模拟吸附在狭缝微孔中的丙烷的微观结构

用巨正则系综MonteCarlo（GCEMC）方法模拟了活性碳孔吸附丙烷时的微观结构．在GCEMC模拟中,非极性丙烷分子采用单点LJ球状分子模型,狭缝活性碳孔墙采用10－4-3势能模型．在温度T＝134．3K下,模拟并观察到了丙烷分子在狭缝活性碳孔中的吸附、脱附以及毛细凝聚现象,得到了吸附等温线和孔中流体的局部密度轮廓图．从分子水平出发,详细分析了吸附、毛细冷凝时孔中流体的微观结构,为认识、理解吸附的微观机理提供了工具与借鉴．     

Thermodynamic Methods and Models to Study Flexible Metal–Organic Frameworks

Much attention has recently been focused on a fascinating subclass of metal‐organic frameworks that behave in a remarkable stimuli‐responsive fashion. These soft porous crystals feature dynamic crystalline frameworks displaying reversible, large‐amplitude structural deformations under external physical constraints such as temperature, electric field or gas exposure. The number of reported syntheses of such materials is rapidly growing and they are promising for practical applications, such as gas capture, purification and fluid separation. Herein, we summarize the recently developed thermodynamic tools that can help understand the process of fluid adsorption and fluid mixture coadsorption in these flexible nanoporous materials. These tools, which include both molecular simulation methods and analytical models, can help rationalize experimental results and predict adsorption properties over a wide range of thermodynamic conditions. A particular focus is given on how these methods can guide the experimental exploration of a large number of materials and working conditions (temperature, pressure, composition) to help design efficient processes relying on fluid adsorption in soft porous crystals.     

氢在多壁碳纳米管中的吸附储存

利用巨正则系综蒙特卡罗(GCMC)的方法模拟了氢在多壁碳纳米管中的吸附,氢气分子之间、氢气分子和碳原子之间的相互作用势能采用Lennard-Jones势能模型。模拟了不同结构参数(管内径、管壁数、管壁间距)的多壁碳纳米管在77K和298K下的吸附等温线,分析了多壁碳纳米管的管内径、管壁数以及管壁间距对吸附性能的影响。模拟结果表明:多壁碳纳米管的管壁数和管壁间距对吸附性能的影响较明显;管壁数越少,管壁间距越大,其吸附性能越好;多壁碳纳米管的管内径对其吸附性能的影响甚微。     

近独立子系系统的统计规律(二)——微正则分布函数

从微正则系统理论出发,导出了任意数目粒子构成的近独立子系系统的分布函数,在粒子数N趋于无限大的极限情况下,得到了麦克斯韦分布律.     

Hybrid Monte Carlo with adaptive temperature in mixed-canonical ensemble: Efficient conformational analysis of RNA

A hybrid Monte Carlo method with adaptive temperature choice is presented that exactly generates the distribution of a mixed-canonical ensemble composed of two canonical ensembles at low and high temperature. The analysis of resulting Markov chains with the reweighting technique shows an efficient sampling of the canonical distribution at low temperature whereas the high temperature component facilitates conformational transitions, which allows shorter simulation times. The algorithm is tested by comparing analytical and numerical results for the small n-butane molecule before simulations are performed for a triribonucleotide. Sampling the complex multiminima energy landscape of this small RNA segment, we observe enforced crossing of energy barriers. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1689–1697, 1998     

Directional quantum random walk induced by coherence

Quantum walk (QW), which is considered as the quantum counterpart of the classical random walk (CRW), is actually the quantum extension of CRW from the single-coin interpretation. The sequential unitary evolution engenders correlation between different steps in QW and leads to a non-binomial position distribution. In this paper, we propose an alternative quantum extension of CRW from the ensemble interpretation, named quantum random walk (QRW), where the walker has many unrelated coins, modeled as two-level systems, initially prepared in the same state. We calculate the walker's position distribution in QRW for different initial coin states with the coin operator chosen as Hadamard matrix. In one-dimensional case, the walker's position is the asymmetric binomial distribution. We further demonstrate that in QRW, coherence leads the walker to perform directional movement. For an initially decoherenced coin state, the walker's position distribution is exactly the same as that of CRW. Moreover, we study QRW in 2D lattice, where the coherence plays a more diversified role in the walker's position distribution.     

Canonical and microcanonical ensemble approaches to Bose-Einstein condensation: The thermodynamics of particles in harmonic traps

The thermodynamic properties of bosons moving in a harmonic trap in an arbitrary number of dimensions are investigated in the grand canonical, canonical and microcanonical ensembles by applying combinatorial techniques developed earlier in statistical nuclear fragmentation models. Thermodynamic functions such as the energy and specific heat are computed exactly in these ensembles. The occupation of the ground or condensed state is also obtained exactly, and signals clearly the phase transition. The application of these techniques to fermionic systems is also briefly discussed. Received 18 August 1998 and Received in final form 14 October 1998     

The topological structure of vortex in BEC

We find that there exists an elementary topological current in Bose-Einstein condensation. Based on the -mapping topological current theory, the implicit function theorem and the Taylor expansion, the topological structure of vortex lines is detailed in the neighborhoods of the bifurcation points of the condensate wave function. Received: 9 April 1998 / Revised: 28 August 1998 / Accepted: 31 August 1998     

On the use of mass scaling for stable and efficient simulated tempering with molecular dynamics

Simulated tempering (ST) is a generalized‐ensemble algorithm that employs trajectories exploring a range of temperatures to effectively sample rugged energy landscapes. When implemented using the molecular dynamics method, ST can require the use of short time steps for ensuring the stability of trajectories at high temperatures. To address this shortcoming, a mass‐scaling ST (MSST) method is presented in which the particle mass is scaled in proportion to the temperature. Mass scaling in the MSST method leads to velocity distributions that are independent of temperature and eliminates the need for velocity scaling after the accepted temperature updates that are required in conventional ST simulations. The homogeneity in time scales with changing temperature improves the stability of simulations and allows for the use of longer time steps at high temperatures. As a result, the MSST is found to be more efficient than the standard ST method, particularly for cases in which a large temperature range is employed. © 2016 Wiley Periodicals, Inc.     

Replica exchange with guided annealing for accelerated sampling of disordered protein conformations

We critically examine a recently proposed convective replica exchange (cRE) method for enhanced sampling of protein conformation based on theoretical and numerical analysis. The results demonstrate that cRE and related replica exchange with guided annealing (RE‐GA) schemes lead to unbalanced exchange attempt probabilities and break detailed balance whenever the system undergoes slow conformational transitions (relative to the temperature diffusion timescale). Nonetheless, numerical simulations suggest that approximate canonical ensembles can be generated for systems with small conformational transition barriers. This suggests that RE‐GA maybe suitable for simulating intrinsically disordered proteins, an important class of newly recognized functional proteins. The efficacy of RE‐GA is demonstrated by calculating the conformational ensembles of intrinsically disordered kinase inducible domain protein. The results show that RE‐GA helps the protein to escape nonspecific compact states more efficiently and provides several fold speedups in generating converged and largely correct ensembles compared to the standard temperature RE. © 2014 Wiley Periodicals, Inc.