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Migration of the Mathematical Collection of Polish Virtual Library of Science to the YADDA Platform

Zamlynska, Katarzyna, Bolikowski, Lukasz, Rosiek, Tomasz (2008)

Towards Digital Mathematics Library. Birmingham, United Kingdom, July 27th, 2008

YADDA framework facilitates information exchange between digital document repositories. YaddaWeb, its web-based interface, provides browse and search functionalities. Content providers use DeskLight application to add or modify metadata and content. Internally, YADDA contains flexible repository aggregation mechanisms, multiple hierarchy support and full-text indexing capabilities. YADDA framework is an excellent solution for Open Access paradigm of content exchange. Migration of the Mathematical...

Multi-core CPU or GPU-accelerated Multiscale Modeling for Biomolecular Complexes

Tao Liao, Yongjie Zhang, Peter M. Kekenes-Huskey, Yuhui Cheng, Anushka Michailova, Andrew D. McCulloch, Michael Holst, J. Andrew McCammon (2013)

Molecular Based Mathematical Biology

Multi-scale modeling plays an important role in understanding the structure and biological functionalities of large biomolecular complexes. In this paper, we present an efficient computational framework to construct multi-scale models from atomic resolution data in the Protein Data Bank (PDB), which is accelerated by multi-core CPU and programmable Graphics Processing Units (GPU). A multi-level summation of Gaussian kernel functions is employed to generate implicit models for biomolecules. The coefficients...

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