Resumen de E-science approaches in molecular science
Computer simulations of the properties of processes and materials are becoming increasingly necessary in several technological and environmental studies. This implies a growing demand of computing resources that severely exploits computational environments in terms of sustainability and reliability of the infrastructure.
The developments in computing hardware and software, in particular the deployment of world-wide reliable Grid Computing infrastructures, the adoption of innovative computing approaches like the General Purpose Graphic Processing Unit (GPGPU) Computing and the High Performance Network environments, stimulate the exploitation of new approaches and methodologies in Computational Sciences. Furthermore the advances made in the World Wide Web, allow the implementation of Web sites from which the simulation of elementary chemical processes at molecular level is performed combining various techniques and computational approaches which are executed on High Throughput Computing (HTC) and/or High Performance Computing (HPC) platforms.
The ubiquity of information and computing resources has impacted on the researchers¿ productivity, in a similar way the same technologies impacted everyone¿s daily life. The E-science technologies facilitate the exchange of information among researchers, enhance the collaborative work and increase the quality of dissemination of results. Several European initiatives are devoted to facilitate researchers¿ work and to establish networks among researchers of the various disciplines, enabling some European research groups to reach leading positions in their disciplines. We have got the support of the EU COST (COllaboration in Science and Technology) Initiative in two Actions devoted to the facilitation of adoption of Grid and Distributed Computing technologies in Molecular and Matter Sciences. In particular I participated to the COST D23 Action: Metachem - Metalaboratories for Complex Computational Applications in Chemistry (2000-2005), and I coordinated the Working Group: Simbex: a metalaboratory for the a priori simulation of crossed molecular Beam Experiments. Furthermore I participated to the COST D37 Action: Grid Computing in Chemistry: GRIDCHEM (2006-2009), and I coordinated the Working Group: ELAMS: E-science and Learning Approaches in Molecular Science.
The outcomes of both COST Actions contributed significantly to establish an active group of Computational Chemistry and Molecular and Matter Science laboratories which adopted the Grid Computing as an innovative computing paradigm for performing massive computational campaigns.
Since 2004 the researchers of such laboratories joined the Virtual Organization (VO) CompChem established on the EGEE Grid Infrastructure, the largest distributed computing environment ever established worldwide, and coordinated by CERN (Conseil Européen pour la Rechèrche Nucléaire). I served as VO Manager since the VO was established, under the coordination of Prof. Antonio Laganà, Department of Chemistry, University of Perugia.
The present thesis covered a long period of research work focused on implementing some e-science instruments to the computational chemistry community, in particular the community of users belonging to the COMPCHEM Virtual Organization active in the EGEE/EGI European Grid Initiative.
The Thesis describes some tools and approaches the author adopted to provide innovative tools to the Computational Chemistry community based on two main pillars:
1. approaches for running large computational campaigns on Grid Infrastructures 2. adopting virtual reality techniques for making more intuitive the interaction with nanoscale computing approaches and simplifying the definition of the initial conditions of the molecular simulations The research work originated 10 research papers, several of them produced as a joint work with European laboratories interested in the implementation of e-science tools for a smart, curious and demanding community like the Computational Chemistry one.
The author has been able to provide a useful view of the molecular world through the use of virtual reality techniques, combined with the most advanced Web technologies, in particular using the ISO standard X3D for the 3D visualization and interaction with a virtual world. These innovative tools enabled the researchers to set up the environment for carrying out complex molecular simulations (as in the case of the Dl-Poly software package) in a intuitive and visual way. Once defined the species interacting in the considered molecular system, represented in a virtual world, the system produce the input file for the simulation and the Dl-Poly program may be launched, possibly on a Grid infrastructure to take benefit of the powerful available computational resources.
In chapters 1, 2 and 3 the various steps toward the implementation of an a-priori molecular simulator on the EGEE/EGI Grid, for the COMPCHEM VO users, are reported.
Molecular Virtual Reality applications are really useful as e-learning support tools for Chemistry students. To this purpose we implemented a Learning Management System based on a semantic web approach, described in chapter 7, and an assessment system, described in chapter 8, which have been used several times to assess the competences of students participating to the Erasmus Mundus Master of Science in Theoretical Chemistry and Computational Modeling. The system enables the coordinators of the Master to monitor the progresses made by the students an a daily basis.
The author has shown how it is possible to use virtual reality approaches to describe a chemical experiment at both human and molecular level using a virtual reality approach. To this end a multi-scale virtual reality approach has been adopted to deal with the description of the physical environment,HVR. The main features of the virtual reality representation of the experiments and the potentiality of associating VRML and X3D with Java engine calculator are outlined in chapter 4.
In chapter 5 an X3D Molecular Virtual Reality environment in which the researcher is able to interact with it by using immersive devices and dynamic gestures is described. By using the gestures the researcher is able to modify the composition of the molecular system by adding or subtracting functions and the molecular properties of the new species are evaluated in real time by invoking a Web Service implementing the simulation environment. This has required the assemblage of an innovative approach coupling the management of immersive devices with Web Services and molecular dynamics packages.
In chapter 6 the author has presented an X3D Molecular Virtual Reality environment which makes usage of the most recent and powerful HTML and Web technologies. The approach implemented takes into account the modern approaches followed in implementing Social Networking environments and showed how useful these approaches are also in implementing scientific environments. We think such type of work is important also in consideration of how our lifestyle is changing, thanks to the ubiquity of the information, the availability of an increasing availability of storage and computing power. The social networking showed us how deep may be the impact of the computing and networking facility in the daily life and similarly the computational science, and the computational chemistry in particular, has to reshape the classical approaches and methodologies in order to gain advantage of the modern computing platforms and the powerfulness of the networking, distributed and mobile environments.
