In this study,a novel lubricant additive nitrogen-doped carbon quantum dot(N-CQD)nanoparticle was prepared by the solvothermal method.The synthesized spherical N-CQD nanoparticles in the diameter of about 10 nm had a ...In this study,a novel lubricant additive nitrogen-doped carbon quantum dot(N-CQD)nanoparticle was prepared by the solvothermal method.The synthesized spherical N-CQD nanoparticles in the diameter of about 10 nm had a graphene oxide(GO)-like structure with various oxygen(O)-and nitrogen(N)-containing functional groups.Then N-CQDs were added to MoS_(2)nanofluid,and the tribological properties for steel/steel friction pairs were evaluated using a pin-on-disk tribometer.Non-equilibrium molecular dynamics(NEMD)simulations for the friction system with MoS_(2)or MoS_(2)+N-CQD nanoparticles were also conducted.The results showed that friction processes with MoS_(2)+N-CQD nanofluids were under the mixed lubrication regime.And MoS_(2)nanofluid containing 0.4 wt%N-CQDs could achieve 30.4%and 31.0%reduction in the friction coefficient and wear rate,respectively,compared to those without N-CQDs.By analyzing the worn surface topography and chemical compositions,the excellent lubrication performance resulted from the formation of tribochemistry-induced tribofilm.The average thickness of tribofilm was about 13.9 nm,and it was composed of amorphous substances,ultrafine crystalline nanoparticles,and self-lubricating FeSO_(4)/Fe2(SO_(4))_(3).NEMD simulation results indicated the interaction between S atoms in MoS_(2)as well as these O-and N-containing functional groups in N-CQDs with steel surfaces enhanced the stability and strength of tribofilm.Thereby the metal surface was further protected from friction and wear.展开更多
Multilayered van der Waals(vdW)materials have attracted increasing interest because of the manipulability of their superior optical,electrical,thermal,and mechanical properties.A mass-spring model(MSM)for elastic wave...Multilayered van der Waals(vdW)materials have attracted increasing interest because of the manipulability of their superior optical,electrical,thermal,and mechanical properties.A mass-spring model(MSM)for elastic wave propagation in multilayered vdW metamaterials is reported in this paper.Molecular dynamics(MD)simulations are adopted to simulate the propagation of elastic waves in multilayered vdW metamaterials.The results show that the graphene/MoS_(2)metamaterials have an elastic wave bandgap in the terahertz range.The MSM for the multilayered vdW metamaterials is proposed,and the numerical simulation results show that this model can well describe the dispersion and transmission characteristics of the multilayered vdW metamaterials.The MSM can predict elastic wave transmission characteristics in multilayered vdW metamaterials stacked with different two-dimensional(2D)materials.The results presented in this paper offer theoretical help for the vibration reduction of multilayered vdW semiconductors.展开更多
Microstructural modification of carbon materials,such as carbon fibers(Cf)and pyrolytically deposited carbon,is important for engineering applications.However,the regulation of these materials is not an effortless tas...Microstructural modification of carbon materials,such as carbon fibers(Cf)and pyrolytically deposited carbon,is important for engineering applications.However,the regulation of these materials is not an effortless task.To understand the impacts of thermal spikes from pulsed laser processing on the structural adaptation of amorphous carbon(a-C),we performed melt quenching by molecular dynamics(MD)simulations.Our results confirm that the vitrification behavior of carbon can be tuned by adjusting the cooling rate(R),which is controlled by the thermal spikes of laser processing.Moreover,we set up a two-step way to locate the critical cooling rate(R_(c))of monoatomic carbon,which is refined by the sharp change in the environmental similarity parameter.Using this novel technique,we demonstrate that the ordering degree and the local atomic motif can be largely modified by going across a bar of 100 K/ps,which is extracted as the critical cooling rate to ensure the complete amorphization of carbon.This approach provides a criterion for both experimentally processing and theoretically simulating a-C structures.Therefore,this work provides guidelines on how to tune the amorphous carbon structures of engineering materials and provides an outlook for the wonderland of amorphous carbon materials.展开更多
Superlubricity and active friction control have been extensively researched in order to reduce the consumption of fossil energy,the failure of moving parts,and the waste of materials.The vibration-induced superlubrici...Superlubricity and active friction control have been extensively researched in order to reduce the consumption of fossil energy,the failure of moving parts,and the waste of materials.The vibration-induced superlubricity(VIS)presents a promising solution for friction reduction since it does not require high-standard environment.However,the mechanism underlying the VIS remains unclear since the atomic-scale information in a buried interface is unavailable to experimental methods.In this paper,the mechanism of VIS was examined via numerical calculation based on the Prandtl-Tomlinson(PT)model and molecular dynamics(MD)simulations.The results revealed that the pushing effect of stick-slip is one of the direct sources of friction reduction ability under vibrational excitation,which was affected by the response amplitude,frequency,and the trace of the tip.Moreover,the proportion of this pushing effect could be modulated by changing the phase difference when applying coupled vibrational excitation in x-and z-axis.This results in a significant change in friction reduction ability with phase.By this way,active friction control from the stick-slip to superlubricity can be achieved conveniently.展开更多
The nanoparticle thermal conductivity and nanoscale thermal contact resistance were investigated by molecular dynamics(MD) simulations to further understand nanoscale porous media thermal conductivity.Macroscale porou...The nanoparticle thermal conductivity and nanoscale thermal contact resistance were investigated by molecular dynamics(MD) simulations to further understand nanoscale porous media thermal conductivity.Macroscale porous media thermal conductivity models were then revised for nanoporous media.The effective thermal conductivities of two packed beds with nanoscale nickel particles and a packed bed with microscale nickel particles were then measured using the Hot Disk.The measured results show that the nano/microscale porous media thermal conductivities were much less than the thermal conductivities of the solid particles.Comparison of the measured and calculated results shows that the revised combined parallel-series model and the revised Hsu-Cheng model can accurately predict the effective thermal conductivities of micro-and nanoparticle packed beds.展开更多
The melting mechanisms of Pt-based multimetallic nanoparticles(NPs)are important to help determine their optimal melting processes.To understand the melting and coalescence behaviors of heterogeneous NPs(Pd-Pt NPs)wit...The melting mechanisms of Pt-based multimetallic nanoparticles(NPs)are important to help determine their optimal melting processes.To understand the melting and coalescence behaviors of heterogeneous NPs(Pd-Pt NPs)with various sizes and compositions,molecular dynamics(MD)simulation was employed.The MD results for larger Pd-Pt NPs with an effective diameter of4.6-7.8 nm show that PtPd alloy can form at Pd/Pt interface before Pd NP melted completely,while for Pt-core/Pdshell NP and Pd-core/Pt-shell NP,PtPd alloy formed only after Pd portion melted completely.For smaller Pd-Pt NPs with an effective diameter of 2.5-4.0 nm,PdPt alloy is not formed until both Pd and Pt NPs melted completely.Besides,the coalescence process of Pd-Pt NPs depends on the melting temperature of Pt NP when Pt composition is higher than 20 at%.Furthermore,the melting mechanisms of Pd/Pt/Ir trimetallic NPs are investigated.A two-step melting process occurs in Pd-Pt-Ir NPs and Ir-core/Ptshell/Pd-shell NP,and the melting sequence of Pd-core/Ptshell/Ir-shell NP and Pt-core/Pd-shell/Ir-shell NP is different from Pd/Pt bimetallic NPs.展开更多
Atomic cluster-based networks represent a promising architecture for the realization of neuromorphic computing systems,which may overcome some of the limitations of the current computing paradigm.The formation and bre...Atomic cluster-based networks represent a promising architecture for the realization of neuromorphic computing systems,which may overcome some of the limitations of the current computing paradigm.The formation and breakage of links between the clusters are of utmost importance for the functioning of these computing systems.This paper reports the results of molecular dynamics simulations of synapse(bridge)formation at elevated temperature and thermal breaking processes between 2.8 nmsized Au1415 clusters deposited on a carbon substrate,a model system.Crucially,we find that the bridge formation process is driven by the diffusion of gold atoms along the substrate,no matter how small the gap between the clusters themselves.The complementary simulations of the bridge breaking process reveal the existence of a threshold bias voltage to activate bridge rupture via Joule heating.These results provide an atomistic-level understanding of the fundamental dynamical processes occurring in neuromorphic cluster arrays.展开更多
Cytochrome P450（CYP） 2El is a dual function monoxygenase with a crucial role in the metabolism of 6% of drugs on the market at present. The enzyme is of tremendous interest for its association with alcohol consumpti...Cytochrome P450（CYP） 2El is a dual function monoxygenase with a crucial role in the metabolism of 6% of drugs on the market at present. The enzyme is of tremendous interest for its association with alcohol consumption, diabetes, obesity and fasting. Despite the abundant experimental mutagenesis data, the molecular origin and the structural motifs for the enzymatic activity deficiencies have not been rationalized at the atomic level. In this regard, we have investigated the effects of mutation on the structural and energetic characteristics upon single point mutations in CYP2E1, N219D and $366C. The molecular dynamics（MD） simulation combined with quantum mechanics/molecular mechanics（QM/MM） and noncovalent interaction（NCI） analysis was carried out on CYP2EI and its two mutants. The results highlight the critical role of Phe207, which is responsible for both structural flexibility and energetic variation, shortening the gap between the theory and the experimentally observed results of enzymatic activity decrease, The underlying molecular mechanism of the enzymatic activity deficiencies for mutants may be attributed to the changes of spatial position of Phe207 in the two mutants. This work provides particular explanations to how mutations affect ligand-receptor interactions based on combined MD and QM/MM calculations. Furthermore, the mutational effects on the activity of CYP2E1 obtained in the present study are beneficial to both the experimental and the computational works of CYPs and may allow researchers to achieve desirable changes in enzymatic activity.展开更多
Swelling clays are found extensively in various parts of the world, and sodium-montmorillonite(NaMMT) is the main constituent of an expansive clay mineral. In this work, the swelling behavior of NaMMT clay with a wide...Swelling clays are found extensively in various parts of the world, and sodium-montmorillonite(NaMMT) is the main constituent of an expansive clay mineral. In this work, the swelling behavior of NaMMT clay with a wide range of organic fluids, high polar through low polar fluids, is studied using a combination of Fourier transform infrared(FTIR) technique and molecular dynamics(MD) simulations.The construction of the representative clayefluid models is carried out, and the nature of nonbonded interactions between clay and fluids is studied using MD. Our FTIR and MD simulations results suggest the significant nonbonded interactions between Na-MMT clay and polar fluids, such as formamide and water. The nonbonded interactions of Na-MMT with methanol and acetone are significantly less than those in Na-MMT with polar fluids. The interactions of the fluids with various entities of the clay such as Sie O, Fee OH, Mge OH, and Ale OH captured via the spectroscopy experiments and modeling provide a finer understanding of the interactions and their contributions to swelling. The MD simulations are able to capture the band shifts observed in the spectra obtained in the spectroscopy experiments. This work also captures the conformations of interlayer sodium ions with formamide, water, methanol, and acetone during swelling. These nonbonded interactions provide insight into the molecular mechanism that the polarity of fluids plays an important role in the initiation of interlayer swelling, alteration in the orientations, and evolution of microstructure of swelling clays at the molecular scale.展开更多
Non-equilibrium molecular dynamics（MD） simulations were performed according to the electronic anti-fouling technology, and some structural parameters and dynamic parameters of CaCl2 aqueous solution were taken as in...Non-equilibrium molecular dynamics（MD） simulations were performed according to the electronic anti-fouling technology, and some structural parameters and dynamic parameters of CaCl2 aqueous solution were taken as indicators to compare the different effect on the anti-fouling performance by applying different electric fields. The results show that electric fields can effectively decrease the viscosity of CaCl2 aqueous solution and enhance the ionic activity by enlarging the self-diffusion coefficient. In addition, with the same electric field strength, the electrostatic field is more effective at decreasing the viscosity of CaCI2 aqueous solution and increasing the self-diffusion coefficient of water molecules, while the alternating electric field is more effective at increasing the self-diffusion coefficient of Ca2＋. Furthermore, an alternating electric field with different frequencies was applied; the results show that an 800 kHz frequency is most effective to decrease the viscosity, and a 700 kHz frequency is most effective to en- hance the self-diffusion coefficient of water molecule. Otherwise, 400 kHz is most effective to enhance the self-diffusion coefficient of Ca2＋. Additionally, by studying the change of structure parameters, it was concluded that an external electric field can enhance the hydration between Ca2＋ and coordinated water molecules, and the alternating electric field is more effective in this respect.展开更多
Atomic motion and surface formation in the nanometric cutting process ofβ-Sn are investigated using molecular dynamics(MD).A stagnation region is observed that changes the shape of the tool edge involved in nanometri...Atomic motion and surface formation in the nanometric cutting process ofβ-Sn are investigated using molecular dynamics(MD).A stagnation region is observed that changes the shape of the tool edge involved in nanometric cutting,resulting in a fluctuation in the cutting forces.It is found that single-crystal tin releases the high compressive stress generated under the tool pressure through slip and phase transformation.The tin transformation proceeds from aβ-Sn structure to a bct-Sn structure.The effects of the cutting speed,undeformed chip thickness(UCT)and tool edge radius on material removal are also explored.A better surface is obtained through material embrittlement caused by a higher speed.In addition,a smaller UCT and sharper tool edge help reduce subsurface damage.展开更多
The dispersion behavior and spatial distribution of nanoparticles(NPs)in ring polymer melts are explored by using molecular dynamics(MD)simulations.As polymer-NP interactions increase,three general categories of polym...The dispersion behavior and spatial distribution of nanoparticles(NPs)in ring polymer melts are explored by using molecular dynamics(MD)simulations.As polymer-NP interactions increase,three general categories of polymer-mediated NP organization are observed,namely,contact aggregation,bridging,and steric dispersion,consistent with the results of equivalent linear ones in previous studies.In the case of direct contact aggregation among NPs,the explicit aggregation-dispersion transition of NPs in ring polymer melts can be induced by increasing the chain stiffness or applying a steady shear flow.Results further indicate that NPs can achieve an optimal dispersed state with the appropriate chain stiffness and shear flow.Moreover,shear flow cannot only improve the dispersion of NPs in ring polymer melts but also control the spatial distribution of NPs into a well-ordered structure.This improvement becomes more evident under stronger polymer-NP interactions.The observed induced-dispersion or ordered distribution of NPs may provide efficient access to the design and manufacture of high-performance polymer nanocomposites(PNCs).展开更多
Drugs SPD-304（6,7-dimethyl-3-{[methyl-（2-{methyl-[1-（3-trifluoromethyl-phenyl）-1H-indol-3-ylme thyl]-amino}-ethyl）-amino]-methyl}-chromen-4-one） and zafirlukast contain a common structural element of 3-substitut...Drugs SPD-304（6,7-dimethyl-3-{[methyl-（2-{methyl-[1-（3-trifluoromethyl-phenyl）-1H-indol-3-ylme thyl]-amino}-ethyl）-amino]-methyl}-chromen-4-one） and zafirlukast contain a common structural element of 3-substituted indole moiety which closely relates to a dehydrogenated reaction catalyzed by cytochrome P450s（CYPs）. It was reported that the dehydrogenation can produce a reactive electrophilic intermediate which cause toxicities and inactivate CYPs. Drug L-745,870（3-{[4-（4-chlorophenyl）piperazin-1-yl]-methyl}-1H-pyrrolo 2,3-β-pyridine） might have similar effect since it contains the same structural element. We used molecular docking approach combined with molecular dynamics（MD） simulation to model three-dimensional（3D） complex structures of SPD-304, zafirlukast and L-745,870 into CYP3A4, respectively. The results show that these three drugs can stably bind into the active site and the 3-methylene carbons of the drugs keep a reasonable reactive distance from the heme iron. The complex structure of SPD-304-CYP3A4 is in agreement with experimental data. For zafirlukast, the calcu lation results indicate that 3-methylene carbon might be the dehydrogenation reaction site. Docking model of L-745,870-CYP3A4 shows a potential possibility of L-745,870 dehydrogenated by CYP3A4 at 3-methylene carbon which is in agreement with experiment in vivo. In addition, residues in the phenylalanine cluster as well as S119 and R212 play a critical role in the ligands binding based on our calculations. The docking models could provide some clues to understand the metabolic mechanism of the drugs by CYP3A4.展开更多
Control of ion transport and fluid flow through nanofluidic devices is of primary importance for energy storage and conversion, drug delivery and a wide range of biological processes. Recent development of nanotechnol...Control of ion transport and fluid flow through nanofluidic devices is of primary importance for energy storage and conversion, drug delivery and a wide range of biological processes. Recent development of nanotechnology, synthesis techniques, purification technologies, and experiment have led to rapid advances in simulation and modeling studies on ion transport properties. In this review, the applications of Poisson-Nernst-Plank （PNP） equations in analyzing transport properties are presented. The molecular dynamics （MD） studies of transport properties of ion and fluidic flow through nanofluidic devices are reported as well.展开更多
Metal ions play critical roles in the interaction between deoxyribonucleic acid(DNA) and protein.The experimental research has demonstrated that the Mg^2+ ion can affect the binding between transcription factor and DN...Metal ions play critical roles in the interaction between deoxyribonucleic acid(DNA) and protein.The experimental research has demonstrated that the Mg^2+ ion can affect the binding between transcription factor and DNA.In our work,by full-atom molecular dynamic simulation, the effects of the Mg^2+ ion on the cyclic adenosine monophosphate(cAMP)response element binding protein(CREB)/cAMP response elements(CRE) complex are investigated.It is illustrated that the number of hydrogen bonds formed at the interface between protein and DNA is significantly increased when the Mg^2+ ion is added.Hence, an obvious change in the structure of the DNA is observed.Then the DNA base groove and base pair parameters are analyzed.We find that, due to the introduction of the Mg2+ ion, the DNA base major groove becomes narrower.A potential mechanism for this observation is proposed.It is confirmed that the Mg^2+ ion can enhance the stability of the DNA–protein complex.展开更多
Molecular Dynamics (MD) simulations of siliceous FAU-type zeolite were carried out at various temperatures. to investigate its thermal behaviors. From the study. we found that pure silicon fanjasite showed different t...Molecular Dynamics (MD) simulations of siliceous FAU-type zeolite were carried out at various temperatures. to investigate its thermal behaviors. From the study. we found that pure silicon fanjasite showed different thermal behaviors below 1500K and above 1500K. its cell volume gradually shrinks with the rising of the temperature below 1500K. the cell volume of the zeolite changes little above 1500K.展开更多
The cytochrome P450 mutant CYP2C9.13（L90P） shows a greatly impaired catalytic activity compared with the wild-type. We constructed the mutants by substitution at residue 90 of CYP2C9, expressed in COS-7 cells, assay...The cytochrome P450 mutant CYP2C9.13（L90P） shows a greatly impaired catalytic activity compared with the wild-type. We constructed the mutants by substitution at residue 90 of CYP2C9, expressed in COS-7 cells, assayed their thermal stability and catalysis activity and analyzed the mutants via molecular dynamic（MD） simulation and flexible docking. Mutant L90E exhibits a significantly lower catalytic activity than the wild-type for the hydroxylation of diclofenac, lornoxicam and luciferin and its molecular dynamics simulation results indicate that the size of the entrance of substrate access was reduced significantly. An increase or minor decrease of catalytic activity was observed for mutants L90Q, L90W, L90R, L90I and L90G, and the sizes of the entrances of substrate access and the active site cavities had a little change in those mutants. The thermal stability and the potential energy of the MD simulation of these mutants showed a similar tendency as the catalysis assays did. Flexible docking results show the fluctuation of interaction energy is due to the change of electrostatic potential distribution. All the above facts show that the changes in the catalysis activity of the mutants caused by the substitution at residue 90 are due to the changes in the size of entrance, the shape and size of active site cavity, electrostatic potential distribution and thermal stability. The residue 90 of CYP2C9 has an important effect on the enzyme catalytic activity.展开更多
The computational cost of numerical methods in microscopic-scales such as molecular dynamics(MD) is a deterrent factor that limits simulations with a large number of particles. Hence, it is desirable to decrease the c...The computational cost of numerical methods in microscopic-scales such as molecular dynamics(MD) is a deterrent factor that limits simulations with a large number of particles. Hence, it is desirable to decrease the computational cost and run time of simulations, especially for problems with a symmetrical domain. However, in microscopic-scales, implementation of symmetric boundary conditions is not straightforward. Previously, the present authors have successfully used a symmetry boundary condition to solve molecular flows in constant-area channels. The results obtained with this approach agree well with the benchmark cases. Therefore, it has provided us with a sound ground to further explore feasibility of applying symmetric solutions of micro-fluid flows in other geometries such as variable-area ducts. Molecular flows are solved for the whole domain with and without the symmetric boundary condition. Good agreement has been reached between the results of the symmetric solution and the whole domain solution. To investigate robustness of the proposed method, simulations are conducted for different values of affecting parameters including an external force, a flow density, and a domain length. The results indicate that the symmetric solution is also applicable to variable-area ducts such as micro-nozzles.展开更多
Extreme ultraviolet(EUV)light plays an important role in various fields such as material characterization and semiconductor manufacturing.It is also a potential approach in material fabrication at atomic and close-to-...Extreme ultraviolet(EUV)light plays an important role in various fields such as material characterization and semiconductor manufacturing.It is also a potential approach in material fabrication at atomic and close-to-atomic scales.However,the material removal mechanism has not yet been fully understood.This paper studies the interaction of a femtosecond EUV pulse with monocrystalline silicon using molecular dynamics(MD)coupled with a two-temperature model(TTM).The photoionization mechanism,an important process occurring at a short wavelength,is introduced to the simulation and the results are compared with those of the traditional model.Dynamical processes including photoionization,atom desorption,and laser-induced shockwave are discussed under various fluencies,and the possibility of single atomic layer removal is explored.Results show that photoionization and the corresponding bond breakage are the main reasons of atom desorption.The method developed can be further employed to investigate the interaction between high-energy photons and the material at moderate fluence.展开更多
The implementation of solid-fluid boundary condition has been a major challenge for dissipative particle dynamics(DPD)method.Current implementations of boundary conditions usually try to approach a uniform density dis...The implementation of solid-fluid boundary condition has been a major challenge for dissipative particle dynamics(DPD)method.Current implementations of boundary conditions usually try to approach a uniform density distribution and a velocity profile close to analytical solution.The density oscillations and slip velocity are intentionally eliminated,and different wall properties disappear in the same analytical solution.This paper develops a new wall model that combines image and frozen particles and a new strategy to emphasize different wall properties especially wettabilities.The strategy first studies the realistic wall-fluid system by molecular dynamics(MD)simulation depending on physical parameters.Then,a DPD simulation is used to match the density and velocity profiles with the new wall model.The obtained DPD parameters can simulate the systems with the same wall and fluid materials.With this method,a simulation of the Poiseuille flow of liquid argon with copper walls is presented.Other walls with super-hydrophilic,hydrophilic,and hydrophobic wettabilities are also simulated.The limitations of the analytical solution and the effect of the wall-fluid interaction are discussed.The results show that the method suggested in this paper can simulate the mesoscale behavior of the microchannel flow related to realistic systems.展开更多
基金This work was supported by the National Natural Science Foundation of China(No.51874036)Beijing Municipal Natural Science Foundation(No.2182041).
文摘In this study,a novel lubricant additive nitrogen-doped carbon quantum dot(N-CQD)nanoparticle was prepared by the solvothermal method.The synthesized spherical N-CQD nanoparticles in the diameter of about 10 nm had a graphene oxide(GO)-like structure with various oxygen(O)-and nitrogen(N)-containing functional groups.Then N-CQDs were added to MoS_(2)nanofluid,and the tribological properties for steel/steel friction pairs were evaluated using a pin-on-disk tribometer.Non-equilibrium molecular dynamics(NEMD)simulations for the friction system with MoS_(2)or MoS_(2)+N-CQD nanoparticles were also conducted.The results showed that friction processes with MoS_(2)+N-CQD nanofluids were under the mixed lubrication regime.And MoS_(2)nanofluid containing 0.4 wt%N-CQDs could achieve 30.4%and 31.0%reduction in the friction coefficient and wear rate,respectively,compared to those without N-CQDs.By analyzing the worn surface topography and chemical compositions,the excellent lubrication performance resulted from the formation of tribochemistry-induced tribofilm.The average thickness of tribofilm was about 13.9 nm,and it was composed of amorphous substances,ultrafine crystalline nanoparticles,and self-lubricating FeSO_(4)/Fe2(SO_(4))_(3).NEMD simulation results indicated the interaction between S atoms in MoS_(2)as well as these O-and N-containing functional groups in N-CQDs with steel surfaces enhanced the stability and strength of tribofilm.Thereby the metal surface was further protected from friction and wear.
基金supported by the National Science Fund for Distinguished Young Scholars of China(No.11925205)the National Natural Science Foundation of China(Nos.51921003 and U2341230)。
文摘Multilayered van der Waals(vdW)materials have attracted increasing interest because of the manipulability of their superior optical,electrical,thermal,and mechanical properties.A mass-spring model(MSM)for elastic wave propagation in multilayered vdW metamaterials is reported in this paper.Molecular dynamics(MD)simulations are adopted to simulate the propagation of elastic waves in multilayered vdW metamaterials.The results show that the graphene/MoS_(2)metamaterials have an elastic wave bandgap in the terahertz range.The MSM for the multilayered vdW metamaterials is proposed,and the numerical simulation results show that this model can well describe the dispersion and transmission characteristics of the multilayered vdW metamaterials.The MSM can predict elastic wave transmission characteristics in multilayered vdW metamaterials stacked with different two-dimensional(2D)materials.The results presented in this paper offer theoretical help for the vibration reduction of multilayered vdW semiconductors.
基金financial support from the National Natural Science Foundation of China(No.52102079)the Hebei Natural Science Foundation(No.E2021203115)+2 种基金the Science and Technology Project of the Hebei Education Department(No.QN2023255)financial support from the National Natural Science Foundation of China(No.52271155)the National Key R&D Program of China(No.2018YFA0703602).
文摘Microstructural modification of carbon materials,such as carbon fibers(Cf)and pyrolytically deposited carbon,is important for engineering applications.However,the regulation of these materials is not an effortless task.To understand the impacts of thermal spikes from pulsed laser processing on the structural adaptation of amorphous carbon(a-C),we performed melt quenching by molecular dynamics(MD)simulations.Our results confirm that the vitrification behavior of carbon can be tuned by adjusting the cooling rate(R),which is controlled by the thermal spikes of laser processing.Moreover,we set up a two-step way to locate the critical cooling rate(R_(c))of monoatomic carbon,which is refined by the sharp change in the environmental similarity parameter.Using this novel technique,we demonstrate that the ordering degree and the local atomic motif can be largely modified by going across a bar of 100 K/ps,which is extracted as the critical cooling rate to ensure the complete amorphization of carbon.This approach provides a criterion for both experimentally processing and theoretically simulating a-C structures.Therefore,this work provides guidelines on how to tune the amorphous carbon structures of engineering materials and provides an outlook for the wonderland of amorphous carbon materials.
基金financially supported by the National Natural Science Foundation of China(Grant Nos.52175175 and 51527901).
文摘Superlubricity and active friction control have been extensively researched in order to reduce the consumption of fossil energy,the failure of moving parts,and the waste of materials.The vibration-induced superlubricity(VIS)presents a promising solution for friction reduction since it does not require high-standard environment.However,the mechanism underlying the VIS remains unclear since the atomic-scale information in a buried interface is unavailable to experimental methods.In this paper,the mechanism of VIS was examined via numerical calculation based on the Prandtl-Tomlinson(PT)model and molecular dynamics(MD)simulations.The results revealed that the pushing effect of stick-slip is one of the direct sources of friction reduction ability under vibrational excitation,which was affected by the response amplitude,frequency,and the trace of the tip.Moreover,the proportion of this pushing effect could be modulated by changing the phase difference when applying coupled vibrational excitation in x-and z-axis.This results in a significant change in friction reduction ability with phase.By this way,active friction control from the stick-slip to superlubricity can be achieved conveniently.
基金supported by the key project fund from the National Natural Science Foundation of China (Grant No. 50736003)the National Natural Science Foundation of China (Grant No. 50676047)
文摘The nanoparticle thermal conductivity and nanoscale thermal contact resistance were investigated by molecular dynamics(MD) simulations to further understand nanoscale porous media thermal conductivity.Macroscale porous media thermal conductivity models were then revised for nanoporous media.The effective thermal conductivities of two packed beds with nanoscale nickel particles and a packed bed with microscale nickel particles were then measured using the Hot Disk.The measured results show that the nano/microscale porous media thermal conductivities were much less than the thermal conductivities of the solid particles.Comparison of the measured and calculated results shows that the revised combined parallel-series model and the revised Hsu-Cheng model can accurately predict the effective thermal conductivities of micro-and nanoparticle packed beds.
基金funding support from the Agency for Science,Technology and Research(A*STAR,No.SERC A1983c0032)AME Individual Research Grant(IRG)the computing resources from National Supercomputing Centre Singapore。
文摘The melting mechanisms of Pt-based multimetallic nanoparticles(NPs)are important to help determine their optimal melting processes.To understand the melting and coalescence behaviors of heterogeneous NPs(Pd-Pt NPs)with various sizes and compositions,molecular dynamics(MD)simulation was employed.The MD results for larger Pd-Pt NPs with an effective diameter of4.6-7.8 nm show that PtPd alloy can form at Pd/Pt interface before Pd NP melted completely,while for Pt-core/Pdshell NP and Pd-core/Pt-shell NP,PtPd alloy formed only after Pd portion melted completely.For smaller Pd-Pt NPs with an effective diameter of 2.5-4.0 nm,PdPt alloy is not formed until both Pd and Pt NPs melted completely.Besides,the coalescence process of Pd-Pt NPs depends on the melting temperature of Pt NP when Pt composition is higher than 20 at%.Furthermore,the melting mechanisms of Pd/Pt/Ir trimetallic NPs are investigated.A two-step melting process occurs in Pd-Pt-Ir NPs and Ir-core/Ptshell/Pd-shell NP,and the melting sequence of Pd-core/Ptshell/Ir-shell NP and Pt-core/Pd-shell/Ir-shell NP is different from Pd/Pt bimetallic NPs.
基金The authors are grateful for partial financial support by the European Commission through the RADON project(GA 872494)within the H2020-MSCA-RISE-2019 callThis article is also based upon work from the COST Action CA20129 MultIChem,supported by COST(European Cooperation in Science and Technology)+1 种基金TP acknowledges Swansea University support via project 74143 of the Research Committee of Aristotle University of ThessalonikiThis work was also supported in part by Deutsche Forschungsgemeinschaft(Project no.415716638).The authors acknowledge the computational support by the Goethe-HLR cluster of the Frankfurt Center for Scientific Computing and by the Supercomputing Wales project,which is part-funded by the European Regional Development Fund(ERDF)via the Welsh Government.
文摘Atomic cluster-based networks represent a promising architecture for the realization of neuromorphic computing systems,which may overcome some of the limitations of the current computing paradigm.The formation and breakage of links between the clusters are of utmost importance for the functioning of these computing systems.This paper reports the results of molecular dynamics simulations of synapse(bridge)formation at elevated temperature and thermal breaking processes between 2.8 nmsized Au1415 clusters deposited on a carbon substrate,a model system.Crucially,we find that the bridge formation process is driven by the diffusion of gold atoms along the substrate,no matter how small the gap between the clusters themselves.The complementary simulations of the bridge breaking process reveal the existence of a threshold bias voltage to activate bridge rupture via Joule heating.These results provide an atomistic-level understanding of the fundamental dynamical processes occurring in neuromorphic cluster arrays.
基金Supported by the National Natural Science Foundation of China（No.21273095）.
文摘Cytochrome P450（CYP） 2El is a dual function monoxygenase with a crucial role in the metabolism of 6% of drugs on the market at present. The enzyme is of tremendous interest for its association with alcohol consumption, diabetes, obesity and fasting. Despite the abundant experimental mutagenesis data, the molecular origin and the structural motifs for the enzymatic activity deficiencies have not been rationalized at the atomic level. In this regard, we have investigated the effects of mutation on the structural and energetic characteristics upon single point mutations in CYP2E1, N219D and $366C. The molecular dynamics（MD） simulation combined with quantum mechanics/molecular mechanics（QM/MM） and noncovalent interaction（NCI） analysis was carried out on CYP2EI and its two mutants. The results highlight the critical role of Phe207, which is responsible for both structural flexibility and energetic variation, shortening the gap between the theory and the experimentally observed results of enzymatic activity decrease, The underlying molecular mechanism of the enzymatic activity deficiencies for mutants may be attributed to the changes of spatial position of Phe207 in the two mutants. This work provides particular explanations to how mutations affect ligand-receptor interactions based on combined MD and QM/MM calculations. Furthermore, the mutational effects on the activity of CYP2E1 obtained in the present study are beneficial to both the experimental and the computational works of CYPs and may allow researchers to achieve desirable changes in enzymatic activity.
基金the support of USDoT,Mountain Plains Consortium,UGPTI under grant No.#69A3551747108
文摘Swelling clays are found extensively in various parts of the world, and sodium-montmorillonite(NaMMT) is the main constituent of an expansive clay mineral. In this work, the swelling behavior of NaMMT clay with a wide range of organic fluids, high polar through low polar fluids, is studied using a combination of Fourier transform infrared(FTIR) technique and molecular dynamics(MD) simulations.The construction of the representative clayefluid models is carried out, and the nature of nonbonded interactions between clay and fluids is studied using MD. Our FTIR and MD simulations results suggest the significant nonbonded interactions between Na-MMT clay and polar fluids, such as formamide and water. The nonbonded interactions of Na-MMT with methanol and acetone are significantly less than those in Na-MMT with polar fluids. The interactions of the fluids with various entities of the clay such as Sie O, Fee OH, Mge OH, and Ale OH captured via the spectroscopy experiments and modeling provide a finer understanding of the interactions and their contributions to swelling. The MD simulations are able to capture the band shifts observed in the spectra obtained in the spectroscopy experiments. This work also captures the conformations of interlayer sodium ions with formamide, water, methanol, and acetone during swelling. These nonbonded interactions provide insight into the molecular mechanism that the polarity of fluids plays an important role in the initiation of interlayer swelling, alteration in the orientations, and evolution of microstructure of swelling clays at the molecular scale.
基金Supported by the National Natural Science Foundation of China（No.51408525）.
文摘Non-equilibrium molecular dynamics（MD） simulations were performed according to the electronic anti-fouling technology, and some structural parameters and dynamic parameters of CaCl2 aqueous solution were taken as indicators to compare the different effect on the anti-fouling performance by applying different electric fields. The results show that electric fields can effectively decrease the viscosity of CaCl2 aqueous solution and enhance the ionic activity by enlarging the self-diffusion coefficient. In addition, with the same electric field strength, the electrostatic field is more effective at decreasing the viscosity of CaCI2 aqueous solution and increasing the self-diffusion coefficient of water molecules, while the alternating electric field is more effective at increasing the self-diffusion coefficient of Ca2＋. Furthermore, an alternating electric field with different frequencies was applied; the results show that an 800 kHz frequency is most effective to decrease the viscosity, and a 700 kHz frequency is most effective to en- hance the self-diffusion coefficient of water molecule. Otherwise, 400 kHz is most effective to enhance the self-diffusion coefficient of Ca2＋. Additionally, by studying the change of structure parameters, it was concluded that an external electric field can enhance the hydration between Ca2＋ and coordinated water molecules, and the alternating electric field is more effective in this respect.
基金by Science Challenge Project(Grant No.TZ2018006-0201-01)National Natural Science Foundation of China(Grant Nos.51605327,51805499)State Administration of Foreign Experts Affairs(Grant No.B07014).
文摘Atomic motion and surface formation in the nanometric cutting process ofβ-Sn are investigated using molecular dynamics(MD).A stagnation region is observed that changes the shape of the tool edge involved in nanometric cutting,resulting in a fluctuation in the cutting forces.It is found that single-crystal tin releases the high compressive stress generated under the tool pressure through slip and phase transformation.The tin transformation proceeds from aβ-Sn structure to a bct-Sn structure.The effects of the cutting speed,undeformed chip thickness(UCT)and tool edge radius on material removal are also explored.A better surface is obtained through material embrittlement caused by a higher speed.In addition,a smaller UCT and sharper tool edge help reduce subsurface damage.
基金Project supported by the National Natural Science Foundation of China(Nos.21674082 and 21973070)the Natural Science Foundation of Zhejiang Province(No.LY19B040006),China。
文摘The dispersion behavior and spatial distribution of nanoparticles(NPs)in ring polymer melts are explored by using molecular dynamics(MD)simulations.As polymer-NP interactions increase,three general categories of polymer-mediated NP organization are observed,namely,contact aggregation,bridging,and steric dispersion,consistent with the results of equivalent linear ones in previous studies.In the case of direct contact aggregation among NPs,the explicit aggregation-dispersion transition of NPs in ring polymer melts can be induced by increasing the chain stiffness or applying a steady shear flow.Results further indicate that NPs can achieve an optimal dispersed state with the appropriate chain stiffness and shear flow.Moreover,shear flow cannot only improve the dispersion of NPs in ring polymer melts but also control the spatial distribution of NPs into a well-ordered structure.This improvement becomes more evident under stronger polymer-NP interactions.The observed induced-dispersion or ordered distribution of NPs may provide efficient access to the design and manufacture of high-performance polymer nanocomposites(PNCs).
基金Supported by the National Natural Science Foundation of China(No.20903045)the Specialized Research Fund for the Doc-toral Program of Higher Education, China(No.20070183046)the Specialized Fund for the Basic Research of Jilin University, China(No.200810018)
文摘Drugs SPD-304（6,7-dimethyl-3-{[methyl-（2-{methyl-[1-（3-trifluoromethyl-phenyl）-1H-indol-3-ylme thyl]-amino}-ethyl）-amino]-methyl}-chromen-4-one） and zafirlukast contain a common structural element of 3-substituted indole moiety which closely relates to a dehydrogenated reaction catalyzed by cytochrome P450s（CYPs）. It was reported that the dehydrogenation can produce a reactive electrophilic intermediate which cause toxicities and inactivate CYPs. Drug L-745,870（3-{[4-（4-chlorophenyl）piperazin-1-yl]-methyl}-1H-pyrrolo 2,3-β-pyridine） might have similar effect since it contains the same structural element. We used molecular docking approach combined with molecular dynamics（MD） simulation to model three-dimensional（3D） complex structures of SPD-304, zafirlukast and L-745,870 into CYP3A4, respectively. The results show that these three drugs can stably bind into the active site and the 3-methylene carbons of the drugs keep a reasonable reactive distance from the heme iron. The complex structure of SPD-304-CYP3A4 is in agreement with experimental data. For zafirlukast, the calcu lation results indicate that 3-methylene carbon might be the dehydrogenation reaction site. Docking model of L-745,870-CYP3A4 shows a potential possibility of L-745,870 dehydrogenated by CYP3A4 at 3-methylene carbon which is in agreement with experiment in vivo. In addition, residues in the phenylalanine cluster as well as S119 and R212 play a critical role in the ligands binding based on our calculations. The docking models could provide some clues to understand the metabolic mechanism of the drugs by CYP3A4.
基金Project supported by the National Natural Science Foundation of China(Grant Nos.11374243 and 11574256)
文摘Control of ion transport and fluid flow through nanofluidic devices is of primary importance for energy storage and conversion, drug delivery and a wide range of biological processes. Recent development of nanotechnology, synthesis techniques, purification technologies, and experiment have led to rapid advances in simulation and modeling studies on ion transport properties. In this review, the applications of Poisson-Nernst-Plank （PNP） equations in analyzing transport properties are presented. The molecular dynamics （MD） studies of transport properties of ion and fluidic flow through nanofluidic devices are reported as well.
基金Project supported by the National Natural Science Foundation of China(Grant Nos.11705064,11675060,and 91730301)the Fundamental Research Funds for the Central Universities,China(Grant Nos.2662016QD005 and 26622018JC017)the Huazhong Agricultural University Scientific and Technological Self-Innovation Foundation Program,China(Grant No.2015RC021)
文摘Metal ions play critical roles in the interaction between deoxyribonucleic acid(DNA) and protein.The experimental research has demonstrated that the Mg^2+ ion can affect the binding between transcription factor and DNA.In our work,by full-atom molecular dynamic simulation, the effects of the Mg^2+ ion on the cyclic adenosine monophosphate(cAMP)response element binding protein(CREB)/cAMP response elements(CRE) complex are investigated.It is illustrated that the number of hydrogen bonds formed at the interface between protein and DNA is significantly increased when the Mg^2+ ion is added.Hence, an obvious change in the structure of the DNA is observed.Then the DNA base groove and base pair parameters are analyzed.We find that, due to the introduction of the Mg2+ ion, the DNA base major groove becomes narrower.A potential mechanism for this observation is proposed.It is confirmed that the Mg^2+ ion can enhance the stability of the DNA–protein complex.
文摘Molecular Dynamics (MD) simulations of siliceous FAU-type zeolite were carried out at various temperatures. to investigate its thermal behaviors. From the study. we found that pure silicon fanjasite showed different thermal behaviors below 1500K and above 1500K. its cell volume gradually shrinks with the rising of the temperature below 1500K. the cell volume of the zeolite changes little above 1500K.
基金Supported by the National Natural Science Foundation of China(Nos.30472062 and 20673044)
文摘The cytochrome P450 mutant CYP2C9.13（L90P） shows a greatly impaired catalytic activity compared with the wild-type. We constructed the mutants by substitution at residue 90 of CYP2C9, expressed in COS-7 cells, assayed their thermal stability and catalysis activity and analyzed the mutants via molecular dynamic（MD） simulation and flexible docking. Mutant L90E exhibits a significantly lower catalytic activity than the wild-type for the hydroxylation of diclofenac, lornoxicam and luciferin and its molecular dynamics simulation results indicate that the size of the entrance of substrate access was reduced significantly. An increase or minor decrease of catalytic activity was observed for mutants L90Q, L90W, L90R, L90I and L90G, and the sizes of the entrances of substrate access and the active site cavities had a little change in those mutants. The thermal stability and the potential energy of the MD simulation of these mutants showed a similar tendency as the catalysis assays did. Flexible docking results show the fluctuation of interaction energy is due to the change of electrostatic potential distribution. All the above facts show that the changes in the catalysis activity of the mutants caused by the substitution at residue 90 are due to the changes in the size of entrance, the shape and size of active site cavity, electrostatic potential distribution and thermal stability. The residue 90 of CYP2C9 has an important effect on the enzyme catalytic activity.
文摘The computational cost of numerical methods in microscopic-scales such as molecular dynamics(MD) is a deterrent factor that limits simulations with a large number of particles. Hence, it is desirable to decrease the computational cost and run time of simulations, especially for problems with a symmetrical domain. However, in microscopic-scales, implementation of symmetric boundary conditions is not straightforward. Previously, the present authors have successfully used a symmetry boundary condition to solve molecular flows in constant-area channels. The results obtained with this approach agree well with the benchmark cases. Therefore, it has provided us with a sound ground to further explore feasibility of applying symmetric solutions of micro-fluid flows in other geometries such as variable-area ducts. Molecular flows are solved for the whole domain with and without the symmetric boundary condition. Good agreement has been reached between the results of the symmetric solution and the whole domain solution. To investigate robustness of the proposed method, simulations are conducted for different values of affecting parameters including an external force, a flow density, and a domain length. The results indicate that the symmetric solution is also applicable to variable-area ducts such as micro-nozzles.
基金supported financially by the National Natural Science Foundation(Grant No.52035009)the‘111’project of the State Administration of Foreign Experts Affairs and the Ministry of Education of China(Grant No.B07014).
文摘Extreme ultraviolet(EUV)light plays an important role in various fields such as material characterization and semiconductor manufacturing.It is also a potential approach in material fabrication at atomic and close-to-atomic scales.However,the material removal mechanism has not yet been fully understood.This paper studies the interaction of a femtosecond EUV pulse with monocrystalline silicon using molecular dynamics(MD)coupled with a two-temperature model(TTM).The photoionization mechanism,an important process occurring at a short wavelength,is introduced to the simulation and the results are compared with those of the traditional model.Dynamical processes including photoionization,atom desorption,and laser-induced shockwave are discussed under various fluencies,and the possibility of single atomic layer removal is explored.Results show that photoionization and the corresponding bond breakage are the main reasons of atom desorption.The method developed can be further employed to investigate the interaction between high-energy photons and the material at moderate fluence.
文摘The implementation of solid-fluid boundary condition has been a major challenge for dissipative particle dynamics(DPD)method.Current implementations of boundary conditions usually try to approach a uniform density distribution and a velocity profile close to analytical solution.The density oscillations and slip velocity are intentionally eliminated,and different wall properties disappear in the same analytical solution.This paper develops a new wall model that combines image and frozen particles and a new strategy to emphasize different wall properties especially wettabilities.The strategy first studies the realistic wall-fluid system by molecular dynamics(MD)simulation depending on physical parameters.Then,a DPD simulation is used to match the density and velocity profiles with the new wall model.The obtained DPD parameters can simulate the systems with the same wall and fluid materials.With this method,a simulation of the Poiseuille flow of liquid argon with copper walls is presented.Other walls with super-hydrophilic,hydrophilic,and hydrophobic wettabilities are also simulated.The limitations of the analytical solution and the effect of the wall-fluid interaction are discussed.The results show that the method suggested in this paper can simulate the mesoscale behavior of the microchannel flow related to realistic systems.
