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Validation of polarizable force field parameters for nucleic acids by inter-molecular interactions

Liaoran Cao,Hong Ren,Jing Miao,Wei Guo,Yan Li,Guohui Li

《化学科学与工程前沿（英文）》 2016年第10卷第2期页码 203-212 doi: 10.1007/s11705-016-1572-4

摘要： Modeling structural and thermodynamic properties of nucleic acids has long been a challenge in the development of force fields. Polarizable force fields are a new generation of potential functions to take charge redistribution and induced dipole into account, and have been proved to be reliable to model small molecules, polypeptides and proteins, but their use on nucleic acids is still rather limited. In this article, the interactions between nucleic acids and a small molecule or ion were modeled by AMOEBAbio09, a modern polarizable force field, and conventional non-polarizable AMBER99sb and CHARMM36 force fields. The resulting intermolecular interaction energies were compared with those calculated by ab initio quantum mechanics methods. Although the test is not sufficient to prove the reliability of the polarizable force field, the results at least validate its capability in modeling energetics of static configurations, which is one basic component in force field parameterization.

关键词： nucleic acid polarizable force field AMOEBA

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mechanisms in the cathode-electrolyte interface layer of lithium manganese oxide batteries from reactive forcefield (ReaxFF) based molecular dynamics

Sahithya REDDIVARI, Christian LASTOSKIE, Ruofei WU, Junliang ZHANG

《能源前沿（英文）》 2017年第11卷第3期页码 365-373 doi: 10.1007/s11708-017-0500-8

摘要： Lithium manganese oxide (LiMn O ) is a principal cathode material for high power and high energy density electrochemical storage on account of its low cost, non-toxicity, and ease of preparation relative to other cathode materials. However, there are well-documented problems with capacity fade of lithium ion batteries containing LiMn O . Experimental observations indicate that the manganese content of the electrolyte increases as an electrochemical cell containing LiMn O ages, suggesting that active material loss by dissolution of divalent manganese from the LiMn O surface is the primary reason for reduced cell life in LiMn O batteries. To improve the retention of manganese in the active material, it is key to understand the reactions that occur at the cathode surface. Although a thin layer of electrolyte decomposition products is known to form at the cathode surface, the speciation and reaction mechanisms of Mn in this interface layer are not yet well understood. To bridge this knowledge gap, reactive force field (ReaxFF) based molecular dynamics was applied to investigate the reactions occurring at the LiMn O cathode surface and the mechanisms that lead to manganese dissolution. The ReaxFFMD simulations reveal that the cathode-electrolyte interface layer is composed of oxidation products of electrolyte solvent molecules including aldehydes, esters, alcohols, polycarbonates, and organic radicals. The oxidation reaction pathways for the electrolyte solvent molecules involve the formation of surface hydroxyl species that react with exposed manganese atoms on the cathode surface. The presence of hydrogen fluoride (HF) induces formation of inorganic metal fluorides and surface hydroxyl species. Reaction products predicted by ReaxFF-based MD are in agreement with experimentally identified cathode-electrolyte interface compounds. An overall cathode-electrolyte interface reaction scheme is proposed based on the molecular simulation results.

关键词： lithium manganese oxide batteries reactive force field (ReaxFF) cathode-electrolyte interface layer molecular dynamics

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论零点振动能与Casimir力

黄志洵

《中国工程科学》 2008年第10卷第5期页码 63-69

摘要：

在真空中放置一对平行的金属板（间距很小），两板会由于一个微弱（可测出）的力而有相互靠近的趋势。这种Casimir效应可用量子理论中的零点能（ZPE）解释。科学家们都认为Casimir力存在，但对其产生的原因却有不同看法。空虚空间是否具有能量，其答案或许将决定宇宙的命运。在自然界和人类实验室中，有许多异常现象可用Casimir效应及挠场理论作出说明。

关键词：零点能零点场真空能 Casimir力挠场理论

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Development, applications and challenges of ReaxFF reactive force field in molecular simulations

You Han, Dandan Jiang, Jinli Zhang, Wei Li, Zhongxue Gan, Junjie Gu

《化学科学与工程前沿（英文）》 2016年第10卷第1期页码 16-38 doi: 10.1007/s11705-015-1545-z

摘要： As an advanced and new technology in molecular simulation fields, ReaxFF reactive force field has been developed and widely applied during the last two decades. ReaxFF bridges the gap between quantum chemistry (QC) and non-reactive empirical force field based molecular simulation methods, and aims to provide a transferable potential which can describe many chemical reactions with bond formation and breaking. This review presents an overview of the development and applications of ReaxFF reactive force field in the fields of reaction processes, biology and materials, including (1) the mechanism studies of organic reactions under extreme conditions (like high temperatures and pressures) related with high-energy materials, hydrocarbons and coals, (2) the structural properties of nanomaterials such as graphene oxides, carbon nanotubes, silicon nanowires and metal nanoparticles, (3) interfacial interactions of solid-solid, solid-liquid and biological/inorganic surfaces, (4) the catalytic mechanisms of many types of metals and metal oxides, and (5) electrochemical mechanisms of fuel cells and lithium batteries. The limitations and challenges of ReaxFF reactive force field are also mentioned in this review, which will shed light on its future applications to a wider range of chemical environments.

关键词： ReaxFF reaction mechanism nanomaterials interfacial interaction catalyst fuel cell

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基于变形力监测数据的残余应力场推断和表征方法

赵智伟, 刘长青, 李迎光, James Gao

《工程（英文）》 2023年第22卷第3期页码 49-59 doi: 10.1016/j.eng.2022.07.018

摘要：

残余应力是材料的基本属性之一，与零件的几何/尺寸稳定性和疲劳寿命直接相关。针对具有高精度要求的大型零件，其残余应力场的准确测量和预测一直是一个挑战。目前的残余应力场测量技术分为基于应变的有损法以及效率和精度较低的无损法。本文提出了一种基于变形力推断残余应力场的无损法。本方法通过能够反映去除材料后不平衡残余应力场整体效应的变形力来推断零件的残余应力场。利用虚功原理建立了变形力与残余应力场之间的力学关系，并引入正则化方法求解残余应力场。为验证方法的有效性，本文进行了理论验证和实际实验验证。实验结果表明，该方法对于大型结构件的残余应力场测量具有可靠的精度和灵活性。在数字化和智能制造的趋势下，该方法的基本原理为利用加工监测数据预测和补偿由残余应力引起的零件加工变形提供了重要参考。

关键词：残余应力场精密加工变形力反问题在位测量

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Review: Tip-based vibrational spectroscopy for nanoscale analysis of emerging energy materials

Amun JARZEMBSKI, Cedric SHASKEY, Keunhan PARK

《能源前沿（英文）》 2018年第12卷第1期页码 43-71 doi: 10.1007/s11708-018-0524-8

摘要： Vibrational spectroscopy is one of the key instrumentations that provide non-invasive investigation of structural and chemical composition for both organic and inorganic materials. However, diffraction of light fundamentally limits the spatial resolution of far-field vibrational spectroscopy to roughly half the wavelength. In this article, we thoroughly review the integration of atomic force microscopy (AFM) with vibrational spectroscopy to enable the nanoscale characterization of emerging energy materials, which has not been possible with far-field optical techniques. The discussed methods utilize the AFM tip as a nanoscopic tool to extract spatially resolved electronic or molecular vibrational resonance spectra of a sample illuminated by a visible or infrared (IR) light source. The absorption of light by electrons or individual functional groups within molecules leads to changes in the sample’s thermal response, optical scattering, and atomic force interactions, all of which can be readily probed by an AFM tip. For example, photothermal induced resonance (PTIR) spectroscopy methods measure a sample’s local thermal expansion or temperature rise. Therefore, they use the AFM tip as a thermal detector to directly relate absorbed IR light to the thermal response of a sample. Optical scattering methods based on scanning near-field optical microscopy (SNOM) correlate the spectrum of scattered near-field light with molecular vibrational modes. More recently, photo-induced force microscopy (PiFM) has been developed to measure the change of the optical force gradient due to the light absorption by molecular vibrational resonances using AFM’s superb sensitivity in detecting tip-sample force interactions. Such recent efforts successfully breech the diffraction limit of light to provide nanoscale spatial resolution of vibrational spectroscopy, which will become a critical technique for characterizing novel energy materials.

关键词： vibrational spectroscopy atomic force microscopy photo-thermal induced resonance scanning near-field optical microscopy tip-enhanced Raman spectroscopy photo-induced force microscopy molecular resonances surface phonon polaritons energy materials

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Modeling limit force capacities of high force to volume lead extrusion dampers

《结构与土木工程前沿（英文）》 2021年第15卷第3期页码 609-622 doi: 10.1007/s11709-021-0724-x

摘要： Lead extrusion dampers are supplemental energy-dissipation devices that are used to mitigate seismic structural damage. Small volumetric sizes and high force capacities define high-force-to-volume (HF2V) devices, which can absorb significant response energy without sacrificial damage. However, the design of such devices for specific force capacities has proven difficult based on the complexities of their internal reaction mechanisms, leading to the adoption of empirical approaches. This study developed upper- and lower-bound force capacity estimates from analytical mechanics based on direct and indirect metal extrusion for guiding design. The derived equations are strictly functions of HF2V device geometric parameters, lead material properties, and extrusion mechanics. The upper-bound estimates from direct and indirect extrusion are denoted as (F_UB,1, F_UB,2) and (F_UB,3, F_UB,4), respectively, and the lower-bound estimates are denoted as (F_LB, F_LB,1) based on the combination of extrusion and friction forces. The proposed models were validated by comparing the predicted bounds to experimental force capacity data from 15 experimental HF2V device tests. The experimental device forces all lie above the lower-bound estimates (F_LB, F_LB,1) and below the upper-bound estimates (F_UB,1, F_UB,2, F_UB,4). Overall, the (F_LB, F_UB,2) pair provides wider bounds and the (F_LB,1, F_UB,4/F_UB,1) pair provides narrower bounds. The (F_LB,1, F_UB,1) pair has a mean lower-bound gap of 36%, meaning the lower bound was 74% of the actual device force on average. The mean upper-bound gap was 33%. The bulge area and cylinder diameter of HF2V devices are key parameters affecting device forces. These relatively tight bounds provide useful mechanics-based predictive design guides for ensuring that device forces are within the targeted design range after manufacturing.

关键词： extrusion lead dampers upper and lower bound analytical modelling limit force

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Review of pantograph and catenary interaction

Weihua ZHANG, Dong ZOU, Mengying TAN, Ning ZHOU, Ruiping LI, Guiming MEI

《机械工程前沿（英文）》 2018年第13卷第2期页码 311-322 doi: 10.1007/s11465-018-0494-x

摘要：

The application of electrified railway directly promotes relevant studies on pantograph-catenary interaction. With the increase of train running speed, the operating conditions for pantograph and catenary have become increasingly complex. This paper reviews the related achievements contributed by groups and institutions around the world. This article specifically focuses on three aspects: The dynamic characteristics of the pantograph and catenary components, the systems’ dynamic properties, and the environmental influences on the pantograph-catenary interaction. In accordance with the existing studies, future research may prioritize the task of identifying the mechanism of contact force variation. This kind of study can be carried out by simplifying the pantograph-catenary interaction into a moving load problem and utilizing the theory of matching mechanical impedance. In addition, developing a computational platform that accommodates environmental interferences and multi-field coupling effects is necessary in order to further explore applications based on fundamental studies.

关键词： electrified railway pantograph and catenary interaction contact force variation moving load problem mechanical impedance multi-field

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静电力驱动的悬臂梁微型电场传感器件 Article

韩志飞, 胡军, 李立浧, 何金良

《工程（英文）》 2023年第24卷第5期页码 184-191 doi: 10.1016/j.eng.2022.06.017

摘要：

随着智能电网和能源互联网的发展，大规模实时电压/电场监测成为电力系统的迫切需求，这依赖于先进传感器件的大规模布置。电场测量在电力系统中具有重要意义。一方面，基于电场测量的电压反演可以实现高电压的非接触式测量，替代传统高压互感器，从而减少测量设备绝缘成本和安装难度；另一方面，电场测量还可以被应用于设备故障诊断、雷电预警、电磁环境测量等应用场景。传统的电场测量设备，如场磨等，往往体积大、成本高，无法大规模灵活布置。本文提出了一种静电力驱动的压阻式微型电场传感器。传感器被设计为四悬臂结构，悬臂在静电力的驱动下产生位移和应变，通过压阻材料转化为可测信
号。所提出的传感器具有尺寸小、成本低、功耗低、易于批量生产的优点。同时，该传感器还具有高信噪比、高分辨率及宽电场测量范围的特点。实验结果表明，所提出的传感器具有1.1~1100.0 kV·m⁻¹的线性测量范围、112 V·m⁻¹·Hz^−1/2的交流电场分辨率以及496 Hz的截止频率。这一微型电场传感器将在智能电网及能源互联网中具有广泛的应用价值。

关键词：微型传感器电气传感器件微加工工艺压阻器件

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Quality control based on electrode displacement and force in resistance spot welding

Chuntao JI, Lipeng DENG

《机械工程前沿（英文）》 2010年第5卷第4期页码 412-417 doi: 10.1007/s11465-010-0114-x

摘要： The behaviors of electrode displacement and force during spot welding under various conditions, such as different weld currents, electrode forces, and welding times, were studied. Tests were conducted on a 170?kVA MFDC spot welder. Data were collected via a multichannel high-speed data acquisition system and were analyzed with MATLAB. Behaviors of 5182 aluminum and mild steel in spot welding were compared. Results show that nugget expansion rate does not reach zero for aluminium as it does for mild steel as nugget grew to a certain size. A linear relationship is found between the nugget size and maximum expansion that facilitates online weld quality evaluation. An electrode force peak is observed and believed relevant to the sufficient nugget size.

关键词： aluminum electrode displacement electrode force nugget size data acquisition

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Visualization of force networks in 2D dense granular materials

Jianguo LIU, Qicheng SUN, Feng JIN,

《结构与土木工程前沿（英文）》 2010年第4卷第1期页码 109-115 doi: 10.1007/s11709-010-0003-8

摘要： Dense granular matter is a conglomeration of discrete solid and closely packed particles. As subjected to external loadings, the stress is largely transmitted by heavily stressed chains of particles forming a sparse network of larger contact forces. To understand the structure and evolution of force chains, a photoelastic technique was improved for determining stresses and strains in the assemblies of photoelastic granular disks in this paper. A two-dimensional vertical slab was designed. It contains 7200 polydispersed photoelastic disks and is subjected to a localized probe penetrating at the top of the slab to mimic the cone penetration test. The interparticle contact force distribution was found a peak around the mean value, a roughly exponential tail for greater force and a dip toward zero for smaller force. The force chain network around the probe tip was depicted, and the contact angle distribution of particles in force chains was found to be well aligned in the directions of major principal stress.

关键词： granular matter force chain multiscale modeling

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Motion/force transmission indices of parallel manipulators

Xinjun LIU, Chao WU, Fugui XIE

《机械工程前沿（英文）》 2011年第6卷第1期页码 89-91 doi: 10.1007/s11465-011-0215-1

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Applications of atomic force microscopy in immunology

Jiping Li, Yuying Liu, Yidong Yuan, Bo Huang

《医学前沿（英文）》 2021年第15卷第1期页码 43-52 doi: 10.1007/s11684-020-0769-6

摘要： Cellular mechanics, a major regulating factor of cellular architecture and biological functions, responds to intrinsic stresses and extrinsic forces exerted by other cells and the extracellular matrix in the microenvironment. Cellular mechanics also acts as a fundamental mediator in complicated immune responses, such as cell migration, immune cell activation, and pathogen clearance. The principle of atomic force microscopy (AFM) and its three running modes are introduced for the mechanical characterization of living cells. The peak force tapping mode provides the most delicate and desirable virtues to collect high-resolution images of morphology and force curves. For a concrete description of AFM capabilities, three AFM applications are discussed. These applications include the dynamic progress of a neutrophil-extracellular-trap release by neutrophils, the immunological functions of macrophages, and the membrane pore formation mediated by perforin, streptolysin O, gasdermin D, or membrane attack complex.

关键词： cellular mechanics atomic force microscopy neutrophil extracellular trap macrophage phagocytosis pore formation

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Non-convex sparse optimization-based impact force identification with limited vibration measurements

《机械工程前沿（英文）》 2023年第18卷第3期 doi: 10.1007/s11465-023-0762-2

摘要： Impact force identification is important for structure health monitoring especially in applications involving composite structures. Different from the traditional direct measurement method, the impact force identification technique is more cost effective and feasible because it only requires a few sensors to capture the system response and infer the information about the applied forces. This technique enables the acquisition of impact locations and time histories of forces, aiding in the rapid assessment of potentially damaged areas and the extent of the damage. As a typical inverse problem, impact force reconstruction and localization is a challenging task, which has led to the development of numerous methods aimed at obtaining stable solutions. The classical

ℓ 2

regularization method often struggles to generate sparse solutions. When solving the under-determined problem,

ℓ 2

regularization often identifies false forces in non-loaded regions, interfering with the accurate identification of the true impact locations. The popular

ℓ 1

sparse regularization, while promoting sparsity, underestimates the amplitude of impact forces, resulting in biased estimations. To alleviate such limitations, a novel non-convex sparse regularization method that uses the non-convex

ℓ 1 − 2

penalty, which is the difference of the

ℓ 1

and

ℓ 2

norms, as a regularizer, is proposed in this paper. The principle of alternating direction method of multipliers (ADMM) is introduced to tackle the non-convex model by facilitating the decomposition of the complex original problem into easily solvable subproblems. The proposed method named

ℓ 1 − 2 -ADMM

is applied to solve the impact force identification problem with unknown force locations, which can realize simultaneous impact localization and time history reconstruction with an under-determined, sparse sensor configuration. Simulations and experiments are performed on a composite plate to verify the identification accuracy and robustness with respect to the noise of the

ℓ 1 − 2 -ADMM

method. Results indicate that compared with other existing regularization methods, the

ℓ 1 − 2 -ADMM

method can simultaneously reconstruct and localize impact forces more accurately, facilitating sparser solutions, and yielding more accurate results.

关键词： impact force identification inverse problem sparse regularization under-determined condition alternating direction method of multipliers

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基于自解耦三明治结构的横向运动栅场效应晶体管微机电系统微力传感器 Article

高文迪, 乔智霞, 韩香广, 王小章, Adnan Shakoor, 刘存朗, 卢德江, 杨萍, 赵立波, 王永录, 王久洪, 蒋庄德, 孙东

《工程（英文）》 2023年第21卷第2期页码 61-74 doi: 10.1016/j.eng.2022.06.018

摘要：

本文介绍了一种基于横向运动栅极场效应晶体管（LMGFET）的新型微型力传感器。文中提出了一种用于小型LMGFET器件性能评估的电气模型，与以前的模型相比，其具有更高精度。由此设计了一种新型的三明治夹层结构，该结构由跨轴解耦Au-栅极阵列层和两个柔性光刻胶SU-8 层组成。通过所提出的双差分传感布置，LMGFET工作时受垂直干扰产生的输出电流被大大消除，所提出传感器的相对输出误差从4.53%（传统差分结构）降低到0.01%。本文还为所提出的传感器开发和模拟了一个可行的制造工艺过程。基于LMGFET的力传感器的灵敏度为4.65 μA∙nN−1，可与垂直可动栅极场效应晶体管（VMGFET）器件相媲美，器件的非线性度提高了0.78%，测量范围扩大为±5.10 μN。上述分析能够为LMGFET器件的电气和结构参数提供全面的设计优化指导，并证明了所提出的传感器在生物医学显微操作应用中具有出色的力传感潜力。

关键词：微力传感器横向运动栅极场效应管柔性光刻胶SU-8 生物医学显微操作