Determination of approximate force field parameters

Methods are described which allow the addition of parameters to an existing force field in order to include new structural units. Data required for the parameterization procedure are mainly taken from quantum mechanical calculations. The methods have been applied to add parameters for aminoalkylphosphonic acids to the GROMOS force field. A molecular dynamics (MD) simulation of 64 aminomethylphosphonic acid molecules in eight unit cells has been carried out. The approximate parameters have also been used for a MD-study of aminomethylphosphonic acid in SPC water at constant temperature and pressure.     

Classical force field parameters for two high-affinity ligands of FKBP12

FKBP12 is an important target in the treatment of transplant rejection and is also a promising target for cancer and neurodegenerative diseases. We determined for two ligands of nanomolar affinity the set of parameters in the CHARMM force field. The fitting procedure was based on reproducing the quantum chemistry data (distances, angles, and energies). Since the dynamical behavior of such ligands strongly depends on the dihedral angles, care was taken to derive the corresponding parameters. Moreover, since each of the central core region of these two ligands is similar to other known ligands or drugs of other proteins, part at least of these parameters could also be useful for these other ligands.     

Interactive graphical optimization of potential energy function parameters in the consistent force field

The performance of a molecular mechanics force field depends on the form of its potential energy function as well as on their parametrization. In the consistent force field (CFF), the fundamentally empirical nature of potential energy functions is recognized by their refinement through optimization which is an integral part of the CFF concept. A graphical interface to the optimization algorithm has been developed with the dual purposes of compressing large amounts of numerical data into one intuitive comprehensible picture of the residue functions and giving the user interactive control of the optimization process. The principles of force field optimization are outlined, with emphasis on the design and realization of the graphical interface.     

Optimization and parallelization of a force field for silicon using OpenMP

The force field by Lenosky and coworkers is the latest force field for silicon which is one of the most studied materials. It has turned out to be highly accurate in a large range of test cases. The optimization and parallelization of this force field using OpenMp and Fortran90 is described here. The optimized program allows us to handle a very large number of silicon atoms in large scale simulations. Since all the parallelization is hidden in a single subroutine that returns the total energies and forces, this subroutine can be called from within a serial program in an user friendly way.     

Cys(x)His(y)-Zn2+ interactions: possibilities and limitations of a simple pairwise force field

In zinc proteins, the Zn2+ cation frequently binds with a tetrahedral coordination to cysteine and histidine side chains. We examine the possibilities and limitations of a classical, pairwise force field for molecular dynamics of such systems. Hartree Fock and density functional calculations are used to obtain geometries, charge distributions, and association energies of side chain analogues bound to Zn2+. Both ionized and neutral cysteines are considered. Two parameterizations are obtained, then tested and compared through molecular dynamics simulations of two small, homologous proteins in explicit solvent: Protein Kinase C and the Cysteine Rich Domain (CRD) of Raf, which have two Cys3His-Zn2+ groups each. The lack of explicit polarizability and charge transfer in the force field leads to poor accuracy for the association energies, and to parameters--including the zinc charge, that depend on the number of bound cysteines and their protonation state. Nevertheless, the structures sampled with the best parameterization are in good overall agreement with experiment, and have zinc coordination geometries compatible with related structures in the Cambridge Structural Database and the Protein Data Bank. Non-optimized parameters lead to poorer structures. This suggests that while a simple force field is not appropriate for processes involving exchange between water and amino acids in the zinc coordination sphere (e.g. protein unfolding), it can be useful for equilibrium simulations of stable Cys3His zinc fingers.     

Optimization of testability parameters

The main objective of this study was to investigate performance models of automatic diagnostic systems taking into consideration its imperfections such as incorrect isolation and false alarms. This was accomplished by developing an optimization model to assist the decision maker in determining the optimal values of testability parameters which maximize his/her utility function. This will provide the decision maker with a tool to evaluate the parameters set forth by the designer and to assess the real capability of the diagnostic system. This tool also will help the decision maker to check if the correct detection and isolation capability of the system, as well as the imperfections of the system, e.g., incorrect isolation and false alarms are acceptable and satisfactory.

An interactive program was developed and help to implement the optimization modedl. This program provides the decision maker with enough flexibility to avaluate different different strategies and to repeat the decision process after changing one or more of the model's parameter. An example will be presented to show the application of this optimization model.     

Optimization of parameters of functional transformations in a signal classification system

A concise mathematical statement of the signal classification problem is given. Within its framework, linear separability criteria are described for a set of points in a finite-dimensional space and then are generalized to an infinite-dimensional space. The problem of synthesis of both linear and nonlinear classification systems is also solved, for which an algorithm is formulated that chooses optimal structures of sequential and parallel functional transformations of uninformative coordinates in a feature vector.     

外激励参数未知系统的同步控制及其参数识别

考虑外激励的振幅和频率未知的混沌系统.把系统未知参数扩张成系统的新的状态量,构造新的驱动系统.用参数自适应控制方法构造一个响应系统,使之与驱动系统的结构相同.基于级联系统的稳定性理论,通过两个步骤来设计控制器和参数自适应律,使得驱动—响应系统能够达到完全同步.当驱动—响应系统达到完全同步时,就可以识别出系统的未知参数振...     

Comparison of wave parameters determined from SILAR images and a pitch and roll buoy

Abstract

The nature of the data recorded by Side-Looking Airborne Radar (SLAR) and that by a pitch and roll buoy differ completely. The radar records a spatial data set at one instant in time, whereas the buoy records a time series on a given point on the sea surface, The spectrum in wave number space of the radar image is transformed to the frequency domain by using the dispersion relation for shallow water waves. With further processing, the radar derived data can be presented in the traditional form of pitch and roll buoy displays a (relative scale) waveheight spectrum, a directional distribution and the directional spreading, all as a function of frequency. Limitations of the method and differences in the results of the sensors are discussed.     

Optimization of the operating parameters of a grass trimming machine

Hand-arm vibration syndrome (HAVS) is very common among the workers operating power tools and doing similar nature of work for long hours. Grass trimming is one of the operations that involves use of vibrating cutter, and results in hand-arm vibration among workers. In this study, the influence of several operating parameters (length of nylon cutting thread, engine speed and handle material) is investigated in terms of HAV. Data are analyzed via orthogonal array, main effect, signal-to-noise (S/N) ratio, and analysis of variance to determine the appropriate operating parameter levels to minimize HAV. Operating parameters under investigation are found to be influential in controlling HAV generation during grass trimming operation. Experiments are carried out for measuring hand-arm vibration using tri-axial accelerometer conforming the effectiveness of this approach. Results show that 100 mm length of nylon thread, 3000 ± 400 rpm of engine speed and ABS handle material combination results in minimum HAV (HARM) of magnitude 2.76 m/s². Through this study not only the optimal operating parameter levels for GTM are obtained, but also the main process parameters that affect the HAV are determined. The optimum HAV obtained through appropriate level selection of operating parameters, significantly reduces the occurrence of HAVS among the grass trimmers.     

Optimization of pantograph mechanisms for force generation

Pantograph mechanisms for force generation, called PMFG, are proposed. They are based on four-bar linkage mechanisms and are effective in saving energy, and simplifying and miniaturizing a total system of force generation. The static relationship between the motion and output force of the mechanism is analysed for optimization of the mechanical dimensions of the structure. For optimization of the pulley shapes, analytical and approximate methods are discussed. The experimental results show that eccentric non-circular pulleys are more effective than circular pulleys in producing an accurate force satisfying the required relations between the force and displacement of the mechanism. The mechanism is applicable to the realization of various kinds of force vs. displacement requirements.     

Stewart六维力传感器优化设计

对Stewart六维力传感器进行了优化设计分析,在有限元分析的基础上,通过球头球窝结构、十字槽结构以及圆环内嵌十字梁结构等形式,增强了传感器整体的抗耦能力。同时,对优化前后的传感器进行了试验比对,在一维加载时,传感器的最大误差由3.28%减小到0.41%;在三维加载时,最大误差由4.76%减小到2.22%。从以上的数据可以看出:改进后的设计更加合理,提高了传感器的精度。     

基于拓扑子集的势场原子类型的派定

对于除了标准氨基酸、核酸残基以外的一般分子,派定分子中原子的原子类型,确定原子类型在不同分子势场之间的转换,这些工作一般是由人工来完成。本文从分子拓扑学的角度解析了分子势场的原子类型(atom type)定义,以基于分子拓扑子集取代原子类型定义的分子片断为途径,实现势场原子类型的计算机自动派定。该方法易于编程,并能满足用户调整原子类型的意愿。     

Optimization of control parameters in micro hot embossing

The key control parameters in hot embossing (such as the imprint pressure, the imprint temperature, the holding time and the demolding temperature) can significantly impact on the pattern quality. The finite element method was used to analyze the embossing, cooling and demolding step to acquire the optimized process parameters. The simulation results show that the polymer flow has a reference to the imprint pressure, the imprint temperature and the holding time. While the adhesion force between the polymer and the mold can significantly influence the replication accuracy. Because of polymer flow, non-uniform pressure distribution can be observed and this results in the pattern height difference. The hydraulic pressure system was designed to acquire uniform pressure. Thermal stress caused by the difference of the thermal expansion coefficients between the mold and the polymer can induce stress concentration at the corner. If the demolding direction is not vertical to horizon, another stress concentration will appear. Excessive stress results in defects and causes fracture at the base part of the pattern during the demolding step. To eliminate the defects, cooling to a relative high temperature was introduced to reduce the stress concentration and an auto-demolding device was used to insure no additional stress was imported at the demolding step. The following experiment showed the successful fabrication of fine patterns with the optimized parameters.     

Stewart六维力传感器解耦算法优化

为满足六维力传感器的高刚度要求,使用固支约束代替铰约束。通过对传感器样机单维加载获得的标定数据进行处理,发现在使用求解标定矩阵或BP神经网络训练的方法时,分别存在维间耦合较大和多维加载误差极大的问题。对此提出一种新的思路,即在标定时同时进行单维加载和多维加载。之后使用上述两种方法进行解耦,对比发现,对新的方法,在使用BP神经网络的方法解耦时,将最大误差降低到了2.27%,证明该方法能够同时解决六维力传感器的维间耦合问题和多维加载问题。     

剪力传感器在铁路计轴领域的应用

提出了一种在铁路计轴领域运用剪力传感器实现计轴的方法,由于剪力传感器具有灵敏度高、精确性好等优点,该方法能运用剪力传感器感应车轮的重力转换为检测信号计算车轴数量,可有效排除不利因素对计轴设备造成的干扰,保证计轴设备检测数据的准确性,提高计轴设备的安全可靠性,保障铁路系统的运输安全.     

HEMP—hand-displacement-based pseudo-haptics: A study of a force field application and a behavioural analysis

This paper introduces a novel pseudo-haptic approach called HEMP—Hand-displacEMent-based Pseudo-haptics. The main idea behind HEMP is to provide haptic-like sensations by dynamically displacing the visual representation of the user's hand. This paper studies the possible application of HEMP to the simulation of force fields (FFs). The proposed hardware solution for simulating the hand displacement is based on an augmented reality configuration, the video see-through head-mounted display. A response model is proposed for controlling the hand displacement. This model adapts to the user's hand movements. It also accounts for a number of perceptual and system constraints. An experiment has been carried out to investigate the potential of the proposed technique. Subjects had to perform an FF strength comparison task and to fill in an illusion evaluation questionnaire. Comparison response results show that different FF strength levels are discriminable and the questionnaire indicates that subjects perceive flow pressure-like sensations. The analysis of arm muscular activity seems to confirm these results.     

Modeling multiple interactions with a Markov random field in query expansion for session search

How to automatically understand and answer users' questions (eg, queries issued to a search engine) expressed with natural language has become an important yet difficult problem across the research fields of information retrieval and artificial intelligence. In a typical interactive Web search scenario, namely, session search, to obtain relevant information, the user usually interacts with the search engine for several rounds in the forms of, eg, query reformulations, clicks, and skips. These interactions are usually mixed and intertwined with each other in a complex way. For the ideal goal, an intelligent search engine can be seen as an artificial intelligence agent that is able to infer what information the user needs from these interactions. However, there still exists a big gap between the current state of the art and this goal. In this paper, in order to bridge the gap, we propose a Markov random field–based approach to capture dependence relations among interactions, queries, and clicked documents for automatic query expansion (as a way of inferring the information needs of the user). An extensive empirical evaluation is conducted on large‐scale web search data sets, and the results demonstrate the effectiveness of our proposed models.     

Effect of geometrical parameters on radiometric force in low-pressure MEMS gas actuator

Microsystem Technologies - In this paper, comprehensive numerical studies are performed to investigate the effects of the geometrical factors on the performance of the low-pressure gas actuator....     

Intmol: Minimization of long range interactions as a function of intermolecular angular parameters

This FORTRAN IV program computes the long range intermolecular energy and its components between two polyelectronic systems and minimizes the intermolecular parameters via the simplex method.The annalytical function of the energy is constructed from the perturbative Rayleigh-Schroödinger theory (2nd order) with the Hamiltonian interaction as a multipole expansion (till r⁻⁷).