Contact maps have been used in ab initio methods for the problem of protein structure prediction problem. Secondary structures and contacts made by the residues are clearly visible in the contact maps where helices are seen as thick bands and the beta sheets are seen as orthogonal to the diagonal. This paper explores the idea of extracting rules from contact maps to represent “protein fold” inf...

I discuss the spectrum of hadrons containing heavy quarks (b or c), and how well the experimental results are matched by theoretical ideas. Useful insights come from potential models and applications of Heavy Quark Symmetry and these can be compared with new numerical results from the ab initio methods of Lattice QCD.

The need to determine phases is a major bottleneck in a fully automated X-ray crystallography pipeline. The problem commonly called phasing can be solved by a computational method called molecular replacement (MR). With the deposition of more and more proteins into the Protein Data Bank (PDB), it has been shown that the MR yields better initial models. In this paper, ab initio first model gener...

The recent discovery of pure boron nanotubes raises questions about their detailed atomic structure. Previous simulations predicted tubular structures with smooth or puckered surfaces. Here, we present some novel results based on ab initio simulations of bundled single–wall zigzag boron nanotubes (ropes). Besides the known smooth and puckered modifications, we found new forms that are radially ...

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In this Letter we investigate boron diffusion as a function of the Fermi-level position in crystalline silicon using ab initio calculations. Based on our results, a new mechanism for B diffusion mediated by Si self-interstitials is proposed. Rather than kick out of B into a mobile channel, we find a direct diffusion mechanism for the boron-interstitial pair for all Fermi-level positions. Our ac...