Effect of chemical potential on the computer simulation of hydrogen storage in single walled carbon nanotubes

Hydrogen is a kind of clean, sustainable and renewable energy carrier. Of the problems to be solved for the utilization of hydrogen energy, how to store and transport hydrogen has been given high priority on the research agenda. Recently, carbon nanotubes (CNTs) were reported to be very promising candidates for hydrogen uptake[1], which may have possibility to satisfy the benchmark set by the US Department of Energy (DOE) Hydrogen Plan for fuel cell powered vehicles: a gravimetric density …     

硬木热解过程中颗粒内部二次反应的数值研究Ⅱ.数值模拟结果

为了研究生物质（硬木）热解过程中颗粒内部的二次反应，对流化床环境下单颗粒生物质热解模型进行了求解。计算针对典型大颗粒和典型小颗粒在流化床反应器反应条件下的热解过程，对不同大小颗粒内部各种产物的生成、消耗、积累以及逃逸行为进行了定量描述。计算结果表明：对于直径为2mm的小颗粒，颗粒内二次裂解的份额可以忽略，但是对于直径10mm的大颗粒，热争过程中有超过20%的一次焦油参加了颗粒内部二次反应，颗粒内二次裂解显著地改变了热解产物分布，改变了热解产物的品质。     

Molecular dynamics simulations of cyclosporin A: The crystal structure and dynamic modelling of a structure in apolar solution based on NMR data

Summary The conformation of the immunosuppressive drug cyclosporin A (CPA), both in apolar solution and in crystalline state, has been studied by computer simulation techniques. Three molecular dynamics (MD) simulations have been performed: one modelling the crystal structure and two modelling the structure in apolar solution, using a restrained MD approach in which data from nuclear magnetic resonance (NMR) and infrared (IR) spectroscopy are taken into account. The simulation of the crystalline state (MDC) concerns a system of 4 unit cells containing 16 cyclosporin A molecules and 22 water molecules, which is simulated using crystalline periodic boundary conditions. The simulations modelling the apolar solvent conformation (MDS) concern one isolated cyclosporin A molecule. In these simulations an extra term in the interatomic potential function is used, which forces the molecule to satisfy a set of 57 atom-atom distance constraints originating from nuclear Overhauser effects (NOEs) obtained from NMR spectroscopy and one distance constraint deduced from IR spectroscopy.From a comparison of the results of the crystal simulation to those of the X-ray experiment in terms of structure, atomic fluctuations, hydrogen bond pattern, etc., it is concluded that the force field that is used yields an adequate representation of crystalline cyclosporin A. Secondly, it is shown that the dynamic modelling technique that is used to obtain a structure in a polar solution from NMR distance information works well. Starting from initial conformations which have a root mean square difference of 0.14 nm both distance restrained MD simulations converge to the same final solution structure. A comparison of the crystal structure of cyclosporin A and the one in apolar solution shows that there are significant differences. The overall difference in atomic positions is 0.09 nm for the C_x atoms and 0.17 nm for all atoms. In apolar solution, the molecule is slightly more bent and the side chains of 1 MeBmt and 10 MeLeu adopt a different conformation.Abbreviations MeBmt (4R)-4[(E)-2-butenyl]-4-methyl-l-Threonine - MD Molecular dynamics - EM Energy minimization - MDC Molecular dynamics simulation of the crystal - MDS1 Restrained molecular dynamics simulation to obtain the structure in solution starting from the crystal structure - MDS2 Like MDS1, but starting from the SMS structure - SMS Proposed structure in solution, obtained by model building - XRAY An X-ray structure - CPA Cyclosporin A - NMR Nuclear magnetic resonance spectroscopy - NOE Nuclear Overhauser enhancement - MDS1 Mean simulated structure obtained by averaging over the time period 20–40 ps of the MDS1 simulation - MDS2 Mean simulated structure obtained by averaging over the time period 10–30 ps of the MDS2 simulation - Mean simulated structure obtained by averaging over the time period 7–15 ps and over the 16 asymmetric units in the computational box of the MDC simulation.     

Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods

A challenge in free energy calculation for complex molecular systems by computer simulation is to obtain a reliable estimate within feasible computational time. In this study, we suggest an answer to this challenge by exploring a simple method, overlap sampling (OS), for producing reliable free-energy results in an efficient way. The formalism of the OS method is based on ensuring sampling of important overlapping phase space during perturbation calculations. This technique samples both forward and reverse free energy perturbation (FEP) to improve the free-energy calculation. It considers the asymmetry of the FEP calculation and features an ability to optimize both the precision and the accuracy of the measurement without affecting the simulation process itself. The OS method is tested at two optimization levels: no optimization (simple OS), and full optimization (equivalent to Bennett's method), and compared to conventional FEP techniques, including the widely used direct FEP averaging method, on three alchemical mutation systems: (a) an anion transformation in water solution, (b) mutation between methanol and ethane, and (c) alchemical change of an adenosine molecule. It is consistently shown that the reliability of free-energy estimates can be greatly improved using the OS techniques at both optimization levels, while the performance of Bennett's method is particularly striking. In addition, the efficiency of a calculation can be significantly improved because the method is able to (a) converge to the right answer quickly, and (b) work for large perturbations. The basic two-stage OS method can be extended to admit additional stages, if needed. We suggest that the OS method can be used as a general perturbation technique for computing free energy differences in molecular simulations.     

Evaluation of the use of consensus values in proficiency testing programmes

Proficiency testing (PT) is an essential tool used by laboratory accreditation bodies to assess the competency of laboratories. Because of limited resources of PT providers or for other reasons, the assigned reference value used in the calculation of z-score values has usually been derived from some sort of consensus value obtained by central tendency estimators such as the arithmetic mean or robust mean. However, if the assigned reference value deviates significantly from the ‘true value’ of the analyte in the test material, laboratories’ performance will be evaluated incorrectly. This paper evaluates the use of consensus values in proficiency testing programmes using the Monte Carlo simulation technique. The results indicated that the deviation of the assigned value from the true value could be as large as 40%, depending on the parameters of the proficiency testing programmes under investigation such as sample homogeneity, number of participant laboratories, concentration level, method precision and laboratory bias. To study how these parameters affect the degree of discrepancy between the consensus value and the true value, a fractional factorial design was also applied. The findings indicate that the number of participating laboratories and the distribution of laboratory bias were the prime two factors affecting the deviation of the consensus value from the true value.     

盐酸拓扑替康与人血清白蛋白的相互作用及分子模拟

用荧光光谱法、分光光度法研究了盐酸拓扑替康(topotecan hydrochloride, 简记为THC)与人血清白蛋白(human serum albumins, HSA)的相互结合反应. 计算了反应的结合常数、结合位点数和热力学常数. 盐酸拓扑替康在人血清白蛋白上的结合位置与色氨酸残基间的距离为3.63 nm. 分子模型研究表明, 盐酸拓扑替康与人血清白蛋白的亚结构域IIA结合, 二者间的作用力主要为疏水作用, 此外, 蛋白质的丙氨酸(Ala-291)残基和天冬氨酸(Asp-256)残基与盐酸拓扑替康之间还存在氢键作用力.     

Topologies of capillary condensation

Calculations are presented to illustrate the dependence of capillary adsorption upon the interactions present in model pores. The sequence of phase transitions at zero temperature is determined for a Lennard-Jones lattice gas in a pore consisting of 4 × 4 × sites. The dependence of the specific filling sequence upon the comparative strength of the gas-pore wall and the gas-gas interaction well-depths is determined. Grand canonical Monte Carlo simulations of sorption at finite temperature in the continuum version of the same model pore are also reported. Both the theory and the simulations were performed with variable gas-solid and gas-gas energy well-depths. At a temperature of 90 K, the gas-solid heterogeneity associated with atoms adsorbed in the corners, on the walls and in the interior pore volume gives rise to sequential adsorption similar to that observed in the lattice gas calculation at 0 K. A gradual approach to non-wetting behavior is observed as the gas-solid well-depth decreases. Values of the gas-solid well-depth needed to produce pore filling at saturation (i.e., pore-wetting) are discussed.     

MONTE CARLO SIMULATION OF TRIBLOCK COPOLYMER/HOMOPOLYMER BLEND FILMS

1. INTRODUCTION The extensive applications of block copolymer have been studied in detail due to their special molecular architecture and characteristic [1,2]. Recently, many studies including theoretical analysis and experimental techniques have addressed the polymer blend system of diblock copolymer/homopolymer [3~9]. An early investigation presented a quantitative analysis of homopolymer distributions in well-ordered copolymer microdomains through mixing polystyrene (PS) or poly methyl…     

Energy decomposition in molecular complexes: implications for the treatment of polarization in molecular simulations

This study examines the contribution of electrostatic and polarization to the interaction energy in a variety of molecular complexes. The results obtained from the Kitaura-Morokuma (KM) energy decomposition analysis at the HF/6-31G(d) level indicate that, for intermolecular distances around the equilibrium geometries, the polarization energy can be determined as the addition of the polarization energies of interacting blocks, as the mixed polarization term is typically negligible. Comparison of KM and QM/MM results shows that the electrostatic energy determined in the KM method is underestimated (in absolute value) by QM/MM methods. The reason of such underestimation can be attributed to the simplified representation of treating the interaction between overlapping charge distribution by the interaction of a QM molecule with a set of point charges. Nevertheless, the polarization energies calculated by KM and QM/MM methods are in close agreement. Finally, a consistent, automated strategy to derive charge distributions that include implicitly polarization effects in pairwise, additive force fields is presented. The strategy relies in the simultaneous fitting of electrostatic and polarization energies computed by placing a suitable perturbing particle at selected points around the molecule. The suitability of these charges to describe molecular interactions is discussed.     

Chemical shift driven geometry optimization

A new method for refinement of 3D molecular structures by geometry optimization is presented. Prerequisites are a force field and a very fast procedure for the calculation of chemical shifts in every step of optimization. To the energy, provided by the force field (COSMOS force field), a pseudoenergy, depending on the difference between experimental and calculated chemical shifts, is added. In addition to the energy gradients, pseudoforces are computed. This requires the derivatives of the chemical shifts with respect to the coordinates. The pseudoforces are analytically derived from the integral expressions of the bond polarization theory. Single chemical shift values attributed to corresponding atoms are considered for structural correction. As a first example, this method is applied for proton position refinement of the D-mannitol X-ray structure. A crystal structure refinement with 13C chemical shift pseudoforces is carried out.