计算机辅助分子模型系统—MMBS

计算机辅助分子模型ＭＭＢＳ采用两种输入方法，线型编码法和二维图形法，模型生成有杉三维碎片子结构构造法，并采用快速子结构匹配实现结构感知。系统具有较强的图形显示和操作功能。     

计算机辅助分子模型系统－MMBS

计算机辅助分子模型系统ＭＭＢＳ采用两种输入方法，线型编码法和二维图形法，模型生成采用三维碎片子结构构造法，并采用快速子结构匹配实现结构感知。系统具有较强的图形显示和操作功能。     

碳-13核磁共振谱图的自动解析研究

为了Ｃ－１３ＮＭＲ的自动解析,ＥＳＥＳＯＣ系统从＾１３ＣＮＭＲ本身的特征出发,提出了不确定层数的子结构模型。即以共振碳原子为中心,以与之相连的完整的官能团为外围环境,对这样的子结构,其外围环境根据官能团的不同可以是一层、或二层乃至多层,即环境层数是可变的。在此子结构模型的基础上,从ＣＩＡＣ－＾１３ＣＮＭＲ谱图数据库统计出＾１３ＣＮＭＲ知识库。     

FX909在无线高速MODEM中的应用

介绍了 ＧＭＳＫ调制解调芯片 ＦＸ ９０９的特点及其在无线高速 ＭＯＤＥＭ中的应用,并给出了相应的硬件框图和主程序流程图。该 ＭＯＤＥＭ可通过音频接口与调频话音电台相接,同时也可与具有标准 ＲＳ－ ２３２ Ｃ接口的数据设备相接,从而通过传统话音电台实现数据信号的无线传输。     

New—UIGMS——界面工具＋方法

本文着重介绍了Ｎｅｗ－ＵＩＧＭＳ在人机界面设计和实现中的作用。Ｎｅｗ－ＵＩＧＭＳ以将界面编辑器和界面动态流程控制设计相结合的方法,向界面设计人员提供了支持。     

测试维护总线(TM-BUS)的研究与实现

测试维护总线是机载计算机测试技术研究的难点和关键技术之一。简要介绍了测试维护总线ＴＭ－ＢＵＳ控制器的设计,重点论述了ＴＭ－ＢＵＳ的实现方案、ＴＭ－ＢＵＳ控制管理机制及ＴＭ－ＢＵＳ应用。应用系统稳定运行表明,所提出的ＴＭ－ＢＵＳ实现方案的正确性以及芯片逻辑功能正确,稳定可靠。     

I-DEAS GM加工——CAMAND的接力棒

ＳＤＲＣ公司是世界上最大的ＣＡＭ软件供应商之一,其ＣＡＭ产品除了享誉业界的ＣＡＭＡＮＤ之外,还有完全集成于Ｉ-ＤＥＡＳ工程环境中的加工模组ＧＭ（ Ｇｅｎｅｒａｔｉｖｅ Ｍａｃｈｉｎｉｎｇ　创成式加工）。ＧＭ不断汲取ＣＡＭＡＮＤ先进的数控技术,融汇其绝大部分功能和优点,形成了全新的刀具路径生成算法,成为ＭＤＡ集成环境下功能超强的加工模组。ＧＭ可以直接利用Ｉ－ＤＥＡＳ产生的实体或曲面几何,或由外部的ＣＡＤ系统输入的实体或曲面集合生成刀具路径;可以建立包含工件、毛坯、装夹和机床再内的完整的制造系统,从而…     

基于GPSS／H和GKS的FMS物流系统的动画仿真

本文介绍了在ｓｕｎ－３工作站上实现的ＦＭＳ动画仿真系统。该系统在开发Ｓｕｎ－３的ＧＰＳＳ／Ｈ及Ｓｕｎ ＧＫＳ软件的基础上，用Ｃ语言编制全部软件，具有良好的人机接口。利用该系统实现ＦＭＳ的动画仿真，具有易于建模和调试，开发周期短，符合标准化，易于验证正确性和可靠性等特点，为开发研制ＦＭＳ提供了有效的手段。这里着重介绍ＦＭＳ物流系统仿真的建模方法，软件设计以及仿真程序与动画程序的软件接口等。     

一种飞行器地面测控系统设计

ＧＭ－２飞行器地面测控系统是一个嵌入式计算机系统,具有对被测对象的测试、控制、模拟功能。本文介绍了ＧＭ－２测控系统的总体设计思想、系统组成、工作原理和主要技术途径。该系统采用ＳＴＤ工业总线标准设计,可靠性高,维修性好,环境适应性强。ＧＭ－２测控系统的设计思路,对今后测控系统及其它测试系统的设计具有较好的借鉴作用。     

XML——新的Web开发工具

ＸＭＬ是当前Ｗｅｂ技术领域的热点,它源于ＳＧＭＬ是ＳＧＭＬ的一个子集,文中,介绍ＸＭＬ的起源和特点,给出一个示例说明怎样书写ＸＭＬ文档,并简要介绍ＸＭＬ的应用和未来。     

Gromacs在神威蓝光超级计算机上的部署及应用

Gromacs是一个大型的分子动力学模拟软件。国家超算济南中心拥有两套高性能计算系统,分别为基于Intel CPU构建的高性能计算集群(理论峰值超过100T),以及基于国产SW1600 CPU构建的MPP超级计算系统(理论峰值超过1P)。本文介绍了Gromacs软件包在两个高性能计算平台的移植、部署,并以生物大分子作为实例在两个平台上进行了分子动力学模拟测试。     

分子模型的建造

本文着重介绍我们在微机上开发的分子模型建造系统.本系统的分子模型建造部分采用三维手工建造和二维自动建造两种方法.使用者选择不同的方法来建造分子的三维模型进行显示或计算.前者的真三维建造界面使分子造型快速、准确,后者采用距离几何算法将二维分子结构式通过计算转化成分子的三维空间结构.     

Investigation of multiscale fluid flow characteristics based on a hybrid atomistic–continuum method

A computer program based on a molecular dynamics–continuum hybrid method has been developed in which the Navier–Stokes equations are solved in the continuum region and the molecular dynamics in the atomistic region. The coupling between the atomistic and continuum is constructed through constrained dynamics within an overlap region where both molecular and continuum equations are solved simultaneously. The simulation geometries are solved in three dimensions and an overlap region is introduced in two directions to improve the choice of using the molecular region in smaller areas. The proposed method is used to simulate steady and start-up Couette flow showing quantitative agreement with results from analytical solutions and full molecular dynamics simulations. The prepared algorithm and the computer code are capable of modeling fluid flows in micro and nano-scale geometries.     

Modified FDP cluster algorithm and its application in protein conformation clustering analysis

We present a modified find density peaks (MFDP) clustering algorithm. In the MFDP, a critical parameter, dc, is auto-defined by minimizing the entropy of all points. By considering both the point density, ρ, and large distance from points with higher densities, δ, the high-dimensional points are transformed into a 2D space. The halo points of the original FDP cluster algorithm are redefined, and a definition of boundary points is introduced to illustrate the intersection region between clusters. To demonstrate the clustering ability, the distance-based K-means clustering and density-based algorithms DBSCAN, original FDP are employed respectively. Four criteria are introduced to evaluate the clustering algorithms quantitatively. For most of the cases, the MFDP provides a superior clustering result than both of the typical clustering algorithms, and FDP in 20 commonly used benchmark datasets, particularly in clearly depicting the intersection region between clusters. Finally, we evaluate the performance of the MFDP in the cluster analysis of conformations in molecular dynamics (MD). In the MD clustering process, eight typical cluster center conformations are selected in six collective variable spaces. Moreover, it is in strong agreement with the experiment results. The clustering results demonstrate the potential for generalized applications of the modified algorithm to similar problems.     

Fragment oriented molecular shapes

Molecular shape is an important concept in drug design and virtual screening. Shape similarity typically uses either alignment methods, which dynamically optimize molecular poses with respect to the query molecular shape, or feature vector methods, which are computationally less demanding but less accurate. The computational cost of alignment can be reduced by pre-aligning shapes, as is done with the Volumetric-Aligned Molecular Shapes (VAMS) method. Here, we introduce and evaluate fragment oriented molecular shapes (FOMS), where shapes are aligned based on molecular fragments. FOMS enables the use of shape constraints, a novel method for precisely specifying molecular shape queries that provides the ability to perform partial shape matching and supports search algorithms that function on an interactive time scale. When evaluated using the challenging Maximum Unbiased Validation dataset, shape constraints were able to extract significantly enriched subsets of compounds for the majority of targets, and FOMS matched or exceeded the performance of both VAMS and an optimizing alignment method of shape similarity search.     

PLUMED 2: New feathers for an old bird

Enhancing sampling and analyzing simulations are central issues in molecular simulation. Recently, we introduced PLUMED, an open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a variety of different enhanced sampling algorithms and collective variables (CVs). The rapid changes in this field, in particular new directions in enhanced sampling and dimensionality reduction together with new hardware, require a code that is more flexible and more efficient. We therefore present PLUMED 2 here—a complete rewrite of the code in an object-oriented programming language (C++). This new version introduces greater flexibility and greater modularity, which both extends its core capabilities and makes it far easier to add new methods and CVs. It also has a simpler interface with the MD engines and provides a single software library containing both tools and core facilities. Ultimately, the new code better serves the ever-growing community of users and contributors in coping with the new challenges arising in the field.     

Method for evaluating thermodynamic and statistical molecular dynamic interactions among the biomolecular particles that participate in gene expression

A mathematical method is introduced for evaluating the biomolecular dynamic interactions in gene expression and the regulation of an artificial life. The theoretical basis was founded on the thermodynamics and statistical molecular dynamics of multicomponent dilute gas systems, which are characterized by the Boltzmann equations and molecular collision integrals. We introduce the mathematical processes for computing shear viscosity, and the thermal conductivity of two interacting biomolecules that have different geometries, number density, and mass, in great detail. The computed normalized shear viscosity, normalized thermal conductivity, self diffusion, and thermal diffusion coefficients showed multimodal complex behaviors as functions of radius, length, mass distribution parameters, number density, and the mass of the second interacting particle. This method and the computed results, in a more generalized version, would give quantitative evaluations of physical collisional interactions among biomolecular particles as the ultimate process of biochemical reactions. This work was presented, in part, at the Sixth International Symposium on Artificial Life and Robotics, Tokyo, Japan, January 15–17, 2001.     

Parallel node placement method by bubble simulation

An efficient Parallel Node Placement method by Bubble Simulation (PNPBS), employing METIS-based domain decomposition (DD) for an arbitrary number of processors is introduced. In accordance with the desired nodal density and Newton’s Second Law of Motion, automatic generation of node sets by bubble simulation has been demonstrated in previous work. Since the interaction force between nodes is short-range, for two distant nodes, their positions and velocities can be updated simultaneously and independently during dynamic simulation, which indicates the inherent property of parallelism, it is quite suitable for parallel computing. In this PNPBS method, the METIS-based DD scheme has been investigated for uniform and non-uniform node sets, and dynamic load balancing is obtained by evenly distributing work among the processors. For the nodes near the common interface of two neighboring subdomains, there is no need for special treatment after dynamic simulation. These nodes have good geometrical properties and a smooth density distribution which is desirable in the numerical solution of partial differential equations (PDEs). The results of numerical examples show that quasi linear speedup in the number of processors and high efficiency are achieved.     

An Improved Hybrid Model for Molecular Image Denoising

In this paper an improved hybrid method for removing noise from low SNR molecular images is introduced. The method provides an improvement over the one suggested by Jian Ling and Alan C. Bovik (IEEE Trans. Med. Imaging, 21(4), [2002]). The proposed model consists of two stages. The first stage consists of a fourth order PDE and the second stage is a relaxed median filter, which processes the output of fourth order PDE. The model enjoys the benefit of both nonlinear fourth order PDE and relaxed median filter. Apart from the method suggested by Ling and Bovik, the proposed method will not introduce any staircase effect and preserves fine details, sharp corners, curved structures and thin lines. Experiments were done on molecular images (fluorescence microscopic images) and standard test images and the results shows that the proposed model performs better even at higher levels of noise.