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Topological data analysis has been recently used to extract meaningful information frombiomolecules. Here we introduce the application of persistent homology, a topological data analysis tool, for computing persistent features (loops) of the RNA folding space. The scaffold of the RNA folding space is a complex graph from which the global features are extracted by completing the graph to a simplicial...
A continuum mechanical model based on the Helfrich Hamiltonian is devised to investigate the coupling between lipid composition and membrane curvature. Each monolayer in the bilayer is modeled as a freely deformable surface with a director field for lipid orientation. A scalar field for the mole fraction of two lipid types accounts for local changes in composition. It allows lipids to access monolayer...
Proteins interact to perform biological functions through specific interface residues. Correctly understanding the mechanisms of interface recognition and prediction are important for many aspects of life science studies. Here, we report a novel architecture to study protein interface residues. In our method, multiple dimensional space was built on some meaningful features. Then we divided the space...
In this work, the existence of a global minimizer for the previous Lagrangian formulation of nonpolar solvation model proposed in [1] has been proved. One of the proofs involves a construction of a phase field model that converges to the Lagrangian formulation. Moreover, an Eulerian formulation of nonpolar solvation model is proposed and implemented under a similar parameterization scheme to that...
Novel approaches for generating and comparing flexible (non-rigid) molecular surface meshes are developed. The mesh-generating method is fast and memory-efficient. The resulting meshes are smooth and accurate, and possess high mesh quality. An isometric-invariant shape descriptor based on the Laplace- Beltrami operator is then explored for mesh comparing. The new shape descriptor is more powerful...
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