An algorithm for two-dimensional mesh generation based on the pinwheel tiling

We propose a new two-dimensional meshing algorithm called PINW able to generate meshes that accurately approximate the distance between any two domain points by paths composed only of cell edges. This technique is based on an extension of pinwheel tilings proposed by Radin and Conway. We prove that the algorithm produces triangles of bounded aspect ratio. This kind of mesh would be useful in cohesive interface finite element modeling when the crack propagation pathis an outcome of a simulation process.Comment: Short version appears in Proceedings of 2004 International Meshing Roundtable at http://www.imr.sandia.go

Study of atmospheric ozone concentration and its longterm variability (Climatology).

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Electrically modulated photoluminescence in ferroelectric liquid crystal

Electrical modulation and switching of photoluminescence (PL) have been demonstrated in pure deformed helix ferroelectric liquid crystal (DHFLC) material. The PL intensity increases and peak position shifts towards lower wavelength above a threshold voltage which continues up to a saturation voltage. This is attributed to the helix unwinding phenomenon in the DHFLC on the application of an electric field. Moreover, the PL intensity could be switched between high intensity (field-on) and low intensity (field-off) positions. These studies would add a new dimension to ferroelectric liquid crystal's application in the area of optical devices.Comment: 4 figure

Intrinsic Curie temperature bistability in ferromagnetic semiconductor resonant tunneling diodes

We predict bistability in the Curie temperature-voltage characteristic of double barrier resonant-tunneling structures with dilute ferromagnetic semiconductor quantum wells. Our conclusions are based on simulations of electrostatics and ballistic quantum transport combined with a mean-field theory description of ferromagnetism in dilute magnetic semiconductors.Comment: 10 pages, 3 figures, submitted to Phys. Rev. B; typo removed in revised version - spurious eq.12 immediately after eq.1

Modulation of the Disordered Conformational Ensembles of the p53 Transactivation Domain by Cancer-Associated Mutations

Citation: Ganguly, D., & Chen, J. H. (2015). Modulation of the Disordered Conformational Ensembles of the p53 Transactivation Domain by Cancer-Associated Mutations. Plos Computational Biology, 11(4), 19. doi:10.1371/journal.pcbi.1004247Intrinsically disordered proteins (IDPs) are frequently associated with human diseases such as cancers, and about one-fourth of disease-associated missense mutations have been mapped into predicted disordered regions. Understanding how these mutations affect the structure-function relationship of IDPs is a formidable task that requires detailed characterization of the disordered conformational ensembles. Implicit solvent coupled with enhanced sampling has been proposed to provide a balance between accuracy and efficiency necessary for systematic and comparative assessments of the effects of mutations as well as post-translational modifications on IDP structure and interaction. Here, we utilize a recently developed replica exchange with guided annealing enhanced sampling technique to calculate well-converged atomistic conformational ensembles of the intrinsically disordered transactivation domain (TAD) of tumor suppressor p53 and several cancer-associated mutants in implicit solvent. The simulations are critically assessed by quantitative comparisons with several types of experimental data that provide structural information on both secondary and tertiary levels. The results show that the calculated ensembles reproduce local structural features of wild-type p53-TAD and the effects of K24N mutation quantitatively. On the tertiary level, the simulated ensembles are overly compact, even though they appear to recapitulate the overall features of transient long-range contacts qualitatively. A key finding is that, while p53-TAD and its cancer mutants sample a similar set of conformational states, cancer mutants could introduce both local and long-range structural modulations to potentially perturb the balance of p53 binding to various regulatory proteins and further alter how this balance is regulated by multisite phosphorylation of p53-TAD. The current study clearly demonstrates the promise of atomistic simulations for detailed characterization of IDP conformations, and at the same time reveals important limitations in the current implicit solvent protein force field that must be sufficiently addressed for reliable description of long-range structural features of the disordered ensembles