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We develop rigorous alternating direction optimization methods for a prototype constrained convex optimization template, which has broad applications in computational sciences. We build upon our earlier work on the model-based gap reduction (MGR) technique ...
Architectural structures such as buildings, towers, bridges and roofs are of fundamental importance in urban environments. Their design, planing, construction and maintenance carry numerous challenges in engineering due to the complex interplay of material ...
Computational approaches are breaking new ground in understanding how embryos form. Here, we discuss recent studies that couple precise measurements in the embryo with appropriately matched modeling and computational methods to investigate classic embryoni ...
Systems biology is a multidisciplinary field that weaves together all the basic sciences through the use of computational and bioinformatics tools, to provide a more integrative view of the complex molecular interactions taking place within and among cells ...
We benchmark the performance of various computational approaches, ranging from the classical nonpolarizable force fields AMBER FF96 and FF99SB, the polarizable force fields AMBER FF02polEP and AMOEBAbio09 to the semiempirical DFT method SCC-DFTB. The test ...
We cast the under-determined convolutive speech separation as sparse approximation of the spatial spectra of the mixing sources. In this framework we compare and contrast the major practical algorithms for structured sparse recovery of speech signal. Speci ...
We consider linear systems A(alpha)x(alpha) - b(alpha) depending on possibly many parameters alpha = (alpha(1), ... , alpha(p)). Solving these systems simultaneously for a standard discretization of the parameter range would require a computational effort ...
Society for Industrial and Applied Mathematics2011
Stochastic models of biological networks properly take the randomness of molecular dynamics in living cells into account. Numerical solution approaches inspired by computational methods from applied probability can efficiently yield accurate results and ha ...
One of the most important advances in biology in recent years may be the discovery of RNAs that can regulate gene expression. As one kind of such functional noncoding RNAs, microRNAs (miRNAs) forma class of endogenous 19–23-nucleotide RNAs that can have im ...
Oxalate decarboxylase (OxDC) catalyzes the Mn-dependent conversion of the oxalate monoanion into CO2 and formate. EPR-based strategies for investigating the catalytic mechanism of decarboxylation are complicated by the difficulty of assigning the signals a ...