The investigation is generalized to clusters with sizes up to 3000 atoms, covering this way the range of sizes experimentally available for low energy cluster beam deposition. The atomic scale modeling is carried on b...The investigation is generalized to clusters with sizes up to 3000 atoms, covering this way the range of sizes experimentally available for low energy cluster beam deposition. The atomic scale modeling is carried on by both Molecular Dynamics and Metropolis Monte Carlo. This represents a huge series of simulations (175 cases) to which further calculations are added by spot when finer tuning of the parameters is necessary. Analyzing the results is a major task which is still in progress. This way, not only a realistic range of sizes is covered, but also the whole range of compositions and the temperature range relevant to the solid and the liquid states.展开更多
For the determination of surface tension of liquid droplets by molecular dynamics simulations, the most timeconsuming part is the calculation of pressure tensor in the transition layer, which makes it difficult to enh...For the determination of surface tension of liquid droplets by molecular dynamics simulations, the most timeconsuming part is the calculation of pressure tensor in the transition layer, which makes it difficult to enhance the precision of the computation. A new method for the calculation of surface tension of liquid droplets to reduce the calculation quantity of pressure tensor in transition layer to the minimum is proposed in this paper. Two thousand particles are taken as example to show how to carry out our scheme.展开更多
Molecular dynamics （MD） simulation has become a powerful tool to investigate the structure- function relationship of proteins and other biological macromolecules at atomic resolution and biologically relevant timesc...Molecular dynamics （MD） simulation has become a powerful tool to investigate the structure- function relationship of proteins and other biological macromolecules at atomic resolution and biologically relevant timescales. MD simulations often produce massive datasets con- taining millions of snapshots describing proteins in motion. Therefore, clustering algorithms have been in high demand to be developed and applied to classify these MD snapshots and gain biological insights. There mainly exist two categories of clustering algorithms that aim to group protein conformations into clusters based on the similarity of their shape （geometric clustering） and kinetics （kinetic clustering）. In this paper, we review a series of frequently used clustering algorithms applied in MD simulations, including divisive algorithms, ag- glomerative algorithms （single-linkage, complete-linkage, average-linkage, centroid-linkage and ward-linkage）, center-based algorithms （K-Means, K-Medoids, K-Centers, and APM）, density-based algorithms （neighbor-based, DBSCAN, density-peaks, and Robust-DB）, and spectral-based algorithms （PCCA and PCCA＋）. In particular, differences between geomet- ric and kinetic clustering metrics will be discussed along with the performances of diflhrent clustering algorithms. We note that there does not exist a one-size-fits-all algorithm in the classification of MD datasets. For a specific application, the right choice of clustering algo- rithm should be based on the purpose of clustering, and the intrinsic properties of the MD conformational ensembles. Therefore, a main focus of our review is to describe the merits and limitations of each clustering algorithm. We expect that this review would be helpful to guide researchers to choose appropriate clustering algorithms for their own MD datasets.展开更多
Understanding of metal oxidation is very critical to corrosion control,catalysis synthesis,and advanced materials engineering.Metal oxidation is a very complex phenomenon,with many different processes which are couple...Understanding of metal oxidation is very critical to corrosion control,catalysis synthesis,and advanced materials engineering.Metal oxidation is a very complex phenomenon,with many different processes which are coupled and involved from the onset of reaction.In this work,the initial stage of oxidation on titanium surface was investigated in atomic scale by molecular dynamics(MD)simulations using a reactive force field(ReaxFF).We show that oxygen transport is the dominant process during the initial oxidation.Our simulation also demonstrate that a compressive stress was generated in the oxide layer which blocked the oxygen transport perpendicular to the Titanium(0001)surface and further prevented oxidation in the deeper layers.The mechanism of initial oxidation observed in this work can be also applicable to other self-limiting oxidation.展开更多
The diffusion dynamics of small two-dimensional atomic clusters Cux （1≤x≤8） on Cu（lll） surface were studied using the molecular dynamics simulations and a modified analytic embedded-atom method in the temperatur...The diffusion dynamics of small two-dimensional atomic clusters Cux （1≤x≤8） on Cu（lll） surface were studied using the molecular dynamics simulations and a modified analytic embedded-atom method in the temperature range from 200 K to 800 K. The cluster size and temperature dependence of the diffusion coefficients and migration energies are presented. Our simulations show that the diffusion migration energy of the CuT cluster is the highest and the prefactor for the CuT cluster is almost three orders of magnitude larger than that for single atom diffusion. This conclusion is consistent with the experimental results for similar metals. In addition, the dependence of cluster diffusion on film growth is also discussed.展开更多
To investigate the microscopicmechanism underlying the influence of surface-chemical gradient on heat andmass recovery,a molecular dynamicsmodel including droplet condensation and transport process has been developed ...To investigate the microscopicmechanism underlying the influence of surface-chemical gradient on heat andmass recovery,a molecular dynamicsmodel including droplet condensation and transport process has been developed to examine heat and mass recovery performance.This work aimed at identify optimal conditions for enhancing heat and mass recovery through the combination of wettability gradient and nanopore transport.For comprehensive analysis,the structure in the simulation was categorized into three distinct groups:a homogeneous structure,a small wettability gradient,and a large wettability gradient.The homogeneous surface demonstrated low efficiency in heat and mass transfer,as evidenced by filmwise condensation.In contrast,the surface with a small wettability gradient experienced a transition from dropwise condensation to filmwise condensation,resulting in a gradual decrease in the efficiency of vapor heat and mass transfer.Only a large wettability gradient could achieve periodic and efficient dropwise condensation heat and mass transfer which was attributed to the rapid droplet coalescence and transport to the nanopore after condensing on the cold surface.展开更多
A comprehensive simulation model -- deposition, diffusion, rotation, reaction and aggregation model is presented to simulate the formation processes of ramified clusters on liquid surfaces, where clusters can disuse a...A comprehensive simulation model -- deposition, diffusion, rotation, reaction and aggregation model is presented to simulate the formation processes of ramified clusters on liquid surfaces, where clusters can disuse and rotate easily. The mobility （including diffusion and rotation） of clusters is related to its mass, which is given by Dm = Dos^-γD and θm = θos^-γθ, respectively. The influence of the reaction probability on the kinetics and structure formation is included in the simulation model. We concentrate on revealing dynamic scaling during ramified cluster formation. For this purpose, the time evolution of the cluster density and the weight-average cluster size as well as the cluster-size distribution scaling function at different time are determined for various conditions. The dependence of the cluster density on the deposition flux and time-dependence of fractal dimension are also investigated. The obtained results are helpful in understanding the formation of clusters or thin film growth on liquid surfaces.展开更多
The effects of the diameters of single-walled carbon nanotubes （SWCNTs） （7.83A to 27.40A） and temperature （20 K-45 K） on the equilibrium structure of an argon cluster are systematically studied by molecular dyna...The effects of the diameters of single-walled carbon nanotubes （SWCNTs） （7.83A to 27.40A） and temperature （20 K-45 K） on the equilibrium structure of an argon cluster are systematically studied by molecular dynamics simulation with consideration of the SWCNTs to be fixed. Since the diameters of SWCNTs with different chiralities increase when temperature is fixed at 20 K, the equilibrium structures of the argon cluster transform from monoatomic chains to helical and then to multishell coaxial cylinders. Chirality has almost no noticeable influence on these cylindrosymmetric structures. The effects of temperature and a non-equilibrium sudden heating process on the structures of argon clusters in SWCNTs are also studied by molecular dynamics simulation.展开更多
Three coalescence processes of Cu57-Cu57, Cu57-Cu58, and Cu5s Cu58 clusters at 300 K are investigated by employing molecular dynamics simulations. According to the evolutions of mean square displacement and local atom...Three coalescence processes of Cu57-Cu57, Cu57-Cu58, and Cu5s Cu58 clusters at 300 K are investigated by employing molecular dynamics simulations. According to the evolutions of mean square displacement and local atom packing, the coalescence process can be separated into three stages including an approaching stage, a coalescing stage, and a coalesced stage. The simulations show that the coalescence processes and the formed products are sensitive to the respective initial structures of, and the relative configuration between, the two coalescing icosahedron-based clusters.展开更多
The grain boundary is an interface and the surface tension is one of its important thermodynamic properties. In this paper, the surface tension of the Σ9 grain boundary for α-Fe at various temperatures and pressures...The grain boundary is an interface and the surface tension is one of its important thermodynamic properties. In this paper, the surface tension of the Σ9 grain boundary for α-Fe at various temperatures and pressures is calculated by means of Computer Molecular Dynamics (CMD). The results agree satisfactorily with the experimental data. It. is shown that the contribution of entropy to surface tension of grain boundary can be ignored.展开更多
Molecular dynamics simulations are performed to observe the evolutions of 512 and 51262 cage-like water clusters filled with or without a methane molecule immersed in bulk liquid water at 250 K and 230 K. The lifetime...Molecular dynamics simulations are performed to observe the evolutions of 512 and 51262 cage-like water clusters filled with or without a methane molecule immersed in bulk liquid water at 250 K and 230 K. The lifetimes of these clusters are calculated according to their Lindemann index δ (t) using the criteria of δ≥0.07. For both the filled and empty clusters, we find the dynamics of bulk water determines the lifetimes of cage-like water clusters, and that the lifetime of 512 62 cage-like cluster is the same as that of 512 cage-like cluster. Although the methane molecule indeed makes the filled cage-like cluster more stable than the empty one, the empty cage-like cluster still has chance to be long-lived compared with the filled clusters. These observations support the labile cluster hypothesis on the formation mechanisms of gas hydrates.展开更多
The phase transition of tungsten(W)under high pressures was investigated with molecular dynamics simulation.The structure was characterized in terms of the pair distribution function and the largest standard cluster a...The phase transition of tungsten(W)under high pressures was investigated with molecular dynamics simulation.The structure was characterized in terms of the pair distribution function and the largest standard cluster analysis(LSCA).It is found that under 40−100 GPa at a cooling rate of 0.1 K/ps a pure W melt first crystallizes into the body-centred cubic(BCC)crystal,and then transfers into the hexagonal close-packed(HCP)crystal through a series of BCC−HCP coexisting states.The dynamic factors may induce intermediate stages during the liquid−solid transition and the criss-cross grain boundaries cause lots of indistinguishable intermediate states,making the first-order BCC−HCP transition appear to be continuous.Furthermore,LSCA is shown to be a parameter-free method that can effectively analyze both ordered and disordered structures.Therefore,LSCA can detect more details about the evolution of the structure in such structure transition processes with rich intermediate structures.展开更多
Depositions of Si, Ge and C atoms onto a preliminary Si （001） substrate at different temperatures are investigated by using the molecular dynamics method. The mechanism of atomic self-assembling occurring locally on...Depositions of Si, Ge and C atoms onto a preliminary Si （001） substrate at different temperatures are investigated by using the molecular dynamics method. The mechanism of atomic self-assembling occurring locally on the flat terraces between steps is suggested. Diffusion and arrangement patterns of adatoms at different temperatures are observed. At 900 K, the deposited atoms are more likely to form dimers in the perpendicular [110] direction due to the more favourable movement along the perpendicular [110] direction. C adatoms are more likely to break or reconstruct the dimers on the substrate surface and have larger diffusion distances than Ge and Si adatoms. Exchange between C adatoms and substrate atoms are obvious and the epitaxial thickness is small. Total potential energies of adatoms and substrate atoms involved in the simulation cell are computed. When a newly arrived adatom reaches the stable position, the potential energy of the system will decrease and the curves turns into a ladder-like shape. It is found that C adatoms can lead to more reduction of the system energy and the potential energy of the system will increase as temperature increases.展开更多
In 1949, Tolman found the relation between the surface tension and Tolman length, which determines the dimensional effect of the surface tension. Tolman length is the difference between the equimolar surface and the s...In 1949, Tolman found the relation between the surface tension and Tolman length, which determines the dimensional effect of the surface tension. Tolman length is the difference between the equimolar surface and the surface of tension. In recent years, the magnitude, expression, and sign of the Tolman length remain an open question. An incompressible and homogeneous liquid droplet model is proposed and the approximate expression and sign for Tolman length are derived in this paper. We obtain the relation between Tolman length and the radius of the surface of tension(R_(s)) and found that they increase with the Rs decreasing. The Tolman length of plane surface tends to zero. Taking argon for example, molecular dynamics simulation is carried out by using the Lennard–Jones(LJ) potential between atoms at a temperature of 90 K. Five simulated systems are used, with numbers of argon atoms being 10140, 10935, 11760, 13500, and 15360, respectively. By methods of theoretical study and molecular dynamics simulation, we find that the calculated value of Tolman length is more than zero, and it decreases as the size is increased among the whole size range. The value of surface tension increases with the radius of the surface of tension increasing, which is consistent with Tolman’s theory. These conclusions are significant for studying the size dependence of the surface tension.展开更多
An analysis of the molecular dynamics of ethanol solvated by water molecules in the absence and presence of a Pt surface has been performed using DL_POLY_2.19 code. The structure and diffusion properties of an ethanol...An analysis of the molecular dynamics of ethanol solvated by water molecules in the absence and presence of a Pt surface has been performed using DL_POLY_2.19 code. The structure and diffusion properties of an ethanol–water system have been studied at various temperatures from 250 to 600 K. We have measured the self-diffusion coefficients of the 50:50% ethanol–water solution;in the absence of a Pt surface our results show an excellent agreement–within an error of 7.4% – with the experimental data. An increase in the self-diffusion coefficients with the inclusion of a Pt surface has been observed. The estimation of the diffusion coefficients of both water and ethanol in the presence of a Pt surface shows that they obey the Arrhenius equation;the calculated activation energies of diffusion of ethanol and water are 2.47 and 2.98 Kcal/mole, respectively. The radial distribution function graphs and density profiles have been built;their correlations with the self-diffusion coefficients of both ethanol and water molecules are also illustrated.展开更多
The human serotonin transporter(SERT)terminates neurotransmission by removing serotonin from the synaptic cleft,which is an essential process that plays an important role in depression.In addition to natural substrate...The human serotonin transporter(SERT)terminates neurotransmission by removing serotonin from the synaptic cleft,which is an essential process that plays an important role in depression.In addition to natural substrate serotonin,SERT is also the target of the abused drug cocaine and,clinically used antidepressants,escitalopram,and paroxetine.To date,few studies have attempted to investigate the unbinding mechanism underlying the orthosteric and allosteric modulation of SERT.In this article,the conserved property of the orthosteric and allosteric sites(S1 and S2)of SERT was revealed by combining the high resolutions of x-ray crystal structures and molecular dynamics(MD)simulations.The residues Tyr95 and Ser438 located within the S1 site,and Arg104 located within the S2 site in SERT illustrate conserved interactions(hydrogen bonds and hydrophobic interactions),as responses to selective serotonin reuptake inhibitors.Van der Waals interactions were keys to designing effective drugs inhibiting SERT and further,electrostatic interactions highlighted escitalopram as a potent antidepressant.We found that cocaine,escitalopram,and paroxetine,whether the S1 site or the S2 site,were more competitive.According to this potential of mean force(PMF)simulations,the new insights reveal the principles of competitive inhibitors that lengths of trails from central SERT to an opening were~18A for serotonin and~22 A for the above-mentioned three drugs.Furthermore,the distance between the natural substrate serotonin and cocaine(or escitalopram)at the allosteric site was~3A.Thus,it can be inferred that the potent antidepressants tended to bind at deeper positions of the S1 or the S2 site of SERT in comparison to the substrate.Continuing exploring the processes of unbinding four ligands against the two target pockets of SERT,this study observed a broad pathway in which serotonin,cocaine,escitalopram(at the S1 site),and paroxetine all were pulled out to an opening between MT1b and MT6a,which may be helpful to understand the dissociation mechanism of antidepressants.展开更多
Superhydrophobic(SH)coatings are intended to resist a surface from corrosion and thereby increases the product life duration.It is also a promising solution to save cleaning costs and time by providing self-clean natu...Superhydrophobic(SH)coatings are intended to resist a surface from corrosion and thereby increases the product life duration.It is also a promising solution to save cleaning costs and time by providing self-clean nature to the surface.This review article provides the most recent updates in designing SH surfaces and their characterizations adopted both in experimental and computational techniques.To gain a comprehensive perspective,the SH surfaces present in nature those are inspiring human beings to mimic such surfaces are introduced at the beginning of this article.Subsequently,different fabrication techniques undertaken recently to design artificial SH surfaces are briefly discussed.Recent progress in computations employed in the development of SH surfaces is then discussed.Next,the limitations in SH surfaces are addressed.Finally,perceptiveness of different strategies and their limitations are presented in the concluding remarks and outlook.Overall,this mini review article brings together and highlights the significant advancements in fabrication of superhydrophobic surfaces which may surely help the early-stage researchers/scientists to plan their work accordingly.展开更多
Within the framework of the embedded-atom method, we performed molecular-dynamics calculations to investigate the structural transformation during melting of two copper clus- ters containing 57 and 58 atoms. The simul...Within the framework of the embedded-atom method, we performed molecular-dynamics calculations to investigate the structural transformation during melting of two copper clus- ters containing 57 and 58 atoms. The simulation results reveal how their different structural changes can strongly influence internal energy and radial distribution functions. The local structural patterns of different regions during the temperature increase, determined by atom density profiles, are identified for the melting of each cluster. The simulations show sensi- tivities of the structural changes for these two small size clusters with different structures.展开更多
Molecular dynamics simulation is carried out to investigate the effects of cooling rate on the final configurations of silver after rapid solidification. The cooling rate for the formation of a silver amorphous phase ...Molecular dynamics simulation is carried out to investigate the effects of cooling rate on the final configurations of silver after rapid solidification. The cooling rate for the formation of a silver amorphous phase is determined by analyzing its pair distribution function, H-A bond index, and the largest crystal cluster. Further, the equilibrium structures of the subcritical nuclei and crystal clusters are studied. The results show that the solidified microstructure is composed of a mixture of crystal clusters and amorphous phases at a certain cooling rate range. The size of the largest crystal cluster decreases with the increasing cooling rate, and it completely disappears when the cooling rate exceeds a critical value. The structures of the subcritical nuclei and the largest crystal cluster are composed of lamellar structures of fcc and hcp atoms, indicating that the lamellar structure of fcc and hcp atoms in the silver crystal originates from nucleation, and not from the growth of crystals.展开更多
文摘The investigation is generalized to clusters with sizes up to 3000 atoms, covering this way the range of sizes experimentally available for low energy cluster beam deposition. The atomic scale modeling is carried on by both Molecular Dynamics and Metropolis Monte Carlo. This represents a huge series of simulations (175 cases) to which further calculations are added by spot when finer tuning of the parameters is necessary. Analyzing the results is a major task which is still in progress. This way, not only a realistic range of sizes is covered, but also the whole range of compositions and the temperature range relevant to the solid and the liquid states.
基金Project supported by the National Natural Science Foundation of China(Grant No.10772189)the Knowledge Innovation Program of Chinese Academy of Sciences
文摘For the determination of surface tension of liquid droplets by molecular dynamics simulations, the most timeconsuming part is the calculation of pressure tensor in the transition layer, which makes it difficult to enhance the precision of the computation. A new method for the calculation of surface tension of liquid droplets to reduce the calculation quantity of pressure tensor in transition layer to the minimum is proposed in this paper. Two thousand particles are taken as example to show how to carry out our scheme.
基金supported by Shenzhen Science and Technology Innovation Committee(JCYJ20170413173837121)the Hong Kong Research Grant Council(HKUST C6009-15G,14203915,16302214,16304215,16318816,and AoE/P-705/16)+2 种基金King Abdullah University of Science and Technology(KAUST) Office of Sponsored Research(OSR)(OSR-2016-CRG5-3007)Guangzhou Science Technology and Innovation Commission(201704030116)Innovation and Technology Commission(ITCPD/17-9and ITC-CNERC14SC01)
文摘Molecular dynamics （MD） simulation has become a powerful tool to investigate the structure- function relationship of proteins and other biological macromolecules at atomic resolution and biologically relevant timescales. MD simulations often produce massive datasets con- taining millions of snapshots describing proteins in motion. Therefore, clustering algorithms have been in high demand to be developed and applied to classify these MD snapshots and gain biological insights. There mainly exist two categories of clustering algorithms that aim to group protein conformations into clusters based on the similarity of their shape （geometric clustering） and kinetics （kinetic clustering）. In this paper, we review a series of frequently used clustering algorithms applied in MD simulations, including divisive algorithms, ag- glomerative algorithms （single-linkage, complete-linkage, average-linkage, centroid-linkage and ward-linkage）, center-based algorithms （K-Means, K-Medoids, K-Centers, and APM）, density-based algorithms （neighbor-based, DBSCAN, density-peaks, and Robust-DB）, and spectral-based algorithms （PCCA and PCCA＋）. In particular, differences between geomet- ric and kinetic clustering metrics will be discussed along with the performances of diflhrent clustering algorithms. We note that there does not exist a one-size-fits-all algorithm in the classification of MD datasets. For a specific application, the right choice of clustering algo- rithm should be based on the purpose of clustering, and the intrinsic properties of the MD conformational ensembles. Therefore, a main focus of our review is to describe the merits and limitations of each clustering algorithm. We expect that this review would be helpful to guide researchers to choose appropriate clustering algorithms for their own MD datasets.
基金Support of this work from the National Natural Science Foundation of China(Grant No.51361009)Work at Ames Laboratory was supported by the US Department of Energy,Basic Energy Sciences,Division of Materials Science and Engineering under Contract No.DE-AC02-07CH11358,including a grant of computer time at the National Energy Research Scientific Computing Centre(NERSC)in Berkeley,CA.
文摘Understanding of metal oxidation is very critical to corrosion control,catalysis synthesis,and advanced materials engineering.Metal oxidation is a very complex phenomenon,with many different processes which are coupled and involved from the onset of reaction.In this work,the initial stage of oxidation on titanium surface was investigated in atomic scale by molecular dynamics(MD)simulations using a reactive force field(ReaxFF).We show that oxygen transport is the dominant process during the initial oxidation.Our simulation also demonstrate that a compressive stress was generated in the oxide layer which blocked the oxygen transport perpendicular to the Titanium(0001)surface and further prevented oxidation in the deeper layers.The mechanism of initial oxidation observed in this work can be also applicable to other self-limiting oxidation.
基金ACKNOWLEDGMENT This work was supported Natural Science Foundation by the Hunan Provincial of China （No.06JJ2100）.
文摘The diffusion dynamics of small two-dimensional atomic clusters Cux （1≤x≤8） on Cu（lll） surface were studied using the molecular dynamics simulations and a modified analytic embedded-atom method in the temperature range from 200 K to 800 K. The cluster size and temperature dependence of the diffusion coefficients and migration energies are presented. Our simulations show that the diffusion migration energy of the CuT cluster is the highest and the prefactor for the CuT cluster is almost three orders of magnitude larger than that for single atom diffusion. This conclusion is consistent with the experimental results for similar metals. In addition, the dependence of cluster diffusion on film growth is also discussed.
基金supported by the National Natural Science Foundation of China(No.52206093)the University Outstanding Youth Fund Project of Anhui Province(Nos.2022AH020028 and 2022AH030037)+2 种基金the Natural Science Foundation of Anhui Province(Nos.1908085QF292 and 2308085ME173)Anhui Province Outstanding Young Talents Support Program(No.gxyqZD2022058)Guangdong Basic and Applied Basic Research Foundation(Nos.2024A1515011379 and 2023A1515110613).
文摘To investigate the microscopicmechanism underlying the influence of surface-chemical gradient on heat andmass recovery,a molecular dynamicsmodel including droplet condensation and transport process has been developed to examine heat and mass recovery performance.This work aimed at identify optimal conditions for enhancing heat and mass recovery through the combination of wettability gradient and nanopore transport.For comprehensive analysis,the structure in the simulation was categorized into three distinct groups:a homogeneous structure,a small wettability gradient,and a large wettability gradient.The homogeneous surface demonstrated low efficiency in heat and mass transfer,as evidenced by filmwise condensation.In contrast,the surface with a small wettability gradient experienced a transition from dropwise condensation to filmwise condensation,resulting in a gradual decrease in the efficiency of vapor heat and mass transfer.Only a large wettability gradient could achieve periodic and efficient dropwise condensation heat and mass transfer which was attributed to the rapid droplet coalescence and transport to the nanopore after condensing on the cold surface.
基金The project supported by the Natural Science Foundation for Young Scientists of Zhejiang Province of China under Grant No. RC02069 .
文摘A comprehensive simulation model -- deposition, diffusion, rotation, reaction and aggregation model is presented to simulate the formation processes of ramified clusters on liquid surfaces, where clusters can disuse and rotate easily. The mobility （including diffusion and rotation） of clusters is related to its mass, which is given by Dm = Dos^-γD and θm = θos^-γθ, respectively. The influence of the reaction probability on the kinetics and structure formation is included in the simulation model. We concentrate on revealing dynamic scaling during ramified cluster formation. For this purpose, the time evolution of the cluster density and the weight-average cluster size as well as the cluster-size distribution scaling function at different time are determined for various conditions. The dependence of the cluster density on the deposition flux and time-dependence of fractal dimension are also investigated. The obtained results are helpful in understanding the formation of clusters or thin film growth on liquid surfaces.
基金Project supported by the National Natural Science Foundation of China(Grant No.11072242)
文摘The effects of the diameters of single-walled carbon nanotubes （SWCNTs） （7.83A to 27.40A） and temperature （20 K-45 K） on the equilibrium structure of an argon cluster are systematically studied by molecular dynamics simulation with consideration of the SWCNTs to be fixed. Since the diameters of SWCNTs with different chiralities increase when temperature is fixed at 20 K, the equilibrium structures of the argon cluster transform from monoatomic chains to helical and then to multishell coaxial cylinders. Chirality has almost no noticeable influence on these cylindrosymmetric structures. The effects of temperature and a non-equilibrium sudden heating process on the structures of argon clusters in SWCNTs are also studied by molecular dynamics simulation.
基金Supported by Special Foundation for State Major Basic Research Program of China (Grant No. G2006CB605103)the Scientific Research Foundation for the Returned Overseas Chinese Scholars,State Education Ministry,China and the Fundamental Research Funds for the Central University (Grant No. 90405001)
文摘Three coalescence processes of Cu57-Cu57, Cu57-Cu58, and Cu5s Cu58 clusters at 300 K are investigated by employing molecular dynamics simulations. According to the evolutions of mean square displacement and local atom packing, the coalescence process can be separated into three stages including an approaching stage, a coalescing stage, and a coalesced stage. The simulations show that the coalescence processes and the formed products are sensitive to the respective initial structures of, and the relative configuration between, the two coalescing icosahedron-based clusters.
基金The project supported by the National Natural Science Foundation of Chinathe Science Foundation of Chinese Academy of Sciences.
文摘The grain boundary is an interface and the surface tension is one of its important thermodynamic properties. In this paper, the surface tension of the Σ9 grain boundary for α-Fe at various temperatures and pressures is calculated by means of Computer Molecular Dynamics (CMD). The results agree satisfactorily with the experimental data. It. is shown that the contribution of entropy to surface tension of grain boundary can be ignored.
基金supported by the National Natural Science Foundation of China(Grant No.40102005 and No.49725205).
文摘Molecular dynamics simulations are performed to observe the evolutions of 512 and 51262 cage-like water clusters filled with or without a methane molecule immersed in bulk liquid water at 250 K and 230 K. The lifetimes of these clusters are calculated according to their Lindemann index δ (t) using the criteria of δ≥0.07. For both the filled and empty clusters, we find the dynamics of bulk water determines the lifetimes of cage-like water clusters, and that the lifetime of 512 62 cage-like cluster is the same as that of 512 cage-like cluster. Although the methane molecule indeed makes the filled cage-like cluster more stable than the empty one, the empty cage-like cluster still has chance to be long-lived compared with the filled clusters. These observations support the labile cluster hypothesis on the formation mechanisms of gas hydrates.
基金Projects(51661005,U1612442)supported by the National Natural Science Foundation of ChinaProject(QKHJC[2017]1025)supported by the Natural Science Foundation of Guizhou Province,ChinaProject(2018JJ3560)supported by the Natural Science Foundation of Hunan Province,China。
文摘The phase transition of tungsten(W)under high pressures was investigated with molecular dynamics simulation.The structure was characterized in terms of the pair distribution function and the largest standard cluster analysis(LSCA).It is found that under 40−100 GPa at a cooling rate of 0.1 K/ps a pure W melt first crystallizes into the body-centred cubic(BCC)crystal,and then transfers into the hexagonal close-packed(HCP)crystal through a series of BCC−HCP coexisting states.The dynamic factors may induce intermediate stages during the liquid−solid transition and the criss-cross grain boundaries cause lots of indistinguishable intermediate states,making the first-order BCC−HCP transition appear to be continuous.Furthermore,LSCA is shown to be a parameter-free method that can effectively analyze both ordered and disordered structures.Therefore,LSCA can detect more details about the evolution of the structure in such structure transition processes with rich intermediate structures.
基金Project supported by the National High Technology Research and Development Program of China (Grant No 2009AA03Z405)the National Natural Science Foundation of China (Grant No 60644004)
文摘Depositions of Si, Ge and C atoms onto a preliminary Si （001） substrate at different temperatures are investigated by using the molecular dynamics method. The mechanism of atomic self-assembling occurring locally on the flat terraces between steps is suggested. Diffusion and arrangement patterns of adatoms at different temperatures are observed. At 900 K, the deposited atoms are more likely to form dimers in the perpendicular [110] direction due to the more favourable movement along the perpendicular [110] direction. C adatoms are more likely to break or reconstruct the dimers on the substrate surface and have larger diffusion distances than Ge and Si adatoms. Exchange between C adatoms and substrate atoms are obvious and the epitaxial thickness is small. Total potential energies of adatoms and substrate atoms involved in the simulation cell are computed. When a newly arrived adatom reaches the stable position, the potential energy of the system will decrease and the curves turns into a ladder-like shape. It is found that C adatoms can lead to more reduction of the system energy and the potential energy of the system will increase as temperature increases.
基金Project supported by the National Key Research and Development Program of China(Grant No.2016YFB0700500)the Scientific Research and Innovation Team of Cangzhou Normal University,China(Grant No.cxtdl1907)+2 种基金the Key Scientific Study Program of Hebei Provincial Higher Education Institution,China(Grant No.ZD2020410)the Cangzhou Natural Science Foundation,China(Grant No.197000001)the General Scientific Research Fund Project of Cangzhou Normal University,China(Grant No.xnjjl1906)。
文摘In 1949, Tolman found the relation between the surface tension and Tolman length, which determines the dimensional effect of the surface tension. Tolman length is the difference between the equimolar surface and the surface of tension. In recent years, the magnitude, expression, and sign of the Tolman length remain an open question. An incompressible and homogeneous liquid droplet model is proposed and the approximate expression and sign for Tolman length are derived in this paper. We obtain the relation between Tolman length and the radius of the surface of tension(R_(s)) and found that they increase with the Rs decreasing. The Tolman length of plane surface tends to zero. Taking argon for example, molecular dynamics simulation is carried out by using the Lennard–Jones(LJ) potential between atoms at a temperature of 90 K. Five simulated systems are used, with numbers of argon atoms being 10140, 10935, 11760, 13500, and 15360, respectively. By methods of theoretical study and molecular dynamics simulation, we find that the calculated value of Tolman length is more than zero, and it decreases as the size is increased among the whole size range. The value of surface tension increases with the radius of the surface of tension increasing, which is consistent with Tolman’s theory. These conclusions are significant for studying the size dependence of the surface tension.
文摘An analysis of the molecular dynamics of ethanol solvated by water molecules in the absence and presence of a Pt surface has been performed using DL_POLY_2.19 code. The structure and diffusion properties of an ethanol–water system have been studied at various temperatures from 250 to 600 K. We have measured the self-diffusion coefficients of the 50:50% ethanol–water solution;in the absence of a Pt surface our results show an excellent agreement–within an error of 7.4% – with the experimental data. An increase in the self-diffusion coefficients with the inclusion of a Pt surface has been observed. The estimation of the diffusion coefficients of both water and ethanol in the presence of a Pt surface shows that they obey the Arrhenius equation;the calculated activation energies of diffusion of ethanol and water are 2.47 and 2.98 Kcal/mole, respectively. The radial distribution function graphs and density profiles have been built;their correlations with the self-diffusion coefficients of both ethanol and water molecules are also illustrated.
基金Project supported by the National Natural Science Foundation of China(Grant Nos.11904036 and 12175081)Fundamental Research Funds for the Central Universities(Grant No.CCNU22QNOO4)。
文摘The human serotonin transporter(SERT)terminates neurotransmission by removing serotonin from the synaptic cleft,which is an essential process that plays an important role in depression.In addition to natural substrate serotonin,SERT is also the target of the abused drug cocaine and,clinically used antidepressants,escitalopram,and paroxetine.To date,few studies have attempted to investigate the unbinding mechanism underlying the orthosteric and allosteric modulation of SERT.In this article,the conserved property of the orthosteric and allosteric sites(S1 and S2)of SERT was revealed by combining the high resolutions of x-ray crystal structures and molecular dynamics(MD)simulations.The residues Tyr95 and Ser438 located within the S1 site,and Arg104 located within the S2 site in SERT illustrate conserved interactions(hydrogen bonds and hydrophobic interactions),as responses to selective serotonin reuptake inhibitors.Van der Waals interactions were keys to designing effective drugs inhibiting SERT and further,electrostatic interactions highlighted escitalopram as a potent antidepressant.We found that cocaine,escitalopram,and paroxetine,whether the S1 site or the S2 site,were more competitive.According to this potential of mean force(PMF)simulations,the new insights reveal the principles of competitive inhibitors that lengths of trails from central SERT to an opening were~18A for serotonin and~22 A for the above-mentioned three drugs.Furthermore,the distance between the natural substrate serotonin and cocaine(or escitalopram)at the allosteric site was~3A.Thus,it can be inferred that the potent antidepressants tended to bind at deeper positions of the S1 or the S2 site of SERT in comparison to the substrate.Continuing exploring the processes of unbinding four ligands against the two target pockets of SERT,this study observed a broad pathway in which serotonin,cocaine,escitalopram(at the S1 site),and paroxetine all were pulled out to an opening between MT1b and MT6a,which may be helpful to understand the dissociation mechanism of antidepressants.
文摘Superhydrophobic(SH)coatings are intended to resist a surface from corrosion and thereby increases the product life duration.It is also a promising solution to save cleaning costs and time by providing self-clean nature to the surface.This review article provides the most recent updates in designing SH surfaces and their characterizations adopted both in experimental and computational techniques.To gain a comprehensive perspective,the SH surfaces present in nature those are inspiring human beings to mimic such surfaces are introduced at the beginning of this article.Subsequently,different fabrication techniques undertaken recently to design artificial SH surfaces are briefly discussed.Recent progress in computations employed in the development of SH surfaces is then discussed.Next,the limitations in SH surfaces are addressed.Finally,perceptiveness of different strategies and their limitations are presented in the concluding remarks and outlook.Overall,this mini review article brings together and highlights the significant advancements in fabrication of superhydrophobic surfaces which may surely help the early-stage researchers/scientists to plan their work accordingly.
文摘Within the framework of the embedded-atom method, we performed molecular-dynamics calculations to investigate the structural transformation during melting of two copper clus- ters containing 57 and 58 atoms. The simulation results reveal how their different structural changes can strongly influence internal energy and radial distribution functions. The local structural patterns of different regions during the temperature increase, determined by atom density profiles, are identified for the melting of each cluster. The simulations show sensi- tivities of the structural changes for these two small size clusters with different structures.
基金supported by the National Natural Science Foundation of China (Grant Nos. 51071115, 50671075)the National Basic Research Program of China ("973" Program) (Grant No. 2006CB605202)
文摘Molecular dynamics simulation is carried out to investigate the effects of cooling rate on the final configurations of silver after rapid solidification. The cooling rate for the formation of a silver amorphous phase is determined by analyzing its pair distribution function, H-A bond index, and the largest crystal cluster. Further, the equilibrium structures of the subcritical nuclei and crystal clusters are studied. The results show that the solidified microstructure is composed of a mixture of crystal clusters and amorphous phases at a certain cooling rate range. The size of the largest crystal cluster decreases with the increasing cooling rate, and it completely disappears when the cooling rate exceeds a critical value. The structures of the subcritical nuclei and the largest crystal cluster are composed of lamellar structures of fcc and hcp atoms, indicating that the lamellar structure of fcc and hcp atoms in the silver crystal originates from nucleation, and not from the growth of crystals.
