The micro-ablation processes and morphological evolution of ablative craters on single-crystal magnesium under subpicosecond laser irradiation are investigated using molecular dynamics(MD) simulations and experiments....The micro-ablation processes and morphological evolution of ablative craters on single-crystal magnesium under subpicosecond laser irradiation are investigated using molecular dynamics(MD) simulations and experiments.The simulation results exhibit that the main failure mode of single-crystal Mg film irradiated by a low fluence and long pulse width laser is the ejection of surface atoms,which has laser-induced high stress.However,under high fluence and short pulse width laser irradiation,the main damage mechanism is nucleation fracture caused by stress wave reflection and superposition at the bottom of the film.In addition,Mg[0001] has higher pressure sensitivity and is more prone to ablation than Mg[0001].The evolution equation of crater depth is established using multi-pulse laser ablation simulation and verified by experiments.The results show that,under multiple pulsed laser irradiation,not only does the crater depth increase linearly with the pulse number,but also the quadratic term and constant term of the fitted crater profile curve increase linearly.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
Metal ions play critical roles in the interaction between deoxyribonucleic acid(DNA) and protein.The experimental research has demonstrated that the Mg^2+ ion can affect the binding between transcription factor and DN...Metal ions play critical roles in the interaction between deoxyribonucleic acid(DNA) and protein.The experimental research has demonstrated that the Mg^2+ ion can affect the binding between transcription factor and DNA.In our work,by full-atom molecular dynamic simulation, the effects of the Mg^2+ ion on the cyclic adenosine monophosphate(cAMP)response element binding protein(CREB)/cAMP response elements(CRE) complex are investigated.It is illustrated that the number of hydrogen bonds formed at the interface between protein and DNA is significantly increased when the Mg^2+ ion is added.Hence, an obvious change in the structure of the DNA is observed.Then the DNA base groove and base pair parameters are analyzed.We find that, due to the introduction of the Mg2+ ion, the DNA base major groove becomes narrower.A potential mechanism for this observation is proposed.It is confirmed that the Mg^2+ ion can enhance the stability of the DNA–protein complex.展开更多
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
All-atom molecular dynamics （MD） simulations and chemical shifts were used to study interactions and structures in the glycine-water system. Radial distribution functions and the hydrogen-bond network were applied i...All-atom molecular dynamics （MD） simulations and chemical shifts were used to study interactions and structures in the glycine-water system. Radial distribution functions and the hydrogen-bond network were applied in MD simulations. Aggregates in the aqueous glycine solution could be classified into different regions by analysis of the hydrogen-bonding network. Temperature-dependent NMR spectra and the viscosity of glycine in aqueous solutions were measured to compare with the results of MD simulations. The variation tendencies of the hydrogen atom chemical shifts and viscosity with concentration of glycine agree with the statistical results of hydrogen bonds in the MD simulations.展开更多
Superhydrophobic(SH)coatings are intended to resist a surface from corrosion and thereby increases the product life duration.It is also a promising solution to save cleaning costs and time by providing self-clea...Superhydrophobic(SH)coatings are intended to resist a surface from corrosion and thereby increases the product life duration.It is also a promising solution to save cleaning costs and time by providing self-clean nature to the surface.This review article provides the most recent updates in designing SH surfaces and their characterizations adopted both in experimental and computational techniques.To gain a comprehensive perspective,the SH surfaces present in nature those are inspiring human beings to mimic such surfaces are introduced at the beginning of this article.Subsequently,different fabrication techniques undertaken recently to design artificial SH surfaces are briefly discussed.Recent progress in computations employed in the development of SH surfaces is then discussed.Next,the limitations in SH surfaces are addressed.Finally,perceptiveness of different strategies and their limitations are presented in the concluding remarks and outlook.Overall,this mini review article brings together and highlights the significant advancements in fabrication of superhydrophobic surfaces which may surely help the early-stage researchers/scientists to plan their work accordingly.展开更多
High entropy alloys(HEAs)attract remarkable attention due to the excellent mechanical performance.However,the origins of their high strength and toughness compared with those of the traditional alloys are still hardly...High entropy alloys(HEAs)attract remarkable attention due to the excellent mechanical performance.However,the origins of their high strength and toughness compared with those of the traditional alloys are still hardly revealed.Here,using a microstructure-based constitutive model and molecular dynamics(MD)simulation,we investigate the unique mechanical behavior and microstructure evolution of FeCoCrNiCu HEAs during the indentation.Due to the interaction between the dislocation and solution,the high dislocation density in FeCoCrNiCu leads to strong work hardening.Plentiful slip systems are stimulated,leading to the good plasticity of FeCoCrNiCu.The plastic deformation of FeCoCrNiCu is basically affected by the motion of dislocation loops.The prismatic dislocation loops inside FeCoCrNiCu are formed by the dislocations with the Burgers vectors of a/6[112]and a/6[112],which interact with each other,and then emit along the<111>slip direction.In addition,the mechanical properties of FeCoCrNiCu HEA can be predicted by constructing the microstructure-based constitutive model,which is identified according to the evolution of the dislocation density and the stress-strain curve.Strong dislocation strengthening and remarkable lattice distortion strengthening occur in the deformation process of FeCoCrNiCu,and improve the strength.Therefore,the origins of high strength and high toughness in FeCoCrNiCu HEAs come from lattice distortion strengthening and the more activable slip systems compared with Cu.These results accelerate the discovery of HEAs with excellent mechanical properties,and provide a valuable reference for the industrial application of HEAs.展开更多
We report the results of protein folding （219M, C34, N36, 2KES, 2KHK） by the method of accelerated molecular dynamics （aMD） at room temperature with the implicit solvent model. Starting from the linear structures,...We report the results of protein folding （219M, C34, N36, 2KES, 2KHK） by the method of accelerated molecular dynamics （aMD） at room temperature with the implicit solvent model. Starting from the linear structures, these proteins successfully fold to the native structure in a lO0-ns aMD simulation. In contrast, they are failed under the traditional MD simulation in the same simulation time. Then we find that the lowest root mean square deviations of helix structures from the native structures are 0.36 A, 0.63 A, 0.52 A, 1.1 A and 0.78 A. What is more, native contacts, cluster and free energy analyses show that the results of the aMD method are in accordance with the experiment very well. All analyses show that the aMD can accelerate the simulation process, thus we may apply it to the field of computer aided drug designs.展开更多
A dynamic quasi-continuum model is presented to analyze free vibration of plate-type cubic crystal nano-materials.According to the Hamilton principle,fundamental governing equations in terms of displacement components...A dynamic quasi-continuum model is presented to analyze free vibration of plate-type cubic crystal nano-materials.According to the Hamilton principle,fundamental governing equations in terms of displacement components and angles of rotations are given.As an application of the model,the cylindrical bending deformation of the structure fixed at two ends is analyzed,and a theoretical formula evaluating the fundamental frequency is obtained by using Galerkin's method.Meanwhile,the solution for the classical continuous plate model is also derived,and the size-dependent elastic modulus and Poisson's ratio are taken in computation.The frequencies corresponding to different atomic layers are numerically presented for the plate-type NaC l nano-materials.Furthermore,a molecular dynamics(MD)simulation is conducted with the code LAMMPS.The comparison shows that the present quasi-continuum model is valid,and it may be used as an alternative model,which reflects scale effects in analyzing dynamic behaviors of such plate-type nano-materials.展开更多
Amorphous carbon films have attracted substantial interest due to their exceptional mechanical and tribological properties.Previous studies revealed that the amorphous carbon films exhibited lower coefficient of frict...Amorphous carbon films have attracted substantial interest due to their exceptional mechanical and tribological properties.Previous studies revealed that the amorphous carbon films exhibited lower coefficient of friction(COF)because of the transformation in bond structure from sp^(3)-C to sp^(2)-C during friction processes.However,the mechanism for such a transformation during friction is not well understood.This study is conducted to get an insight into the metastable transformation in amorphous carbon film during friction by means of experiments and molecular dynamics(MD)simulation.Relevant wear tests showed that wear of the film changed from an abrasive wear mode to a mixture of abrasion and adhesive wear,resulting in a decrease in growth rate of the wear rate after the running-in stage.It is worth noting that the sp^(3)-C atoms were increased during the running-in stage when the films contained lower sp^(3)/sp^(2) ratios.However,the formed sp^(3)-C atoms could only be short-lived and gradually transformed to sp^(2)-C atoms with the graphitization generated on the wearing surface of the films.The radial distribution function and translational order parameter indicated that the films'high sp^(3)/sp^(2) ratio led to an increased sp^(2)-C proportion on the wear scar after friction,which caused an increased structural ordering.展开更多
文摘The micro-ablation processes and morphological evolution of ablative craters on single-crystal magnesium under subpicosecond laser irradiation are investigated using molecular dynamics(MD) simulations and experiments.The simulation results exhibit that the main failure mode of single-crystal Mg film irradiated by a low fluence and long pulse width laser is the ejection of surface atoms,which has laser-induced high stress.However,under high fluence and short pulse width laser irradiation,the main damage mechanism is nucleation fracture caused by stress wave reflection and superposition at the bottom of the film.In addition,Mg[0001] has higher pressure sensitivity and is more prone to ablation than Mg[0001].The evolution equation of crater depth is established using multi-pulse laser ablation simulation and verified by experiments.The results show that,under multiple pulsed laser irradiation,not only does the crater depth increase linearly with the pulse number,but also the quadratic term and constant term of the fitted crater profile curve increase linearly.
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Project supported by the National Natural Science Foundation of China(Grant Nos.11705064,11675060,and 91730301)the Fundamental Research Funds for the Central Universities,China(Grant Nos.2662016QD005 and 26622018JC017)the Huazhong Agricultural University Scientific and Technological Self-Innovation Foundation Program,China(Grant No.2015RC021)
文摘Metal ions play critical roles in the interaction between deoxyribonucleic acid(DNA) and protein.The experimental research has demonstrated that the Mg^2+ ion can affect the binding between transcription factor and DNA.In our work,by full-atom molecular dynamic simulation, the effects of the Mg^2+ ion on the cyclic adenosine monophosphate(cAMP)response element binding protein(CREB)/cAMP response elements(CRE) complex are investigated.It is illustrated that the number of hydrogen bonds formed at the interface between protein and DNA is significantly increased when the Mg^2+ ion is added.Hence, an obvious change in the structure of the DNA is observed.Then the DNA base groove and base pair parameters are analyzed.We find that, due to the introduction of the Mg2+ ion, the DNA base major groove becomes narrower.A potential mechanism for this observation is proposed.It is confirmed that the Mg^2+ ion can enhance the stability of the DNA–protein complex.
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Supported by the National Natural Science Foundation of China(No.20903026)the Talents Introduction Foundation for Universities of Guangdong Province(2011)Scientific Research Foundation of the Natural Science Foundation of Guangdong Province(No.S2011010002483)
文摘All-atom molecular dynamics （MD） simulations and chemical shifts were used to study interactions and structures in the glycine-water system. Radial distribution functions and the hydrogen-bond network were applied in MD simulations. Aggregates in the aqueous glycine solution could be classified into different regions by analysis of the hydrogen-bonding network. Temperature-dependent NMR spectra and the viscosity of glycine in aqueous solutions were measured to compare with the results of MD simulations. The variation tendencies of the hydrogen atom chemical shifts and viscosity with concentration of glycine agree with the statistical results of hydrogen bonds in the MD simulations.
文摘Superhydrophobic(SH)coatings are intended to resist a surface from corrosion and thereby increases the product life duration.It is also a promising solution to save cleaning costs and time by providing self-clean nature to the surface.This review article provides the most recent updates in designing SH surfaces and their characterizations adopted both in experimental and computational techniques.To gain a comprehensive perspective,the SH surfaces present in nature those are inspiring human beings to mimic such surfaces are introduced at the beginning of this article.Subsequently,different fabrication techniques undertaken recently to design artificial SH surfaces are briefly discussed.Recent progress in computations employed in the development of SH surfaces is then discussed.Next,the limitations in SH surfaces are addressed.Finally,perceptiveness of different strategies and their limitations are presented in the concluding remarks and outlook.Overall,this mini review article brings together and highlights the significant advancements in fabrication of superhydrophobic surfaces which may surely help the early-stage researchers/scientists to plan their work accordingly.
基金the Foundation for Innovative Research Groups of the National Natural Science Foundation of China(No.51621004)the National Natural Science Foundation of China(Nos.12072109,51871092,and 11772122)。
文摘High entropy alloys(HEAs)attract remarkable attention due to the excellent mechanical performance.However,the origins of their high strength and toughness compared with those of the traditional alloys are still hardly revealed.Here,using a microstructure-based constitutive model and molecular dynamics(MD)simulation,we investigate the unique mechanical behavior and microstructure evolution of FeCoCrNiCu HEAs during the indentation.Due to the interaction between the dislocation and solution,the high dislocation density in FeCoCrNiCu leads to strong work hardening.Plentiful slip systems are stimulated,leading to the good plasticity of FeCoCrNiCu.The plastic deformation of FeCoCrNiCu is basically affected by the motion of dislocation loops.The prismatic dislocation loops inside FeCoCrNiCu are formed by the dislocations with the Burgers vectors of a/6[112]and a/6[112],which interact with each other,and then emit along the<111>slip direction.In addition,the mechanical properties of FeCoCrNiCu HEA can be predicted by constructing the microstructure-based constitutive model,which is identified according to the evolution of the dislocation density and the stress-strain curve.Strong dislocation strengthening and remarkable lattice distortion strengthening occur in the deformation process of FeCoCrNiCu,and improve the strength.Therefore,the origins of high strength and high toughness in FeCoCrNiCu HEAs come from lattice distortion strengthening and the more activable slip systems compared with Cu.These results accelerate the discovery of HEAs with excellent mechanical properties,and provide a valuable reference for the industrial application of HEAs.
基金Supported by the National Natural Science Foundation of China under Grant Nos 31200545,11274206 and 11574184
文摘We report the results of protein folding （219M, C34, N36, 2KES, 2KHK） by the method of accelerated molecular dynamics （aMD） at room temperature with the implicit solvent model. Starting from the linear structures, these proteins successfully fold to the native structure in a lO0-ns aMD simulation. In contrast, they are failed under the traditional MD simulation in the same simulation time. Then we find that the lowest root mean square deviations of helix structures from the native structures are 0.36 A, 0.63 A, 0.52 A, 1.1 A and 0.78 A. What is more, native contacts, cluster and free energy analyses show that the results of the aMD method are in accordance with the experiment very well. All analyses show that the aMD can accelerate the simulation process, thus we may apply it to the field of computer aided drug designs.
文摘A dynamic quasi-continuum model is presented to analyze free vibration of plate-type cubic crystal nano-materials.According to the Hamilton principle,fundamental governing equations in terms of displacement components and angles of rotations are given.As an application of the model,the cylindrical bending deformation of the structure fixed at two ends is analyzed,and a theoretical formula evaluating the fundamental frequency is obtained by using Galerkin's method.Meanwhile,the solution for the classical continuous plate model is also derived,and the size-dependent elastic modulus and Poisson's ratio are taken in computation.The frequencies corresponding to different atomic layers are numerically presented for the plate-type NaC l nano-materials.Furthermore,a molecular dynamics(MD)simulation is conducted with the code LAMMPS.The comparison shows that the present quasi-continuum model is valid,and it may be used as an alternative model,which reflects scale effects in analyzing dynamic behaviors of such plate-type nano-materials.
基金This work was co-supported by the National Natural Science Foundation of China(No.51905466)Aeronautical Science Foundation of China(No.201945099002)+1 种基金Natural Science Foundation of Hebei Province,China(Nos.E2021203191 and E2020203184)Youth Top Talent Project of Hebei Province Higher Education,China(No.BJ2019058).
文摘Amorphous carbon films have attracted substantial interest due to their exceptional mechanical and tribological properties.Previous studies revealed that the amorphous carbon films exhibited lower coefficient of friction(COF)because of the transformation in bond structure from sp^(3)-C to sp^(2)-C during friction processes.However,the mechanism for such a transformation during friction is not well understood.This study is conducted to get an insight into the metastable transformation in amorphous carbon film during friction by means of experiments and molecular dynamics(MD)simulation.Relevant wear tests showed that wear of the film changed from an abrasive wear mode to a mixture of abrasion and adhesive wear,resulting in a decrease in growth rate of the wear rate after the running-in stage.It is worth noting that the sp^(3)-C atoms were increased during the running-in stage when the films contained lower sp^(3)/sp^(2) ratios.However,the formed sp^(3)-C atoms could only be short-lived and gradually transformed to sp^(2)-C atoms with the graphitization generated on the wearing surface of the films.The radial distribution function and translational order parameter indicated that the films'high sp^(3)/sp^(2) ratio led to an increased sp^(2)-C proportion on the wear scar after friction,which caused an increased structural ordering.
