GridMol: a grid application for molecular modeling and visualization

In this paper we present GridMol, an extensible tool for building a high performance computational chemistry platform in the grid environment. GridMol provides computational chemists one-stop service for molecular modeling, scientific computing and molecular information visualization. GridMol is not only a visualization and modeling tool but also simplifies control of remote Grid software that can access high performance computing resources. GridMol has been successfully integrated into China National Grid, the most powerful Chinese Grid Computing platform. In Section “Grid computing” of this paper, a computing example is given to show the availability and efficiency of GridMol. GridMol is coded using Java and Java3D for portability and cross-platform compatibility (Windows, Linux, MacOS X and UNIX). GridMol can run not only as a stand-alone application, but also as an applet through web browsers. In this paper, we will present the techniques for molecular visualization, molecular modeling and grid computing. GridMol is available free of charge under the GNU Public License (GPL) from our website: Contact:      

Avoiding the van der Waals endpoint problem using serial atomic insertion

In the past analyses of the so-called van der Waals end point problem focused on thermodynamic integration. Here we investigate which of the recommendations, such as the need for soft-core potentials, are still valid when Bennett's acceptance ratio method is used. We show that in combination with Bennett's acceptance ratio method intermediate states characterized by the coupling parameter λ can be replaced by intermediate states in which Lennard-Jones interactions are turned on or off on an "atom by atom" basis. By doing so, there is no necessity to use soft-core potentials. In fact, one can compute free energy differences without dedicated code, making it possible to use any molecular dynamics program to compute alchemical free energy differences. Such an approach, which we illustrate by several examples, makes it possible to exploit the tremendous computational power of the graphics processing unit.     

Merits of random forests emerge in evaluation of chemometric classifiers by external validation

Real-world applications will inevitably entail divergence between samples on which chemometric classifiers are trained and the unknowns requiring classification. This has long been recognized, but there is a shortage of empirical studies on which classifiers perform best in ‘external validation’ (EV), where the unknown samples are subject to sources of variation relative to the population used to train the classifier. Survey of 286 classification studies in analytical chemistry found only 6.6% that stated elements of variance between training and test samples. Instead, most tested classifiers using hold-outs or resampling (usually cross-validation) from the same population used in training. The present study evaluated a wide range of classifiers on NMR and mass spectra of plant and food materials, from four projects with different data properties (e.g., different numbers and prevalence of classes) and classification objectives. Use of cross-validation was found to be optimistic relative to EV on samples of different provenance to the training set (e.g., different genotypes, different growth conditions, different seasons of crop harvest). For classifier evaluations across the diverse tasks, we used ranks-based non-parametric comparisons, and permutation-based significance tests. Although latent variable methods (e.g., PLSDA) were used in 64% of the surveyed papers, they were among the less successful classifiers in EV, and orthogonal signal correction was counterproductive. Instead, the best EV performances were obtained with machine learning schemes that coped with the high dimensionality (914–1898 features). Random forests confirmed their resilience to high dimensionality, as best overall performers on the full data, despite being used in only 4.5% of the surveyed papers. Most other machine learning classifiers were improved by a feature selection filter (ReliefF), but still did not out-perform random forests.     

Parallel Fock matrix construction program for molecular orbital calculation--specific computer with a hierarchical network

A parallel Fock matrix construction program for a hierarchical network has been developed on the molecular orbital calculation-specific EHPC system. To obtain high parallelization efficiency on the hierarchical network system, a multilevel dynamic load-balancing scheme was adopted, which provides equal load balance and localization of communications on a tree-structured hierarchical network. The parallelized Fock matrix construction routine was implemented into a GAMESS program on the EHPC system, which has a tree-structured hierarchical network. Benchmark results on a 63-processor system showed high parallelization efficiency even on the tree-structured hierarchical network.     

隆回富硒区山银花不同花期硒分布规律研究

通过分析山银花不同花期硒含量,探讨了山银花中硒的积蓄规律与土壤硒之间的关系。选择湖南省隆回县小沙江地区加油站北和岩背村两处土壤硒含量分别为0.968 mg/kg和0.837mg/kg的山地,种植灰毡毛忍冬的两个不同品种:白云一号和金蕾一号,在花期内连续采收绿蕾期、白蕾期、白花期和金花期样本,脱水后,用电化学法测定硒含量。结果表明,白云一号和金蕾一号的绿蕾期、白蕾期、白花期和金花期硒平均含量分别为0.111、0.191、0.191、0.295 mg/kg和0.146、0.260、0.272、0.363 mg/kg,金蕾一号的硒积蓄能力优于白云一号。结论是富硒区山银花中硒的积蓄量与品种、花期密切相关,但与土壤中硒含量无明显相关性。     

Complex equilibria of molybdenum(VI) with 2,3-dihydroxynaphthalene

Equilibria of Mo(VI) in acid aqueous solutions with excess of 2,3-dihydroxynaphthalene (DHN)c _DHN /c _Mo = 2.3–107 (I = 0.6 mol 1^–1 (NaClO₄), 0.6% v/v ethanol) were studied spectrophotometrically. Formation constants of MoO₂R ₂ ^2– (logK ₀₁₂ = 5.89±0.01) and presumed MoO₂(OH)(OH₂)R^– (logK ₁₁₁ = 7.79±0.01) chelates were evaluated using SQUAD-G program.     

DNA labelled graphs with DNA computing

Let k≥2, 1≤i≤k andα≥1 be three integers. For any multiset which consists of some k-long oligonucleotides, a DNA labelled graph is defined as follows: each oligonucleotide from the multiset becomes a point; two points are connected by an arc from the first point to the second one if the i rightmost uucleotides of the first point overlap with the i leftmost nucleotides of the second one. We say that a directed graph D can be(k, i;α)-labelled if it is possible to assign a label(l_1(x),..., l_k(x))to each point x of D such that l_j(x)∈{0,...,a-1}for any j∈{1,...,k}and(x,y)∈E(D)if and only if(l_k-i 1(x),..., l_k(x))=(l_1(y),..., l_i(y)). By the biological background, a directed graph is a DNA labelled graph if there exist two integers k, i such that it is(k, i; 4)-labelled. In this paper, a detailed discussion of DNA labelled graphs is given. Firstly, we study the relationship between DNA labelled graphs and some existing directed graph classes. Secondly, it is shown that for any DNA labelled graph, there exists a positive integer i such that it is(2i, i; 4)-labelled. Furthermore, the smallest i is determined, and a polynomial-time algorithm is introduced to give a(2i, i; 4)-labelling for a given DNA labelled graph. Finally, a DNA algorithm is given to find all paths from one given point to another in a(2i, i; 4)-labelled directed graph.     

Self-Organized Task Allocation for Service Tasks in Computing Systems with Reconfigurable Components

A self-organized scheme for the allocation service tasks in adaptive or organic computing systems is proposed. Such computing systems are highly self-organized and the components ideally adapt to the needs of users or the environment. Typically, the components of such systems need some service from time to time in order perform their work efficiently. Since the type of service tasks will often change in this systems it is attractive to use reconfigurable hardware to perform the service tasks. The studied system consists of normal worker components and the helper components which have reconfigurable hardware and can perform different service tasks. The speed with which a service task is executed by a helper depends on its actual configuration. Different strategies for the helpers to decide about service task acceptance and reconfiguration are proposed. These task acceptance strategies are inspired by stimulus-threshold models that are used to explain task allocation in social insects. Analytical results for a system with two reconfigurable helpers are presented together with simulation results for larger systems. This work was supported by the German Research Foundation (DFG) through the project Organisation and Control of Self-Organising Systems in Technical Compounds within SPP 1183.