The transport properties of fluid argon in micropores, i.e. diffusivity and viscosity, were studied by molecular dynamics simulations. The effects of pore width, temperature and density on diffusivity and viscosity we...The transport properties of fluid argon in micropores, i.e. diffusivity and viscosity, were studied by molecular dynamics simulations. The effects of pore width, temperature and density on diffusivity and viscosity were analyzed in micropores with pore widths from 0.8 to 4.0 nm. The results show that the diffusivity in micropores is much lower than the bulk diffusivity, and it decreases as the pore width decreases; but the viscosity in micropores is significantly larger than the bulk one, and it increases sharply in narrow micropores. The diffusivity in channel parallel direction is obviously larger than that in channel perpendicular direction. The temperature and density are important factors that obviously affect diffusivity and viscosity in micropores.展开更多
The model of ion transportation through graphene nanochannels is established by the molecular dynamics simulation method. Statistics of the electric potential and charge distribution are made, respectively, on both si...The model of ion transportation through graphene nanochannels is established by the molecular dynamics simulation method. Statistics of the electric potential and charge distribution are made, respectively, on both sides of graphene nanopore with various diameters. Then, their changing relationship with respect to the nanopore diameter is determined. When applying a uniform electric field, polar water molecules are rearranged so that the corresponding relationship between the polarized degree of these molecules and the nanopore diameter can be created. Based on the theoretical model of ion transportation through nanochannels,the changing relationship between the concentration of anions/cations in nanochannels and bulk solution concentration is quantitatively analyzed. The results show that the increase of potential drop and charge accumulation, as well as a more obvious water polarization, will occur with the decrease of nanopore diameter. In addition, hydrogen ion concentration has a large proportion in nanochannels with a sodium chloride（NaCl） solution at a relative low concentration. As the NaCl concentration increases, the concentration appreciation of sodium ions tends to be far greater than the concentration drop of chloride ions. Therefore, sodium ion concentration makes more contribution to ionic conductance.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
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
Control of ion transport and fluid flow through nanofluidic devices is of primary importance for energy storage and conversion, drug delivery and a wide range of biological processes. Recent development of nanotechnol...Control of ion transport and fluid flow through nanofluidic devices is of primary importance for energy storage and conversion, drug delivery and a wide range of biological processes. Recent development of nanotechnology, synthesis techniques, purification technologies, and experiment have led to rapid advances in simulation and modeling studies on ion transport properties. In this review, the applications of Poisson-Nernst-Plank （PNP） equations in analyzing transport properties are presented. The molecular dynamics （MD） studies of transport properties of ion and fluidic flow through nanofluidic devices are reported as well.展开更多
Objective:To study the transmembrane transport of chemical components of Chinese herbs and to explore the function of platycodin D (PD) on biomembranes.Methods:Interaction between PD and the dipalmitoylphosphatidylcho...Objective:To study the transmembrane transport of chemical components of Chinese herbs and to explore the function of platycodin D (PD) on biomembranes.Methods:Interaction between PD and the dipalmitoylphosphatidylcholine (DPPC) bilayer was reproduced by molecular dynamics simulation with the Martini force field.A model validation and methodological study were first performed,and were based on simulation investigations of transmembrane transport for three herbal compounds with distinct hydrophilic properties.Results:PD increased the mobility of the DPPC bilayer since its aglycone strongly interacted with the hydrophobic layer,which broke the structure of the gate layer,and weakened the ordered performance of hydrophobic tails.Conclusion:The Martini force field was successfully applied to the study of the interaction between herbal compounds and a biological membrane.By combining the dynamics equilibrium morphology,the distribution of drugs inside and outside the biomembrane,and the interaction sites of drugs on the DPPC bilayer,factors influencing transmembrane transport of drugs were elucidated and the function of platycodin D in a biological membrane was reproduced.展开更多
The diffusivity and viscosity of water confined in micropores were studied by molecular dynamics simulations. The effects of pore width and density were analyzed at pore widths from 0.9 to 2.6 nm. The diffusivity in m...The diffusivity and viscosity of water confined in micropores were studied by molecular dynamics simulations. The effects of pore width and density were analyzed at pore widths from 0.9 to 2.6 nm. The diffusivity in micropores is lower than that of the bulk, and it decreases as pore width decreases and as density increases. But the viscosity in micropores is much larger than that of the bulk, and it increases as pore width decreases and as density increases. The diffusivity in channel parallel direction is obviously larger than that in channel perpendicular directions.展开更多
The thermal conductivity of GaN nanofilm is simulated by using the molecular dynamics(MD)method to explore the influence of the nanofilm thickness and the pre-strain field under different temperatures.It is demonstrat...The thermal conductivity of GaN nanofilm is simulated by using the molecular dynamics(MD)method to explore the influence of the nanofilm thickness and the pre-strain field under different temperatures.It is demonstrated that the thermal conductivity of GaN nanofilm increases with the increase of nanofilm thickness,while decreases with the increase of temperature.Meanwhile,the thermal conductivity of strained GaN nanofilms is weakened with increasing the tensile strain.The film thickness and environment temperature can affect the strain effect on the thermal conductivity of GaN nanofilms.In addition,the analysis of phonon properties of GaN nanofilm shows that the phonon dispersion and density of states of GaN nanofilms can be significantly modified by the film thickness and strain.The results in this work can provide the theoretical supports for regulating the thermal properties of GaN nanofilm through tailoring the geometric size and strain engineering.展开更多
The equation of states,diffusions,and viscosities of strongly coupled Fe at 80 and 240 eV with densities from 1.6 to 40 g/cm^(3) are studied by orbital-free molecular dynamics,classical molecular dynamics with a corre...The equation of states,diffusions,and viscosities of strongly coupled Fe at 80 and 240 eV with densities from 1.6 to 40 g/cm^(3) are studied by orbital-free molecular dynamics,classical molecular dynamics with a corrected Yukawa potential and compared with the results from average atom model.A new local pseudopotential is generated for orbital free calculations.For low densities,the Yukawa model captures the correct ionic interaction behavior around the first peak of the radial distribution function(RDF),thus it gives correct RDFs and transport coefficients.For higher densities,the scaled transformation of the Yukawa potential or adding a short range repulsion part to the Yukawa potential can give correct RDFs and transport coefficients.The corrected potentials are further validated by the force matching method.展开更多
Magnesium(Mg)and its composites have been widely used in different fields,but the mechanical properties and deformation mechanisms of polycrystalline Mg(polyMg)at the atomic scale are poorly understood.In this paper,t...Magnesium(Mg)and its composites have been widely used in different fields,but the mechanical properties and deformation mechanisms of polycrystalline Mg(polyMg)at the atomic scale are poorly understood.In this paper,the effects of grain size,temperature,and strain rate on the tensile properties of polyMg are explored and discussed by theMolecular dynamics(MD)simulation method.The calculated results showed that there exists a critical grain size of 10 nm for the mechanical properties of polyMg.The flow stress decreases with the increase of grain size if the average grain size is larger than 10 nm,which shows the Hall-Petch effect,and the deformation mechanism of large grain-sized polyMg is mainly dominated by the movement of dislocations.When the average grain size is less than 10 nm,it shows the reverse Hall-Petch effect that the flow stress decreases with the decrease of grain size,and the deformation mode of polyMg with small grain-size is the movement and deformation of atoms at the grain boundary.Due to the more active motion of atoms as the system temperature increases,the material can easily reach the plastic stage under tensile loading,and the mechanical properties of polyMg decrease at high temperatures.The strain rate has a hardening effect on the properties of composite.Based on our calculated results,it can provide theoretical guidance for the applications of Mg metal and Mg matrix composites.展开更多
The perfluorosulfonic acid(PFSA) membrane doped with two-dimensional conductive filler Ti_(3)C_(2)T_(x) is a fuel cell proton exchange membrane with high application potential. Experimental studies showed that the pro...The perfluorosulfonic acid(PFSA) membrane doped with two-dimensional conductive filler Ti_(3)C_(2)T_(x) is a fuel cell proton exchange membrane with high application potential. Experimental studies showed that the proton conductivity of Nafion/Ti_(3)C_(2)T_(x) composite membrane is improved significantly compared with that in pure Nafion. However, the microscopic mechanism of doping on the enhancement of membrane performance is remain unclear now. In this work, molecular dynamics simulation was used to investigate the microscopic morphology and proton transport behaviors of Nafion/Ti_(3)C_(2)T_(x) composite membrane at the molecular level. The results shown that there were significant differences about the diffusion kinetics of water molecules and hydroxium ions in Nafion/Ti_(3)C_(2)T_(x) at low and high hydration levels in the nanoscale region.With the increase of water content, Ti_(3)C_(2)T_(x) in membrane was gradually surrounded by ambient water molecules to form a hydration layer, and forming a relatively continuous proton transport channel between Nafion polymer and Ti_(3)C_(2)T_(x) monomer. The continuous proton transport channel could increase the number of binding sites of proton and thus achieving high proton conductivity and high mobility of water molecules at higher hydration level. The current work can provide a theoretical guidance for designing new type of Nafion composite membranes.展开更多
The exploration of performance and prediction of environmentally friendly refrigerant physical properties represents a critical endeavor.Equilibriummolecular dynamics simulationswere employed to investigate the densit...The exploration of performance and prediction of environmentally friendly refrigerant physical properties represents a critical endeavor.Equilibriummolecular dynamics simulationswere employed to investigate the density and transport properties of propane and ethane at ultra-low temperatures under evaporative pressure conditions.The results of the density simulation of the evaporation conditions of the blends proved the validity of the simulation method.Under identical temperature and pressure conditions,increasing the proportion of R170 in the refrigerant blends leads to a density decrease while the temperature range in which the gas-liquid phase transition occurs is lower.The analysis of simulated results pertaining to viscosity,thermal conductivity,and self-diffusion coefficient reveals heightened deviation levels within the phase transition temperature zone.This increase in deviation attributed to intensified molecular activity.In terms of uncovering the physical mechanism of gas-liquid phase transition,the work illustrates the macroscopic phenomenon of the intensified existing disorder during phase transitions at the molecular level.Molecular dynamics simulations analyzing the thermophysical properties of refrigerant blends from a microscopic point of view can deepen the comprehension of the thermal optimization of refrigeration processes.展开更多
Molecular dynamics(MD)simulations are conducted to study the thermo-mechanical properties of a family of thermosetting epoxy-amines.The crosslinked epoxy resin EPON862 with a series of cross-linkers is built and simul...Molecular dynamics(MD)simulations are conducted to study the thermo-mechanical properties of a family of thermosetting epoxy-amines.The crosslinked epoxy resin EPON862 with a series of cross-linkers is built and simulated under the polymer consistent force field(PCFF).Three types of curing agents(rigidity1,3-phenylenediamine(1,3-P),4,4-diaminodiphenylmethane(DDM),and phenol-formaldehyde-ethylenediamine(PFE))with different numbers of active sites are selected in the simulations.We focus on the effects of the cross-linkers on thermo-mechanical properties such as density,glass transition temperature(T_(g)),elastic constants,and strength.Our simulations show a significant increase in the Tg,Young’s modulus and yield stress with the increase in the degree of conversion.The simulation results reveal that the mechanical properties of thermosetting polymers are strongly dependent on the molecular structures of the cross-linker and network topological properties,such as end-to-end distance,crosslinking density and degree of conversion.展开更多
We design a nanostructure composing of two nanoscale graphene sheets parallelly immersed in water.Using molecular dynamics simulations,we demonstrate that the wet/dry state between the graphene sheets can be self-latc...We design a nanostructure composing of two nanoscale graphene sheets parallelly immersed in water.Using molecular dynamics simulations,we demonstrate that the wet/dry state between the graphene sheets can be self-latched;moreover,the wet→dry/dry→wet transition takes place when applying an external electric field perpendicular/parallel to the graphene sheets(E;/E;).This structure works like a flash memory device(a non-volatile memory):the stored information(wet and dry states)of the system can be kept spontaneously,and can also be rewritten by external electric fields.On the one hand,when the distance between the two nanosheets is close to a certain distance,the free energy barriers for the transitions dry→wet and wet→dry can be quite large.As a result,the wet and dry states are self-latched.On the other hand,an E;and an E;will respectively increase and decrease the free energy of the water located in-between the two nanosheets.Consequently,the wet→dry and dry→wet transitions are observed.Our results may be useful for designing novel information memory devices.展开更多
Based on the EAM potential, a molecular dynamics study on the tensile properties of ultrathin nickel nanowires in the （100〉 orientation with diameters of 3.94, 4.95 and 5.99 nm was presented at different temperature...Based on the EAM potential, a molecular dynamics study on the tensile properties of ultrathin nickel nanowires in the （100〉 orientation with diameters of 3.94, 4.95 and 5.99 nm was presented at different temperatures and strain rates. The temperature and strain rate dependences of tensile properties were investigated. The simulation results show that the elastic modulus and the yield strength are gradually decreasing with the increase of temperature, while with the increase of the strain rate, the stress--strain curves fluctuate more intensely and the ultrathin nickel nanowires rupture at one smaller and smaller strain. At an ideal temperature of 0.01 K, the yield strength of the nanowires drops rapidly with the increase of strain rate, and at other temperatures the strain rate has a little influence on the elastic modulus and the yield strength. Finally, the effects of size on the tensile properties of ultrathin nickel nanowires were briefly discussed.展开更多
The structural and magnetic properties of Fe80P9B11 amorphous alloy are investigated through ab initio molecular dynamic simulation. The structure evolution of Fe（80）P9B（11） amorphous alloy can be described in the...The structural and magnetic properties of Fe80P9B11 amorphous alloy are investigated through ab initio molecular dynamic simulation. The structure evolution of Fe（80）P9B（11） amorphous alloy can be described in the framework of topological fluctuation theory, and the fluctuation of atomic hydrostatic stress gradually decreases upon cooling. The left sub peak of the second peak of Fe–B partial pair distribution functions（PDFs） becomes pronounced below the glass transition temperature, which may be the major reason why B promotes the glass formation ability significantly. The magnetization mainly originates from Fe 3d states, while small contribution results from metalloid elements P and B. This work may be helpful for developing Fe-based metallic glasses with both high saturation flux density and glass formation ability.展开更多
Over the past few decades,significant progress has been made in micro-and nanoscale heat transfer.Numerous computational methods have been developed to quantitatively characterize the thermal transport in bulk materia...Over the past few decades,significant progress has been made in micro-and nanoscale heat transfer.Numerous computational methods have been developed to quantitatively characterize the thermal transport in bulk materials and across the interfaces,which benefit the thermal management design in microelectronics and energy conversion in thermoelectrics largely.In this paper,the methods and studies on quantifying thermal transport properties using molecular dynamics simulations are comprehensively reviewed.Two classical methods based on molecular dynamics simulations are first introduced,i.e.,equilibrium molecular dynamics and nonequilibrium molecular dynamics,to calculate the thermal transport properties in bulk materials and across the interfaces.The spectroscopy methods are then reviewed,which are developed in the framework of equilibrium molecular dynamics(i.e.,time domain normal mode analysis,spectral energy density,Green-Kubo modal analysis) and methods proposed based on the nonequilibrium molecular dynamics(i.e.,time domain direct decompose method,frequency domain direct decompose method and spectral heat flux method).In the subsequent section,the calculations of spectral thermal conductivities using these computational methods in various systems are presented,including simple crystals,low-dimensional materials,complex materials and nanostructures.Following that,spectral thermal transport across the interfacial systems is discussed,which includes solid/solid interfaces,solid/solid interfaces with interfacial engineering and solid/liquid interfaces.Some fundamental challenges in molecular dynamics simulations,such as including quantum effects and quantifying the anharmonic contributions,are discussed as well.Finally,some open problems on spectroscopy thermal transport properties in the framework of molecular dynamics simulations are given in the summary.展开更多
基金Project supported by the National Natural Science Foundation of China (No. 20176048).
文摘The transport properties of fluid argon in micropores, i.e. diffusivity and viscosity, were studied by molecular dynamics simulations. The effects of pore width, temperature and density on diffusivity and viscosity were analyzed in micropores with pore widths from 0.8 to 4.0 nm. The results show that the diffusivity in micropores is much lower than the bulk diffusivity, and it decreases as the pore width decreases; but the viscosity in micropores is significantly larger than the bulk one, and it increases sharply in narrow micropores. The diffusivity in channel parallel direction is obviously larger than that in channel perpendicular direction. The temperature and density are important factors that obviously affect diffusivity and viscosity in micropores.
基金The National Basic Research Program of China(973Program)(No.2011CB707600)the National Natural Science Founda tion of China(No.51435003,51375092)+1 种基金the Natural Science Foundation of Jiangsu Province(No.BK20160935)the Natural Science Foundation of Higher Education Institutions of Jiangsu Province(No.16KJB460015)
文摘The model of ion transportation through graphene nanochannels is established by the molecular dynamics simulation method. Statistics of the electric potential and charge distribution are made, respectively, on both sides of graphene nanopore with various diameters. Then, their changing relationship with respect to the nanopore diameter is determined. When applying a uniform electric field, polar water molecules are rearranged so that the corresponding relationship between the polarized degree of these molecules and the nanopore diameter can be created. Based on the theoretical model of ion transportation through nanochannels,the changing relationship between the concentration of anions/cations in nanochannels and bulk solution concentration is quantitatively analyzed. The results show that the increase of potential drop and charge accumulation, as well as a more obvious water polarization, will occur with the decrease of nanopore diameter. In addition, hydrogen ion concentration has a large proportion in nanochannels with a sodium chloride（NaCl） solution at a relative low concentration. As the NaCl concentration increases, the concentration appreciation of sodium ions tends to be far greater than the concentration drop of chloride ions. Therefore, sodium ion concentration makes more contribution to ionic conductance.
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.
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.
基金Project supported by the National Natural Science Foundation of China(Grant Nos.11374243 and 11574256)
文摘Control of ion transport and fluid flow through nanofluidic devices is of primary importance for energy storage and conversion, drug delivery and a wide range of biological processes. Recent development of nanotechnology, synthesis techniques, purification technologies, and experiment have led to rapid advances in simulation and modeling studies on ion transport properties. In this review, the applications of Poisson-Nernst-Plank （PNP） equations in analyzing transport properties are presented. The molecular dynamics （MD） studies of transport properties of ion and fluidic flow through nanofluidic devices are reported as well.
基金The experiment was financially supported by the National Natural Science Foundation of China(81473364)Beijing Natural Science Foundation(7162122)Excellent Talents Training Subsidy Scheme of Beijing(2013D009999000003).
文摘Objective:To study the transmembrane transport of chemical components of Chinese herbs and to explore the function of platycodin D (PD) on biomembranes.Methods:Interaction between PD and the dipalmitoylphosphatidylcholine (DPPC) bilayer was reproduced by molecular dynamics simulation with the Martini force field.A model validation and methodological study were first performed,and were based on simulation investigations of transmembrane transport for three herbal compounds with distinct hydrophilic properties.Results:PD increased the mobility of the DPPC bilayer since its aglycone strongly interacted with the hydrophobic layer,which broke the structure of the gate layer,and weakened the ordered performance of hydrophobic tails.Conclusion:The Martini force field was successfully applied to the study of the interaction between herbal compounds and a biological membrane.By combining the dynamics equilibrium morphology,the distribution of drugs inside and outside the biomembrane,and the interaction sites of drugs on the DPPC bilayer,factors influencing transmembrane transport of drugs were elucidated and the function of platycodin D in a biological membrane was reproduced.
文摘The diffusivity and viscosity of water confined in micropores were studied by molecular dynamics simulations. The effects of pore width and density were analyzed at pore widths from 0.9 to 2.6 nm. The diffusivity in micropores is lower than that of the bulk, and it decreases as pore width decreases and as density increases. But the viscosity in micropores is much larger than that of the bulk, and it increases as pore width decreases and as density increases. The diffusivity in channel parallel direction is obviously larger than that in channel perpendicular directions.
基金Project supported by the National Natural Science Foundation of China(Grant Nos.11772294 and 11621062)the Fundamental Research Funds for the Central Universities(Grant No.2017QNA4031)。
文摘The thermal conductivity of GaN nanofilm is simulated by using the molecular dynamics(MD)method to explore the influence of the nanofilm thickness and the pre-strain field under different temperatures.It is demonstrated that the thermal conductivity of GaN nanofilm increases with the increase of nanofilm thickness,while decreases with the increase of temperature.Meanwhile,the thermal conductivity of strained GaN nanofilms is weakened with increasing the tensile strain.The film thickness and environment temperature can affect the strain effect on the thermal conductivity of GaN nanofilms.In addition,the analysis of phonon properties of GaN nanofilm shows that the phonon dispersion and density of states of GaN nanofilms can be significantly modified by the film thickness and strain.The results in this work can provide the theoretical supports for regulating the thermal properties of GaN nanofilm through tailoring the geometric size and strain engineering.
基金This work is supported by the National Basic Research Program of China(973 Program)under grant no.2013CB922203the National NSFC under grant Nos.11422432 and 11774429+1 种基金Science Challenge Project under grant no.JCKY2016212A501the Advanced Research Foundation of National University of Defense Technology under grant no.JQ14-02-01.
文摘The equation of states,diffusions,and viscosities of strongly coupled Fe at 80 and 240 eV with densities from 1.6 to 40 g/cm^(3) are studied by orbital-free molecular dynamics,classical molecular dynamics with a corrected Yukawa potential and compared with the results from average atom model.A new local pseudopotential is generated for orbital free calculations.For low densities,the Yukawa model captures the correct ionic interaction behavior around the first peak of the radial distribution function(RDF),thus it gives correct RDFs and transport coefficients.For higher densities,the scaled transformation of the Yukawa potential or adding a short range repulsion part to the Yukawa potential can give correct RDFs and transport coefficients.The corrected potentials are further validated by the force matching method.
文摘Magnesium(Mg)and its composites have been widely used in different fields,but the mechanical properties and deformation mechanisms of polycrystalline Mg(polyMg)at the atomic scale are poorly understood.In this paper,the effects of grain size,temperature,and strain rate on the tensile properties of polyMg are explored and discussed by theMolecular dynamics(MD)simulation method.The calculated results showed that there exists a critical grain size of 10 nm for the mechanical properties of polyMg.The flow stress decreases with the increase of grain size if the average grain size is larger than 10 nm,which shows the Hall-Petch effect,and the deformation mechanism of large grain-sized polyMg is mainly dominated by the movement of dislocations.When the average grain size is less than 10 nm,it shows the reverse Hall-Petch effect that the flow stress decreases with the decrease of grain size,and the deformation mode of polyMg with small grain-size is the movement and deformation of atoms at the grain boundary.Due to the more active motion of atoms as the system temperature increases,the material can easily reach the plastic stage under tensile loading,and the mechanical properties of polyMg decrease at high temperatures.The strain rate has a hardening effect on the properties of composite.Based on our calculated results,it can provide theoretical guidance for the applications of Mg metal and Mg matrix composites.
基金financially supported by the National Key R&D Program of China (Nos.2020YFB1505500 and 2020YFB1505503)。
文摘The perfluorosulfonic acid(PFSA) membrane doped with two-dimensional conductive filler Ti_(3)C_(2)T_(x) is a fuel cell proton exchange membrane with high application potential. Experimental studies showed that the proton conductivity of Nafion/Ti_(3)C_(2)T_(x) composite membrane is improved significantly compared with that in pure Nafion. However, the microscopic mechanism of doping on the enhancement of membrane performance is remain unclear now. In this work, molecular dynamics simulation was used to investigate the microscopic morphology and proton transport behaviors of Nafion/Ti_(3)C_(2)T_(x) composite membrane at the molecular level. The results shown that there were significant differences about the diffusion kinetics of water molecules and hydroxium ions in Nafion/Ti_(3)C_(2)T_(x) at low and high hydration levels in the nanoscale region.With the increase of water content, Ti_(3)C_(2)T_(x) in membrane was gradually surrounded by ambient water molecules to form a hydration layer, and forming a relatively continuous proton transport channel between Nafion polymer and Ti_(3)C_(2)T_(x) monomer. The continuous proton transport channel could increase the number of binding sites of proton and thus achieving high proton conductivity and high mobility of water molecules at higher hydration level. The current work can provide a theoretical guidance for designing new type of Nafion composite membranes.
基金supported by the Open Project of the Shanghai Key Laboratory of Multiphase Flow and Heat Transfer in Power Engineering and the Central Guidance on Local Science and Technology Development Fund of Shanghai City(No.YDZX20213100003002)the Special Project of Independent Innovation of Qingdao City(21-1-2-6-NSH).
文摘The exploration of performance and prediction of environmentally friendly refrigerant physical properties represents a critical endeavor.Equilibriummolecular dynamics simulationswere employed to investigate the density and transport properties of propane and ethane at ultra-low temperatures under evaporative pressure conditions.The results of the density simulation of the evaporation conditions of the blends proved the validity of the simulation method.Under identical temperature and pressure conditions,increasing the proportion of R170 in the refrigerant blends leads to a density decrease while the temperature range in which the gas-liquid phase transition occurs is lower.The analysis of simulated results pertaining to viscosity,thermal conductivity,and self-diffusion coefficient reveals heightened deviation levels within the phase transition temperature zone.This increase in deviation attributed to intensified molecular activity.In terms of uncovering the physical mechanism of gas-liquid phase transition,the work illustrates the macroscopic phenomenon of the intensified existing disorder during phase transitions at the molecular level.Molecular dynamics simulations analyzing the thermophysical properties of refrigerant blends from a microscopic point of view can deepen the comprehension of the thermal optimization of refrigeration processes.
基金supported by the National Natural Science Foundation of China(Grant No.11772043)。
文摘Molecular dynamics(MD)simulations are conducted to study the thermo-mechanical properties of a family of thermosetting epoxy-amines.The crosslinked epoxy resin EPON862 with a series of cross-linkers is built and simulated under the polymer consistent force field(PCFF).Three types of curing agents(rigidity1,3-phenylenediamine(1,3-P),4,4-diaminodiphenylmethane(DDM),and phenol-formaldehyde-ethylenediamine(PFE))with different numbers of active sites are selected in the simulations.We focus on the effects of the cross-linkers on thermo-mechanical properties such as density,glass transition temperature(T_(g)),elastic constants,and strength.Our simulations show a significant increase in the Tg,Young’s modulus and yield stress with the increase in the degree of conversion.The simulation results reveal that the mechanical properties of thermosetting polymers are strongly dependent on the molecular structures of the cross-linker and network topological properties,such as end-to-end distance,crosslinking density and degree of conversion.
基金supported by the National Natural Science Foundation of China(Grant No.11704328)。
文摘We design a nanostructure composing of two nanoscale graphene sheets parallelly immersed in water.Using molecular dynamics simulations,we demonstrate that the wet/dry state between the graphene sheets can be self-latched;moreover,the wet→dry/dry→wet transition takes place when applying an external electric field perpendicular/parallel to the graphene sheets(E;/E;).This structure works like a flash memory device(a non-volatile memory):the stored information(wet and dry states)of the system can be kept spontaneously,and can also be rewritten by external electric fields.On the one hand,when the distance between the two nanosheets is close to a certain distance,the free energy barriers for the transitions dry→wet and wet→dry can be quite large.As a result,the wet and dry states are self-latched.On the other hand,an E;and an E;will respectively increase and decrease the free energy of the water located in-between the two nanosheets.Consequently,the wet→dry and dry→wet transitions are observed.Our results may be useful for designing novel information memory devices.
基金Project(51205302)supported by the National Natural Science Foundation of ChinaProject(2013JM7017)supported by the Natural Science Basic Research Plan in Shanxi Province of ChinaProject(K5051304006)supported by the Fundamental Research Funds for the Central Universities,China
文摘Based on the EAM potential, a molecular dynamics study on the tensile properties of ultrathin nickel nanowires in the （100〉 orientation with diameters of 3.94, 4.95 and 5.99 nm was presented at different temperatures and strain rates. The temperature and strain rate dependences of tensile properties were investigated. The simulation results show that the elastic modulus and the yield strength are gradually decreasing with the increase of temperature, while with the increase of the strain rate, the stress--strain curves fluctuate more intensely and the ultrathin nickel nanowires rupture at one smaller and smaller strain. At an ideal temperature of 0.01 K, the yield strength of the nanowires drops rapidly with the increase of strain rate, and at other temperatures the strain rate has a little influence on the elastic modulus and the yield strength. Finally, the effects of size on the tensile properties of ultrathin nickel nanowires were briefly discussed.
基金supported by the National Natural Science Foundation of China(Grant No.51571115)a Project Funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions
文摘The structural and magnetic properties of Fe80P9B11 amorphous alloy are investigated through ab initio molecular dynamic simulation. The structure evolution of Fe（80）P9B（11） amorphous alloy can be described in the framework of topological fluctuation theory, and the fluctuation of atomic hydrostatic stress gradually decreases upon cooling. The left sub peak of the second peak of Fe–B partial pair distribution functions（PDFs） becomes pronounced below the glass transition temperature, which may be the major reason why B promotes the glass formation ability significantly. The magnetization mainly originates from Fe 3d states, while small contribution results from metalloid elements P and B. This work may be helpful for developing Fe-based metallic glasses with both high saturation flux density and glass formation ability.
基金financially supported by the ASPIRE Seed Fund (No.ASPIRE2022#1) from the ASPIRE Leaguethe HKUST Central High-Performance Computing Cluster.the Project of Hetao Shenzhen-Hong Kong Science,Technology Innovation Cooperation Zone (No.HZQB-KCZYB-2020083)the fund from Research Grants Council of the Hong Kong Special Administrative Region (Nos.C6020-22G and C7002-22Y)。
文摘Over the past few decades,significant progress has been made in micro-and nanoscale heat transfer.Numerous computational methods have been developed to quantitatively characterize the thermal transport in bulk materials and across the interfaces,which benefit the thermal management design in microelectronics and energy conversion in thermoelectrics largely.In this paper,the methods and studies on quantifying thermal transport properties using molecular dynamics simulations are comprehensively reviewed.Two classical methods based on molecular dynamics simulations are first introduced,i.e.,equilibrium molecular dynamics and nonequilibrium molecular dynamics,to calculate the thermal transport properties in bulk materials and across the interfaces.The spectroscopy methods are then reviewed,which are developed in the framework of equilibrium molecular dynamics(i.e.,time domain normal mode analysis,spectral energy density,Green-Kubo modal analysis) and methods proposed based on the nonequilibrium molecular dynamics(i.e.,time domain direct decompose method,frequency domain direct decompose method and spectral heat flux method).In the subsequent section,the calculations of spectral thermal conductivities using these computational methods in various systems are presented,including simple crystals,low-dimensional materials,complex materials and nanostructures.Following that,spectral thermal transport across the interfacial systems is discussed,which includes solid/solid interfaces,solid/solid interfaces with interfacial engineering and solid/liquid interfaces.Some fundamental challenges in molecular dynamics simulations,such as including quantum effects and quantifying the anharmonic contributions,are discussed as well.Finally,some open problems on spectroscopy thermal transport properties in the framework of molecular dynamics simulations are given in the summary.
