Effect of the solvent on the conformational behavior of the alanine dipeptide deduced from MD simulations

In general, peptides do not exhibit a well-defined conformational profile in solution. However, despite the experimental blurred picture associated with their structure, compelling spectroscopic evidence shows that peptides exhibit local order. The conformational profile of a peptide is the result of a balance between intramolecular interactions between different atoms of the molecule and intermolecular interactions between atoms of the molecule and the solvent. Accordingly, the conformational profile of a peptide will change upon the properties of the solvent it is soaked. To get insight into the balance between intra- and intermolecular interactions on the conformational preferences of the peptide backbone we have studied the conformational profile of the alanine dipeptide in diverse solvents using molecular dynamics as sampling technique. Solvents studied include chloroform, methanol, dimethyl sulfoxide, water and N-methylacetamide. Different treatments of the solvent have been studied in the present work including explicit solvent molecules, a generalized Born model and using the bulk dielectric constant of the solvent. The diverse calculations identify four major conformations with different populations in the diverse solvents: the C₇^eq only sampled in chloroform; the C₅ or extended conformation; the polyproline (PII) conformation and the right-handed α-helix conformation (α_R). The results of present calculations permit to analyze how the balance between intra- and intermolecular interactions explains the populations of the diverse conformations observed.     

Efficient parallel implementation of Ewald summation in molecular dynamics simulations on multi-core platforms

We present a multi-step computation method to implement the Ewald summation for long-range electrostatic interactions in molecular dynamic simulations on a multi-core machine. Our methodology is based on the OpenMP programming model. It partitions computations of real-space summation among threads so that the global force of a single particle cannot be modified by more than one thread simultaneously. It requires neither a private copy of the force array for each thread nor an inspector at runtime. Compared with some other methods that can parallelise reduction operations on a force-array, our method achieves relatively higher speedups and lower L2 cache miss and bus utilisation ratios.     

基于理论线性溶剂化能关系研究两类局部麻醉药物的疏水性质

用理论线性溶剂化能关系建立了两类局部麻醉药物 (咪唑烷二酮类和苄醇类 )的结构—疏水性关系。结果表明 :分子的体积越大 ,两类化合物的亲脂性越强。另外 ,对咪唑烷二酮而言 ,分子的氢键碱度与其LogP值呈负相关 ,而苄醇类化合物的氢键酸度越大 ,对亲脂性越有利。     

Modeling and Managing Interactions among Business Processes

Most workflow management systems (WfMSs) only support the separate andindependent execution of business processes. However, processes often needto interact with each other, in order to synchronize the execution of theiractivities, to exchange process data, to request execution of services, orto notify progresses in process execution. Recent market trends also raisethe need for cooperation and interaction between processes executed in differentorganizations, posing additional challenges. In fact, in order to reduce costsand provide better services, companies are pushed to increase cooperation and toform virtual enterprises, where business processes span across organizationalboundaries and are composed of cooperating workflows executed in differentorganizations. Workflow interaction in a cross-organizational environment iscomplicated by the heterogeneity of workflow management platforms on top ofwhich workflows are defined and executed and by the different and possiblycompeting business policies and business goals that drive process executionin each organization.In this paper we propose a model and system that enable interactionbetween workflows executed in the same or in different organizations. Weextend traditional workflow models by allowing workflows to publish andsubscribe to events, and by enabling the definition of points in the processexecution where events should be sent or received. Event notifications aremanaged by a suitable event service that is capable of filtering andcorrelating events, and of dispatching them to the appropriate targetworkflow instances. The extended model can be easily mapped onto anyworkflow model, since event specific constructs can be specified by means ofordinary workflow activities, for which we provide the implementation. Inaddition, the event service is easily portable to different platforms, anddoes not require integration with the WfMS that supports the cooperatingworkflows. Therefore, the proposed approach is applicable in virtually anyenvironment and is independent on the specific platform adopted     

Chemical cross-linking and mass spectrometry to map three-dimensional protein structures and protein-protein interactions

Closely related to studying the function of a protein is the analysis of its three-dimensional structure and the identification of interaction sites with its binding partners. An alternative approach to the high-resolution methods for three-dimensional protein structure analysis, such as X-ray crystallography and NMR spectroscopy, consists of covalently connecting two functional groups of the protein(s) under investigation. The location of the created cross-links imposes a distance constraint on the location of the respective side chains and allows one to draw conclusions on the three-dimensional structure of the protein or a protein complex. Recently, chemical cross-linking of proteins has been combined with a mass spectrometric analysis of the created cross-linked products. This review article describes the most popular cross-linking reagents for protein structure analysis and gives an overview of the different available strategies that employ chemical cross-linking and different mass spectrometric techniques. The challenges for mass spectrometry caused by the enormous complexity of the cross-linking reaction mixtures are emphasized. The various approaches described in the literature to facilitate the mass spectrometric detection of cross-linked products as well as computer software for data analyses are reviewed.     

Combining ergonomics, culture and scenario for the design of a cooperation platform

Analyzing the way computer technologies are used is crucial for their development. Such analyses make it possible to evaluate these technologies and enhance their evolution. The present article presents some ideas drawn from the development of a cooperation platform for elementary school children (10–11 years old). On the basis of an obvious ergonomic requirement, we worked on two other dimensions: cultural aspects and the teaching scenario. The goal was to set up observation situations and analyze the conversations produced during those situations, in order to understand what using the platform meant to both the pupils and their teachers.

Cynipid gall-wasp communities correlate with oak chemistry

Host-plant association data, gathered from field surveys conducted throughout Florida and from the literature, were used to identify the specificity of cynipid gall inducers to one or more of six Quercus species that occur at Archbold Biological Station, Lake Placid, Florida, USA, including the red oaks Q. laevis, Q. myrtifolia, and Q. inopina, and the white oaks Q. chapmanii, Q. geminata, and Q. minima. Quercus myrtifolia had the highest cynipid richness and diversity (37 cynipid species, Shannon H = 3.61, Simpson's D = 0.97), followed by Q. chapmanii, Q. laevis, Q. inopina, Q. geminata, and finally Q. minima (10 species, H = 2.30, D = 0.90). All cynipid species showed strong fidelity to a particular host plant or a restricted set of host plants. An ordination of gall-wasp host associations indicated that the cynipid communities of each oak species were distinct and specific to a given oak species. Leaf samples taken from each oak species were analyzed for condensed and hydrolyzable tannins, total phenolics, lignin, cellulose and hemicellulose, nitrogen, and carbon. All of these chemical traits, with the exception of carbon, differed by oak species, and the differences were strongly correlated with the axes of the cynipid--species ordination. These results suggest that gall-wasp occurrence is influenced by oak chemistry and imply that experimental studies of cynipid gall inducers that examine host-plant chemistry and female oviposition choice and larval performance will yield useful insights.     

Fault prediction and the discriminative powers of connectivity-based object-oriented class cohesion metrics

Context

Several metrics have been proposed to measure the extent to which class members are related. Connectivity-based class cohesion metrics measure the degree of connectivity among the class members.

Objective

We propose a new class cohesion metric that has higher discriminative power than any of the existing cohesion metrics. In addition, we empirically compare the connectivity and non-connectivity-based cohesion metrics.

Method

The proposed class cohesion metric is based on counting the number of possible paths in a graph that represents the connectivity pattern of the class members. We theoretically and empirically validate this path connectivity class cohesion (PCCC) metric. The empirical validation compares seven connectivity-based metrics, including PCCC, and 11 non-connectivity-based metrics in terms of discriminative and fault detection powers. The discriminative-power study explores the probability that a cohesion metric will incorrectly determine classes to be cohesively equal when they have different connectivity patterns. The fault detection study investigates whether connectivity-based metrics, including PCCC, better explain the presence of faults from a statistical standpoint in comparison to other non-connectivity-based cohesion metrics, considered individually or in combination.

Results

The theoretical validation demonstrates that PCCC satisfies the key cohesion properties. The results of the empirical studies indicate that, in contrast to other connectivity-based cohesion metrics, PCCC is much better than any comparable cohesion metric in terms of its discriminative power. In addition, the results also indicate that PCCC measures cohesion aspects that are not captured by other metrics, wherein it is considerably better than other connectivity-based metrics but slightly worse than some other non-connectivity-based cohesion metrics in terms of its ability to predict faulty classes.

Conclusion

PCCC is more useful in practice for the applications in which practitioners need to distinguish between the quality of different classes or the quality of different implementations of the same class.     

基于一致性算法的多智能体系统能控性性质

针对多智能体系统能控性方面的问题,采用图论及矩阵的方法研究了多智能体系统在对称拓扑和多领航者情况下的能控性,给出了拓扑结构为对称的系统能控性的几个性质。在领航者为多个时,指出了不对称的拓扑结构不再是多智能体系统能控性的必要条件。证明结果表明,图中连通枝的对称性（不是整个图对称）将导致系统的不能控以及在领航者是多个的情况下,如果领航者是来自任意的单元素单元,那么系统是不能控的。该结果为分析基于一致性算法的多智能体能控性提供了新的启示。     

H-Solid State NMR Studies of Tunneling Phenomena and Isotope Effects in Transition Metal Dihydrides

In many transition metal dihydrides and dihydrogen complexes the hydrogens are relatively weakly bound and exhibit a fairly high mobility, in particular with respect to their mutual exchange. Part of this high mobility is due to the exchange symmetry of the two hydrogens, which causes an energy splitting into even and odd spatial energy eigenfunctions, resulting in the typical coherent tunneling of a two-level system. Owing to the quantum mechanical symmetry selection principles the eigenfunctions are connected to the possible nuclear spin states of the system. If the tunneling frequency is in the proper frequency window it is thus possible to observe these tunneling transitions by NMR at very low temperatures, where no thermally induced exchange reactions overshadow the tunneling. The first part of this review gives an introduction into the interplay of chemical kinetics and tunneling phenomena in general, rotational tunneling of dihydrogen in a two-fold potential in particular and the Bell tunnel model, followed by a summary of solid state NMR techniques for the observation of these tunnel processes. Then a discussion of the effects of these processes on the ²H NMR line shape is given. The second part of the review reports results of a ²H-solid state NMR spectroscopy and T₁ relaxatiometry study of trans-[Ru(D₂)Cl(PPh₂CH₂CH₂PPh₂)₂]PF₆, in the temperature regime from 5.4 to 320 K. In the Ru-D₂ sample coherent tunneling and incoherent exchange processes on the time scale of the quadrupolar interaction are observed. From the spectra and T₁-data the height of the tunneling barrier is determined. Next results of ²H-spin–lattice relaxation measurements for a selectively η² − D₂ labeled isotopomer of the complex W(PCy₃)₂(CO)₃)(η² − D₂) are presented and discussed. The relaxation measurements are analyzed in terms of a simple one dimensional Bell tunnel model and comparison to incoherent neutron scattering (INS) data from the H₂ complex. The comparison reveals a strong isotope effect of 2 × 10³ for the exchange rates of the deuterons versus hydrons.