0.5 kJ·mol^(-1)-which aligns with theoretical estimation from MD simulations.We contrast the behavior of Gdm^(+) with that of NH_(4)^(+) cations,which exhibit no contact ion pairing in water.DFT calculations predict that the NMR chemical shift of Gdm^(+) dimers is different than that of monomers,in agreement with NMR titration curves that display a nonlinear Langmuir-like behavior.Additionally,we conducted cryo-electron microscopy-to our knowledge,for the first time-on concentrated oligoarginines R9,which,unlike nona-lysines K9,exhibit aggregation in water.These results point to like charge pairing of the guanidinium side chain groups,as corroborated also by MD simulations and free energy calculations.展开更多
Due to their chiral structure,carbon nanosprings possess unique properties that are promising for nanotechnology applications.The structural transformations of carbon nanosprings in the form of spiral macromolecules d...Due to their chiral structure,carbon nanosprings possess unique properties that are promising for nanotechnology applications.The structural transformations of carbon nanosprings in the form of spiral macromolecules derived from planar coronene and kekulene molecules(graphene helicoids and spiral nanoribbons)are analyzed using molecular dynamics simulations.The interatomic interactions are described by a force field including valence bonds,bond angles,torsional and dihedral angles,as well as van derWaals interactions.While the tension/compression of such nanosprings has been analyzed in the literature,this study investigates other modes of deformation,including bending and twisting.Depending on the geometric characteristics of the carbon nanosprings,the formation of structural and helix reversal topological defects is described.During these structural transformations of the nanosprings,only van der Waals bonds break and recover,but breaking or recovery of covalent bonds does not take place.It is found that nanosprings demonstrate a significantly higher coefficient of axial thermal expansion than many metals and alloys.Under axial compression,Euler instability leads to lateral bending with continuous deformation of the nanospring axis at relatively low compression,while at high compression,bending kinks form.Various types of topological defects form on the instantly released nanospring during its relaxation from a highly stretched configuration.These results are useful for the development of nanosensors operating over a wide temperature range.展开更多
In Chin.Phys.B 34114704(2025),Eq.(7)and the associated unit notation were incorrect.The correct ones are present here.Since Eq.(7)is an in-built expression in the simulation package,the correction is purely typographi...In Chin.Phys.B 34114704(2025),Eq.(7)and the associated unit notation were incorrect.The correct ones are present here.Since Eq.(7)is an in-built expression in the simulation package,the correction is purely typographical and does not affect the simulation procedure,numerical results,or the conclusions.展开更多
THE mechanical response and deformation mechanisms of pure nickel under nanoindentation were systematically investigated using molecular dynamics(MD)simulations,with a particular focus on the novel interplay between c...THE mechanical response and deformation mechanisms of pure nickel under nanoindentation were systematically investigated using molecular dynamics(MD)simulations,with a particular focus on the novel interplay between crystallographic orientation,grain boundary(GB)proximity,and pore characteristics(size/location).This study compares single-crystal nickel models along[100],[110],and[111]orientations with equiaxed polycrystalline models containing 0,1,and 2.5 nm pores in surface and subsurface configurations.Our results reveal that crystallographic anisotropy manifests as a 24.4%higher elastic modulus and 22.2%greater hardness in[111]-oriented single crystals compared to[100].Pore-GB synergistic effects are found to dominate the deformation behavior:2.5 nm subsurface pores reduce hardness by 25.2%through stress concentration and dislocation annihilation at GBs,whereas surface pores enable mechanical recovery via accelerated dislocation generation post-collapse.Additionally,size-dependent deformation regimes were identified,with 1 nm pores inducing negligible perturbation due to rapid atomic rearrangement,in contrast with persistent softening in 2.5 nm pores.These findings establish atomic-scale design principles for defect engineering in nickel-based aerospace components,demonstrating how crystallographic orientation,pore configuration,and GB interactions collectively govern nanoindentation behavior.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
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 von Hippel-Lindau tumor suppressor(VHL)has been extensively used to develop degraders targeting numerous proteins of interest.However,studies on the rational design of VHL-proteolysis-targeting chimeras(PROTACs)re...The von Hippel-Lindau tumor suppressor(VHL)has been extensively used to develop degraders targeting numerous proteins of interest.However,studies on the rational design of VHL-proteolysis-targeting chimeras(PROTACs)remain scarce.This study aimed to develop strategies to investigate VHL-recruiting PROTACs connecting with varying attachment sites on VHL ligands,which could be utilized for KRAS^(G12C) degraders development and expanded to additional targets.We developed a molecular dynamics(MD)-based strategy to explore the stability of ternary complexes induced by KRAS^(G12C) PROTACs with four distinct attachment sites of VH032.We found a potent degrader namely YN14-H,linked to hydroxyl group on VH032 benzene ring,exhibited the most superior ability of inducing ternary complexes,reflected by the lowest dissociation constant(Kd)for ternary complex induction and the highest AlphaScreen(AS)-based interaction.YN14-H inhibited cell growth with low nanomolar half maximal inhibitory concentration(IC_(50))and half maximal degradation concentration(DC_(50))values as well as>98%of maximum degradation(D_(max))in NCI-H358 and MIA PaCa-2 cells harboring KRAS^(G12C)-mutation.Mechanistically,YN14-H significantly induced apoptosis and inhibited the migratory capacity.Notably,YN14-H demonstrated favorable pharmacokinetic properties and excellent antitumor activity in vivo.Furthermore,bromodomain-containing protein 7(BRD7)and Bruton tyrosine kinase(BTK)degraders attached to distinct sites on VH032 further verified the rationality and universality of our MD-based strategies.Our findings demonstrated that YN14-H could serve as a promising candidate for the treatment of tumors with KRAS^(G12C)-mutation and present a strategy for the rational design of VHL-recruiting PROTACs that target additional proteins at distinct attachment sites.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
MgO has been shown to facilitate the precipitation of MgO-rich crystalline phases within the MgO-CaO-Al_(2)O_(3)-SiO_(2)(MCAS)glassy inclusion system,which possesses a high liquidus temperature and a significant Young...MgO has been shown to facilitate the precipitation of MgO-rich crystalline phases within the MgO-CaO-Al_(2)O_(3)-SiO_(2)(MCAS)glassy inclusion system,which possesses a high liquidus temperature and a significant Young’s modulus.The underlying linkage between the structural evolution and the crystallization characteristics of the MCAS system was systematically investigated using molecular dynamics simulation and thermodynamic calculation.The results revealed that Mg^(2+) ions played a dual role,constructing networks through the formation of tricluster oxygens while consuming bridging oxygens(BOs)in a mechanism similar to Ca^(2+) ions.However,despite this dual role,the network connectivity was still decreased with the increase in MgO/(MgO+Al_(2)O_(3))(M/(M+A))and CaO/(CaO+SiO_(2))(C/(C+S))ratios,primarily due to the reduction in BOs.This microscopic structural evolution resulted in a reduction in viscosity and an enhancement of crystallization ability.Furthermore,the remarkable diffusion capability of Mg^(2+) ions,coupled with the increased proportion of 6-coordinated Mg^(2+)ions,unveiled the mechanism underlying the precipitation of MgSiO_(3) and Mg_(2)SiO_(4) crystals,which exhibited high Young’s moduli of 165.23 and 196.67 GPa,respectively.To prevent the precipitation of MgO-rich crystalline phases,it was crucial to maintain the M/(M+A)ratio below 0.42 and the C/(C+S)ratio below 0.16 within the MCAS system.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
Ionic liquids(ILs)have exhibited great application potential in many fields due to their unique properties.Molecular dynamics(MD)simulation has been widely employed to investigate their microscopic structure.However,c...Ionic liquids(ILs)have exhibited great application potential in many fields due to their unique properties.Molecular dynamics(MD)simulation has been widely employed to investigate their microscopic structure.However,classical molecular dynamics simulations struggle to accurately describe the complex interactions in ILs using the existing parameterized force fields.Recently,the MD simulations based on machine learning force fields(MLFFs)trained by first-principles calculations have attracted considerable attentions due to their abilities to balance computational accuracy and efficiency.Herein,we report the Bayesian-based MLFFs which can be successfully applied in IL systems and accelerate MD simulation.The calculated atomic forces,structures,and vibrational behaviors were validated to match the accuracy of firstprinciples calculations.Properties of the imidazolium-based ILs,including density,self-diffusion coefficients,viscosity,and radial distribution functions were predicted at the extended scales.Z-bonds that describe the unique structures in ILs were analyzed and the influences of Cpositions,temperature,and solvent H2O on Z-bonding configurations were systematically investigated.Our results confirmed that MLFFs presented the strong feasibility to investigate the large and complex systems,especially to predict structures and properties of the ILs.And the procedure described for MLFFs provides valuable guidance for researchers who are studying ILs.展开更多
The global energy demand is increasing rapidly,and it is imperative to develop shale hydrocarbon re-sources vigorously.The prerequisite for enhancing the exploitation efficiency of shale reservoirs is the systematic e...The global energy demand is increasing rapidly,and it is imperative to develop shale hydrocarbon re-sources vigorously.The prerequisite for enhancing the exploitation efficiency of shale reservoirs is the systematic elucidation of the occurrence characteristics,flow behavior,and enhanced oil recovery(EOR)mechanisms of shale oil within commonly developed nanopores.Molecular dynamics(MD)technique can simulate the occurrence,flow,and extraction processes of shale oil at the nanoscale,and then quantitatively characterize various fluid properties,flow characteristics,and action mechanisms under different reservoir conditions by calculating and analyzing a series of MD parameters.However,the existing review on the application of MD simulation in shale oil reservoirs is not systematic enough and lacks a summary of technical challenges and solutions.Therefore,recent MD studies on shale oil res-ervoirs were summarized and analyzed.Firstly,the applicability of force fields and ensembles of MD in shale reservoirs with different reservoir conditions and fluid properties was discussed.Subsequently,the calculation methods and application examples of MD parameters characterizing various properties of fluids at the microscale were summarized.Then,the application of MD simulation in the study of shale oil occurrence characteristics,flow behavior,and EOR mechanisms was reviewed,along with the elucidation of corresponding micro-mechanisms.Moreover,influencing factors of pore structure,wall properties,reservoir conditions,fluid components,injection/production parameters,formation water,and inorganic salt ions were analyzed,and some new conclusions were obtained.Finally,the main challenges associated with the application of MD simulations to shale oil reservoirs were discussed,and reasonable prospects for future MD research directions were proposed.The purpose of this review is to provide theoretical basis and methodological support for applying MD simulation to study shale oil reservoirs.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
Increasing evidence showed that histone deacetylase 6(HDAC6)dysfunction is directly associated with the onset and progression of various diseases,especially cancers,making the development of HDAC6-targeted anti-tumor ...Increasing evidence showed that histone deacetylase 6(HDAC6)dysfunction is directly associated with the onset and progression of various diseases,especially cancers,making the development of HDAC6-targeted anti-tumor agents a research hotspot.In this study,artificial intelligence(AI)technology and molecular simulation strategies were fully integrated to construct an efficient and precise drug screening pipeline,which combined Voting strategy based on compound-protein interaction(CPI)prediction models,cascade molecular docking,and molecular dynamic(MD)simulations.The biological potential of the screened compounds was further evaluated through enzymatic and cellular activity assays.Among the identified compounds,Cmpd.18 exhibited more potent HDAC6 enzyme inhibitory activity(IC_(50)=5.41 nM)than that of tubastatin A(TubA)(IC_(50)=15.11 nM),along with a favorable subtype selectivity profile(selectivity index z 117.23 for HDAC1),which was further verified by the Western blot analysis.Additionally,Cmpd.18 induced G2/M phase arrest and promoted apoptosis in HCT-116 cells,exerting desirable antiproliferative activity(IC_(50)=2.59 mM).Furthermore,based on long-term MD simulation trajectory,the key residues facilitating Cmpd.18's binding were identified by decomposition free energy analysis,thereby elucidating its binding mechanism.Moreover,the representative conformation analysis also indicated that Cmpd.18 could stably bind to the active pocket in an effective conformation,thus demonstrating the potential for in-depth research of the 2-(2-phenoxyethyl)pyridazin-3(2H)-one scaffold.展开更多
The extraordinary strength of metal/graphene composites is significantly determined by the characteristic size,distribution and morphology of graphene.However,the effect of the graphene size/distribution on the mechan...The extraordinary strength of metal/graphene composites is significantly determined by the characteristic size,distribution and morphology of graphene.However,the effect of the graphene size/distribution on the mechanical properties and related strengthening mechanisms has not been fully elucidated.Herein,under the same volume fraction and distribution conditions of graphene,molecular dynamics simulations were used to investigate the effect of graphene sheet size on the hardness and deformation behavior of Cu/graphene composites under complex stress field.Two models of pure single crystalline Cu and graphene fully covered Cu matrix composite were constructed for comparison.The results show that the strengthening effect changes with varying the graphene sheet size.Besides the graphene dislocation blocking effect and the load-bearing effect,the deformation mechanisms change from stacking fault tetrahedron,dislocation bypassing and dislocation cutting to dislocation nucleation in turn with decreasing the graphene sheet size.The hardness of Cu/graphene composite,with the graphene sheet not completely covering the metal matrix,can even be higher than that of the fully covered composite.The extra strengthening mechanisms of dislocation bypassing mechanism and the stacking fault tetrahedra pinning dislocation mechanism contribute to the increase in hardness.展开更多
Carbon nanotube formation exemplifies atomically precise self-assembly,where atomic interactions dynamically engineer nanoscale architectures with emergent properties that transcend classical material boundaries.Howev...Carbon nanotube formation exemplifies atomically precise self-assembly,where atomic interactions dynamically engineer nanoscale architectures with emergent properties that transcend classical material boundaries.However,elucidating the transient molecular intermediates remains a critical mechanistic frontier.This study investigates the atomic-scale nucleation process of single-walled carbon nanotubes(SWCNTs)from acetylene on iron(Fe)clusters,utilizing GFN(-x)TB-based nanoreactor molecular dynamics simulations.The simulations reveal a consistent nucleation pathway,regardless of iron cluster size(Fe_(13),Fe_(38),Fe_(55)),where the chemisorption and dissociation of acetylene molecules on the Fe clusters lead to the formation of C_(2)H and C_(2)intermediates.These species then undergo oligomerization,initiating the growth of carbon chains.As the chains cross-link and cyclize,five-membered carbon rings are preferentially formed,which eventually evolve into six-membered rings and more complex sp2-hybridized carbon networks,resembling the cap structures of nascent SWCNTs.Although the nucleation mechanism remains similar across all cluster sizes,larger clusters show enhanced catalytic activity,leading to higher molecular weight hydrocarbons and more extensive carbocyclic networks due to their higher density of active sites per reacting molecule.Crucially,the study highlights the role of C_(2)H as the key active species in the carbon network formation process.These findings offer critical insights into the initial stages of SWCNT nucleation,contributing to a deeper understanding of the mechanisms driving SWCNT growth and guiding the development of optimized synthetic strategies.展开更多
Background:In this present study,we have screened major phytoconstituents of Nilavembu Kudineer against critical COVID-19 target proteins that cause severe pneumonia globally.In addition,a human receptor protein that ...Background:In this present study,we have screened major phytoconstituents of Nilavembu Kudineer against critical COVID-19 target proteins that cause severe pneumonia globally.In addition,a human receptor protein that facilitates viral entry into the host cell was also targeted.Methods:Phytoconstituents derived from Nilavembu Kudineer formulation were docked against 12 major proteins,which help viral entry,viral proliferation,and a human receptor facilitate the viral entry into the host cells.The major metabolites of Nilavembu Kudineer were retrieved based on literature from the PubChem database.The docked complex was subjected to MD simulation studies to verify its binding mode and the stability of the interactions.The binding energy analysis was performed to estimate the binding affinity between the compounds and their respective receptors using MM/GBSA.Results:Docking studies have shown that three major plants in the polyherbal formulation,Andrographis paniculata,Mollugo cerviana,and Zingiber officinale,have 14 potential compounds that have better binding affinity against COVID-19 proteins and their host receptor protein.MD studies and binding energy calculations also confirmed that these compounds possess better stability and strong binding energy with these proteins.Conclusion:In silico analyses suggest that phytoconstituents from Nilavembu Kudineer possess promising multi-target antiviral activity against COVID-19.These findings provide a rationale for further experimental studies to validate their therapeutic potential for the treatment of COVID-19.展开更多
A microscopic understanding of the complex solute-defect interaction is pivotal for optimizing the alloy’s macroscopic mechanical properties.Simulating solute segregation in a plastically deformed crystalline system ...A microscopic understanding of the complex solute-defect interaction is pivotal for optimizing the alloy’s macroscopic mechanical properties.Simulating solute segregation in a plastically deformed crystalline system at atomic resolution remains challenging.The objective is to efficiently model and predict a phys-ically informed segregated solute distribution rather than simulating a series of diffusion kinetics.To ad-dress this objective,we coupled molecular dynamics(MD)and Monte Carlo(MC)methods using a novel method based on virtual atoms technique.We applied our MD-MC coupling approach to model off-lattice carbon(C)solute segregation in nanoindented Fe-C samples containing complex dislocation networks.Our coupling framework yielded the final configuration through efficient parallelization and localized en-ergy computations,showing C Cottrell atmospheres near dislocations.Different initial C concentrations resulted in a consistent trend of C atoms migrating from less crystalline distortion to high crystalline distortion regions.Besides unraveling the strong spatial correlation between local C concentration and defect regions,our results revealed two crucial aspects of solute segregation preferences:(1)defect ener-getics hierarchy and(2)tensile strain fields near dislocations.The proposed approach is generic and can be applied to other material systems as well.展开更多
This study explores green and low-viscosity deep eutectic solvents(DESs) for the efficient extraction of quinoline(QUI) from wash oil.The hydrogen bond donors and acceptors constituting DESs were initially screened ba...This study explores green and low-viscosity deep eutectic solvents(DESs) for the efficient extraction of quinoline(QUI) from wash oil.The hydrogen bond donors and acceptors constituting DESs were initially screened based on thermodynamic properties predicted by the conductor-like screening model for real solvents(COSMO-RS),followed by further selection considering the viscosity and cost of the formed DESs.Phase equilibrium experiments showed that the DES composed of triethylmethylammonium chloride and formic acid exhibited the best extraction performance among the selected candidates.Key extraction parameters were optimized experimentally,achieving a maximum QUI extraction efficiency of 97.18% under mild conditions.Molecular dynamics simulations revealed that the interactions between quaternary ammonium cations and QUI play a crucial role in the extraction mechanism.This study provides insights into the use of DESs for QUI extraction and demonstrates their potential for application to other coal tar derivatives.展开更多
基金support from the project“National Institute of Virology and Bacteriology(Program EXCELES,ID Project No.LX22NPO5103)Funded by the European Union-Next Generation EU".D.B.also acknowledges VSB-Technical University of Ostrava,IT4Innovations National Supercomputing Center,Czech Republic,for awarding this project access to the LUMI supercomputer,owned by the EuroHPC Joint Undertaking,hosted by CSC(Finland)and the LUMI consortium through the Ministry of Education,Youth and Sports of the Czech Republic through the e-INFRA CZ(Grant ID:90254)+4 种基金project OPEN-35-3.M.V.and J.H.acknowledge the Czech Science Foundation for support via grant number 25-16117S and the project"The Energy Conversion and Storage"funded as project No.CZ.02.01.01/00/22_008/0004617 by Programme Johannes Amos Comeniuscall Excellent Research.M.V.also acknowledges support by the Ministry of Education,Youth and Sports of the Czech Republic through the e-INFRA CZ(ID:90254)Project OPEN-30-53.P.J.acknowledges support from the European Research Council via an ERC Advanced Grant no.101095957The authors would like to acknowledge the contribution of COST Action CA21169,supported by COST(European Cooperation in Science and Technology).
文摘Like-charge pairing is a physical manifestation of the unique solvation properties of certain ion pairs in water.Water's high dielectric constant and related charge screening capability significantly influence the interaction between like-charged ions,with the possibility to transform it-in exceptional cases when noncovalent interactions are involved-from repulsion to attraction.Guanidinium cations(Gdm^(+))represent a quintessential example of such like-charge pairing due to their specific geometry and electronic structure.In this work,we present experimental validation and quantification of Gdm^(+)-Gdm contact ion pairing in water utilizing nuclear magnetic resonance(NMR)spectroscopy complemented by molecular dynamics(MD)simulations and density functional theory(DFT)calculations.The observed Gdm^(+)-Gdm^(+)interaction is attractive albeit weak-about 0.5 kJ·mol^(-1)-which aligns with theoretical estimation from MD simulations.We contrast the behavior of Gdm^(+) with that of NH_(4)^(+) cations,which exhibit no contact ion pairing in water.DFT calculations predict that the NMR chemical shift of Gdm^(+) dimers is different than that of monomers,in agreement with NMR titration curves that display a nonlinear Langmuir-like behavior.Additionally,we conducted cryo-electron microscopy-to our knowledge,for the first time-on concentrated oligoarginines R9,which,unlike nona-lysines K9,exhibit aggregation in water.These results point to like charge pairing of the guanidinium side chain groups,as corroborated also by MD simulations and free energy calculations.
基金funded by the Russian Science Foundation(RSF),grant No.25-73-20038(conceptualization,methodology,manuscript writing).
文摘Due to their chiral structure,carbon nanosprings possess unique properties that are promising for nanotechnology applications.The structural transformations of carbon nanosprings in the form of spiral macromolecules derived from planar coronene and kekulene molecules(graphene helicoids and spiral nanoribbons)are analyzed using molecular dynamics simulations.The interatomic interactions are described by a force field including valence bonds,bond angles,torsional and dihedral angles,as well as van derWaals interactions.While the tension/compression of such nanosprings has been analyzed in the literature,this study investigates other modes of deformation,including bending and twisting.Depending on the geometric characteristics of the carbon nanosprings,the formation of structural and helix reversal topological defects is described.During these structural transformations of the nanosprings,only van der Waals bonds break and recover,but breaking or recovery of covalent bonds does not take place.It is found that nanosprings demonstrate a significantly higher coefficient of axial thermal expansion than many metals and alloys.Under axial compression,Euler instability leads to lateral bending with continuous deformation of the nanospring axis at relatively low compression,while at high compression,bending kinks form.Various types of topological defects form on the instantly released nanospring during its relaxation from a highly stretched configuration.These results are useful for the development of nanosensors operating over a wide temperature range.
文摘In Chin.Phys.B 34114704(2025),Eq.(7)and the associated unit notation were incorrect.The correct ones are present here.Since Eq.(7)is an in-built expression in the simulation package,the correction is purely typographical and does not affect the simulation procedure,numerical results,or the conclusions.
基金The National Natural Science Foundation of China(Grant No.12462006)Beijing Institute of Structure and Environment Engineering Joint Innovation Fund(No.BQJJ202414).
文摘THE mechanical response and deformation mechanisms of pure nickel under nanoindentation were systematically investigated using molecular dynamics(MD)simulations,with a particular focus on the novel interplay between crystallographic orientation,grain boundary(GB)proximity,and pore characteristics(size/location).This study compares single-crystal nickel models along[100],[110],and[111]orientations with equiaxed polycrystalline models containing 0,1,and 2.5 nm pores in surface and subsurface configurations.Our results reveal that crystallographic anisotropy manifests as a 24.4%higher elastic modulus and 22.2%greater hardness in[111]-oriented single crystals compared to[100].Pore-GB synergistic effects are found to dominate the deformation behavior:2.5 nm subsurface pores reduce hardness by 25.2%through stress concentration and dislocation annihilation at GBs,whereas surface pores enable mechanical recovery via accelerated dislocation generation post-collapse.Additionally,size-dependent deformation regimes were identified,with 1 nm pores inducing negligible perturbation due to rapid atomic rearrangement,in contrast with persistent softening in 2.5 nm pores.These findings establish atomic-scale design principles for defect engineering in nickel-based aerospace components,demonstrating how crystallographic orientation,pore configuration,and GB interactions collectively govern nanoindentation behavior.
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supported by National Natural Science Foundation of China(No.82404417)State Key Laboratory of National Security Specially Needed Medicines Program(No.LTMC2022Zz006).
文摘The von Hippel-Lindau tumor suppressor(VHL)has been extensively used to develop degraders targeting numerous proteins of interest.However,studies on the rational design of VHL-proteolysis-targeting chimeras(PROTACs)remain scarce.This study aimed to develop strategies to investigate VHL-recruiting PROTACs connecting with varying attachment sites on VHL ligands,which could be utilized for KRAS^(G12C) degraders development and expanded to additional targets.We developed a molecular dynamics(MD)-based strategy to explore the stability of ternary complexes induced by KRAS^(G12C) PROTACs with four distinct attachment sites of VH032.We found a potent degrader namely YN14-H,linked to hydroxyl group on VH032 benzene ring,exhibited the most superior ability of inducing ternary complexes,reflected by the lowest dissociation constant(Kd)for ternary complex induction and the highest AlphaScreen(AS)-based interaction.YN14-H inhibited cell growth with low nanomolar half maximal inhibitory concentration(IC_(50))and half maximal degradation concentration(DC_(50))values as well as>98%of maximum degradation(D_(max))in NCI-H358 and MIA PaCa-2 cells harboring KRAS^(G12C)-mutation.Mechanistically,YN14-H significantly induced apoptosis and inhibited the migratory capacity.Notably,YN14-H demonstrated favorable pharmacokinetic properties and excellent antitumor activity in vivo.Furthermore,bromodomain-containing protein 7(BRD7)and Bruton tyrosine kinase(BTK)degraders attached to distinct sites on VH032 further verified the rationality and universality of our MD-based strategies.Our findings demonstrated that YN14-H could serve as a promising candidate for the treatment of tumors with KRAS^(G12C)-mutation and present a strategy for the rational design of VHL-recruiting PROTACs that target additional proteins at distinct attachment sites.
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support from the National Key R&D Program of China(Grant Nos.2023YFB3709900 and 2023YFB3709903)the National Natural Science Foundation of China(Grant Nos.52174293 and U22A20171)+1 种基金the High Steel Center(HSC)at North China University of TechnologyUniversity of Science and Technology Beijing(USTB).
文摘MgO has been shown to facilitate the precipitation of MgO-rich crystalline phases within the MgO-CaO-Al_(2)O_(3)-SiO_(2)(MCAS)glassy inclusion system,which possesses a high liquidus temperature and a significant Young’s modulus.The underlying linkage between the structural evolution and the crystallization characteristics of the MCAS system was systematically investigated using molecular dynamics simulation and thermodynamic calculation.The results revealed that Mg^(2+) ions played a dual role,constructing networks through the formation of tricluster oxygens while consuming bridging oxygens(BOs)in a mechanism similar to Ca^(2+) ions.However,despite this dual role,the network connectivity was still decreased with the increase in MgO/(MgO+Al_(2)O_(3))(M/(M+A))and CaO/(CaO+SiO_(2))(C/(C+S))ratios,primarily due to the reduction in BOs.This microscopic structural evolution resulted in a reduction in viscosity and an enhancement of crystallization ability.Furthermore,the remarkable diffusion capability of Mg^(2+) ions,coupled with the increased proportion of 6-coordinated Mg^(2+)ions,unveiled the mechanism underlying the precipitation of MgSiO_(3) and Mg_(2)SiO_(4) crystals,which exhibited high Young’s moduli of 165.23 and 196.67 GPa,respectively.To prevent the precipitation of MgO-rich crystalline phases,it was crucial to maintain the M/(M+A)ratio below 0.42 and the C/(C+S)ratio below 0.16 within the MCAS system.
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 National Natural Science Foundation of China(Nos.22278397)the Fundamental Research Funds for the Central Universities(2024SMECP01).
文摘Ionic liquids(ILs)have exhibited great application potential in many fields due to their unique properties.Molecular dynamics(MD)simulation has been widely employed to investigate their microscopic structure.However,classical molecular dynamics simulations struggle to accurately describe the complex interactions in ILs using the existing parameterized force fields.Recently,the MD simulations based on machine learning force fields(MLFFs)trained by first-principles calculations have attracted considerable attentions due to their abilities to balance computational accuracy and efficiency.Herein,we report the Bayesian-based MLFFs which can be successfully applied in IL systems and accelerate MD simulation.The calculated atomic forces,structures,and vibrational behaviors were validated to match the accuracy of firstprinciples calculations.Properties of the imidazolium-based ILs,including density,self-diffusion coefficients,viscosity,and radial distribution functions were predicted at the extended scales.Z-bonds that describe the unique structures in ILs were analyzed and the influences of Cpositions,temperature,and solvent H2O on Z-bonding configurations were systematically investigated.Our results confirmed that MLFFs presented the strong feasibility to investigate the large and complex systems,especially to predict structures and properties of the ILs.And the procedure described for MLFFs provides valuable guidance for researchers who are studying ILs.
基金supported by the National Natural Science Foundation of China(52304021,52104022,52204031)the Natural Science Foundation of Sichuan Province(2022NSFSC0205,2024NSFSC0201,2023NSFSC0947)the National Science and Technology Major Projects of China(2017ZX05049006-010).
文摘The global energy demand is increasing rapidly,and it is imperative to develop shale hydrocarbon re-sources vigorously.The prerequisite for enhancing the exploitation efficiency of shale reservoirs is the systematic elucidation of the occurrence characteristics,flow behavior,and enhanced oil recovery(EOR)mechanisms of shale oil within commonly developed nanopores.Molecular dynamics(MD)technique can simulate the occurrence,flow,and extraction processes of shale oil at the nanoscale,and then quantitatively characterize various fluid properties,flow characteristics,and action mechanisms under different reservoir conditions by calculating and analyzing a series of MD parameters.However,the existing review on the application of MD simulation in shale oil reservoirs is not systematic enough and lacks a summary of technical challenges and solutions.Therefore,recent MD studies on shale oil res-ervoirs were summarized and analyzed.Firstly,the applicability of force fields and ensembles of MD in shale reservoirs with different reservoir conditions and fluid properties was discussed.Subsequently,the calculation methods and application examples of MD parameters characterizing various properties of fluids at the microscale were summarized.Then,the application of MD simulation in the study of shale oil occurrence characteristics,flow behavior,and EOR mechanisms was reviewed,along with the elucidation of corresponding micro-mechanisms.Moreover,influencing factors of pore structure,wall properties,reservoir conditions,fluid components,injection/production parameters,formation water,and inorganic salt ions were analyzed,and some new conclusions were obtained.Finally,the main challenges associated with the application of MD simulations to shale oil reservoirs were discussed,and reasonable prospects for future MD research directions were proposed.The purpose of this review is to provide theoretical basis and methodological support for applying MD simulation to study shale oil reservoirs.
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funded by Central Guidance on Local Science and Technology Development Fund of Hebei Province,China(Grant No.:226Z2605G)the Key Project from Hebei Provincial Department of Science and Technology,China(Grant No.:21372601D)+6 种基金Graduate Student Innovation Grant Program of Hebei Medical University,China(Grant No.:XCXZZB202303)Science Research Project of Hebei Education Department,China(Grant Nos.:BJ2025046,and CYZD202501)Program for Young Scientists in the Field of Natural Science of Hebei Medical University,China(Program Nos.:CYCZ2023010,CYCZ2023011,CYQD2021011,CYQD2021015 and CYQD2023012)Traditional Chinese Medicine Administration Project of Hebei Province,China(Project No.:2025427)National Natural Science Foundation of China(Grant No.:32100771)the Hebei Provincial Medical Science Research Project Plan,China(Project Nos.:20240241 and 20220200)Shijiazhuang Science and Technology Bureau,China(Grant Nos.:241200487A,and 07202204).
文摘Increasing evidence showed that histone deacetylase 6(HDAC6)dysfunction is directly associated with the onset and progression of various diseases,especially cancers,making the development of HDAC6-targeted anti-tumor agents a research hotspot.In this study,artificial intelligence(AI)technology and molecular simulation strategies were fully integrated to construct an efficient and precise drug screening pipeline,which combined Voting strategy based on compound-protein interaction(CPI)prediction models,cascade molecular docking,and molecular dynamic(MD)simulations.The biological potential of the screened compounds was further evaluated through enzymatic and cellular activity assays.Among the identified compounds,Cmpd.18 exhibited more potent HDAC6 enzyme inhibitory activity(IC_(50)=5.41 nM)than that of tubastatin A(TubA)(IC_(50)=15.11 nM),along with a favorable subtype selectivity profile(selectivity index z 117.23 for HDAC1),which was further verified by the Western blot analysis.Additionally,Cmpd.18 induced G2/M phase arrest and promoted apoptosis in HCT-116 cells,exerting desirable antiproliferative activity(IC_(50)=2.59 mM).Furthermore,based on long-term MD simulation trajectory,the key residues facilitating Cmpd.18's binding were identified by decomposition free energy analysis,thereby elucidating its binding mechanism.Moreover,the representative conformation analysis also indicated that Cmpd.18 could stably bind to the active pocket in an effective conformation,thus demonstrating the potential for in-depth research of the 2-(2-phenoxyethyl)pyridazin-3(2H)-one scaffold.
基金Foundation of Northwest Institute for Nonferrous Metal Research(ZZXJ2203)Capital Projects of Financial Department of Shaanxi Province(YK22C-12)+3 种基金Innovation Capability Support Plan in Shaanxi Province(2023KJXX-083)Key Research and Development Projects of Shaanxi Province(2024GXYBXM-351,2024GX-YBXM-356)National Natural Science Foundation of China(62204207,12204383)Xi'an Postdoctoral Innovation Base Funding Program。
文摘The extraordinary strength of metal/graphene composites is significantly determined by the characteristic size,distribution and morphology of graphene.However,the effect of the graphene size/distribution on the mechanical properties and related strengthening mechanisms has not been fully elucidated.Herein,under the same volume fraction and distribution conditions of graphene,molecular dynamics simulations were used to investigate the effect of graphene sheet size on the hardness and deformation behavior of Cu/graphene composites under complex stress field.Two models of pure single crystalline Cu and graphene fully covered Cu matrix composite were constructed for comparison.The results show that the strengthening effect changes with varying the graphene sheet size.Besides the graphene dislocation blocking effect and the load-bearing effect,the deformation mechanisms change from stacking fault tetrahedron,dislocation bypassing and dislocation cutting to dislocation nucleation in turn with decreasing the graphene sheet size.The hardness of Cu/graphene composite,with the graphene sheet not completely covering the metal matrix,can even be higher than that of the fully covered composite.The extra strengthening mechanisms of dislocation bypassing mechanism and the stacking fault tetrahedra pinning dislocation mechanism contribute to the increase in hardness.
基金supported by the National Key R&D Program of China(2022YFA1604100)the National Natural Science Foundation of China(22302220,22372187,1972157,21972160,22402218)+2 种基金the National Science Fund for Distinguished Young Scholars of China(22225206)the Fundamental Research Program of Shanxi Province(202203021222403)the Youth Innovation Promotion Association CAS(2020179)。
文摘Carbon nanotube formation exemplifies atomically precise self-assembly,where atomic interactions dynamically engineer nanoscale architectures with emergent properties that transcend classical material boundaries.However,elucidating the transient molecular intermediates remains a critical mechanistic frontier.This study investigates the atomic-scale nucleation process of single-walled carbon nanotubes(SWCNTs)from acetylene on iron(Fe)clusters,utilizing GFN(-x)TB-based nanoreactor molecular dynamics simulations.The simulations reveal a consistent nucleation pathway,regardless of iron cluster size(Fe_(13),Fe_(38),Fe_(55)),where the chemisorption and dissociation of acetylene molecules on the Fe clusters lead to the formation of C_(2)H and C_(2)intermediates.These species then undergo oligomerization,initiating the growth of carbon chains.As the chains cross-link and cyclize,five-membered carbon rings are preferentially formed,which eventually evolve into six-membered rings and more complex sp2-hybridized carbon networks,resembling the cap structures of nascent SWCNTs.Although the nucleation mechanism remains similar across all cluster sizes,larger clusters show enhanced catalytic activity,leading to higher molecular weight hydrocarbons and more extensive carbocyclic networks due to their higher density of active sites per reacting molecule.Crucially,the study highlights the role of C_(2)H as the key active species in the carbon network formation process.These findings offer critical insights into the initial stages of SWCNT nucleation,contributing to a deeper understanding of the mechanisms driving SWCNT growth and guiding the development of optimized synthetic strategies.
文摘Background:In this present study,we have screened major phytoconstituents of Nilavembu Kudineer against critical COVID-19 target proteins that cause severe pneumonia globally.In addition,a human receptor protein that facilitates viral entry into the host cell was also targeted.Methods:Phytoconstituents derived from Nilavembu Kudineer formulation were docked against 12 major proteins,which help viral entry,viral proliferation,and a human receptor facilitate the viral entry into the host cells.The major metabolites of Nilavembu Kudineer were retrieved based on literature from the PubChem database.The docked complex was subjected to MD simulation studies to verify its binding mode and the stability of the interactions.The binding energy analysis was performed to estimate the binding affinity between the compounds and their respective receptors using MM/GBSA.Results:Docking studies have shown that three major plants in the polyherbal formulation,Andrographis paniculata,Mollugo cerviana,and Zingiber officinale,have 14 potential compounds that have better binding affinity against COVID-19 proteins and their host receptor protein.MD studies and binding energy calculations also confirmed that these compounds possess better stability and strong binding energy with these proteins.Conclusion:In silico analyses suggest that phytoconstituents from Nilavembu Kudineer possess promising multi-target antiviral activity against COVID-19.These findings provide a rationale for further experimental studies to validate their therapeutic potential for the treatment of COVID-19.
基金the funding from the Ger-man Research Foundation(DFG)-BE 5360/1-1 and ThyssenKrupp Europe.
文摘A microscopic understanding of the complex solute-defect interaction is pivotal for optimizing the alloy’s macroscopic mechanical properties.Simulating solute segregation in a plastically deformed crystalline system at atomic resolution remains challenging.The objective is to efficiently model and predict a phys-ically informed segregated solute distribution rather than simulating a series of diffusion kinetics.To ad-dress this objective,we coupled molecular dynamics(MD)and Monte Carlo(MC)methods using a novel method based on virtual atoms technique.We applied our MD-MC coupling approach to model off-lattice carbon(C)solute segregation in nanoindented Fe-C samples containing complex dislocation networks.Our coupling framework yielded the final configuration through efficient parallelization and localized en-ergy computations,showing C Cottrell atmospheres near dislocations.Different initial C concentrations resulted in a consistent trend of C atoms migrating from less crystalline distortion to high crystalline distortion regions.Besides unraveling the strong spatial correlation between local C concentration and defect regions,our results revealed two crucial aspects of solute segregation preferences:(1)defect ener-getics hierarchy and(2)tensile strain fields near dislocations.The proposed approach is generic and can be applied to other material systems as well.
基金financially supported by the Natural Science Foundation of Shanxi Province (20210302123167)National Key Research and Development Program (2022YFC3902505)。
文摘This study explores green and low-viscosity deep eutectic solvents(DESs) for the efficient extraction of quinoline(QUI) from wash oil.The hydrogen bond donors and acceptors constituting DESs were initially screened based on thermodynamic properties predicted by the conductor-like screening model for real solvents(COSMO-RS),followed by further selection considering the viscosity and cost of the formed DESs.Phase equilibrium experiments showed that the DES composed of triethylmethylammonium chloride and formic acid exhibited the best extraction performance among the selected candidates.Key extraction parameters were optimized experimentally,achieving a maximum QUI extraction efficiency of 97.18% under mild conditions.Molecular dynamics simulations revealed that the interactions between quaternary ammonium cations and QUI play a crucial role in the extraction mechanism.This study provides insights into the use of DESs for QUI extraction and demonstrates their potential for application to other coal tar derivatives.
