Management of Web and Associated Grid Technologies for Quantum Chemistry Computation

The European Young Chemist Award 2012

In the research area of grid computing and workflow technology, workflow products based on Web-service technology can work as grid services in grid architecture. A new algorithm of scheduling grid resource with workflow engine is discussed in this paper. The QoS, executing time of process, cost and workload of grid resources are the key factors in grid resources scheduling. Dynamic feed back mechanism and executing time estimation are applied in this algorithm, which can keep the grid resources in a good balance and advance the whole performance of the grid application with workflow service.

Computational Quantum Chemistry has developed into a powerful, efficient, reliable and increasingly routine tool for exploring the structure and properties of small to medium sized molecules. Many thousands of calculations are performed every day, some offering results which approach experimental accuracy. However, in contrast to other disciplines, such as crystallography, or bioinformatics, where standard formats and well-known, unified databases exist, this QC data is generally destined to remain locally held in files which are not designed to be machine-readable. Only a very small subset of these results will become accessible to the wider community through publication.In this paper we describe how the Quixote Project is developing the infrastructure required to convert output from a number of different molecular quantum chemistry packages to a common semantically rich, machine-readable format and to build respositories of QC results. Such an infrastructure offers benefits at many levels. The standardised representation of the results will facilitate software interoperability, for example making it easier for analysis tools to take data from different QC packages, and will also help with archival and deposition of results. The repository infrastructure, which is lightweight and built using Open software components, can be implemented at individual researcher, project, organisation or community level, offering the exciting possibility that in future many of these QC results can be made publically available, to be searched and interpreted just as crystallography and bioinformatics results are today.Although we believe that quantum chemists will appreciate the contribution the Quixote infrastructure can make to the organisation and and exchange of their results, we anticipate that greater rewards will come from enabling their results to be consumed by a wider community. As the respositories grow they will become a valuable source of chemical data for use by other disciplines in both research and education.The Quixote project is unconventional in that the infrastructure is being implemented in advance of a full definition of the data model which will eventually underpin it. We believe that a working system which offers real value to researchers based on tools and shared, searchable repositories will encourage early participation from a broader community, including both producers and consumers of data. In the early stages, searching and indexing can be performed on the chemical subject of the calculations, and well defined calculation meta-data. The process of defining more specific quantum chemical definitions, adding them to dictionaries and extracting them consistently from the results of the various software packages can then proceed in an incremental manner, adding additional value at each stage.Not only will these results help to change the data management model in the field of Quantum Chemistry, but the methodology can be applied to other pressing problems related to data in computational and experimental science.

U.S. environmental regulations require the collection, statistical evaluation, and reporting of data associated with ground-water monitoring at hazardous waste facilities. Desktop personal computers are capable of managing the large volume of data and automatically generating the required reports. A functional data base for ground-water monitoring data has been developed for the Apple II personal computer. Design emphasis was placed on error-checking during data entry and on simplicity and consistency of all operations available to the user. This should be considered an integral part of quality assurance/quality control considerations, not only throughout the operations of sampling and chemical and physical measurements, but also throughout all operations involving data entry, storage, manipulation, and reporting. The programming language used in data base development (a structured BASIC) was chosen to facilitate testing and debugging of program modules. A major design objective was to assure that all operations involved in entry, storage, manipulation, and statistical evaluation of data are well-documented and “bug-free.”

This grant was $12500 for partial support of an international conference, Molecular Quantum Mechanics 2010, which was held on the campus of the University of California, Berkeley, from 24 to 29 May 2010. The conference involved more than 250 participants. The conference schedule ran from as early as 8:00 AM to as late as 10:30 PM at night, in order to accommodate six historical lectures, 16 plenary lectures, 42 invited talks and two very strong poster sessions containing 143 contributed posters. Since 1989, the Molecular Quantum Mechanics (MQM) series of international conferences has show- cased the frontiers of research in quantum chemistry with a strong focus on basic theory and algorithms, as well as highlights of topical applications. Both were strongly in evidence at MQM 2010. At the same time as embracing the future, the MQM conferences also honour the lifetime contributions of some of the most prominent scientists in the field of theoretical and computational quantum chemistry. MQM 2010 recognised the work of Prof. Henry F. ‘Fritz’ Schaefer of the Center for Computational Chemistry at the University of Georgia, who was previously on the faculty at Berkeley The travel of invited speakers was partially covered by sponsorships from Dell Computer, Hewlett-Packard, Journal of Chemical Theory and Computation, Virginia Tech College of Science, Molecular Physics, Q-Chem Inc and the American Institute of Physics. By contrast, the conference grant from the Department of Energy was used to provide fellowships and scholarships to enable graduate students and postdoctoral fellows to attend the meeting, and thereby broaden the participation of young scientists at a meeting where in the past most of the attendees have been more senior faculty researchers. We believe that we were very successful in this regard: 118 students and postdocs attended out of the total of 256 participants. In detail, the DOE sponsorship money was partially used for dormitory scholarships that covered the cost of shared accommodation for students and postdocs at Berkeley dormitories. This covered the $200-$305 cost of a shared room for the 5-day duration of the conference. The only condition of these scholarships was that the awardee must present a poster at the meeting. Approximately $7565 was spent for these dormitory scholarships. The remaining expenditures of $4800 was used for 12 merit scholarships which were awarded to students whose poster presentations were judged the best at the conference. This amount covered a significant part of their travel and registration fees.

The key trends and prospects of development of computational chemistry that formed in the early 2010s are considered. The most advanced methods for solution of various types of challenges in the computational and quantum chemistry by calculations in the distributed environments (Grid) and on high-performance supercomputer installations and the application methods of parallel and distributed computations are demonstrated; the tailor-made technologies developed for these calculations are described.

This paper gives a description of building a Grid middleware portal infrastructure in CCLRC to allow computational scientists, researchers and application users access to resources via an easy to use Web based portal interfaces. The goal is to develop common Grid application components that can be used by portal developers and administrators to build and deploy on open source portal frameworks. This will allow users to authenticate securely to remote resources and provide transparent access via Grid related tools to manage their tasks efficiently. The current portal technology, JSR 168, is described for the development of Java based applications. The work is substantiated by giving an example of building the UK National Grid Service (NGS) portal. NGS Portal itself works as middleware; it "glues" different Grid Resources together in a single location. Portals and portlets are not confined to a Web-based solution, through Web Services for Remote Portlets WSRP [8] portlets offered by different portal framworks can be consumed in software ranging from desktop to PDA.

Computational chemistry methods and tools have enabled studies of biological processes and chemical reactions to get insights from detailed atomic structures and reaction mechanisms. In this thesis, two biological problems are attacked by the classical force fields simulations and two homogeneous catalysis problems are studied by quantum chemical calculations. In all four problems, new insights have been revealed by the computational results. Chapter 1 briefly reviews the computational chemistry theories and methods developed and popularized in the past few decades. Chapter 2 addresses the protein-protein interaction problem in the onset of meningitis where E. coli OmpA interacts with FcγRI α-chain (FcγRIa) to invade macrophages. Computationally predicted three-dimensional structure of the OmpA-FcγRIa complex showed the role of three N-glycans in FcγRIa in the interaction. Chapter 3 studies the molecular origin of the bitter aftertaste of a kind of natural sweetener called steviol glycosides. By examining the predicted binding complexes between the human bitter taste receptors 2R4 and 2R14 which could be activated by steviol glycosides, a general activation model is proposed to explain the structure-function relationship and to predict new natural sweeteners with less bitterness. Chapter 4 investigated the reaction mechanisms of methane to methanol conversion by a biomimetic tricopper cluster compound. An unusual exchange-stabilized multiradical state is found to be responsible for the hydrogen abstraction reactivity and a methyl radical rebound mechanism is proposed for methane oxidation. Calculations also show interesting spin crossing during the reaction cycle with high spin state forbidden for methyl rebound. Chapter 5 examines the reaction mechanisms in olefin hydrosilylation by the Pt-based Karstedt’s catalyst. An unexpected rate-determining step of agostic bond dissociation is found in between the elementary reaction steps proposed previously. The regioselectivity of the products are studied. An alternative reaction cycle which is kinetically unflavored is proposed. Oxygen stability is studied.

This European Conference on Computational Chemistry (EUCO-CC5) is the fifth in a series, following the previous ones held in Nancy, Lisboa, Budapest, and Assisi. These meetings, organized by the Working Party on Computational Chemistry (WPCC) of the Federation of the European Chemical Societies (FECS), are intended to give a broad view of the present-day achievements and capabilities of computational chemistry, whose strength depends on the strong interaction between theoretical and computational aspects. In fact, as a result of the rapid evolution of computational algorithms and computer technology, this science now covers a much larger field than the original one, which was essentially restricted to quantum chemistry. For this reason, in the present edition of the European Conference on Computational Chemistry, different aspects of this discipline have been covered, ranging from spectroscopy, thermodynamics, or molecular modeling to chemiometrics or grid computation. These themes were introduced by plenary lectures given by scientists from seven European countries and covered by communications and poster sessions. This conference could not have been organized without the valuable support of the Universities Paul Sabatier, Toulouse; de Provence and Paul Cézanne, Marseille; and the Laboratoire de Physique Quantique, Toulouse. The organizing committees of the Laboratoire de Physique Quantique, Toulouse (Jean-Pierre Daudey, Stefano Evangelisti, Nadine Halberstadt, Sophie Hoyau, Franck Jolibois, Thierry Leininger, Laurent Maron, Colin Marsden, Romuald Poteau, Fernand Spiegelman, and Christian Teichteil) and of the Groupe de Chimie Théorique et Modélisation Moléculaire, Marseille (Alain Allouche, Nicolas Ferré, Stéphane Humbel, Anouk Siri, and Didier Siri) thank Mrs. Gisèle Dedieu for her kind and precious help. Finally, we thank the editors, and especially Professor Erkki Brändas, for the publication of the proceedings of the conference in this Special Issue of the International Journal of Quantum Chemistry.

This paper describes research work carried out with the aim to investigate dynamically evolving database environments and corresponding schemata, allowing storage and manipulation of variable length data, a variable number of fields per record, variable length records, manipulation of authority records and links between records and fields, and dynamically defined objects (relations in the traditional sense). The paper proposes a new framework for the definition of a unified schema that eliminates completely the need for reorganisation at both logical and internal levels. Retrieval of data is optimised through self‐contained storage chunks that also vary dynamically.

Unmanned aerial vehicles (UAVs) offer important strategic advantages in the Internet of Military Things (IoMT). On the other hand, the use of the UAV by an untrusted party may threaten security and perhaps endanger the vital operation of the IoMT network. The IoMT network additionally faces significant challenges from data falsification and manipulation through unauthorised access. For the purpose of addressing these challenges, this research presents a blockchain-based architecture and user authentication mechanism for the purpose of identifying and keeping track of unauthorized UAVs in the IoMT network. Blockchain technology not only stores data on the central control server but also forbids unauthorized access, data manipulation, and illegal intrusions. Additionally, a unique consensus model for UAV communication has been created. By streamlining the resource-constrained mining process, the created consensus can improve the efficiency of blockchain transactions between UAVs.

Extreme-scale simulations and high-resolution instruments have been generating an increasing amount of data, which poses significant challenges to not only data storage during the run, but also post-processing where data will be repeatedly retrieved and analyzed for a long period of time. The challenges in satisfying a wide range of post-hoc analysis needs while minimizing the I/O overhead caused by inappropriate and/or excessive data retrieval should never be left unmanaged. In this paper, we propose a data refactoring, compressing, and retrieval framework capable of 1) fine-grained data refactoring with regard to precision; 2) incrementally retrieving and recomposing the data in terms of various error bounds; and 3) adaptively retrieving data in multi-precision and multi-resolution with respect to different analysis. With the progressive data re-composition and the adaptable retrieval algorithms, our framework significantly reduces the amount of data retrieved when multiple incremental precision are requested and/or the downstream analysis time when coarse resolution is used. Experiments show that the amount of data retrieved under the same progressively requested error bound using our framework is 64% less than that using state-of-the-art single-error-bounded approaches. Parallel experiments with up to 1, 024 cores and ~ 600 GB data in total show that our approach yields 1.36× and 2.52× performance over existing approaches in writing to and reading from persistent storage systems, respectively.

For the past few years, the pharmaceutical industry has made rapid growth. The changes are being made in information technology each passing day. This development has automated almost all the data storage and retrieval tasks on different levels. This paper has discussed a case study on “Merck-Medco,” whose operational employees faced difficulties in data retrieval. This paper has analogies from a research paper that have also been put forward on Merck-Medco. According to this research report, Merck-Medco has an ineffective implementation of Customer Relationship Management. This study discusses all the major and minor problems regarding this and suggests some solutions that can be proved beneficial to improve Customer Relationship Management’s efficiency. This study has recommended solutions that would improve the integration of systems. Also, this paper put forward the proof on how information technology can play such a vital role to boost Customer Relationship Management’s Operational efficiency by analyzing all present market dynamics such as differentiation strategies, Firms value chain analysis, and porters five forces.

This paper proposes a data storage method that cost-efficiently manages a massive amount of short lifetime data continuously generated typically by IoT devices (called Live Data, e.g., surveillance camera images) considering real-time data retrieval. Along with the rapid growth of the IoT, many users expect to shift to an Open IoT in which they can share enormous amounts of Live Data. To efficiently use Live Data, it is important to use both hot and cold data storage. Data should be stored in cold storage, which is less expensive but has slow access speeds than hot storage, only if the data are unlikely to be used. The proposed method virtualizes distributed hot storage to provide two data placement mechanisms; (1) an original-data-only optimized allocation according to demand by migrating original data to the appropriate distributed hot storage, and (2) integrated data replacement in the case of capacity overflow by migrating data to the distributed hot storage storing less useful data. As a result of a performance evaluation, compared with a cache algorithm often used for traditional data, the proposed method can reduce operational costs (transmission costs for data migration and retrieval and miss–hit penalty costs) when the ratio of single miss–hit penalty costs to 1-hop transmission costs is more than 6.

With the fast development of industrial Internet of things (IIoT), a large amount of data is being generated continuously by different sources. Storing all the raw data in the IIoT devices locally is unwise considering that the end devices’ energy and storage spaces are strictly limited. In addition, the devices are unreliable and vulnerable to many threats because the networks may be deployed in remote and unattended areas. In this paper, we discuss the emerging challenges in the aspects of data processing, secure data storage, efficient data retrieval and dynamic data collection in IIoT. Then, we design a flexible and economical framework to solve the problems above by integrating the fog computing and cloud computing. Based on the time latency requirements, the collected data are processed and stored by the edge server or the cloud server. Specifically, all the raw data are first preprocessed by the edge server and then the time-sensitive data (e.g., control information) are used and stored locally. The non-time-sensitive data (e.g., monitored data) are transmitted to the cloud server to support data retrieval and mining in the future. A series of experiments and simulation are conducted to evaluate the performance of our scheme. The results illustrate that the proposed framework can greatly improve the efficiency and security of data storage and retrieval in IIoT.