We discuss part-of-speech (POS) tagging in presence of large, fine-grained label sets using conditional random fields (CRFs). We propose improving tagging accuracy by utilizing dependencies within sub-components of the fine-grained labels. These sub-label dependencies are incorporated into the CRF model via a (relatively) straightforward feature extraction scheme. Experiments on five languages ...

Normal mode analysis (NMA) with coarse-grained model, such as elastic network model (ENM), has allowed the quantitative understanding of protein dynamics. As the protein size is increased, there emerges the expensive computational process to find the dynamically important low-frequency normal modes due to diagonalization of massive Hessian matrix. In this study, we have provided the domain deco...

this research was performed to determine the efficiency effect of sedimentary environment of kerman city area on soil structure bycomparing natural and reconstituted consolidation curves. in this regard, four different criteria such as sensitivity strength, stresssensitivity, schmertman criteria and the result of the uniaxial compression test were used. the base of these criteria is to compare ...

Conformational sampling is one of the bottlenecks in fragment-based protein structure prediction approaches. They generally start with a coarse-grained optimization where mainchain atoms and centroids of side chains are considered, followed by a fine-grained optimization with an all-atom representation of proteins. It is during this coarse-grained phase that fragment-based methods sample intens...

We have used systematic structure-based coarse graining to derive effective site-site potentials for a 10-site coarse-grained dimyristoylphosphatidylcholine (DMPC) lipid model and investigated their state point dependence. The potentials provide for the coarse-grained model the same site-site radial distribution functions, bond and angle distributions as those computed in atomistic simulations ...

The recently discovered twist-bend nematic phase of achiral bent-shaped molecules, NTB, has a doubly degenerate ground-state with a periodically modulated heliconical structure and unusual distortion elasticity, the theoretical description of which is still debated. We show that the NTB phase has the same macroscopic symmetry as another periodic mesophase, the chiral smectic-A, SmA*. Based on t...

A coarse-grained geometrical model for protein secondary-structure description and analysis is presented which uses only the positions of the C(α) atoms. A space curve connecting these positions by piecewise polynomial interpolation is constructed and the folding of the protein backbone is described by a succession of screw motions linking the Frenet frames at consecutive C(α) positions. Using ...