Interweaving Markov Chain Monte Carlo Strategies for Efficient Estimation of Dynamic Linear Models

In dynamic linear models (DLMs) with unknown fixed parameters, a standard Markov chain Monte Carlo (MCMC) sampling strategy is to alternate sampling of latent states conditional on fixed parameters and sampling of fixed parameters conditional on latent states. In some regions of the parameter space, this standard data augmentation (DA) algorithm can be inefficient. To improve efficiency, we apply the interweaving strategies of Yu and Meng to DLMs. For this, we introduce three novel alternative DAs for DLMs: the scaled errors, wrongly scaled errors, and wrongly scaled disturbances. With the latent states and the less well known scaled disturbances, this yields five unique DAs to employ in MCMC algorithms. Each DA implies a unique MCMC sampling strategy and they can be combined into interweaving and alternating strategies that improve MCMC efficiency. We assess these strategies using the local level model and demonstrate that several strategies improve efficiency relative to the standard approach and the most efficient strategy interweaves the scaled errors and scaled disturbances. Supplementary materials are available online for this article.     

Improving the Q2MM method for transition state force field modeling

The Quantum‐to‐molecular mechanics method (Q2MM) for converting quantum mechanical transition states (TSs) to molecular mechanical minima has been modified to allow a fit to the “natural” reaction mode eigenvalue. The resulting force field gives an improved representation of the energy curvature at the TS, but can potentially give false responses to steric interactions. Ways to address this problem while staying close to the “natural” TS force field are discussed. © 2014 Wiley Periodicals, Inc.     

基于特征正交分解的材料微结构参数化表征模型及等效性能优化设计

随着计算能力的不断发展,近年来基于材料微结构图像的材料等效性能数值模拟越来越受到学者们的重视.在此背景下,提出了一种针对材料微结构图像的高效参数化表征模型.通过特征正交分解(proper orthogonal decomposition,POD)对已有材料微结构图像数据进行特征分析,得到近似描述该类材料微结构的特征缩减基.应用移动最小二乘(moving least squares,MLS)法建立特征缩减基映射系数的响应面模型,拟合得到任意给定参量相应的缩减基映射系数.利用拟合缩减基系数可获得任意给定参量对应的微结构图像矩阵.该参数化表征模型被用于表征含椭球夹杂的两相材料(2-phase composite)的二维情形, 并进一步应用于这类复合材料宏观等效力学性能的优化设计.     

A systematic approach to calibrate a transferable polarizable force field parameter set for primary alcohols

In this work, parameters are optimized for a charge‐on‐spring based polarizable force field for linear alcohols. We show that parameter transferability can be obtained using a systematic approach in which the effects of parameter changes on physico‐chemical properties calculated from simulation are predicted. Our previously described QM/MM calculations are used to attribute condensed‐phase polarizabilities, and starting from the non‐polarizable GROMOS 53A5/53A6 parameter set, van der Waals and Coulomb interaction parameters are optimized to reproduce pure‐liquid (thermodynamic, dielectric, and transport) properties, as well as hydration free energies. For a large set of models, which were obtained by combining small perturbations of 10 distinct parameters, values for pure‐liquid properties of the series methanol to butanol were close to experiment. From this large set of models, we selected 34 models without special repulsive van der Waals parameters to distinguish between hydrogen‐bonding and non‐hydrogen‐bonding atom pairs, to make the force field simple and transparent. © 2017 Wiley Periodicals, Inc.     

Force-field development and molecular dynamics simulations of ferrocene-peptide conjugates as a scaffold for hydrogenase mimics

The increasing importance of hydrogenase enzymes in the new energy research field has led us to examine the structure and dynamics of potential hydrogenase mimics, based on a ferrocene-peptide scaffold, using molecular dynamics (MD) simulations. To enable this MD study, a molecular mechanics force field for ferrocene-bearing peptides was developed and implemented in the CHARMM simulation package, thus extending the usefulness of the package into peptide-bioorganometallic chemistry. Using the automated frequency-matching method (AFMM), optimized intramolecular force-field parameters were generated through quantum chemical reference normal modes. The partial charges for ferrocene were derived by fitting point charges to quantum-chemically computed electrostatic potentials. The force field was tested against experimental X-ray crystal structures of dipeptide derivatives of ferrocene-1,1'-dicarboxylic acid. The calculations reproduce accurately the molecular geometries, including the characteristic C2-symmetrical intramolecular hydrogen-bonding pattern, that were stable over 0.1 micros MD simulations. The crystal packing properties of ferrocene-1-(D)alanine-(D)proline-1'-(D)alanine-(D)proline were also accurately reproduced. The lattice parameters of this crystal were conserved during a 0.1 micros MD simulation and match the experimental values almost exactly. Simulations of the peptides in dichloromethane are also in good agreement with experimental NMR and circular dichroism (CD) data in solution. The developed force field was used to perform MD simulations on novel, as yet unsynthesized peptide fragments that surround the active site of [Ni-Fe] hydrogenase. The results of this simulation lead us to propose an improved design for synthetic peptide-based hydrogenase models. The presented MD simulation results of metallocenes thereby provide a convincing validation of our proposal to use ferrocene-peptides as minimal enzyme mimics.     

基于物理的变形曲线在结构形状优化中的应用

用各向异性模型定义NURBS曲线的变形能,基于所提出的变形能模型,用有限元法对NURBS曲线表达的设计边界进行模态计算,然后,将设计边界用模态向量的线性组合参数化表示。将这种基于边界特征向量的几何形状表示方法应用于优化参数定义．提出了一种适用于结构形状优化的自适应几何精化方法,它有效地将户型有限元分析、优化方法和设计边界的形状表达集成在一起。     

MCMC Estimation of Restricted Covariance Matrices

This article is motivated by the difficulty of applying standard simulation techniques when identification constraints or theoretical considerations induce covariance restrictions in multivariate models. To deal with this difficulty, we build upon a decomposition of positive definite matrices and show that it leads to straightforward Markov chain Monte Carlo samplers for restricted covariance matrices. We introduce the approach by reviewing results for multivariate Gaussian models without restrictions, where standard conjugate priors on the elements of the decomposition induce the usual Wishart distribution on the precision matrix and vice versa. The unrestricted case provides guidance for constructing efficient Metropolis–Hastings and accept-reject Metropolis–Hastings samplers in more complex settings, and we describe in detail how simulation can be performed under several important constraints. The proposed approach is illustrated in a simulation study and two applications in economics. Supplemental materials for this article (appendixes, data, and computer code) are available online.     

半干旱草原下垫面动量和感热总体输送系数参数化关系研究

本文利用锡林郭勒草原2008年春季近地层涡旋相关系统和铁塔的风、 温平均梯度观测资料, 分析了总体输送系数随梯度Richardson数的变化特征, 建立了动量总体输送系数随大气稳定度、近地层风速以及感热总体输送系数随大气稳定度和近地层气温的关系. 中性条件下, 半干旱草原植被下垫面动量总体输送系数与近地层大气动力状态之间存在明显的相互作用, 总体输送系数与近地面层风速之间满足二次曲线拟合关系; 风速较小时, 大气动力特征对地表粗糙度长度的改变不是很明显, 动量总体输送系数随气流增强而增大; 而当风速较大时, 强风速会使植被高度发生改变, 动量总体输送系数随气流增强而减小. 另外, 感热总体输送系数与近地层气温之间也存在二次曲线关系. 动量总体输送系数与近地层风速之间的关系、感热总体输送系数与近地层气温之间关系的建立为总体输送系数参数化提供了重要途径, 同时该方案避免了对动力学粗糙度长度和热力学粗糙度长度的求解. 关键词： 总体输送系数 参数化 湍流通量 相似性函数     

MATCH: an atom-typing toolset for molecular mechanics force fields

We introduce a toolset of program libraries collectively titled multipurpose atom-typer for CHARMM (MATCH) for the automated assignment of atom types and force field parameters for molecular mechanics simulation of organic molecules. The toolset includes utilities for the conversion of multiple chemical structure file formats into a molecular graph. A general chemical pattern-matching engine using this graph has been implemented whereby assignment of molecular mechanics atom types, charges, and force field parameters are achieved by comparison against a customizable list of chemical fragments. While initially designed to complement the CHARMM simulation package and force fields by generating the necessary input topology and atom-type data files, MATCH can be expanded to any force field and program, and has core functionality that makes it extendable to other applications such as fragment-based property prediction. In this work, we demonstrate the accurate construction of atomic parameters of molecules within each force field included in CHARMM36 through exhaustive cross validation studies illustrating that bond charge increment rules derived from one force field can be transferred to another. In addition, using leave-one-out substitution it is shown that it is also possible to substitute missing intra and intermolecular parameters with ones included in a force field to complete the parameterization of novel molecules. Finally, to demonstrate the robustness of MATCH and the coverage of chemical space offered by the recent CHARMM general force field (Vanommeslaeghe, et al., J Comput Chem 2010, 31, 671), one million molecules from the PubChem database of small molecules are typed, parameterized, and minimized.