Processes of DNA condensation induced by multivalent cations： Approximate annealing experiments and molecular dynamics simulations

The condensation of DNA induced by spermine is studied by atomic force microscopy （AFM） and molecular dynamics （MD） simulation in this paper. In our experiments, an equivalent amount of multivalent cations is added to the DNA solutions in different numbers of steps, and we find that the process of DNA condensation strongly depends on the speed of adding cations. That is, the slower the spermine cations are added, the slower the DNA aggregates. The MD and steered molecular dynamics （SMD） simulation results agree well with the experimental results, and the simulation data also show that the more steps of adding multivalent cations there are, the more compact the condensed DNA structure will be. This investigation can help us to control DNA condensation and understand the complicated structures of DNA--cation complexes.     

方解石纳米孔隙内二氧化碳毛细凝聚的分子模拟

在二氧化碳地质封存、增产非常规油气以及孔隙材料表征测量方面,纳米孔隙中二氧化碳相态的准确预测具有重要意义.然而,由于纳米尺度下毛细力、分离压等作用力占据主导因素,流体在孔隙中的相行为与体相流体存在根本不同.已有实验和模拟表明,Kelvin毛细凝聚理论无法预测特征尺度10 nm下的,孔隙内流体凝聚压力与体相饱和蒸气压的偏...     

晶粒棱长、尺寸与拓扑学特征之间关系的Monte Carlo仿真研究

采用Potts模型Monte Carlo方法研究了晶粒棱长、尺寸与拓扑学特征之间的统计关系.结果表明,晶粒棱长与晶粒面数之间呈线性统计关系,并且平均N面体晶粒模型和Poisson-Voronoi组织均支持该结论.不同时刻的晶粒长大仿真数据表明,在准稳态晶粒长大阶段晶粒棱长的分布具有自相似性.个体晶粒的平均棱长随晶粒面数（或晶粒尺寸）的增加而逐渐增大,这说明一些理论模型中采用的“不同面数的晶粒平均棱长均相等”的假设具有局限性.仿真数据和纯铁实验数据均表明,晶粒尺寸与晶粒面数之间的统计关系表现为一条单调递增的凸曲线.关键词：晶粒棱长晶粒尺寸拓扑学Monte Carlo仿真     

Tracer diffusion in the presence of segregating obstacles

Tracer diffusion in an alloy in which the trajectories of one of the species is biased is examined as a model of mass transport with attendant segregation to extended defects (e.g., dynamic strain ageing, grain-boundary segregation). More specifically, we employ Monte Carlo simulation to describe the nonequilibrium diffusive behavior of the components of a two-dimensional lattice gas comprising A and B atoms wherein one of the species (B) interacts with randomly distributed line defects to create equilibrium atmospheres at late times. Various kinetic assumptions and defect densities are explored to highlight the role of B-atom mobility and defect interaction strength on the transport behavior of the A atoms. From the calculated instantaneous diffusivity, several diffusive regimes are then identified and related to evolving segregation profiles and, in particular, to the free area available for diffusion.     

Magnetic Properties of the Infinitely Repulsive Hubbard Model Near Half Filling

Many theoretical works discuss the magnetic properties of the strongly repulsive Hubbard model near half filling. Several authors suggest that the system which contains a few holes does not behave as a ferromagnet, unlike in the one-hole case described by Nagaoka's famous result. We discuss the finite temperature properties of finite lattices. Using an efficient Monte Carlo method magnetic and specific heat results are presented for a 10 by 10 lattice with two holes. Our results show that the magnetization increases with decreasing temperature for such a finite system.     

低能电子在固体表面背散射系数的直接Monte Carlo方法模拟

应用单次碰撞的直接Monte Carlo方法计算能量范围从100 eV~10 keV的电子在固体Al,Si,Au表面的背散射系数,其中低能电子在固体中的弹性散射和非弹性散射截面分别应用Mott散射截面和Born近似下的广义振子强度计算模型得到.通过与压缩历史Monte Carlo方法的模拟计算结果及实验值的比较,结果表明,对于100 eV~10 keV范围的低能区电子,采用直接方法计算得到的电子背散射系数与实验值符合较好,直接方法比压缩历史方法更适合于能量在10 keV以下的电子输运计算.     

不对称钴纳米环磁特性及涡旋态控制的蒙特卡罗模拟

利用Monte Carlo模拟方法研究不同外加磁场方向对不对称钴纳米环磁特性的影响.主要研究磁化反转过程中畴壁运动可控制机制、磁滞回线及涡旋态的形成.模拟结果表明:①不同的外加磁场方向对不对称钴纳米环在磁化反转过程中畴壁的运动和涡旋态的形成及稳定性有较大的影响;②可利用畴壁能的变化及外加磁场的方向控制纳米环畴壁的运动;③磁化反转过程中涡旋态的形成及稳定性存在明显的尺寸效应.     

采用壳层效应屏蔽长度Monte Carlo方法计算溅射产额

使用ACAT模拟程序计算了不同离子碰撞在单原子材料上的溅射产额.采用山村等人提出的考虑壳层效应的理论屏蔽长度,原子间作用势用Moliére势.并将计算结果与实验数据和山村等的经验公式进行了比较.     

低维螺旋磁体纳米条带中磁场驱动的磁结构演变规律

利用蒙特卡洛方法研究了低维螺旋磁体纳米条带中磁场驱动的磁结构演变规律,以及偶极相互作用对螺旋磁体纳米条带中磁结构的影响。研究表明,螺旋磁体纳米条带中的自旋结构由自旋的面内取向平行或垂直于边界的边缘态和中间聚集态两部分构成。在一定范围内增加外磁场,条带边缘平行于边界的自旋排列将增多,最终将在条带外围形成大的磁涡旋环,该涡旋环十分稳定,即使在很强的外磁场下仍然存在。处于条带中间的聚集态随着外磁场的增大,从磁螺旋态逐步过渡到Skyrmions态,最终形成铁磁态。Skyrmions的排列状况与条带尺寸密切相关。此外,偶极相互作用对磁矩平行于边界且首尾顺次连接的排列起积极作用,在无外磁场作用下,随着偶极相互作用的增大,体系终将形成涡旋态。     

“Antiferromagnetism” in social relations and Bonabeau model

We here present a fixed agents version of an original model of the emergence of hierarchies among social agents first introduced by Bonabeau et al. Having interactions occurring on a social network rather than among “walkers” does not drastically alter the dynamics. But it makes social structures more stable and give a clearer picture of the social organisation in a “mixed” regime, where finite ordered domains appear.     

低维螺旋磁体纳米条带中磁场驱动的磁结构演变规律

利用蒙特卡洛方法研究了低维螺旋磁体纳米条带中磁场驱动的磁结构演变规律,以及偶极相互作用对螺旋磁体纳米条带中磁结构的影响。研究表明,螺旋磁体纳米条带中的自旋结构由自旋的面内取向平行或垂直于边界的边缘态和中间聚集态两部分构成。在一定范围内增加外磁场,条带边缘平行于边界的自旋排列将增多,最终将在条带外围形成大的磁涡旋环,该涡旋环十分稳定,即使在很强的外磁场下仍然存在。处于条带中间的聚集态随着外磁场的增大,从磁螺旋态逐步过渡到Skyrmions态,最终形成铁磁态。Skyrmions的排列状况与条带尺寸密切相关。此外,偶极相互作用对磁矩平行于边界且首尾顺次连接的排列起积极作用,在无外磁场作用下,随着偶极相互作用的增大,体系终将形成涡旋态。     

低维螺旋磁体纳米条带中磁场驱动的磁结构演变规律

利用蒙特卡洛方法研究了低维螺旋磁体纳米条带中磁场驱动的磁结构演变规律,以及偶极相互作用对螺旋磁体纳米条带中磁结构的影响.研究表明,螺旋磁体纳米条带中的自旋结构由自旋的面内取向平行或垂直于边界的边缘态和中间聚集态两部分构成.在一定范围内增加外磁场,条带边缘平行于边界的自旋排列将增多,最终将在条带外围形成大的磁涡旋环,该涡旋环十分稳定,即使在很强的外磁场下仍然存在.处于条带中间的聚集态随着外磁场的增大,从磁螺旋态逐步过渡到Skyrmions态,最终形成铁磁态.Skyrmions的排列状况与条带尺寸密切相关.此外,偶极相互作用对磁矩平行于边界且首尾顺次连接的排列起积极作用,在无外磁场作用下,随着偶极相互作用的增大,体系终将形成涡旋态.     

Monte Carlo simulation for temperature dependence of Ga diffusion length on GaAs(0 0 1)

Diffusion length of Ga on the GaAs(0 0 1)-(2×4)β2 is investigated by a newly developed Monte Carlo-based computational method. The new computational method incorporates chemical potential of Ga in the vapor phase and Ga migration potential on the reconstructed surface obtained by ab initio calculations; therefore we can investigate the adsorption, diffusion and desorption kinetics of adsorbate atoms on the surface. The calculated results imply that Ga diffusion length before desorption decreases exponentially with temperature because Ga surface lifetime decreases exponentially. Furthermore, Ga diffusion length L along and [1 1 0] on the GaAs(0 0 1)-(2×4)β2 are estimated to be and L_[110]200 nm, respectively, at the incorporation–desorption transition temperature (T860 K).     

General-purpose event generators for LHC physics

We review the physics basis, main features and use of general-purpose Monte Carlo event generators for the simulation of proton-proton collisions at the Large Hadron Collider. Topics included are: the generation of hard scattering matrix elements for processes of interest, at both leading and next-to-leading QCD perturbative order; their matching to approximate treatments of higher orders based on the showering approximation; the parton and dipole shower formulations; parton distribution functions for event generators; non-perturbative aspects such as soft QCD collisions, the underlying event and diffractive processes; the string and cluster models for hadron formation; the treatment of hadron and tau decays; the inclusion of QED radiation and beyond Standard Model processes. We describe the principal features of the Ariadne, Herwig++, Pythia 8 and Sherpa generators, together with the Rivet and Professor validation and tuning tools, and discuss the physics philosophy behind the proper use of these generators and tools. This review is aimed at phenomenologists wishing to understand better how parton-level predictions are translated into hadron-level events as well as experimentalists seeking a deeper insight into the tools available for signal and background simulation at the LHC.