Linear expansions of correlated functions: Variational Monte Carlo case study

The relative performance of trial wave functions expressed as linear combination of correlated exponentials has been tested on a variety of systems. The results are compared against other correlated functions commonly used in the literature to assess the capabilities of the proposed ansatz. A possible departure from the simple exponential functional form used in previous works is discussed, along with its advantages and drawbacks. We also discuss how to implement an efficient optimization procedure for this correlated basis set. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 74: 23–33, 1999     

Monte Carlo study of three-dimensional organization of water molecules around DNA fragments

Interactions with water molecules are important for the stabilization of three-dimensional structures of nucleic acids and for their functioning. The first hydration shells of macromolecules can be considered as structural parts of nucleic acid. We performed a Monte Carlo study of systems containing a nucleic acid base or base pair with water molecules using improved potential functions. These potential functions enable experimental data on both single base–single water interaction energies and enthalpies of base hydration to be reproduced. Hydration shell structures of base pairs are dependent on the pair geometry. Structural elements of hydration shells can contribute to the pair stability and hence to the probability of mispair formation during nucleic acid biosynthesis. The distribution of water molecules around bases and base pairs is essentially nonhomogeneous.From the Proceedings of the 28th Congreso de Químicos Teóricos de Expresión Latina (QUITEL 2002).     

Protection of nano-powders by adsorbed surfactants: A Monte Carlo study

The production of high-performance ceramics requires the protection of powder particles against chemical reactions. Hydrolysis and oxidation of nanoscaled non-oxidic powders can be impeded by a coating consisting of a dense adsorbed layer of amphiphilic molecules. Using Monte Carlo simulations for a coarse grained model the adsorption equilibrium of differently shaped amphiphiles in apolar and polar solvents is investigated. For estimating the protection capability of the adsorbed surfactant film in aqueous environment we study the diffusion of small hydrophilic particles through the adsorbed surfactant film. The surfactants considered as coating agents differ in the number of hydrocarbon tails. It is found that amphiphiles with a single hydrocarbon tail or at most two branches are more suitable to protect particle surfaces than amphiphiles with three or four branches, although the adsorption energy of amphiphiles with many branches is higher.     

Diffusion Monte Carlo study of correlation in the hydrogen molecule

The diffusion Monte Carlo (DMC) method shows that correlation in H₂ produces a set of three spatial changes: (i) an enhancement in the electron density distribution n( r ) in the left and right anti‐binding regions that include separately the immediate vicinity of each of the two nuclei, (ii) a reduction in n( r ) in the binding region intervening between the two nuclei as a counterbalance, and (iii) a concomitant increase in the equilibrium internuclear separation. It is stressed that the correlation energy E^c (= T^c + V^c) for diatomic molecules be defined by the difference in the total energy between the exact and the Hartree–Fock (HF) variational calculations that are performed at individually optimized internuclear separations. It is this definition that makes it possible to involve a significant contribution from a correlation‐induced change in the equilibrium internuclear separation as part of the correlation energy and to relate (i) and (ii) to (iii) in consistency with the electrostatic theorem. The present calculations fulfill the virial theorem to an accuracy of ?V/T = 2.00 for DMC and ?V^HF/T^HF = 2.000 for HF. The present correlation energy E^c = ?0.0408 hartree is not only in good agreement with the most accurate value previously reported, but also can be analyzed into all its components in accordance with the correlational virial theorem 2T^c + V^c = 0. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

量子Monte Carlo处理激发态

提出了用于电子激发态的剩余函数变分量子ＭｏｎｔｅＣａｒｌｏ（ＳＦＶＭＣ）方法,已经证明：若激发态的初始波函数与基态的初始波函数属于对称性不同的不可约表示时,该激发态的ＳＦＶＭＣ方法与基态的ＳＦＶＭＣ方法完全相同;若激发态的初始波函数与基态的初始波函数有相同的对称性时,只要对激发态的初始波函数作正交性修正,则其态的ＳＦＶＭＣ方法亦可推到该激发态的情况。文章导出了这第二类激发态的ＳＦＶＭＣ方法的详细计     

Optimized Monte Carlo sampling in forward-backward semiclassical dynamics

Forward-backward semiclassical dynamics (FBSD) provides a rigorous and powerful methodology for calculating time correlation functions in condensed phase systems characterized by substantial quantum mechanical effects associated with zero-point motion, quantum dispersion, or identical particle exchange symmetries. The efficiency of these simulations arises from the use of classical trajectories to capture all dynamical information. However, full quantization of the density operator makes these calculations rather expensive compared to fully classical molecular dynamics simulations. This article discusses the convergence properties of various correlation functions and introduces an optimal Monte Carlo sampling scheme that leads to a significant reduction of statistical error. A simple and efficient procedure for normalizing the FBSD results is also discussed. Illustrative examples on model systems are presented.     

用变分Monte Carlo方法处理分子

对变分量子Ｍｏｎｔｅ Ｃａｒｔｏ方法提出了一种种算法：将传统的Ｈａｒｔｒｅｅ－Ｆｏｅｋ方法与量子Ｍｏｎｔｅ Ｃａｒｌｏ方法有机结合在一起；导出了“局部能”的解析式；使用了一种新的相关函数和随机数发生器。我们用这个新算法计算了Ｈ２、ＬｉＨ、Ｌｉ２、Ｈ２Ｏ、Ｆ２分子的基态和ＣＨ２分子的＾３Ｂ１、＾１Ａ１态的能量。计算结果表明，这个新算法在精度和统计误差两个方面比一般ＶＭＣ过程都要好得多。     

变分量子Monte Carlo的一个新算法

提出变分量子MonteCarlo(VMC)计算的新算法-极小化方差(MV)方法.它从局域能的内部结构出发,直接削减其波动以达到将VMC的方差减到极小的目的.给出了局域能的分析表达式,导出VMC的极小方差原理,并建立方差极小化的计算步骤.     

自优化扩散量子Monte Carlo差值法

提出了自优化扩散量子MonteCarlo差值法,这是一个集优化、扩散和相关取样三项技术于一身的MonteCarlo新算法.这个算法能够在扩散过程中直接计算两个体系之间的能量差,且使计算结果的统计误差达到10^-5hartree数量级,获得相关能达80%以上.应用该方法研究分子势能面,使用"刚性移动"模型,利用Jacobi变换使分子两个几何构型的能量计算具有很好的正相关性,因而能得到准确的能量差值和分子势能面.另外,我们还首创了"平衡后留样"技术,可节省50%以上的计算量.该算法还可应用于分子光谱、化学反应能量变化值等领域的研究.     

自优化剩余函数量子Monte Carlo方法

提出剩余函数量子Monte Carlo的一个新算法，这是一个自优化和自改善的过程.与以前的算法相比，本算法中的试探函数的优化是在剩余函数方法中同步进行的，而不是在变分Monte Carlo计算之前.为了优化试探函数，使用一种改进了的速降法，这是一个步长能够自动调节，超线性收敛的优化技术.在这个算法中,还使用了一种新的相关函数，它满足电子与电子以及电子与核奇点条件.此方法已被用于计算H2、LiH、Li2、H2O分子的基态以及CH2的X 3B1态、1 1A1态和2 1A1态的能量值.     

Influence of the presence of small gas molecules in the structure of comblike polyacrylates: a Monte Carlo study

A theoretical strategy has been developed to study the motion of small molecules through ordered polymeric systems. The strategy, which has been incorporated into a computer program denoted MCDP/2, is especially useful to study comblike polymers organized in biphasic arrangements. This is because it is based on a configurational bias Monte Carlo algorithm, which is more efficient than conventional methods to study dense systems. The MCDP/2 program has been used to investigate the influence of CH(4) and CO(2) gas molecules in the structure of isotactic poly(octadecyl acrylate), a typical comblike polymer. For this purpose, the pure polymer and different molecular systems constituted by several gas molecules dissolved in the polymer matrix have been simulated. Results indicated that the structural relaxation of the polymer is not coupled to the motion of gas molecules. The importance of these results in the field of molecular modeling of transport properties in comblike polymers is discussed.     

Quantum Monte Carlo calculations of bond dissociation energies for some nitro and amino molecules

Bond dissociation energies (BDEs) for some nitro or amino contained prototypical molecules in energetic materials are computed by fixed‐node diffusion quantum Monte Carlo method. The nodes are determined from a Slater determinant calculated within density functional theory at the B3LYP/6‐311G** level. The possible errors, the nodal error, and the cancellation of nodal errors in calculating BDE are discussed, and the accuracy is compared with other available ab initio computations and experimental results. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Monte Carlo correction programme for PC

A Monte Carlo correction program for quantitative microanalysis on PC computer is introduced in this paper. The elastic scattering is described by the screened Rutherford cross section. Instead of computing the energy loss according to the actual path between two scatterings we have defined the Bethe inelastic cross section determined by the Bethe-slowing-down approximation. It is assumed that it causes no angular departure of the scattered electron. In the second model we took into account the angular dependence of inelastic scattering assuming that the primary electron interacts with quasi-free atom electrons. On the basis of these two models analytical Monte Carlo programmes were developed and experimentally tested on some oxide glass. Our results are fully comparable to those obtained by ten world microprobe laboratories using classical ZAF correction or Bence-Albee methods. We have found that introducing angular part of the inelastic cross section analytical results did not significantly change. All of our results were carried out for bulk specimens but extending it to layers is under the development.     

Thermodynamic properties of small rare gas clusters by path integral Monte Carlo simulations: a preliminary study

A strategy for reducing the risk of non-ergodic simulations in Monte Carlo calculations of the thermodynamic properties of clusters is discussed with the support of some examples. The results obtained attest the significance of the approach for the low-temperature regime, as non-ergodic sampling of potential energy surfaces is a particularly insidious occurrence. Fourier path integral Monte Carlo techniques for taking into account quantum effects are adopted, in conjunction with suitable tricks for improving the procedure reliability. Applications are restricted to Lennard-Jones clusters of rare-gas systems.     

高分子链形状与尺寸关联的Monte Carlo模拟

运用MonteCarlo方法对线型高分子链格点模型的构型进行了模拟,研究了构型的尺寸(采用平方末端距R²,平方回转半径S²来表征)和形状(由非球形因子A表征)之间的关联.对任何长度的高分子链,其关联系数CA,R²和CA,S²均为正值,表明高分子链的形状与尺寸之间存在正关联,即尺寸小的构型其非球形因子A一般也小,反之尺寸大的构型其非球形因子A一般也大.关联系数CA,R²和CA,S²均随链长的增大而减小,近似地与链长的倒数(n^-1)成正比.研究还表明,关联系数的极限值(链长n很大时)与格点的类型无关,与链样本产生的方式也无关,但与链是否考虑排斥体积有关,考虑了排斥体积后,关联系数增大.     

Monte Carlo study of polyelectrolyte gels

The discontinuous transition between dense and dilute phases in polyelectrolyte gels is observed in Bond-Fluctuation Method Monte Carlo simulations of gels. The transition is driven by the competition between local attractive interactions of a poor-quality solvent and global repulsive interactions from counter-ion pressure. A procedure is introduced that prevents local attractive interactions from destroying ergodicity. Under good solvent conditions, lengths and volumes of gels are found to follow self-avoiding random walk scaling. © 1996 John Wiley & Sons, Inc.     

精确固定节面量子Monte Carlo差值法

提出了精确固定节面量子Monte Carlo差值法, 这个新算法能够在精确固定节面量子Monte Carlo方法的基础上直接计算两个体系之间的能量差, 且使计算结果的统计误差达到10-5 hartree 数量级, 获得电子相关能90%以上. 我们把这个新算法应用于分子势能面的研究中, 使用一个“刚性移动”模型, 利用Jacobi变换使分子两个几何构型的能量计算具有很好的正相关性, 因而能得到准确的能量差值, 由此就可以得到精确的分子势能面.     

蒙特卡洛模拟在分子模拟教学中的应用*

以有机化合物的模板诱导沉积实验为例,介绍了蒙特卡洛模拟在分子模拟教学中的应用。本实验在有机化合物诱导沉积实验的基础上,将诱导沉积实验、蒙特卡洛模拟方法系统综合在一个实验教学中,让学生在学习蒙特卡洛模拟方法的同时,更直观、形象地理解分子间相互作用对有机分子聚集形貌的影响,加深学生对有机分子自组装概念的理解。通过实际上机操作,学生还能初步了解Dev-C++,RasMol等相关软件的使用,并加深学生对结构化学及计算化学课程相关知识的理解。     

Alignment of molecules by the Monte Carlo optimization of molecular similarity indices

3D-QSAR uses statistical techniques to correlate calculated structural properties with target properties like biological activity. The comparison of calculated structural properties is dependent upon the relative orientations of molecules in a given data set. Typically molecules are aligned by performing an overlap of common structural units. This “alignment rule” is adequate for a data set, that is closely related structurally, but is far more difficult to apply to either a diverse data set or on the basis of some structural property other than shape, even for sterically similar molecules. In this work we describe a new algorithm for molecular alignment based upon optimization of molecular similarity indices. We show that this Monte Carlo based algorithm is more effective and robust than other optimizers applied previously to the similarity based alignment problem. We show that QSARs derived using the alignments generated by our algorithm are superior to QSARs derived using the more common alignment of fitting of common structural units. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18 : 1344–1353, 1997