Molecular dynamics simulation study of nitrogen vacancy color centers prepared by carbon ion implantation into diamond

Nitrogen vacancy(NV)color centers in diamond have useful applications in quantum sensing andfluorescent marking.They can be gen-erated experimentally by ion implantation,femtosecond lasers,and chemical vapor deposition.However,there is a lack of studies of the yield of NV color centers at the atomic scale.In the molecular dynamics simulations described in this paper,NV color centers are pre-pared by ion implantation in diamond with pre-doped nitrogen and subsequent annealing.The differences between the yields of NV color centers produced by implantation of carbon(C)and nitrogen(N)ions,respectively,are investigated.It is found that C-ion implantation gives a greater yield of NV color centers and superior location accuracy.The effects of different pre-doping concentrations(400–1500 ppm)and implantation energies(1.0–3.0 keV)on the NV color center yield are analyzed,and it is shown that a pre-doping concentra-tion of 1000 ppm with 2 keV C-ion implantation can produce a 13%yield of NV color centers after 1600 K annealing for 7.4 ns.Finally,a brief comparison of the NV color center identification methods is presented,and it is found that the error rate of an analysis utiliz-ing the identify diamond structure coordination analysis method is reduced by about 7%compared with conventional identification+methods.

Subpicosecond laser ablation behavior of a magnesium target and crater evolution:Molecular dynamics study and experimental validation

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.

Exploring unbinding mechanism of drugs from SERT via molecular dynamics simulation and its implication in antidepressants

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.

Effects of Mg2+ on the binding of the CREB/CRE complex:Full-atom molecular dynamics simulations

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.

Theoretical studies and molecular dynamics simulations on ion transport properties in nanochannels and nanopores

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.

Studies on the Structures and Hydrogen-bonding Interactions in Aqueous Glycine Solutions Using All-atom Molecular Dynamics Simulations and NMR Spectroscopy

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.

Recent Progress in Superhydrophobic Coatings Using Molecular Dynamics Simulations and Experimental Techniques

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.

Solid−solid phase transition of tungsten induced by high pressure:A molecular dynamics simulation

The phase transition of tungsten(W)under high pressures was investigated with molecular dynamics simulation.The structure was characterized in terms of the pair distribution function and the largest standard cluster analysis(LSCA).It is found that under 40−100 GPa at a cooling rate of 0.1 K/ps a pure W melt first crystallizes into the body-centred cubic(BCC)crystal,and then transfers into the hexagonal close-packed(HCP)crystal through a series of BCC−HCP coexisting states.The dynamic factors may induce intermediate stages during the liquid−solid transition and the criss-cross grain boundaries cause lots of indistinguishable intermediate states,making the first-order BCC−HCP transition appear to be continuous.Furthermore,LSCA is shown to be a parameter-free method that can effectively analyze both ordered and disordered structures.Therefore,LSCA can detect more details about the evolution of the structure in such structure transition processes with rich intermediate structures.

Microstructural evolution and mechanical properties of FeCoCrNiCu high entropy alloys:a microstructure-based constitutive model and a molecular dynamics simulation study

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.

All-Atom Direct Folding Simulation for Proteins Using the Accelerated Molecular Dynamics in Implicit Solvent Model

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.

分子动力学模拟在沥青体系中的应用研究进展

随着计算机技术的飞速发展,分子模拟方法已被广泛应用于各个领域。本文总结了沥青分子模型、老化沥青模型、集料模型的构建方法以及基质沥青模型的验证方法。通过分子动力学(MD)模拟,探讨了沥青的性质与性能、沥青的扩散现象、改性剂对沥青的改性作用、沥青老化与再生以及沥青与集料的界面相互作用。MD模拟方法能够预测沥青材料的性能,包括基质沥青的力学性能、低温性能、抗老化性能、自愈合性能,基质沥青与改性剂的相容性以及沥青与集料界面的力学性能、黏附性等性能,架起了宏观和微观行为之间的桥梁,为MD模拟在沥青材料的广泛应用提供了指导。但MD模拟在沥青体系中还需要进一步完善,如初始模型的建立、力场的优化和模型验证等,目前分子动力学模拟只关注沥青材料与改性剂之间的物理作用,缺少对两者之间化学作用的研究。此外,分子动力学在沥青混合料中的应用目前只限于沥青与集料界面之间的研究。最后,对MD模拟在沥青体系中的未来发展方向进行了展望,在未来需要使用MD方法来研究沥青的高温流变性能、沥青与改性剂的界面模拟以及多种改性剂与沥青之间的相互作用。此外,还需要探究多种因素(如裂缝宽度、改性剂、温度和再生剂)共同作用下对沥青自愈合性能的影响,为了探究沥青与改性剂之间的化学相互作用,建议结合量子力学等其他模拟方法进行研究,在沥青混合料方面建议结合有限元等模拟方法来研究沥青混合料的性能。

Cu_(50)Ni_(50)合金凝固过程中的空位捕获

通过分子动力学(molecular dynamics,MD)模拟,研究了Cu_(50)Ni_(50)合金在不同温度下凝固及其退火过程的空位捕获.结果发现:凝固过程中的空位捕获效应,即被捕获空位浓度的过饱和现象非常明显;随着凝固温度的降低,空位浓度显著上升,与平衡浓度随温度的变化规律正好相反;Cu_(50)Ni_(50)存在一个特征温度T∗,在T>T∗浅过冷温度下,凝固速度随着凝固温度的降低快速增加,在T<T∗深过冷温度下,凝固速度随着凝固温度的降低缓慢下降,表明空位浓度并不是界面生长速度的单值函数;作为合金元素,Cu比Ni更倾向于形成空位原子(vacancy atom,VA).

不同模型下HMX晶体结构和性能的MD研究

用分子动力学(MD)方法,在COMPASS力场和295K-NPT系综下,对奥克托今(HMX)(4×2×4)和(4×4×4)超晶胞及其沿各自(1 0 0)晶面构成的共6种模型进行了模拟,求得它们的平衡结构、引发键键长分布、引发键连双原子作用能和弹性力学性能。结果表明,引发键呈近似对称的高斯型分布,平均键长(L ave)与实验值很接近;随着体系中原子数目增加,引发键连双原子作用能E N—N单调增加;除柯西压外,各模型的力学性能比较稳定一致。

力调控FLNa-Ig21/αⅡbβ3-CT复合物结构稳定性的分子动力学研究

目的探究力对FLNa-Ig21/αⅡbβ3-CT稳定性的影响及调控机制。方法FLNa-Ig21/αⅡbβ3-CT晶体结构取自PDB数据库。通过平衡和拉伸分子动力学模拟,分析复合物生理环境下稳定性以及力诱导的解折叠路径和力学稳定性。结果平衡过程中,FLNa-Ig21和αⅡbβ3-CT之间大部分盐桥和氢键的生存率小于0.5,其结合强度相对较弱;恒速度拉伸过程中,复合物可承受170~380 pN的拉力,其力学强度与力诱导的解离路径有关;在0~60 pN恒力条件下,复合物呈现“滑移键”趋势,且力的增加有利于αⅡbβ3近膜端R995-D723盐桥的解离和整合素的活化。结论力诱导的αⅡbβ3-CT近膜端异构可增强复合物的力学强度和解离时间的后移;突破20 pN阈值后,力正向调控整合素的活化。研究结果为深入揭示整合素αⅡbβ3活化的分子机制及相关靶向药物开发提供参考。

不同温度下PETN晶体感度判别和力学性能预测的MD研究

为从理论上寻求典型硝酸酯炸药太安(PETN)晶体的感度判据和力学性能,在NPT系综下,用COMPASS力场对PETN(4×3×4)超晶胞和沿其(100)晶面切割的两种模型,实施了5个温度(195,245,295,345,395K)的周期性分子动力学(MD)模拟。结果表明,随温度升高,它们的引发键O—NO2的最大键长(Lmax)递增,引发键连双原子作用能(EO-N)和内聚能密度(CED)递减,与感度随温度升高而增大的实验事实相一致。Lmax、EO-N和CED在一定条件下,确可用作高能物质热和撞击感度相对大小的理论判据。随温度升高,弹性系数与弹性模量递减,刚性减小,柔性递增,符合实验事实,表明,以切割分面模型进行MD模拟能获得较符合实际的确定结果。

2,6-二氨基-3,5-二硝基吡啶-1-氧化物晶体形貌的MD模拟

为探讨溶剂对炸药晶体形貌的影响机制和溶剂的选择依据,采用附着能(AE)模型预测2,6-二氨基-3,5-二硝基吡啶-1-氧化物(ANPyO)在真空的晶体形貌,确定其主要生长晶面;并运用分子动力学(MD)模拟研究ANPyO晶面与溶剂N,N-二甲基甲酰胺(DMF)的相互作用及其本质,进而通过修正的AE模型预测其在DMF中的晶体形貌。结果表明:ANPyO在真空中的晶体形状接近椭圆,主要生长晶面为(110)、(100)、(11-2)及(10-1)面。溶剂与晶面间存在较强相互作用,径向分布函数分析表明相互作用能主要包括范德华作用,库仑作用和氢键。在溶剂DMF中,晶面的修正附着能绝对值顺序为(110)<(11-2)<(10-1)<(100),ANPyO晶体形貌接近片状,与已有实验结果一致。此外,DMF分子在ANPyO晶面的扩散系数研究结果表明,扩散系数与修正附着能绝对值成线性关系,晶体生长形貌亦受溶剂扩散能力的影响。

ε-CL-20不同晶面与PVA、PEG复合物的MD模拟

为探讨和比较在ε-CL-20(六硝基六氮杂异伍兹烷)(001)、(110)和(020)晶面上的ε-CL-20/PVA(聚乙烯醇)与ε-CL-20/PEG(聚乙二醇)复合物的稳定性和力学性能,在COMPASS力场下,对ε-CL-20/PVA与ε-CL-20/PEG进行了常温常压分子动力学(MD)模拟研究。求得其内聚能密度(CED),结合能(E_(bind))和弹性参数(拉伸模量E、剪切模量G、体积模量K、泊松比ν和柯西压C_(12)-C_(44))。结果表明,在相同晶面上,ε-CL-20/PEG的CED比ε-CL-20/PVA的大,表明前者稳定性优于后者。对于同一复合物,其CED排序为(020)>(001)>(110)。在相同晶面上,PEG与晶面的E_(bind)比PVA的大。对同一复合物,其E_(bind)大小次序为(001)>(110)>(020)。依据泊松比和K/G值,ε-CL-20/PEG的弹性和延展性均优于ε-CL-20/PVA。

Dynamic quasi-continuum model for plate-type nano-materials and analysis of fundamental frequency

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.

浅析MD模拟方法理论

随着理论和计算化学以及计算机的发展,量子力学计算已深入发展到运用适合于材料科学研究中。尤其是MD分子模拟技术已被越来越广泛地用于预测一些高能化合物难以用实验测定的热物理性质、力学性质和在极端条件下的分解现象等。文中对分子动力学(MD)方法进行了理论概述,并对分子模拟技术进行了简要分析和总结,展望了未来趋势。

第一类鱼抗冻蛋白与天然气水合物吸附结合过程中局部结构变化研究

采用分子动力学模拟方法,计算分析第一类鱼抗冻蛋白(AFP-Ⅰ)在与天然气水合物吸附结合过程中局部结构的变化,并通过AFP-Ⅰ氨基酸突变体模拟结果来进一步说明AFP-Ⅰ抑制水合物生长的作用机理。结果表明,在AFP-Ⅰ与水合物结合过程中分子局部结构发生改变,水合物结合位点(Hydrate-binding site,HBS)处部分氨基酸残基的甲基发生迁移以适应水合物的笼状结构并取代甲烷分子与水合物表面结合。此外,氨基酸突变体模拟表明AFP-Ⅰ侧链上的甲基的缺失会减弱抗冻蛋白与水合物的结合能力。研究结果对研发可降解的天然产物类水合物抑制剂具有参考意义。