保持C2连续的一类弧长参数化方法

讨论了C^2参数曲线的弧长参数化。在弧长区间选择性地取若干插值节点，利用原参数曲线的C^2连续性质，构造一类局部性Hermite插值三次样条，反插值参数曲线的弧长函数。所导致的近似弧长参数方程几何上完全描述原参数曲线，且自然地保持C^2连续。近似弧长参数化曲线对于精确弧长参数曲线具有实际应用所期望的逼近性质。     

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.     

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.     

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.     

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.     

Chordal cubic spline interpolation is fourth-order accurate

^** Email: michaelf{at}ifi.uio.no It is well known that complete cubic spline interpolation offunctions with four continuous derivatives is fourth-order accurate.In this paper we show that this kind of interpolation, whenused to construct parametric spline curves through sequencesof points in any space dimension, is again fourth-order accurateif the parameter intervals are chosen by chord length. We alsoshow how such chordal spline interpolants can be used to approximatethe arc-length derivatives of a curve and its length.     

Development and testing of a general amber force field

We describe here a general Amber force field (GAFF) for organic molecules. GAFF is designed to be compatible with existing Amber force fields for proteins and nucleic acids, and has parameters for most organic and pharmaceutical molecules that are composed of H, C, N, O, S, P, and halogens. It uses a simple functional form and a limited number of atom types, but incorporates both empirical and heuristic models to estimate force constants and partial atomic charges. The performance of GAFF in test cases is encouraging. In test I, 74 crystallographic structures were compared to GAFF minimized structures, with a root-mean-square displacement of 0.26 A, which is comparable to that of the Tripos 5.2 force field (0.25 A) and better than those of MMFF 94 and CHARMm (0.47 and 0.44 A, respectively). In test II, gas phase minimizations were performed on 22 nucleic acid base pairs, and the minimized structures and intermolecular energies were compared to MP2/6-31G* results. The RMS of displacements and relative energies were 0.25 A and 1.2 kcal/mol, respectively. These data are comparable to results from Parm99/RESP (0.16 A and 1.18 kcal/mol, respectively), which were parameterized to these base pairs. Test III looked at the relative energies of 71 conformational pairs that were used in development of the Parm99 force field. The RMS error in relative energies (compared to experiment) is about 0.5 kcal/mol. GAFF can be applied to wide range of molecules in an automatic fashion, making it suitable for rational drug design and database searching.     

雷达高度表灵敏度测试系统的参数化设计方法

提出了一种参数化设计方法,实现了雷达高度表接收机灵敏度的自动化测试,提高了接收机灵敏度的测试效率和测试准确度。利用计算机程序通过GPIB协议控制直流稳压电源、信号源、示波器等标准仪器,实现了雷达高度表的加电和断电、雷达回波信号的模拟、雷达高度表输出端信号的检测。针对测试需求,充分考虑接收机灵敏度测试方案的通用性和可扩展性,设计了通用的测试模型,据此开发的软件可自动给出测试结论。在程序中设计了求取灵敏度最优频点和灵敏度的优化迭代算法,节省了测试时间。利用数据库技术对被测雷达高度表相关信息和测试数据进行管理,便于将测试结果与历史数据进行比对。