Displaying similar documents to “TEAMLOG in Action: a Case Study in Teamwork”

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

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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....

Vibrational properties of nanographene

Sandeep Kumar Singh, F.M. Peeters (2013)

Nanoscale Systems: Mathematical Modeling, Theory and Applications

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The eigenmodes and the vibrational density of states of the ground state configuration of graphene clusters are calculated using atomistic simulations. The modified Brenner potential is used to describe the carbon-carbon interaction and carbon-hydrogen interaction in case of H-passivated edges. For a given configuration of the C-atoms the eigenvectors and eigenfrequencies of the normal modes are obtained after diagonalisation of the dynamical matrix whose elements are the second derivative...

Analysis of fast boundary-integral approximations for modeling electrostatic contributions of molecular binding

Amelia B. Kreienkamp, Lucy Y. Liu, Mona S. Minkara, Matthew G. Knepley, Jaydeep P. Bardhan, Mala L. Radhakrishnan (2013)

Molecular Based Mathematical Biology

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We analyze and suggest improvements to a recently developed approximate continuum-electrostatic model for proteins. The model, called BIBEE/I (boundary-integral based electrostatics estimation with interpolation), was able to estimate electrostatic solvation free energies to within a mean unsigned error of 4% on a test set of more than 600 proteins¶a significant improvement over previous BIBEE models. In this work, we tested the BIBEE/I model for its capability to predict residue-by-residue...

Theory, Experiment and Computation of Half Metals for Spintronics: Recent Progress in Si-based Materials

C. Y. Fong, M. Shaughnessy, L. Damewood, L. H. Yang (2012)

Nanoscale Systems: Mathematical Modeling, Theory and Applications

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Since the term “spintronics” was conceived in 1996, there have been several directions taken to develop new semiconductor-based magnetic materials for device applications using spin, or spin and charge, as the operational paradigm. Anticipating their integration into mature semiconductor technologies, one direction is to make use of materials involving Si. In this review, we focus on the progress made, since 2005, in Si-based half metallic spintronic materials. In addition to commenting...