Final Report: NWACC 2008 Project: Interactive Visualizations of Crystal Structures and Morphologies in the Wikipedia Approach Prof. Peter Moeck, Department of Physics, Portland State University (PSU) phone: 503 725 4227, e-mail:
[email protected], April 10, 2009
Summary of our achievements on the basis of funding from the North West Academic Computing Consortium (NWAAC) The project web site is located at http://nanocrystallography.research.pdx.edu/ (the NWACC logo is displayed prominently on all web pages that belong to this site,) see bottom of Fig. 1. Note that our site is rather popular as demonstrated by the more than 35,000 hits since January 1, 2008. We provide at http://nanocrystallography.research.pdx.edu/CIF-searchable/, Fig. 1, free access to a subset of the open-access Crystallography Open Database (COD [1], where I am a member of the international advisory board) and our own three additional (and the COD complementing) Internet based crystallographic databases. Our databases at Portland State University (PSU) contain the records of approximately 25,000 structure determinations. Queries of all of these databases can be downloaded in the standard Crystallographic Information File (CIF) format [2] and displayed in a variety of modes (including anaglyph stereo) by java based applets. We have been identified by World Science News (www.world-science.net) as a high-traffic scientific-data dissemination site and were kindly asked to provide a link to their open-access science news services. Reciprocally we (the Nanocrystallography Group, Portland State University, Ore.) are acknowledged as a supporter of their site (at http://www.world-science.net/x01). Our databases are a mainly inorganic and educational subset of the COD, a dedicated “Nano-Crystallography Database” (NCD), a dedicated “Crystal Morphology Database” (CMD), and the “world’s first” open-access crystallography database “Wiki-CD” in the “wikipedia format”. The latter of these databases has been set up initially with approximately 9,000 minerals and over the last year grown in its detailed information content by some 10%. Mineral data have initially been uploaded to our “Wiki-CD” by us because there are many people interested in mineralogy and many active mineral collectors worldwide. On the basis of the computing infrastructure we made openly available with funds from the NWAAC, there is now a worldwide sharing of knowledge about minerals and inorganic crystals by anonymous contributors. This is possible because our databases utilize the so-called “CIF format”. The CIF (for Crystallographic Information File) format and the associated CIF dictionaries [2] are the outcome of major efforts by the International Union of Crystallography (IUCr, which is
a non-profit organization that represents the common interests of the world’s crystallographers and is also the main publisher of crystallographic reference books and journals). CIF is in essence a kind of “language” in which everything about a crystal can be communicated between human beings (who also read English), between human beings and computers, and between computers alone. In order to facilitate the upload of date by people who are not familiar with the CIF language, we provide both a simple and an advanced CIF Editor/Upload Protocol, Fig. 2. Our Nano-Crystallography Database (NCD), on the other hand, is a research database with registered users from the community of nanocrystallographers. While access if free to the general public, the uploading of data requires registration. We also improved significantly the displays of the crystal structures for all of our databases (by e.g. providing capabilities for 3D anaglyph, Fig. 3, stereo displays). Our Crystal Morphology Database (CMD) has a strong educational component and is topical because there is a renewed interest in the knowledge of crystal morphology that is driven by the demonstration that not only the size of a nanocrystal matters with respect to its properties, but also its morphology. (Catalytic properties of nanocrystals have, for example, recently been shown to be controlled by crystal morphology, ref. [3]!). Early mineralogists and crystallographers did develop a comprehensive and systematic crystal morphology description on the basis of the spatial arrangement of symmetry elements about 100 years ago. The same framework can now be reused and expanded for nanocrystals, but needs to be popularized within the community of researchers and educators that deal with nanocrystals. Figure 4 shows our crystal morphology display program in action. Lattice fringe fingerprinting is now also better supported by our open-access databases, Fig. 5. The goals that I identified in the original proposal have all been met. Figure 6 finally illustrates my group’s involvement in the COP project, with funds from the NWACC, we set up the first mirror of the COD in the Americas, at the respective site at Portland state, we are just 16 entries shy of 75,000 comprehensive crystallographic datasets.
Closing financial statement All funds will be expended according to the guidelines defined by the NWACC. Currently there is unused balance of approximately $1500 in the respective research account at Portland State University. In the week after Easter, I will be chairing the symposium “Electron Crystallography for Materials Research” (http://www.mrs.org/s_mrs/doc.asp?CID=17622&DID=228231) at the spring 2009 Meeting of the Materials Research Society (http://www.mrs.org/s_mrs/sec.asp?CID=17870&DID=231212). During this symposium, I will also give a talk on “Structural Fingerprinting in the Transmission Electron Microscope” which will also cover world wide efforts in open access crystallographic databases and parts of my research group’s work that were sponsored by the NWAAC. Similarly, only a few weeks later, I will give two talks and present two posters about my research group’s work a the annual meeting of the Nano Science and Technology Institute (http://www.nsti.org/Nanotech2009/). The parts of my research group’s work that received funding from the NWAAC will constitute the main parts of one of these talks and of one of the posters (http://www.nsti.org/Nanotech2009/program/equipment.html). The results of this year’s NWACC project will therefore be represented in 3 conference proceedings papers. Partial reimbursement of members of my research group and of myself for attending these
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conferences will result in a state of affairs that all project fund will have been completely utilized according to the guidelines defined by the NWACC.
Other colleges or universities that are utilizing the project results There were more than 35,000 hits on the webpages of this project since we started registering the accesses. The respective colleges and universities are not precisely known. From the distribution of the hits over the course of a day, I can estimate that about 50% of all hits originate in Asia, 20% in Europe and Africa, and 30% in the Americas. It is not precisely known how the results of the project are being utilized in teaching, research, and/or student learning that is going on in other departments and schools around the world. I know personally that at least two faculty members of the Department of Physics and one faculty member of the Department of Chemical Engineering at Oregon State University utilize the project’s results in their teaching and research.
Additional funding (from within the institution or from external granting agencies) attained partially as a result of the NWACC grant Partially as a result of completing this project I am about to receive: about $120,000 from the Army Research Labs, and about $60,000 from the Oregon Nanoscience and Microtechnologies Institute. So far in the last academic year, I received: $5,500 from the Portland State University Venture Fund, $6,000 from the Portland State University Venture Fund, and $7,032 from the Portland State University Faculty Enhancement Fund partially as a result of this NWACC project.
References [1] S. Grazulis, D. Chateigner, R. T. Downs, A. F. T. Yokochi, M. Quirós. L. Lutterotti, E. Manakova, J. Butkus, P. Moeck, A. Le Bail, Crystallography Open Database: an open access collection of crystal structures. A tribute to Micheal Berndt, J. Appl. Cryst. 2009, in press [2] International Tables for Crystallography, Volume G, Definition and exchange of crystallographic data, S. Hall and B. McMahon, eds., Springer, Dordrecht, 2005 [3] N. Tian, Z.-Y. Zhou, S.-G. Sun, Y. Ding, Z. L. Wang: Synthesis of Tetrahexahedral Platinum Nanocrystals with High-Index Facets and High ElectroOxidation Activity, Science 316 (2007) 732-735 3
Figure 1: Screen shot from the page that gives access to PSU’s four open-access crystallographic databases, (http://nanocrystallography.research.pdx.edu/CIF-searchable/). Note that as of April 10, 2009, the different web pages that constitute the whole website were accessed over 35,000 times. 4
Figure 2: Screenshot of our simple CIF editor. This editor allows for the creation of CIF entries for our databases (including the WikiCrystallography Database) by the “crystal and minerals loving” general public.
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Figure 3: Visualization (in one of the anaglyph three-dimensional display modes) of a crystal structure from our open access database (at the atomic level). The opened Java Applet demonstrates the versatility of our new display mode (left hand side). The PI of this project demonstrating a crystal structure (in the large extra-window format) from our open-access databases to a group of visiting physics professors and instructors from the People’s Republic of China where we all wear anaglyph glasses (right hand side).
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Figure 4: Screenshot of our interactive 3D Crystal Morphology Visualization program. 7
Figure 5: Screenshot of our Lattice fringe fingerprint search-match program.
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Figure 6: Screenshot of the opening screens of two of the four mirrors of the Crystallography Open Database new; (background and left hand side) mirror in Caen/France, (forefront and inset on the right hand side) our new mirror in Portland/Oregon. The COD comprises now the records of nearly 75,000 full crystal structure determinations.
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