Adaptive resolution molecular dynamics simulation through coupling to an internal particle reservoir

For simulation studies of (macro) molecular liquids it would be of significant interest to be able to adjust or increase the level of resolution within one region of space, while allowing for the free exchange of molecules between open regions of different resolution or representation. We generalize the adaptive resolution idea and suggest an interpretation in terms of an effective generalized grand canonical approach. The method is applied to liquid water at ambient conditions.     

Recoiling DNA molecule: simulation and experiment

Single molecule DNA experiments often generate data from force versus extension measurements involving the tethering of a microsphere to one end of a single DNA molecule while the other is attached to a substrate. We show that the persistence length of single DNA molecules can also be measured based on the recoil dynamics of these DNA-microsphere complexes if appropriate corrections are made to the friction coefficient of the microsphere in the vicinity of the substrate. Comparison between computer simulated recoil curves, generated from the corresponding Langevin equation, and experimental recoils are used to assure the validity of data analysis.     

铂纳米粒子热稳定性的原子级模拟研究

本文采用分子动力学结合嵌入原子多体势,模拟了铂纳米粒子在升温过程中的热稳定性和熔化机制,并利用共近邻分析方法分析了它的微结构演化过程。模拟的结果表明：铂纳米粒子的熔点明显低于体材料的熔点;由于表面层原子的结合力较弱,在升温过程中表面会首先出现预熔;纳米粒子的熔化是从表面层开始的,并随着温度的升高,熔化的表面层会逐渐向内部扩展,最终导致纳米粒子整体转变为液态结构;当温度低于表面预熔温度时,纳米粒子保持良好的晶态结构。     

金属纳米线应力分布特征的原子级模拟研究

运用分子静力学方法结合量子修正Sutten-Chen多体力场研究了Ni纳米线在平衡状态下的应力分布特征，考虑了三种不同取向的纳米线，即轴线方向分别沿［100］，［110］和［111］方向的纳米线.计算的结果表明：由于表面张应力的作用，纳米线在弛豫过程中沿轴线方向长度发生收缩；纳米线从表面向中心区域呈现出由张应力向压应力连续分布的特征.随着纳米线直径的增加，纳米线的表面区域的张应力先上升，然后略有下降，并趋向一个非零的常值；而中心区域的应力则属于压应力，其值随着直径的增加显著地减小，并趋向于零值.无论是轴向     

金属纳米线应力分布特征的原子级模拟研究

运用分子静力学方法结合量子修正Sutten-Chen多体力场研究了Ni纳米线在平衡状态下的应力分布特征,考虑了三种不同取向的纳米线,即轴线方向分别沿［100］,［110］和［111］方向的纳米线.计算的结果表明：由于表面张应力的作用,纳米线在弛豫过程中沿轴线方向长度发生收缩;纳米线从表面向中心区域呈现出由张应力向压应力连续分布的特征.随着纳米线直径的增加,纳米线的表面区域的张应力先上升,然后略有下降,并趋向一个非零的常值;而中心区域的应力则属于压应力,其值随着直径的增加显著地减小,并趋向于零值.无论是轴向 关键词： 纳米线 应力分布 分子静力学     

Investigation of a Kubo-formula-based approach to estimate DNA conductance in an atomistic model

A novel approach to estimate DNA conductance based upon Kubo formula is presented and discussed. Using this approach, the effects of base pair mismatches, different conformational changes and base pair sequence on DNA electrical properties were investigated. The results were compared with the data from other methods. The new approach makes possible very fast estimation of conductance spectra for oligonucleotides with hundreds of base pairs and can easily be extended to treat arbitrary chemical modifications of DNA.     

DNA molecule as an elastic Heisenberg chain

A DNA molecule is simulated by an anisotropic elastic fiber which defines the configuration of the molecule central line and is supplemented with a chain of quantum two-level systems imitating hydrogen bonds between two polynucleotide chains in the DNA double helix. The system Hamiltonian consists of Kirchhoff’s classical elastic energy and the energy of a quantum anisotropic chain of “spins” 1/2. The two-level systems and macroscopic vector variables which determine the conformation of the central line are coupled by a classical vector field q, which is introduced to take into account the existence of two polynucleotide strands. Averaging over fast (microscopic) variables yields an effective potential U(q). In the approximation of weak coupling between the systems, the spectrum of elementary excitations and effective potential U(q) have been calculated in explicit form. The relation between elementary excitations in the “magnetic” subsystem and so-called breathing modes [C. Mandel, N. R. Kallenbach, and S. W. Englander, J. Mol. Biol. 135, 391 (1980); G. Manning, Biopolymers 22, 689 (1983)] corresponding to low-frequency excitations in DNA molecules is discussed. Zh. éksp. Teor. Fiz. 111, 1833–1844 (May 1997)     

The elastic properties and energy characteristics of Au nanowires: an atomistic simulation study

This paper have performed molecular static calculations with the quantum corrected Sutten Chen type many body potential to study size effects on the elastic modulus of Au nanowires with [100], [110] and [111] crystallographic directions, and to explore the preferential growth orientation of Au nanowires. The main focus of this work is the size effects on their surface characteristics. Using the common neighbour analysis, this paper deduces that surface region approximately consists of two layer atoms. Further, it extracts the elastic modulus of surface, and calculate surface energy of nanowire. The results show that for all three directions the Young＇s modulus of nanowire increases as the diameter increases. Similar trend has been observed for the Young＇s modulus of surface. However, the atomic average potential energy of nanowire shows an opposite change. Both the potential and surface energy of [110] nanowire are the lowest among all three orlentational nanowires, which helps to explain why Au nanowires possess a [110] preferred orientation during the experimental growth proceeds.     

Statistical analysis of DNA duplex structures in solution derived by high resolution NMR

An initial statistical analysis has been performed on the helical parameters for the solution structures of three DNA duplexes recently solved in this laboratory by proton NMR. Local conformations in these structures belong to the B family of forms; nevertheless they display a strong sequence-dependent heterogeneity akin to that found in single crystals and by theoretical calculations. However, average helical parameters as well as their variations are quite different for short DNA fragments in solution and in crystal. Average helical twist in three NMR-refined oligonucleotides is 34.6°, in remarkable agreement with independent solution-state data, while helical twist is 36° for DNA in crystals. Other characteristic features of solution DNA conformations are negative slide, systematically open minor groove (for almost all sequences), and decreased helical rise. The latter, rather unexpected finding, is correlated with a surprisingly strong non-flatness of Watson-Crick base pairs. Deviations of base pairs from planarity proved to be a significant source of conformational variability; of particular importance is base stagger, which is often missed in structural analysis of DNA. Several new structural parameters have been introduced for dinucleotide steps, characterizing non-planar geometries of constituent base pairs; these parameters show a significant degree of correlation with traditional step parameters (twist, tillt roll, shift, slide, rise). Many sequence-dependent features are observed in solution structures; variation of roll and slide parameters occurs according to “Calladine’s rules”, while variation of helical twist appears to oppose them. However, a larger set of solution structures is needed to complete the analysis of sequence dependence of DNA conformation.     

Influence of adding salt on ultrasonic atomization in an ethanol-water solution

Ethanol was enriched by ultrasonic atomization. Enrichment ratios were increased by adding salt to the ethanol solution. Different enrichment ratios were observed for different types of salts in a range of low ethanol concentrations. The enrichment ratio was significantly improved by adding K(2)CO(3) or (NH(4))(2)SO(4). It is concluded that this is due to enhanced interfacial adsorption of the ethanol. Addition of Na(2)CO(3) to the ethanol solution also enhanced the interfacial adsorption of the ethanol, but the effect was relatively small. Addition of NaCl to the ethanol solution did not enhance the interfacial adsorption of the ethanol.     

High resolution spectrum of DyO molecule

Emission spectrum of DyO molecule has been photographed under high resolution in the wavelength region 5000 to 6300 A. The observed bands have been arranged into three different band systems. The rotational structure in the (0, 0) band of system I is partially resolved and analysed. Isotopic shifts have been calculated for various isotopic molecules and compared with observations. Electronic states involved in the transitions have been discussed.     

Laser ablation of gold: Experiment and atomistic simulation

The interaction of radiation of a picosecond X-ray laser (wavelength λ = 13.9 nm) with targets made of a thick gold film has been studied theoretically and experimentally. It has been shown experimentally that the action of individual X-ray laser pulses with a fluence of F ≈ 21 mJ/cm² initiates the nanostructuring of the gold surface. Explicitly taking into account the electron subsystem, we have proposed an atomistic model of ablation that makes it possible to adequately describe the experimental results. The atomistic simulation involves the ion-ion potential depending on the electron temperature T _e . The use of such a potential makes it possible to take into account an increase in the pressure in the system with increasing T _e and to reveal two laser ablation mechanisms.     

Thermal stability of silicon nanowires: atomistic simulation study

Using the Stillinger--Weber (SW) potential model, we investigate the thermal stability of pristine silicon nanowires based on classical molecular dynamics (MD) simulations. We explore the structural evolutions and the Lindemann indices of silicon nanowires at different temperatures in order to unveil atomic-level melting behaviour of silicon nanowires. The simulation results show that silicon nanowires with surface reconstructions have higher thermal stability than those without surface reconstructions, and that silicon nanowires with perpendicular dimmer rows on the two (100) surfaces have somewhat higher thermal stability than nanowires with parallel dimmer rows on the two (100) surfaces. Furthermore, the melting temperature of silicon nanowires increases as their diameter increases and reaches a saturation value close to the melting temperature of bulk silicon. The value of the Lindemann index for melting silicon nanowires is 0.037.     

Spectral-luminescence study of the formation of QD-sulfophthalocyanine molecule complexes in an aqueous solution

The spectral-luminescence manifestations of the formation of quantum dot (QD)-phthalocyanine complexes as a result of electrostatic interaction have been investigated. Effective QD luminescence quenching has been found in complexes of this type. The luminescence of the molecules associated in complexes with QDs is also partially quenched. A mathematical model of the formation of QD-organic molecule complexes is proposed.     

Atomistic simulation of the transition from atomistic to macroscopic cratering

Using large-scale atomistic simulations, we show that the macroscopic cratering behavior emerges for projectile impacts on Au at projectile sizes between 1000 and 10000 Au atoms at impact velocities comparable to typical meteoroid velocities. In this size regime, we detect a compression of material in Au nanoparticle impacts similar to that observed for hypervelocity macroscopic impacts. The simulated crater volumes agree with the values calculated using the macroscopic crater size scaling law, in spite of a downwards extrapolation over more than 15 orders of magnitude in terms of the impactor volume. The result demonstrates that atomistic simulations can be used as a tool to understand the strength properties of materials in cases where only continuum models have been possible before.     

Plastic deformation behaviour of layer-grained silver polycrystalline from atomistic simulation

Two types of nanocrystalline polycrystalline silver models in bulk, film and nanowire forms were constructed with layer-grained or equiaxed grain morphologies and average grain sizes of ~7.8 and ~14.7 nm. Uniaxial tensile deformation was performed to investigate the effect of grain morphology and free surface on the plastic deformation behaviour under the strain rate of 5 × 10⁸ and 10⁷ s^?1 at 0.1 K. Grain Boundary (GB) orientation and dimensions in layer-grained morphology promoted the formation of sessile dislocation structures. Some dislocations interacted with each other and some dislocations got obstructed by stacking faults. However, the resulting configurations did not last long enough to cause strain hardening. Strain softening was observed in all models except for the layer-grained models in bulk form, where steady plastic flow was observed after yield. The location and orientation of free surfaces with respect to GBs imposed geometric constraints on the deformation mechanisms (GB sliding and formation of sessile dislocations) which produced asymmetric stress states that influenced the elastic as well as plastic response of the material. The yield stress and flow stress were much smaller at lower strain rate simulations. The proportion of perfect dislocations increased as the strain rate decreased from 5 × 10⁸ to 10⁷ s^?1 due to the decrease of applied stress. Dislocations were mainly emitted from grain boundaries or triple junctions at both high and low strain rate deformations. These results provided insights into the understanding of layer-grained nanocrystalline materials and the synthesis of materials with both high strength and ductility.