Molecular dynamics simulations were carried out to study the configuration energy and radial distribution functions of mmonium dihydrogen phosphate solution at different temperatures. The dihydrogen phosphate ion was ...Molecular dynamics simulations were carried out to study the configuration energy and radial distribution functions of mmonium dihydrogen phosphate solution at different temperatures. The dihydrogen phosphate ion was treated as a seven-site model and the ammonium ion was regarded as a five-site model, while a simple-point-charge model for water molecule. An unusually local particle number density fluctuation was observed in the system at saturation temperature. It can be found that the potential energy increases slowly with the temperature from 373 K to 404 K, which indicates that the ammonium dihydrogen phosphate has partly decomposed. The radial distribution function between the hydrogen atom of ammonium cation and the oxygen atom of dihydrogen phosphate ion at three different temperatures shows obvious difference, which indicates that the average H-bond number changes obviously with the temperature. The temperature has an influence on the combination between hydrogen atoms and phosphorus atoms of dihydrogen phosphate ion and there are much more growth units at saturated solutions.展开更多
The microstructures and thermodynamic properties of mixed systems comprising pyridinium ionic liquid[HPy][BF_(4)]and acetonitrile at different mole fractions were studied using molecular dynamics simulation in this wo...The microstructures and thermodynamic properties of mixed systems comprising pyridinium ionic liquid[HPy][BF_(4)]and acetonitrile at different mole fractions were studied using molecular dynamics simulation in this work.The following properties were determined:density,self-diffusion coefficient,excess molar volume,and radial distribution function.The results show that with an increase in the mole fraction of[HPy][BF_(4)],the self-diffusion coefficient decreases.Additionally,the excess molar volume initially decreases,reaches a minimum,and then increases.The rules of radial distribution functions(RDFs)of characteristic atoms are different.With increasing the mole fraction of[HPy][BF_(4)],the first peak of the RDFs of HA1-F decreases,while that of CT6-CT6 rises at first and then decreases.This indicates that the solvent molecules affect the polar and non-polar regions of[HPy][BF_(4)]differently.展开更多
The mechanical property and deformation mechanism of twinned gold nanowire with non-uniform distribution of twinned boundaries(TBs)are studied by the molecular dynamics(MD)method.It is found that the twin boundary spa...The mechanical property and deformation mechanism of twinned gold nanowire with non-uniform distribution of twinned boundaries(TBs)are studied by the molecular dynamics(MD)method.It is found that the twin boundary spacing(TBS)has a great effect on the strength and plasticity of the nanowires with uniform distribution of TBs.And the strength enhances with the decrease of TBS,while its plasticity declines.For the nanowires with non-uniform distribution of TBs,the differences in distribution among different TBSs have little effect on the Young's modulus or strength,and the compromise in strength appears.But the differences have a remarkable effect on the plasticity of twinned gold nanowire.The twinned gold nanowire with higher local symmetry ratio has better plasticity.The initial dislocations always form in the largest TBS and the fracture always appears at or near the twin boundaries adjacent to the smallest TBS.Some simulation results are consistent with the experimental results.展开更多
The realization of protein functional movement is usually accompanied by specific conformational changes,and there exist some key residues that mediate and control the functional motions of proteins in the allosteric ...The realization of protein functional movement is usually accompanied by specific conformational changes,and there exist some key residues that mediate and control the functional motions of proteins in the allosteric process.In the present work,the perturbation-response scanning method developed by our group was combined with the molecular dynamics(MD)simulation to identify the key residues controlling the functional movement of proteins.In our method,a physical quantity that is directly related to protein specific function was introduced,and then based on the MD simulation trajectories,the perturbation-response scanning method was used to identify the key residues for functional motions,in which the residues that highly correlated with the fluctuation of the function-related quantity were identified as the key residues controlling the specific functional motions of the protein.Two protein systems,i.e.,the heat shock protein 70 and glutamine binding protein,were selected as case studies to validate the effectiveness of our method.Our calculated results are in good agreement with the experimental results.The location of the key residues in the two proteins are similar,indicating the similar mechanisms behind the performance of their biological functions.展开更多
The distributions of local structural units of calcium silicate melts were quantified by means of classical molecular dynamics simulation and a newly constructed structural thermodynamic model. The distribution of fiv...The distributions of local structural units of calcium silicate melts were quantified by means of classical molecular dynamics simulation and a newly constructed structural thermodynamic model. The distribution of five kinds of Si-O tetrahedra Qi from these two methods was compared with each other and also with the experimental Raman spectra, an excellent agreement was achieved. These not only displayed the panorama distribution of microstructural units in the whole composition range, but also proved that the thermodynamic model is suitable for the utilization as the subsequent application model of spectral experiments for the thermodynamic calculation. Meanwhile, the five refined regions mastered by different disproportionating reactions were obtained. Finally, the distributions of two kinds of connections between Qi were obtained, denoted as Qi-Ca-Qj and Qi-[Ob]-Qj, from the thermodynamic model, and a theoretical verification was given that the dominant connections for any composition are equivalent connections.展开更多
Molecular dynamics （MD） simulations are performed to study the stability of structure H clathrate-hydrates of methane＋large-molecule vip substance （LMGS） at temperatures of 270, 273, 278 and 280 K under canonic...Molecular dynamics （MD） simulations are performed to study the stability of structure H clathrate-hydrates of methane＋large-molecule vip substance （LMGS） at temperatures of 270, 273, 278 and 280 K under canonical （NVT-） ensemble condition in a 3×3×3 structure H unit cell replica with 918 TIP4P water molecules. The studied LMGS are 2-methylbutane （2-MB）, 2,3-dimethylbutane （2,3-DMB）, neohexane （NH）, methylcyclohexane （MCH）, adamantane and tert-butyl methyl ether （TBME）. In the process of MD simulation, achieving equilibrium of the studied system is recognized by stability in calculated pressure for NVT-ensemble. So, for the accuracy of MD simulations, the obtained pressures are compared with the experimental phase diagrams. Therefore, the obtained equilibrium pressures by MD simulations are presented for studying the structure H clathrate-hydrates. The results show that the calculated temperature and pressure conditions by MD simulations are consistent with the experimental phase diagrams. Also, the radial distribution functions （RDFs） of host-host, host-vip and vip-vip molecules are used to analysis the characteristic configurations of the structure H clathrate-hydrate.展开更多
Molecular dynamics simulation has been performed to simulate the interaction between PESA and the （001） face of anhydrite crystal CaSO4 at different temperatures with the presence of various number of H2O molecules....Molecular dynamics simulation has been performed to simulate the interaction between PESA and the （001） face of anhydrite crystal CaSO4 at different temperatures with the presence of various number of H2O molecules. The results show that PESA can effectively prevent the growth of CaSO4 scale at 323-343 K. At the same temperature, the binding energy between PESA and the （001） face of CaSO4 for systems with various number of H2O has the order of E-bind（OH2O）〉Ebind（200-400H2O）〉E, bind（lOOH2O）. For the same system at different temperatures the binding energies are close and are mainly contributed from the Coulomb interaction, including ionic bonds. The bonds are formed between the calcium atoms of anhydrite scale crystal and the Hydrogen bonds are formed between the O oxygen atoms of the carboxyl group of PESA. atoms of the carboxyl group of PESA and the H atoms of H2O. van der Waals interaction is conducive to the stability of the system of PESA, H2O, and CaSO4. The radial distribution functions of O（carbonyl of PESA）-H（H2O）, O（CaSO4）-H（H2O）, and O（CaSO4）-H（PESA） imply that solvents have effects on the anti-scale performance of PESA to CaSO4.展开更多
In the purpose to design novel antituberculosis (anti-TB) drugs agents against Mycobacterium tuberculosis (Mtb), we have built a molecular library around 42 Halimane Diterpenoids isolated from natural sources. Two Mtb...In the purpose to design novel antituberculosis (anti-TB) drugs agents against Mycobacterium tuberculosis (Mtb), we have built a molecular library around 42 Halimane Diterpenoids isolated from natural sources. Two Mtb enzymes drug targets (Mtb Mycothiol S-transferase and Mtb Homoserine transacetylase) have been adopted. The pharmacological potential was investigated through molecular docking, molecular dynamics simulation, density functional theory (gas phase and water) and ADMET analysis. Our results indicate that (2R,5R,6S)-1,2,3,4,5,6,7,8-octahydro-5-((E)-5-hydroxy-3-methylpent-3-enyl)-1,1,5,6-tetramethylnaphtha-lene-2-ol (compound 20) has displays higher docking score with each of the selected drug targets. In addition, this molecule exhibits a satisfactory drug potential activity and a good chemical reactivity. Its improved kinetic stability in the Mtb Mycothiol S-transferase enzyme reflects its suitability as a novel inhibitor of Mtb growth. This molecule has displayed a good absorption potential. Our results also show that its passive passage of the intestinal permeability barrier is more effective than that of first-line treatments (ethambutol, isoniazid). In the same way, this anti-TB druglikeness has shown to be able to cross the blood brain barrier.展开更多
The thermal stability of Ti@A1 core/shell nanoparticles with different sizes and components during continuous heating and cooling processes is examined by a molecular dynamics simulation with embedded atom method. The...The thermal stability of Ti@A1 core/shell nanoparticles with different sizes and components during continuous heating and cooling processes is examined by a molecular dynamics simulation with embedded atom method. The thermodynamic properties and structure evolution during continuous heating and cooling processes are investigated through the character- ization of the potential energy, specific heat distribution, and radial distribution function （RDF）. Our study shows that, for fixed Ti core size, the melting temperature decreases with A1 shell thickness, while the crystallizing temperature and glass formation temperature increase with A1 shell thickness. Diverse melting mechanisms have been discovered for different Ti core sized with fixed A1 shell thickness nanoparticles. The melting temperature increases with the Ti core radius. The trend agrees well with the theoretical phase diagram of bimetallic nanoparticles. In addition, the glass phase formation of A1-Ti nanoparticles for the fast cooling rate of 12 K/ps, and the crystal phase formation for the low cooling rate of 0.15 K/ps. The icosahedron structure is formed in the frozen 4366 A1-Ti atoms for the low cooling rate.展开更多
The microstructure and intermolecular interaction of toluene(TOL), methyl ethyl ketone(MEK), lube oil, TOL-MEK solvents, and TOL-MEK-oil solutions were studied by molecular simulation. Some simulation results agree we...The microstructure and intermolecular interaction of toluene(TOL), methyl ethyl ketone(MEK), lube oil, TOL-MEK solvents, and TOL-MEK-oil solutions were studied by molecular simulation. Some simulation results agree well with the experiment, which suggests that the simulation method we adopted is a powerful tool to obtain microscopic property of the systems. The density functional theory(DFT) calculation results suggest that the interaction group of toluene and MEK is the methyl group of theirs. And the interaction between toluene and MEK is attractive. The contribution of van der Waals interaction to the change of total energy of the TOL-MEK system is major, and the second is electrostatic interaction. Molecular dynamics(MD) simulation analyzes the solubility parameter(SP), mean square displacement(MSD), radius of gyration(RG), and radial distribution function(RDF) of solvents and solutions. The results are that the solubility parameter of the blend solvents decreases with temperature, and increases with the proportion of methyl ethyl ketone in principle, and that of lube oil also trends to decrease with temperature. The MSD results give one reason of why the transmission rate of MEK is greater in membrane separation process of recovery toluene and MEK and the permeation flux increases with MEK:TOL. The RG analysis predicts that the permeability of the oil molecule is likely to rise with temperature during dewaxing solvent recovery process by membrane. The analysis of RDFs shows that the intermolecular interaction of C···C, O···O and C···O makes a major contribution to the total interaction energy.展开更多
The dynamical progresses involved in ultra-short laser pulse ablation of face-centered cubic metals under stress confinement condition are described completely using molecular dynamics method. The laser beam absorptio...The dynamical progresses involved in ultra-short laser pulse ablation of face-centered cubic metals under stress confinement condition are described completely using molecular dynamics method. The laser beam absorption and thermal energy turning into kinetics energy of. atoms are taken into account to give a detailed picture of laser metal interaction. Superheating phenomenon is observed, and the phase change from solid to liquid is characterized by a destroyed atom configuration and a decreased number density. The steep velocity gradients are found in the systems of Cu and Ni after pulse in consequence of located heating and exponential decrease of fluences following the Lambert-Beer expression. The shock wave velocities are predicted to be about 5 000 m/s in Cu and 7 200 m/s in Ni. The higher ablation rates are obtained from simulations compared with experimental data as a result of a well-defined crystalline surface irradiated by a single pulse. Simulation results show that the main mechanisms of ablation are evaporation and thermoelastic stress due to located heating.展开更多
The lumped time distribution functions were proposed, which can be used for describing the dynamicsystems with two or more than two states of the end of growing polymer chain during chain addition polymerization.Numer...The lumped time distribution functions were proposed, which can be used for describing the dynamicsystems with two or more than two states of the end of growing polymer chain during chain addition polymerization.Numerical analysis of the lumped time distribution functions was carried out. The method for calculating molecularweight distribution of polymer in the stable free radical polymerization and more general cases was developed basedon the lumped time distribution functions.展开更多
The interface properties of Fe(101)/zinc silicate modified by organo-siloxane(KH-570)was studied by using the method of molecular dynamics simulation.By calculating the temperature and energy fluctuation of equilibriu...The interface properties of Fe(101)/zinc silicate modified by organo-siloxane(KH-570)was studied by using the method of molecular dynamics simulation.By calculating the temperature and energy fluctuation of equilibrium state,equilibrium concentration distribution,MSD of layer and different groups,and interaction energy of two interface models,the influencing mechanism on the interface properties of adding organosiloxane into coating system was studied at the atomic scale.It shows that the temperature and energy of interface oscillated in a small range and it was exited in a state of dynamic equilibrium within the initial simulation stage(t<20 ps).It can be seen from the multiple peak states of concentration distribution that the iron substrate,organo-siloxane and zinc silicate are distributed in the form of a concentration gradient in the real environment.The rapid diffusion of free zinc powder in zinc silicate coating was the essential reason that affected the comprehensive properties of coating.The interface thickness decreased from 7.45 to 6.82Å,the MSD of free zinc powder was effectively reduced,and the interfacial energy was increased from 104.667 to 347.158 kcal/mol after being modified by organo-siloxane.展开更多
Molecular dynamic simulation was employed to predict the melting points Tm of TNAD/HMX, TNAD/RDX, TNAD/DINA, and TNAD/DNP systems （tans-1,4,5,8- tetranitro-1,4,5,8-tetraazadacalin （TNAD）, dinitropiperazine （DNP）,...Molecular dynamic simulation was employed to predict the melting points Tm of TNAD/HMX, TNAD/RDX, TNAD/DINA, and TNAD/DNP systems （tans-1,4,5,8- tetranitro-1,4,5,8-tetraazadacalin （TNAD）, dinitropiperazine （DNP）, cyclotetramethylenetetranitroamine （HMX）, cyclotrimethylenetrinitramine （RDX）, and N-nitrodihydroxyethylaminedinitrate （DINA））. Tm was determined from the inflexion point on the curve of mean specific volume vs. temperature. The result shows that the Tm values of TNAD/HMX, TNAD/RDX, and TNAD/DINA systems are 500, 536, and 488 K, respectively. The TNAD/DNP system has no obvious Tm value, which shows the system is insoluble. Using Tm, the solubility of the four systems was analyzed. The radial distribution functions of the four systems were analyzed and the main intermolecular forces between TNAD and other energetic components are short-range interactions. The better the solubility is, the stronger the intermoleenlar interaction is. In addition, the force field energy at different temperature was also analyzed to predict Tm of the four systems.展开更多
Molecular dynamics simulations were carried out to study the internal energy and microstructure of potassium dihydrogen phosphates （KDP） solution at different temperatures. The water molecule was treated as a simple...Molecular dynamics simulations were carried out to study the internal energy and microstructure of potassium dihydrogen phosphates （KDP） solution at different temperatures. The water molecule was treated as a simple-point-charge model, while a seven-site model for the dihydrogen phosphate ion was adopted. The internal energy functions and the radial distribution functions of the solution were studied in detail. An unusually large local particle number density fluctuation was observed in the system at saturation temperature. It has been found that the specific heat of oversaturated solution is higher than that of unsaturated solution, which indicates the solution experiences a crystallization process below saturation temperature. The radial distribution function between the oxygen atom of water and the hydrogen atom of the dihydrogen phosphate ion shows a very strong hydrogen bond structure. There are strong interactions between potassium cation and oxygen atom of dihydrogen phosphate ion in KDP solution, and much more ion pairs were formed in saturated solution.展开更多
Monolayer molybdenum disulfide(MoS2) is a novel two-dimensional material that exhibits potential application in lubrication technology. In this work, molecular dynamics was used to investigate the lubrication behaviou...Monolayer molybdenum disulfide(MoS2) is a novel two-dimensional material that exhibits potential application in lubrication technology. In this work, molecular dynamics was used to investigate the lubrication behaviour of different polar fluid molecules(i.e., water, methanol and decane) confined in monolayer Mo S2 nanoslits. The pore width effect(i.e., 1.2, 1.6 and 2.0 nm) was also evaluated. Results revealed that decane molecules exhibited good lubricating performance compared to the other two kinds of molecules. The friction coefficient followed the order of decane b methanol b water, and decreased evidently as the slit width increased, except for decane. Analysis of the spatial distribution and mobility of different confined fluid molecules showed that a solid-like layer was formed near the slit wall. This phenomenon led to the extra low friction coefficient of confined decane molecules.展开更多
The inhibitory mechanism of copper（Ⅱ） on the aggegation of amyloid β-peptide （Aβ） was investigated by molecular dynamics simulations. The binding mode ofcopper（Ⅱ） with Aβ is characterized by the imidazole n...The inhibitory mechanism of copper（Ⅱ） on the aggegation of amyloid β-peptide （Aβ） was investigated by molecular dynamics simulations. The binding mode ofcopper（Ⅱ） with Aβ is characterized by the imidazole nitrogen atom, Nπ, of the histidine residue H 13, acting as the anchoring site, and the backbone＇s deprotoned amide nitogen atoms as the main binding sites. Drove by the coordination bonds and their induced hydrogen bond net, the conformations of Aβ converted from β-sheet non-β-sheet conformations, which destabilized the aggregation of Aβ into fibrils.展开更多
The microstructure, IR spectrum, as well as rotation dynamics of water molecule in sodium tetrafluoroborate （NaBF4）/water mixture at room temperatures were studied with molecular dynamics simulation. Different conce...The microstructure, IR spectrum, as well as rotation dynamics of water molecule in sodium tetrafluoroborate （NaBF4）/water mixture at room temperatures were studied with molecular dynamics simulation. Different concentrations of water （6.25%, 25.0%, 50.0%, 75.0%, 90.0%, and 99.6%） in NaBF4/water mixture were simulated to understand the structure and dynamics. It was shown that water molecules tend to be isolated from each other in mixtures with more ions than water molecules in both liquids. With increase of the molar fraction of water in the mixture, the rotation bands and the bending bands of water display red shift whereas the O-H stretch bands show blue shift, and the decay of the reorientation correlation function becomes slower. This suggests that the molecules are hindered and their motions are difficult and slow, due to the hydrogen-bond interactions and the inharmonic interactions between the interor intra-molecular modes.展开更多
Integrin activation,the transition from a low to a high affinity state,regulates the numerous cellular responses consequent to integrin engagement by extracellular matrix proteins.Kindlin proteins,play crucial roles i...Integrin activation,the transition from a low to a high affinity state,regulates the numerous cellular responses consequent to integrin engagement by extracellular matrix proteins.Kindlin proteins,play crucial roles in the integrin-signaling pathway by directly interacting with and activating integrins,which mediate the cell-extracellular matrix adhesion and signaling.As a widely distributed PTB domain protein and a major member of the kindlin family,kindlin2 interacts withβ3-tail,bridges talin-activated integrins to promote integrin aggregation,and enhances talin-induced integrin activation.Thus,kindlin2 is identified as a coactivator of integrins.Unlike talins,kindlin2 cannot directly alter the conformation of the integrin transmembrane helix and fail to activate integrin alone.Nevertheless,although it is widely accepted that kindlins and talins synergistically promote integrin activation,the underlying mechanism is unclear.Thus,the study of the force dissociation of the kindlin2/β3-tail complex and the conformation stabilization under different mechanical micro-environments should be of great significance for the further understanding of the structural basis of its synergistically activation of integrin.To reveal the molecular dynamics mechanism of interaction between kindlin2 andβ3-tail,we perform molecular dynamics(MD)simulations for this complex with different computing strategies interaction.In MD simulations,the available crystal structures of Kindlin-2/β3-tail complex(Protein Data Bank code 5XQ1)was downloaded from the PDB database.Two software packages,VMD for visualization and modeling and NAMD 2.13 for energy minimizations and MD simulations,were used here.The steadystate conformation of the complex was obtained from the equilibrium simulation.The dissociation event was observed by the constant velocity simulation,and the mechanical stability of the complex was observed by the constant force simulation.Our results showed that,during the equilibrium of the kindlin2-F3/β34ail complex,the residue MET612,LYS613 and TRP615 on the F3 domain of kindlin2 contributed to hydrogen-bonding with the corresponding residues onβ3 integrin.These bonds exhibit moderate or strong stability through steered molecular dynamics(SMD)simulation.During the constant velocity simulation,the complex exhibits a variety of unfolding pathways against tension applications,which are mainly distinguished by the disruption of hydrogen-bonds between the F3 domain a1/a2 helixes andβ1/β2 sheets.During the constant force simulation,the different phases of the composite force dissociation have different dissociation probabilities,which shows the biphasic force-dependent characteristics.And,the key residues in the pulling were recognized according not only to the number of interacting residue pairs,but also to their bond strength.Using molecular dynamics simulation,we showed the steady state of the kindlin2-F3/β3-tail complex under different tensile forces,and observe the dynamic process of molecular interaction.A possible underlying biophysical mechanism is that,the dissociation of Kindlin2-F3/β3-tail complex is biphasic force-dependent,and the conformations under different stretching states have different binding affinities.This study not only provides insights into the structural basis and mechanical regulation mechanisms of the kindlin/integrin interaction,in understanding in kindlin/integrin-related signaling in different cellular biological processes,but also provides new ideas for novel drug design and the treatment of related diseases.展开更多
Molecular dynamics （MD） simulations of monocrystalline copper （100） surface during nanomachining process were performed based on a new 3D simulation model. The material removal mechanism and system temperature dis...Molecular dynamics （MD） simulations of monocrystalline copper （100） surface during nanomachining process were performed based on a new 3D simulation model. The material removal mechanism and system temperature distribution were discussed. The simulation results indicate that the system temperature distribution presents a roughly concentric shape, a steep temperature gradient is observed in diamond cutting tool, and the highest temperature is located in chip. Centrosymmetry parameter method was used to monitor defect structures. Dislocations and vacancies are the two principal types of defect structures. Residual defect structures impose a major change on the workpiece physical properties and machined surface quality. The defect structures in workpiece are temperature dependent. As the temperature increases, the dislocations are mainly mediated from the workpiece surface, while the others are dissociated into point defects. The relatively high cutting speed used in nanomachining results in less defect structures, beneficial to obtain highly machined surface quality.展开更多
文摘Molecular dynamics simulations were carried out to study the configuration energy and radial distribution functions of mmonium dihydrogen phosphate solution at different temperatures. The dihydrogen phosphate ion was treated as a seven-site model and the ammonium ion was regarded as a five-site model, while a simple-point-charge model for water molecule. An unusually local particle number density fluctuation was observed in the system at saturation temperature. It can be found that the potential energy increases slowly with the temperature from 373 K to 404 K, which indicates that the ammonium dihydrogen phosphate has partly decomposed. The radial distribution function between the hydrogen atom of ammonium cation and the oxygen atom of dihydrogen phosphate ion at three different temperatures shows obvious difference, which indicates that the average H-bond number changes obviously with the temperature. The temperature has an influence on the combination between hydrogen atoms and phosphorus atoms of dihydrogen phosphate ion and there are much more growth units at saturated solutions.
文摘The microstructures and thermodynamic properties of mixed systems comprising pyridinium ionic liquid[HPy][BF_(4)]and acetonitrile at different mole fractions were studied using molecular dynamics simulation in this work.The following properties were determined:density,self-diffusion coefficient,excess molar volume,and radial distribution function.The results show that with an increase in the mole fraction of[HPy][BF_(4)],the self-diffusion coefficient decreases.Additionally,the excess molar volume initially decreases,reaches a minimum,and then increases.The rules of radial distribution functions(RDFs)of characteristic atoms are different.With increasing the mole fraction of[HPy][BF_(4)],the first peak of the RDFs of HA1-F decreases,while that of CT6-CT6 rises at first and then decreases.This indicates that the solvent molecules affect the polar and non-polar regions of[HPy][BF_(4)]differently.
基金the National Natural Science Foundation of China(Grant No.51771033).
文摘The mechanical property and deformation mechanism of twinned gold nanowire with non-uniform distribution of twinned boundaries(TBs)are studied by the molecular dynamics(MD)method.It is found that the twin boundary spacing(TBS)has a great effect on the strength and plasticity of the nanowires with uniform distribution of TBs.And the strength enhances with the decrease of TBS,while its plasticity declines.For the nanowires with non-uniform distribution of TBs,the differences in distribution among different TBSs have little effect on the Young's modulus or strength,and the compromise in strength appears.But the differences have a remarkable effect on the plasticity of twinned gold nanowire.The twinned gold nanowire with higher local symmetry ratio has better plasticity.The initial dislocations always form in the largest TBS and the fracture always appears at or near the twin boundaries adjacent to the smallest TBS.Some simulation results are consistent with the experimental results.
文摘The realization of protein functional movement is usually accompanied by specific conformational changes,and there exist some key residues that mediate and control the functional motions of proteins in the allosteric process.In the present work,the perturbation-response scanning method developed by our group was combined with the molecular dynamics(MD)simulation to identify the key residues controlling the functional movement of proteins.In our method,a physical quantity that is directly related to protein specific function was introduced,and then based on the MD simulation trajectories,the perturbation-response scanning method was used to identify the key residues for functional motions,in which the residues that highly correlated with the fluctuation of the function-related quantity were identified as the key residues controlling the specific functional motions of the protein.Two protein systems,i.e.,the heat shock protein 70 and glutamine binding protein,were selected as case studies to validate the effectiveness of our method.Our calculated results are in good agreement with the experimental results.The location of the key residues in the two proteins are similar,indicating the similar mechanisms behind the performance of their biological functions.
基金Project(2012CB722805)supported by the National Basic Research Program of ChinaProjects(50504010,50974083,51174131,51374141)supported by the National Natural Science Foundation of China+1 种基金Project(50774112)supported by the Joint Fund of NSFC and Baosteel,ChinaProject(07QA4021)supported by the Shanghai"Phosphor"Science Foundation,China
文摘The distributions of local structural units of calcium silicate melts were quantified by means of classical molecular dynamics simulation and a newly constructed structural thermodynamic model. The distribution of five kinds of Si-O tetrahedra Qi from these two methods was compared with each other and also with the experimental Raman spectra, an excellent agreement was achieved. These not only displayed the panorama distribution of microstructural units in the whole composition range, but also proved that the thermodynamic model is suitable for the utilization as the subsequent application model of spectral experiments for the thermodynamic calculation. Meanwhile, the five refined regions mastered by different disproportionating reactions were obtained. Finally, the distributions of two kinds of connections between Qi were obtained, denoted as Qi-Ca-Qj and Qi-[Ob]-Qj, from the thermodynamic model, and a theoretical verification was given that the dominant connections for any composition are equivalent connections.
文摘Molecular dynamics （MD） simulations are performed to study the stability of structure H clathrate-hydrates of methane＋large-molecule vip substance （LMGS） at temperatures of 270, 273, 278 and 280 K under canonical （NVT-） ensemble condition in a 3×3×3 structure H unit cell replica with 918 TIP4P water molecules. The studied LMGS are 2-methylbutane （2-MB）, 2,3-dimethylbutane （2,3-DMB）, neohexane （NH）, methylcyclohexane （MCH）, adamantane and tert-butyl methyl ether （TBME）. In the process of MD simulation, achieving equilibrium of the studied system is recognized by stability in calculated pressure for NVT-ensemble. So, for the accuracy of MD simulations, the obtained pressures are compared with the experimental phase diagrams. Therefore, the obtained equilibrium pressures by MD simulations are presented for studying the structure H clathrate-hydrates. The results show that the calculated temperature and pressure conditions by MD simulations are consistent with the experimental phase diagrams. Also, the radial distribution functions （RDFs） of host-host, host-vip and vip-vip molecules are used to analysis the characteristic configurations of the structure H clathrate-hydrate.
文摘Molecular dynamics simulation has been performed to simulate the interaction between PESA and the （001） face of anhydrite crystal CaSO4 at different temperatures with the presence of various number of H2O molecules. The results show that PESA can effectively prevent the growth of CaSO4 scale at 323-343 K. At the same temperature, the binding energy between PESA and the （001） face of CaSO4 for systems with various number of H2O has the order of E-bind（OH2O）〉Ebind（200-400H2O）〉E, bind（lOOH2O）. For the same system at different temperatures the binding energies are close and are mainly contributed from the Coulomb interaction, including ionic bonds. The bonds are formed between the calcium atoms of anhydrite scale crystal and the Hydrogen bonds are formed between the O oxygen atoms of the carboxyl group of PESA. atoms of the carboxyl group of PESA and the H atoms of H2O. van der Waals interaction is conducive to the stability of the system of PESA, H2O, and CaSO4. The radial distribution functions of O（carbonyl of PESA）-H（H2O）, O（CaSO4）-H（H2O）, and O（CaSO4）-H（PESA） imply that solvents have effects on the anti-scale performance of PESA to CaSO4.
文摘In the purpose to design novel antituberculosis (anti-TB) drugs agents against Mycobacterium tuberculosis (Mtb), we have built a molecular library around 42 Halimane Diterpenoids isolated from natural sources. Two Mtb enzymes drug targets (Mtb Mycothiol S-transferase and Mtb Homoserine transacetylase) have been adopted. The pharmacological potential was investigated through molecular docking, molecular dynamics simulation, density functional theory (gas phase and water) and ADMET analysis. Our results indicate that (2R,5R,6S)-1,2,3,4,5,6,7,8-octahydro-5-((E)-5-hydroxy-3-methylpent-3-enyl)-1,1,5,6-tetramethylnaphtha-lene-2-ol (compound 20) has displays higher docking score with each of the selected drug targets. In addition, this molecule exhibits a satisfactory drug potential activity and a good chemical reactivity. Its improved kinetic stability in the Mtb Mycothiol S-transferase enzyme reflects its suitability as a novel inhibitor of Mtb growth. This molecule has displayed a good absorption potential. Our results also show that its passive passage of the intestinal permeability barrier is more effective than that of first-line treatments (ethambutol, isoniazid). In the same way, this anti-TB druglikeness has shown to be able to cross the blood brain barrier.
基金Project supported by the National Natural Science Foundation of China(Grant No.21401064)the Science&Technology Development Program of Henan Province,China(Grant No.142300410282)the Program of Henan Educational Committee,China(Grant No.13B140986)
文摘The thermal stability of Ti@A1 core/shell nanoparticles with different sizes and components during continuous heating and cooling processes is examined by a molecular dynamics simulation with embedded atom method. The thermodynamic properties and structure evolution during continuous heating and cooling processes are investigated through the character- ization of the potential energy, specific heat distribution, and radial distribution function （RDF）. Our study shows that, for fixed Ti core size, the melting temperature decreases with A1 shell thickness, while the crystallizing temperature and glass formation temperature increase with A1 shell thickness. Diverse melting mechanisms have been discovered for different Ti core sized with fixed A1 shell thickness nanoparticles. The melting temperature increases with the Ti core radius. The trend agrees well with the theoretical phase diagram of bimetallic nanoparticles. In addition, the glass phase formation of A1-Ti nanoparticles for the fast cooling rate of 12 K/ps, and the crystal phase formation for the low cooling rate of 0.15 K/ps. The icosahedron structure is formed in the frozen 4366 A1-Ti atoms for the low cooling rate.
基金supported by Beijing Key Laboratory of Energy Environmental Catalysis Beijing University of Chemical Technology Beijing of ChinaYanshan Branch of Beijing Research Institute of Chemical Industry,Sinopec
文摘The microstructure and intermolecular interaction of toluene(TOL), methyl ethyl ketone(MEK), lube oil, TOL-MEK solvents, and TOL-MEK-oil solutions were studied by molecular simulation. Some simulation results agree well with the experiment, which suggests that the simulation method we adopted is a powerful tool to obtain microscopic property of the systems. The density functional theory(DFT) calculation results suggest that the interaction group of toluene and MEK is the methyl group of theirs. And the interaction between toluene and MEK is attractive. The contribution of van der Waals interaction to the change of total energy of the TOL-MEK system is major, and the second is electrostatic interaction. Molecular dynamics(MD) simulation analyzes the solubility parameter(SP), mean square displacement(MSD), radius of gyration(RG), and radial distribution function(RDF) of solvents and solutions. The results are that the solubility parameter of the blend solvents decreases with temperature, and increases with the proportion of methyl ethyl ketone in principle, and that of lube oil also trends to decrease with temperature. The MSD results give one reason of why the transmission rate of MEK is greater in membrane separation process of recovery toluene and MEK and the permeation flux increases with MEK:TOL. The RG analysis predicts that the permeability of the oil molecule is likely to rise with temperature during dewaxing solvent recovery process by membrane. The analysis of RDFs shows that the intermolecular interaction of C···C, O···O and C···O makes a major contribution to the total interaction energy.
基金the Ministerial Level Advanced Research Foundation (ABAQ440261)
文摘The dynamical progresses involved in ultra-short laser pulse ablation of face-centered cubic metals under stress confinement condition are described completely using molecular dynamics method. The laser beam absorption and thermal energy turning into kinetics energy of. atoms are taken into account to give a detailed picture of laser metal interaction. Superheating phenomenon is observed, and the phase change from solid to liquid is characterized by a destroyed atom configuration and a decreased number density. The steep velocity gradients are found in the systems of Cu and Ni after pulse in consequence of located heating and exponential decrease of fluences following the Lambert-Beer expression. The shock wave velocities are predicted to be about 5 000 m/s in Cu and 7 200 m/s in Ni. The higher ablation rates are obtained from simulations compared with experimental data as a result of a well-defined crystalline surface irradiated by a single pulse. Simulation results show that the main mechanisms of ablation are evaporation and thermoelastic stress due to located heating.
文摘The lumped time distribution functions were proposed, which can be used for describing the dynamicsystems with two or more than two states of the end of growing polymer chain during chain addition polymerization.Numerical analysis of the lumped time distribution functions was carried out. The method for calculating molecularweight distribution of polymer in the stable free radical polymerization and more general cases was developed basedon the lumped time distribution functions.
基金supported by the National Science Fundation of China(No.U1937601),and the National Natural Science Foundation of China(Grant No.NSFC51905471).
文摘The interface properties of Fe(101)/zinc silicate modified by organo-siloxane(KH-570)was studied by using the method of molecular dynamics simulation.By calculating the temperature and energy fluctuation of equilibrium state,equilibrium concentration distribution,MSD of layer and different groups,and interaction energy of two interface models,the influencing mechanism on the interface properties of adding organosiloxane into coating system was studied at the atomic scale.It shows that the temperature and energy of interface oscillated in a small range and it was exited in a state of dynamic equilibrium within the initial simulation stage(t<20 ps).It can be seen from the multiple peak states of concentration distribution that the iron substrate,organo-siloxane and zinc silicate are distributed in the form of a concentration gradient in the real environment.The rapid diffusion of free zinc powder in zinc silicate coating was the essential reason that affected the comprehensive properties of coating.The interface thickness decreased from 7.45 to 6.82Å,the MSD of free zinc powder was effectively reduced,and the interfacial energy was increased from 104.667 to 347.158 kcal/mol after being modified by organo-siloxane.
基金V. ACKNOWLEDGMENTS This work was supported by the National Natural Science Foundation of China （No.U1304111）, the Laboratory of Science and Technology on Combustion and Explosion （No.9140C3501021101）, China Postdoctoral Science Foundation （No.2013M531361）, and Jiangsu Planned Projects for Postdoctoral Research Funds （No.1201015B）.
文摘Molecular dynamic simulation was employed to predict the melting points Tm of TNAD/HMX, TNAD/RDX, TNAD/DINA, and TNAD/DNP systems （tans-1,4,5,8- tetranitro-1,4,5,8-tetraazadacalin （TNAD）, dinitropiperazine （DNP）, cyclotetramethylenetetranitroamine （HMX）, cyclotrimethylenetrinitramine （RDX）, and N-nitrodihydroxyethylaminedinitrate （DINA））. Tm was determined from the inflexion point on the curve of mean specific volume vs. temperature. The result shows that the Tm values of TNAD/HMX, TNAD/RDX, and TNAD/DINA systems are 500, 536, and 488 K, respectively. The TNAD/DNP system has no obvious Tm value, which shows the system is insoluble. Using Tm, the solubility of the four systems was analyzed. The radial distribution functions of the four systems were analyzed and the main intermolecular forces between TNAD and other energetic components are short-range interactions. The better the solubility is, the stronger the intermoleenlar interaction is. In addition, the force field energy at different temperature was also analyzed to predict Tm of the four systems.
文摘Molecular dynamics simulations were carried out to study the internal energy and microstructure of potassium dihydrogen phosphates （KDP） solution at different temperatures. The water molecule was treated as a simple-point-charge model, while a seven-site model for the dihydrogen phosphate ion was adopted. The internal energy functions and the radial distribution functions of the solution were studied in detail. An unusually large local particle number density fluctuation was observed in the system at saturation temperature. It has been found that the specific heat of oversaturated solution is higher than that of unsaturated solution, which indicates the solution experiences a crystallization process below saturation temperature. The radial distribution function between the oxygen atom of water and the hydrogen atom of the dihydrogen phosphate ion shows a very strong hydrogen bond structure. There are strong interactions between potassium cation and oxygen atom of dihydrogen phosphate ion in KDP solution, and much more ion pairs were formed in saturated solution.
基金Supported by the National NaturalScience Foundation of China(21576130,21490584)Project of Jiangsu Natural Science Foundation of China(BK20171464)+1 种基金Qing Lan ProjectJiangsu Overseas Visiting Scholar Program for University Prominent Young&Middleaged Teachers and Presidents
文摘Monolayer molybdenum disulfide(MoS2) is a novel two-dimensional material that exhibits potential application in lubrication technology. In this work, molecular dynamics was used to investigate the lubrication behaviour of different polar fluid molecules(i.e., water, methanol and decane) confined in monolayer Mo S2 nanoslits. The pore width effect(i.e., 1.2, 1.6 and 2.0 nm) was also evaluated. Results revealed that decane molecules exhibited good lubricating performance compared to the other two kinds of molecules. The friction coefficient followed the order of decane b methanol b water, and decreased evidently as the slit width increased, except for decane. Analysis of the spatial distribution and mobility of different confined fluid molecules showed that a solid-like layer was formed near the slit wall. This phenomenon led to the extra low friction coefficient of confined decane molecules.
基金This work was supported by the National Natural Science Foundation of China(Nos.30470408 and 20637010).
文摘The inhibitory mechanism of copper（Ⅱ） on the aggegation of amyloid β-peptide （Aβ） was investigated by molecular dynamics simulations. The binding mode ofcopper（Ⅱ） with Aβ is characterized by the imidazole nitrogen atom, Nπ, of the histidine residue H 13, acting as the anchoring site, and the backbone＇s deprotoned amide nitogen atoms as the main binding sites. Drove by the coordination bonds and their induced hydrogen bond net, the conformations of Aβ converted from β-sheet non-β-sheet conformations, which destabilized the aggregation of Aβ into fibrils.
基金The authors are grateful to Professor Jiu-shu Shao at Beijing Normal University for his encourage and help reading the manuscript. We also would like to thank Prof. Jian-min Tao and Guo-bao Li for their kind help. This work was supported by the National Natural Science Foundation of China （No.50564006）, the Key program of Natural Science Foundation of Yunnan Provine （No.2005EOOO4Z）, the Natural Science Foundation of Yunnan Provine （No.2008E0049M）, the Foundation of the Education Department of Yunnan Province （No.07Z40082）, and the Foundation of Kunming University of Science and Technology （No.2007-16）.
文摘The microstructure, IR spectrum, as well as rotation dynamics of water molecule in sodium tetrafluoroborate （NaBF4）/water mixture at room temperatures were studied with molecular dynamics simulation. Different concentrations of water （6.25%, 25.0%, 50.0%, 75.0%, 90.0%, and 99.6%） in NaBF4/water mixture were simulated to understand the structure and dynamics. It was shown that water molecules tend to be isolated from each other in mixtures with more ions than water molecules in both liquids. With increase of the molar fraction of water in the mixture, the rotation bands and the bending bands of water display red shift whereas the O-H stretch bands show blue shift, and the decay of the reorientation correlation function becomes slower. This suggests that the molecules are hindered and their motions are difficult and slow, due to the hydrogen-bond interactions and the inharmonic interactions between the interor intra-molecular modes.
基金supported by the National Natural Science Foundation of China ( 116272109, 11432006)
文摘Integrin activation,the transition from a low to a high affinity state,regulates the numerous cellular responses consequent to integrin engagement by extracellular matrix proteins.Kindlin proteins,play crucial roles in the integrin-signaling pathway by directly interacting with and activating integrins,which mediate the cell-extracellular matrix adhesion and signaling.As a widely distributed PTB domain protein and a major member of the kindlin family,kindlin2 interacts withβ3-tail,bridges talin-activated integrins to promote integrin aggregation,and enhances talin-induced integrin activation.Thus,kindlin2 is identified as a coactivator of integrins.Unlike talins,kindlin2 cannot directly alter the conformation of the integrin transmembrane helix and fail to activate integrin alone.Nevertheless,although it is widely accepted that kindlins and talins synergistically promote integrin activation,the underlying mechanism is unclear.Thus,the study of the force dissociation of the kindlin2/β3-tail complex and the conformation stabilization under different mechanical micro-environments should be of great significance for the further understanding of the structural basis of its synergistically activation of integrin.To reveal the molecular dynamics mechanism of interaction between kindlin2 andβ3-tail,we perform molecular dynamics(MD)simulations for this complex with different computing strategies interaction.In MD simulations,the available crystal structures of Kindlin-2/β3-tail complex(Protein Data Bank code 5XQ1)was downloaded from the PDB database.Two software packages,VMD for visualization and modeling and NAMD 2.13 for energy minimizations and MD simulations,were used here.The steadystate conformation of the complex was obtained from the equilibrium simulation.The dissociation event was observed by the constant velocity simulation,and the mechanical stability of the complex was observed by the constant force simulation.Our results showed that,during the equilibrium of the kindlin2-F3/β34ail complex,the residue MET612,LYS613 and TRP615 on the F3 domain of kindlin2 contributed to hydrogen-bonding with the corresponding residues onβ3 integrin.These bonds exhibit moderate or strong stability through steered molecular dynamics(SMD)simulation.During the constant velocity simulation,the complex exhibits a variety of unfolding pathways against tension applications,which are mainly distinguished by the disruption of hydrogen-bonds between the F3 domain a1/a2 helixes andβ1/β2 sheets.During the constant force simulation,the different phases of the composite force dissociation have different dissociation probabilities,which shows the biphasic force-dependent characteristics.And,the key residues in the pulling were recognized according not only to the number of interacting residue pairs,but also to their bond strength.Using molecular dynamics simulation,we showed the steady state of the kindlin2-F3/β3-tail complex under different tensile forces,and observe the dynamic process of molecular interaction.A possible underlying biophysical mechanism is that,the dissociation of Kindlin2-F3/β3-tail complex is biphasic force-dependent,and the conformations under different stretching states have different binding affinities.This study not only provides insights into the structural basis and mechanical regulation mechanisms of the kindlin/integrin interaction,in understanding in kindlin/integrin-related signaling in different cellular biological processes,but also provides new ideas for novel drug design and the treatment of related diseases.
基金Project (50925521) supported by the National Natural Science Fund for Distinguished Young Scholars of China
文摘Molecular dynamics （MD） simulations of monocrystalline copper （100） surface during nanomachining process were performed based on a new 3D simulation model. The material removal mechanism and system temperature distribution were discussed. The simulation results indicate that the system temperature distribution presents a roughly concentric shape, a steep temperature gradient is observed in diamond cutting tool, and the highest temperature is located in chip. Centrosymmetry parameter method was used to monitor defect structures. Dislocations and vacancies are the two principal types of defect structures. Residual defect structures impose a major change on the workpiece physical properties and machined surface quality. The defect structures in workpiece are temperature dependent. As the temperature increases, the dislocations are mainly mediated from the workpiece surface, while the others are dissociated into point defects. The relatively high cutting speed used in nanomachining results in less defect structures, beneficial to obtain highly machined surface quality.
