The CGU (convex global underestimator) global optimization method is used to predict the minimum energy structures, i.e. folded states, of small protein sequences. Computational results obtained from the CGU method applied to actual protein sequences using a detailed polypeptide model and a differentiable form of the Sun/Thomas/Dill potential energy function are presented. This potential functi...

A protein backbone has two degrees of conformational freedom per residue, described by its ϕ,ψ-angles. Accordingly, the energy landscape of a blocked peptide unit can be mapped in two dimensions, as shown by Ramachandran, Sasisekharan, and Ramakrishnan almost half a century ago. With atoms approximated as hard spheres, the eponymous Ramachandran plot demonstrated that steric clashes alone elimi...

We present a contraction algorithm for finding a minimal set of arcs or vertices that break all cycles in a digraph. The algorithm is (essentially) an extension to the contraction algorithm for the feedback vertex set problem introduced by Levy and Lew (Levy & Lew 1988). The algorithm’s time complexity of O (m log n) is preserved, while allowing both (weighted) feedback vertices and arcs. As th...

Cyclic peptides are a promising class of molecules that can be used to target specific protein-protein interactions. A computational method to accurately predict their structures would substantially advance the development of cyclic peptides as modulators of protein-protein interactions. Here, we develop a computational method that integrates bias-exchange metadynamics simulations, a Boltzmann ...

The pathology of Alzheimer's disease can ultimately be traced to the increased aggregation stability of Aβ42 peptides which possess two extra residues (Ile 41 &Ala 42) that the non-pathological strain (Aβ40) lacks. We have found Aβ42 fibrils to exhibit stronger energies in inter-chain interactions and we have also identified the cause for this increase to be the result of different Ramachandran...

We have theoretically and experimentally demonstrated that the resonant wavelength of long period fiber gratings (LPG) can be shifted by a large magnitude by coating with only a nm-thick thin-film that has a refractive index higher than that of the glass cladding. The resonant wavelength shift can result from either the variation of the thickness of the film and/or the variation of its refracti...