The strategic dispersion of carbon nanotubes(CNTs)within triblock copolymer matrix is key to fabricating nanocomposites with the desired electrical properties.This study investigated the self-assembly and electrical b...The strategic dispersion of carbon nanotubes(CNTs)within triblock copolymer matrix is key to fabricating nanocomposites with the desired electrical properties.This study investigated the self-assembly and electrical behavior of a polystyrene-polybutadiene-polystyrene(SBS)matrix with CNTs of different aspect ratios using hybrid particle-field molecular dynamics simulations.Structural factor analysis of the nanocomposites indicated that CNTs with higher aspect ratios promoted the transition of the SBS matrix from a bicontinuous to a lamellar phase.The resistor network algorithm method showed that the electrical conductivity of SBS and CNTs nanocomposites was influenced by the interplay between the CNTs aspect ratios,concentrations,and domain sizes of the triblock copolymer SBS.Our research sheds light on the relationship between CNTs dispersion and the electrical behavior of SBS/CNTs nanocomposites,guiding the engineering of materials to achieve desired electrical properties through the modulation of CNTs aspect ratios and tailored sizing of triblock copolymer domains.展开更多
Molecular simulations using MEAM(Modified Embedded Atom Method) potentials have been applied to research the interfacial properties of the different(hkl) Cu substrate in the soldering.In the simulation,the surface ene...Molecular simulations using MEAM(Modified Embedded Atom Method) potentials have been applied to research the interfacial properties of the different(hkl) Cu substrate in the soldering.In the simulation,the surface energies and the process of Sn spreading on the different(hkl) copper plate surface were simulated,and the results show that the different(hkl) plane substrates have few effects to the soldering spreading process,the solid-liquid interfacial energy is still the dominant ingredient practically in the wetting process.展开更多
Our researches are based on the fact that the systems composed of polyacrylamide and montmorillonite under a kind of shear state often appear in some important practical processes like drilling well etc. The viscosity...Our researches are based on the fact that the systems composed of polyacrylamide and montmorillonite under a kind of shear state often appear in some important practical processes like drilling well etc. The viscosity of polyacrylamide is usually the most important one among the characteristics to decide if the practical processes succeed or not. Therefore, we studied the effect of hydrated montmorillonite on the viscosities of polyacrylamide with temperature and shear rate varying under confined shear by molecular simulation method. Adopting the condition of confined shear in the research could make our simulations and the practical processes as similar as possible. First, the model of one polyacrylamide polymer chain with 20 monomers linearly linking surrounded by water molecules between two of montmorillonite layers was constructed. Then canonical ensemble （NVT） MD simulations were carried out for the built model at different temperatures and shear rates. From the gained simulation results, we calculated the polymer＇s structural property-radius of gyration, which was directly related to the viscosity property of polyacrylamide polymer. It was found that the viscosity of the polyacrylamide polymer between hydrated clay layers decreased with the temperature increasing from 298 to 343 K under the condition of confined shear. The variation trend of viscosity from simulation results was also confirmed by our experiments. Besides, the viscosity of the polyacrylamide between hydrated clay layers decreased with the shear rate increasing within the range of higher shear rates.展开更多
Molecular simulation plays an increasingly important role in studying the properties of complex fluid systems containing charges,such as ions,piezoelectric materials,ionic liquids,ionic surfactants,polyelectrolytes,zw...Molecular simulation plays an increasingly important role in studying the properties of complex fluid systems containing charges,such as ions,piezoelectric materials,ionic liquids,ionic surfactants,polyelectrolytes,zwitterionic materials,nucleic acids,proteins,biomembranes and etc.,where the electrostatic interactions are of special significance.Several methods have been available for treating the electrostatic interactions in explicit and implicit solvent models.Accurate and efficient treatment of such interactions has therefore always been one of the most challenging issues in classical molecular dynamics simulations due to their inhomogeneity and long-range characteristics.Currently,two major challenges remain in the application field of electrostatic interactions in molecular simulations;(i)improving the representation of electrostatic interactions while reducing the computational costs in molecular simulations;(ii)revealing the role of electrostatic interactions in regulating the specific properties of complex fluids.In this review,the calculation methods of electrostatic interactions,including basic principles,applicable conditions,advantages and disadvantages are summarized and compared.Subsequently,the specific role of electrostatic interactions in governing the properties and behaviors of different complex fluids is emphasized and explained.Finally,challenges and perspective on the computational study of charged systems are given.展开更多
Molecular simulations are now an essential part of modern chemistry and physics,especially for the investigation of macromolecules.They have evolved into mature approaches that can be used effectively to understand th...Molecular simulations are now an essential part of modern chemistry and physics,especially for the investigation of macromolecules.They have evolved into mature approaches that can be used effectively to understand the structure-to-property relationships of diverse macromolecular systems.In this article,we provide a tutorial on molecular simulations,focusing on the technical and practical aspects.Several prominent and classical simulation methods and software are introduced.The applications of molecular simulations in various directions of macromolecular science are thenfeatured by representative systems,including self-assembly,crystallization,chemical reaction,and some typical non-equilibrium systems.This tutorial paper provides a useful overview of molecular simulations in the rapid progress of macromolecular science,and suggests guidance for researchers who start exploiting molecular simulations in their study.展开更多
Adsorption of FCC dry gas components, hydrogen(H_2), nitrogen(N_2), methane(CH_4), ethane(C_2H_6) and ethylene(C_2H_4) in zeolite Y was studied by performing the Grant Canonical Monte Carlo(GCMC) simulations at 298K a...Adsorption of FCC dry gas components, hydrogen(H_2), nitrogen(N_2), methane(CH_4), ethane(C_2H_6) and ethylene(C_2H_4) in zeolite Y was studied by performing the Grant Canonical Monte Carlo(GCMC) simulations at 298K and 823K and under a pressure range up to 10 MPa. Simulation results were analyzed using the Langmuir model, which presented fitting of dry gas components adsorption to be suggested as the monolayer adsorption. C_2H_4 presented most single adsorption amount, which reached 7.63 mol/kg at 298K under a pressure of 200kPa. Thermodynamic parameters of the Gibbs free energy change, enthalpy change and entropy change were analyzed based on adsorption equilibrium constant obtained from the GCMC simulations. The results suggested that it was more favorable for C_2H_4 to be adsorbed in zeolite Y. Adsorption molecules were in ordered arrangement in the zeolite, and C_2H_4 exhibited a more orderly arrangement than other components. Additionally, a competition in the adsorption of a mixture of dry gas components was found, and supercages were the priority adsorption space. The competition was favorable to CH_4 and C_2H_6, and the competitive power was affected by temperature.展开更多
Zeolites have been widely applied in many chemical processes owing to their featured microporous framework structures.Organic structure-directing agents(OSDAs) play an important role during of the formation of zeolite...Zeolites have been widely applied in many chemical processes owing to their featured microporous framework structures.Organic structure-directing agents(OSDAs) play an important role during of the formation of zeolite frameworks via non-bonding host-vip interactions.Understanding these interactions is crucial to the design of OSDAs and the synthesis of target zeolites.Here,we report a molecular simulation study in the host-vip interactions between zeolite framework STW and 21 alkylated imidazolium and pyrazolium cations that have been used as the OSDAs for the synthesis of STW-type zeolites.We find that OSDAs that have successfully directed the formation of STW exhibit stronger host-vip interactions than unsuccessful ones.Furthermore,we find all successful OSDAs possess relatively more negative atomic charges on nitrogen atoms and smaller dipole moments.According to this finding,we have designed seven new alkylated imidazolium and pyrazolium cations that may be suitable for zeolite STW,and verified their structure-directing capability by molecular simulation calculations.展开更多
Protein XPA plays critical roles in nucleotide excision repair pathway.Recent experimental work showed that the functional dynamics of XPA involves the one-dimensional diffusion along DNA to search the damage site.Her...Protein XPA plays critical roles in nucleotide excision repair pathway.Recent experimental work showed that the functional dynamics of XPA involves the one-dimensional diffusion along DNA to search the damage site.Here,we investigate the involved dynamical process using extensive coarse-grained molecular simulations at various salt concentrations.The results demonstrated strong salt concentration dependence of the diffusion mechanisms.At low salt concentrations,the one-dimensional diffusion with rotational coupling is the dominant mechanism.At high salt concentrations,the diffusion by three-dimensional mechanism becomes more probable.At wide range of salt concentrations,the residues involved in the DNA binding are similar and the one-dimensional diffusion of XPA along DNA displays sub-diffusive feature.This sub-diffusive feature is tentatively attributed to diverse strengths of XPA-DNA interactions.In addition,we showed that both binding to DNA and increasing salt concentration tend to stretch the conformation of the XPA,which increases the exposure extent of the sites for the binding of other repair proteins.展开更多
Amyloid β-protein(Aβ) and Tau, two common pathogenic proteins associated with Alzheimer’s disease(AD), cross-interact, and thus co-assemble into hybrid aggregates. However, molecular mechanism of the cross-interact...Amyloid β-protein(Aβ) and Tau, two common pathogenic proteins associated with Alzheimer’s disease(AD), cross-interact, and thus co-assemble into hybrid aggregates. However, molecular mechanism of the cross-interactions remains unclear. To explore the issue, docking and molecular dynamics(MD) simulations were coupled to study the cross-interactions between Aβ pentamer and Tau pentamer. Four stable hybrid decamer conformations including double layer, single layer, block, and part-in were obtained by protein-protein docking software HADDOCK 2.2. Then, MD simulations were used to explore the molecular mechanism of cross-interactions between Aβ pentamer and Tau pentamer. The results of MD simulations showed that the part-in structure was the most stable among all the above four representative ones. The binding energy between Aβ and Tau was about-759.77 kJ·mol-1in the part-in structure. Moreover, the part-in conformation would undergo conformational transition, which would improve its hydrophobicity and make the structure more compact. This work offers a structural understanding of cross-interactions between Aβ and Tau linked to AD.展开更多
1,2,3-TrI[Cis-9-Hexadecenoyl](GTM)is a common oiliness additive.In this paper,the anti-wear property of GTM was found poor when it was directly used as lubricating oil for titanium alloy.However,when it was added to w...1,2,3-TrI[Cis-9-Hexadecenoyl](GTM)is a common oiliness additive.In this paper,the anti-wear property of GTM was found poor when it was directly used as lubricating oil for titanium alloy.However,when it was added to water and made into oil-in-water(OW)emulsion,it could play an effective role.The wear volume of titanium alloy sample lubricated by the emulsion was reduced by 75%compared to that lubricated by pure oil.It was difficult to fully uncover the underlying mechanism of these phenomena by experimental methods alone.With the help of molecular simulation method,the changes of GTM in chemical activity and adsorption capacity caused by water medium were revealed on atomic scale.The adsorption energies between GTM and titanium alloy under different temperature were quantitatively calculated.The superior anti-wear performance of the emulsions was related to following three aspects:(1)Water medium enhanced the adsorption capacity of GTM;(2)water medium changed the composition of lubrication film;and(3)the adsorption film in the water medium was less affected by temperature.Based on above results,an approach to predict tribological properties of oiliness additive was proposed.Using this method,the lubrication effects of several oiliness additives were successfully predicted.展开更多
Self-assembly of block copolymers(BCPs)is highly intricate and is adsorbing extensive experimental and simulation efforts to reveal it for maximizing structural order and device performances.The coarse-grained(CG)mole...Self-assembly of block copolymers(BCPs)is highly intricate and is adsorbing extensive experimental and simulation efforts to reveal it for maximizing structural order and device performances.The coarse-grained(CG)molecular dynamics(MD)simulation offers a microscopic angle to view the self-assembly of BCPs.Although some molecular details are sacrificed during CG processes,this method exhibits remarkable computational efficiency.In this study,a comprehensive CG model for polystyrene-block-poly(2-vinylpyridine),PS-b-P2VP,one of the most extensively studied BCPs for its high Flory-Huggins interaction parameter,is constructed,with parameters optimized using target values derived from all-atom MD simulations.The CG model precisely coincides with various classical self-assembling morphologies observed in experimental studies,matching the theoretical phase diagrams.Moreover,the conformational asymmetry of the experimental phase diagram is also clearly revealed by our simulation results,and the phase boundaries obtained from simulations are highly consistent with experimental results.The CG model is expected to extend to simulate the self-assembly behaviors of other BCPs in addition to PS-b-P2VP,thus increasing understanding of the microphase separation of BCPs from the molecular level.展开更多
Shale gas serves as a significant strategic successor resource for future oil and gas reserves and production in China.Thus,a profound understanding of the adsorption mechanism of shale gas in shale reservoirs is cruc...Shale gas serves as a significant strategic successor resource for future oil and gas reserves and production in China.Thus,a profound understanding of the adsorption mechanism of shale gas in shale reservoirs is crucial to accurately predict and evaluate shale gas reserves.In this study,we utilized two simulation methods,molecular dynamics simulation and Giant Canonical Monte Carlo simulation to examine the adsorption characteristics of kerogen under varying temperature and pressure conditions.We compared the results under identical temperature and pressure conditions for different mineral-kerogen composite models.Moreover,we examined the effects of temperature,pressure,and mineral species on the kerogen adsorption mechanism.The results indicate that shale formations with high organic matter content and a substantial proportion of non-clay inorganic minerals,as well as those subjected to higher temperature and pressure conditions than the shallow layer,possess a greater capacity to accommodate shale gas.This study examined the adsorption mechanism of methane in shale gas using different mineral-kerogen composite models.The findings of this study provide more accurate guidance and support for efficient development of shale gas.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
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
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
MRI is an indispensable diagnostic tool in modern medicine;however,understanding the molecular-level processes governing NMR relaxation of water in the presence of MRI contrast agents remains a challenge,hindering the...MRI is an indispensable diagnostic tool in modern medicine;however,understanding the molecular-level processes governing NMR relaxation of water in the presence of MRI contrast agents remains a challenge,hindering the molecularguided development of more effective contrast agents.By using quantum-based polarizable force fields,the first-of-its-kind molecular dynamics(MD)simulations of Gadobutrol are reported where the ^(1)H NMR longitudinal relaxivity r_(1) of the aqueous phase is determined without any adjustable parameters.The MD simulations of r_(1) dispersion(i.e.,frequency dependence)show good agreement with measurements at frequencies of interest in clinical MRI.Importantly,the simulations reveal key insights into the molecular level processes leading to r_(1) dispersion by decomposing the NMR dipole−dipole autocorrelation function G(t)into a discrete set of molecular modes,analogous to the eigenmodes of a quantum harmonic oscillator.The molecular modes reveal important aspects of the underlying mechanisms governing r_(1),such as its multiexponential nature and the importance of the second eigenmodal decay.By simply analyzing the MD trajectories on a parameter-free approach,the Gadobutrol simulations show that the outer-shell water contributes∼50%of the total relaxivity r_(1) compared to the inner-shell water,in contrast to simulations of(nonchelated)gadolinium-aqua where the outer shell contributes only∼15%of r_(1).The deviation between simulations and measurements of r_(1) below clinical MRI frequencies is used to determine the low-frequency electron-spin relaxation time for Gadobutrol,in good agreement with independent studies.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 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financially supported by the National Natural Science Foundation of China(Nos.52273019,62173065,22133002,22273031,and 12274056)Fundamental Research Funds for the Central Universities(No.04442024074)+2 种基金NationalKey R&D Program of China(No.2022YFB3707300)Beijing Natural Science Foundation(No.4242040)Scientific Research Funds Project of Liaoning Provincial Department of Education(No.LJKZ0034)。
文摘The strategic dispersion of carbon nanotubes(CNTs)within triblock copolymer matrix is key to fabricating nanocomposites with the desired electrical properties.This study investigated the self-assembly and electrical behavior of a polystyrene-polybutadiene-polystyrene(SBS)matrix with CNTs of different aspect ratios using hybrid particle-field molecular dynamics simulations.Structural factor analysis of the nanocomposites indicated that CNTs with higher aspect ratios promoted the transition of the SBS matrix from a bicontinuous to a lamellar phase.The resistor network algorithm method showed that the electrical conductivity of SBS and CNTs nanocomposites was influenced by the interplay between the CNTs aspect ratios,concentrations,and domain sizes of the triblock copolymer SBS.Our research sheds light on the relationship between CNTs dispersion and the electrical behavior of SBS/CNTs nanocomposites,guiding the engineering of materials to achieve desired electrical properties through the modulation of CNTs aspect ratios and tailored sizing of triblock copolymer domains.
文摘Molecular simulations using MEAM(Modified Embedded Atom Method) potentials have been applied to research the interfacial properties of the different(hkl) Cu substrate in the soldering.In the simulation,the surface energies and the process of Sn spreading on the different(hkl) copper plate surface were simulated,and the results show that the different(hkl) plane substrates have few effects to the soldering spreading process,the solid-liquid interfacial energy is still the dominant ingredient practically in the wetting process.
基金Funded by the National Natural Science Foundation of China(No.30871988)the Jiangsu Provincial Science and Technology Project(No.BK2014147110)
文摘Our researches are based on the fact that the systems composed of polyacrylamide and montmorillonite under a kind of shear state often appear in some important practical processes like drilling well etc. The viscosity of polyacrylamide is usually the most important one among the characteristics to decide if the practical processes succeed or not. Therefore, we studied the effect of hydrated montmorillonite on the viscosities of polyacrylamide with temperature and shear rate varying under confined shear by molecular simulation method. Adopting the condition of confined shear in the research could make our simulations and the practical processes as similar as possible. First, the model of one polyacrylamide polymer chain with 20 monomers linearly linking surrounded by water molecules between two of montmorillonite layers was constructed. Then canonical ensemble （NVT） MD simulations were carried out for the built model at different temperatures and shear rates. From the gained simulation results, we calculated the polymer＇s structural property-radius of gyration, which was directly related to the viscosity property of polyacrylamide polymer. It was found that the viscosity of the polyacrylamide polymer between hydrated clay layers decreased with the temperature increasing from 298 to 343 K under the condition of confined shear. The variation trend of viscosity from simulation results was also confirmed by our experiments. Besides, the viscosity of the polyacrylamide between hydrated clay layers decreased with the shear rate increasing within the range of higher shear rates.
基金supported by the National Natural Science Foundation of China(21776093,21376089,41976203,21506178,21908066)。
文摘Molecular simulation plays an increasingly important role in studying the properties of complex fluid systems containing charges,such as ions,piezoelectric materials,ionic liquids,ionic surfactants,polyelectrolytes,zwitterionic materials,nucleic acids,proteins,biomembranes and etc.,where the electrostatic interactions are of special significance.Several methods have been available for treating the electrostatic interactions in explicit and implicit solvent models.Accurate and efficient treatment of such interactions has therefore always been one of the most challenging issues in classical molecular dynamics simulations due to their inhomogeneity and long-range characteristics.Currently,two major challenges remain in the application field of electrostatic interactions in molecular simulations;(i)improving the representation of electrostatic interactions while reducing the computational costs in molecular simulations;(ii)revealing the role of electrostatic interactions in regulating the specific properties of complex fluids.In this review,the calculation methods of electrostatic interactions,including basic principles,applicable conditions,advantages and disadvantages are summarized and compared.Subsequently,the specific role of electrostatic interactions in governing the properties and behaviors of different complex fluids is emphasized and explained.Finally,challenges and perspective on the computational study of charged systems are given.
基金financially supported by the National Natural Science Foundation of China(Nos.22025302 and 21873053).
文摘Molecular simulations are now an essential part of modern chemistry and physics,especially for the investigation of macromolecules.They have evolved into mature approaches that can be used effectively to understand the structure-to-property relationships of diverse macromolecular systems.In this article,we provide a tutorial on molecular simulations,focusing on the technical and practical aspects.Several prominent and classical simulation methods and software are introduced.The applications of molecular simulations in various directions of macromolecular science are thenfeatured by representative systems,including self-assembly,crystallization,chemical reaction,and some typical non-equilibrium systems.This tutorial paper provides a useful overview of molecular simulations in the rapid progress of macromolecular science,and suggests guidance for researchers who start exploiting molecular simulations in their study.
基金financial support from the National Natural Science Foundation of China (No. 41302101 and No. 21476263)
文摘Adsorption of FCC dry gas components, hydrogen(H_2), nitrogen(N_2), methane(CH_4), ethane(C_2H_6) and ethylene(C_2H_4) in zeolite Y was studied by performing the Grant Canonical Monte Carlo(GCMC) simulations at 298K and 823K and under a pressure range up to 10 MPa. Simulation results were analyzed using the Langmuir model, which presented fitting of dry gas components adsorption to be suggested as the monolayer adsorption. C_2H_4 presented most single adsorption amount, which reached 7.63 mol/kg at 298K under a pressure of 200kPa. Thermodynamic parameters of the Gibbs free energy change, enthalpy change and entropy change were analyzed based on adsorption equilibrium constant obtained from the GCMC simulations. The results suggested that it was more favorable for C_2H_4 to be adsorbed in zeolite Y. Adsorption molecules were in ordered arrangement in the zeolite, and C_2H_4 exhibited a more orderly arrangement than other components. Additionally, a competition in the adsorption of a mixture of dry gas components was found, and supercages were the priority adsorption space. The competition was favorable to CH_4 and C_2H_6, and the competitive power was affected by temperature.
基金the National Natural Science Foundation of China(Nos.21622102,21621001 and 21920102005)the National Key Research and Development Program of China(No.2016YFB0701100)+1 种基金the National 111 Project(No.B17020)Program for JLUSTIRT and High Performance Computing Center of Jilin University。
文摘Zeolites have been widely applied in many chemical processes owing to their featured microporous framework structures.Organic structure-directing agents(OSDAs) play an important role during of the formation of zeolite frameworks via non-bonding host-vip interactions.Understanding these interactions is crucial to the design of OSDAs and the synthesis of target zeolites.Here,we report a molecular simulation study in the host-vip interactions between zeolite framework STW and 21 alkylated imidazolium and pyrazolium cations that have been used as the OSDAs for the synthesis of STW-type zeolites.We find that OSDAs that have successfully directed the formation of STW exhibit stronger host-vip interactions than unsuccessful ones.Furthermore,we find all successful OSDAs possess relatively more negative atomic charges on nitrogen atoms and smaller dipole moments.According to this finding,we have designed seven new alkylated imidazolium and pyrazolium cations that may be suitable for zeolite STW,and verified their structure-directing capability by molecular simulation calculations.
基金supported by the National Natural Science Foundation of China(Grant Nos.11974173 and 11774158)the HPC center of Nanjing University。
文摘Protein XPA plays critical roles in nucleotide excision repair pathway.Recent experimental work showed that the functional dynamics of XPA involves the one-dimensional diffusion along DNA to search the damage site.Here,we investigate the involved dynamical process using extensive coarse-grained molecular simulations at various salt concentrations.The results demonstrated strong salt concentration dependence of the diffusion mechanisms.At low salt concentrations,the one-dimensional diffusion with rotational coupling is the dominant mechanism.At high salt concentrations,the diffusion by three-dimensional mechanism becomes more probable.At wide range of salt concentrations,the residues involved in the DNA binding are similar and the one-dimensional diffusion of XPA along DNA displays sub-diffusive feature.This sub-diffusive feature is tentatively attributed to diverse strengths of XPA-DNA interactions.In addition,we showed that both binding to DNA and increasing salt concentration tend to stretch the conformation of the XPA,which increases the exposure extent of the sites for the binding of other repair proteins.
基金funded by the National Natural Science Foundation of China (21908165 and 21878234)Regional Innovation System Project (21ZYQCSY00050)。
文摘Amyloid β-protein(Aβ) and Tau, two common pathogenic proteins associated with Alzheimer’s disease(AD), cross-interact, and thus co-assemble into hybrid aggregates. However, molecular mechanism of the cross-interactions remains unclear. To explore the issue, docking and molecular dynamics(MD) simulations were coupled to study the cross-interactions between Aβ pentamer and Tau pentamer. Four stable hybrid decamer conformations including double layer, single layer, block, and part-in were obtained by protein-protein docking software HADDOCK 2.2. Then, MD simulations were used to explore the molecular mechanism of cross-interactions between Aβ pentamer and Tau pentamer. The results of MD simulations showed that the part-in structure was the most stable among all the above four representative ones. The binding energy between Aβ and Tau was about-759.77 kJ·mol-1in the part-in structure. Moreover, the part-in conformation would undergo conformational transition, which would improve its hydrophobicity and make the structure more compact. This work offers a structural understanding of cross-interactions between Aβ and Tau linked to AD.
基金financially supported by the National Natural Science Foundation of China(Grant Nos.51925506 and 52205203).
文摘1,2,3-TrI[Cis-9-Hexadecenoyl](GTM)is a common oiliness additive.In this paper,the anti-wear property of GTM was found poor when it was directly used as lubricating oil for titanium alloy.However,when it was added to water and made into oil-in-water(OW)emulsion,it could play an effective role.The wear volume of titanium alloy sample lubricated by the emulsion was reduced by 75%compared to that lubricated by pure oil.It was difficult to fully uncover the underlying mechanism of these phenomena by experimental methods alone.With the help of molecular simulation method,the changes of GTM in chemical activity and adsorption capacity caused by water medium were revealed on atomic scale.The adsorption energies between GTM and titanium alloy under different temperature were quantitatively calculated.The superior anti-wear performance of the emulsions was related to following three aspects:(1)Water medium enhanced the adsorption capacity of GTM;(2)water medium changed the composition of lubrication film;and(3)the adsorption film in the water medium was less affected by temperature.Based on above results,an approach to predict tribological properties of oiliness additive was proposed.Using this method,the lubrication effects of several oiliness additives were successfully predicted.
基金supported by the National Natural Science Foundation of China(22438005,22108117).
文摘Self-assembly of block copolymers(BCPs)is highly intricate and is adsorbing extensive experimental and simulation efforts to reveal it for maximizing structural order and device performances.The coarse-grained(CG)molecular dynamics(MD)simulation offers a microscopic angle to view the self-assembly of BCPs.Although some molecular details are sacrificed during CG processes,this method exhibits remarkable computational efficiency.In this study,a comprehensive CG model for polystyrene-block-poly(2-vinylpyridine),PS-b-P2VP,one of the most extensively studied BCPs for its high Flory-Huggins interaction parameter,is constructed,with parameters optimized using target values derived from all-atom MD simulations.The CG model precisely coincides with various classical self-assembling morphologies observed in experimental studies,matching the theoretical phase diagrams.Moreover,the conformational asymmetry of the experimental phase diagram is also clearly revealed by our simulation results,and the phase boundaries obtained from simulations are highly consistent with experimental results.The CG model is expected to extend to simulate the self-assembly behaviors of other BCPs in addition to PS-b-P2VP,thus increasing understanding of the microphase separation of BCPs from the molecular level.
基金supported by the National Natural Science Foundation of China(Grant No.42102145)the Science Foundation of China University of Petroleum,Beijing(Grant No.2462022YXZZ007)。
文摘Shale gas serves as a significant strategic successor resource for future oil and gas reserves and production in China.Thus,a profound understanding of the adsorption mechanism of shale gas in shale reservoirs is crucial to accurately predict and evaluate shale gas reserves.In this study,we utilized two simulation methods,molecular dynamics simulation and Giant Canonical Monte Carlo simulation to examine the adsorption characteristics of kerogen under varying temperature and pressure conditions.We compared the results under identical temperature and pressure conditions for different mineral-kerogen composite models.Moreover,we examined the effects of temperature,pressure,and mineral species on the kerogen adsorption mechanism.The results indicate that shale formations with high organic matter content and a substantial proportion of non-clay inorganic minerals,as well as those subjected to higher temperature and pressure conditions than the shallow layer,possess a greater capacity to accommodate shale gas.This study examined the adsorption mechanism of methane in shale gas using different mineral-kerogen composite models.The findings of this study provide more accurate guidance and support for efficient development of shale gas.
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 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Ken Kennedy Institute,the Rice University Creative Ventures Fund(Faculty Initiatives Fund)the Robert A.Welch Foundation for the financial support.
文摘MRI is an indispensable diagnostic tool in modern medicine;however,understanding the molecular-level processes governing NMR relaxation of water in the presence of MRI contrast agents remains a challenge,hindering the molecularguided development of more effective contrast agents.By using quantum-based polarizable force fields,the first-of-its-kind molecular dynamics(MD)simulations of Gadobutrol are reported where the ^(1)H NMR longitudinal relaxivity r_(1) of the aqueous phase is determined without any adjustable parameters.The MD simulations of r_(1) dispersion(i.e.,frequency dependence)show good agreement with measurements at frequencies of interest in clinical MRI.Importantly,the simulations reveal key insights into the molecular level processes leading to r_(1) dispersion by decomposing the NMR dipole−dipole autocorrelation function G(t)into a discrete set of molecular modes,analogous to the eigenmodes of a quantum harmonic oscillator.The molecular modes reveal important aspects of the underlying mechanisms governing r_(1),such as its multiexponential nature and the importance of the second eigenmodal decay.By simply analyzing the MD trajectories on a parameter-free approach,the Gadobutrol simulations show that the outer-shell water contributes∼50%of the total relaxivity r_(1) compared to the inner-shell water,in contrast to simulations of(nonchelated)gadolinium-aqua where the outer shell contributes only∼15%of r_(1).The deviation between simulations and measurements of r_(1) below clinical MRI frequencies is used to determine the low-frequency electron-spin relaxation time for Gadobutrol,in good agreement with independent studies.
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.
