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Full-Text Articles in Computer Engineering
Phage-Induced Alignment Of Membrane Proteins Enables The Measurement And Structural Analysis Of Residual Dipolar Couplings With Dipolar Waves And Lambda-Maps, Sang Ho Park, Woo Sung Son, Rishi Mukhopadhyay, Homayoun Valafar, Stanley J. Opella
Phage-Induced Alignment Of Membrane Proteins Enables The Measurement And Structural Analysis Of Residual Dipolar Couplings With Dipolar Waves And Lambda-Maps, Sang Ho Park, Woo Sung Son, Rishi Mukhopadhyay, Homayoun Valafar, Stanley J. Opella
Faculty Publications
At pH > 6 added filamentous bacteriophage fd is compatible with many of the detergents used to solubilize membrane proteins for solution NMR studies of membrane proteins and, therefore, serves as an alignment media. In combination with strained polyacrylamide gel alignment, Dipolar Waves can be used to directly assess the secondary structure and a λ-map extracts the order tensors for de novo structure calculation of membrane proteins without distance restraints.
Gene Order Phylogeny And The Evolution Of Methanogens, Haiwei Luo, Zhiyi Sun, William Arndt, Jian Shi, Robert Friedman, Jijun Tang
Gene Order Phylogeny And The Evolution Of Methanogens, Haiwei Luo, Zhiyi Sun, William Arndt, Jian Shi, Robert Friedman, Jijun Tang
Faculty Publications
Methanogens are a phylogenetically diverse group belonging to Euryarchaeota. Previously, phylogenetic approaches using large datasets revealed that methanogens can be grouped into two classes, “Class I” and “Class II”. However, some deep relationships were not resolved. For instance, the monophyly of “Class I” methanogens, which consist of Methanopyrales, Methanobacteriales and Methanococcales, is disputable due to weak statistical support. In this study, we use MSOAR to identify common orthologous genes from eight methanogen species and a Thermococcale species (outgroup), and apply GRAPPA and FastME to compute distance-based gene order phylogeny. The gene order phylogeny supports two classes of methanogens, but it …
Exploiting Matrix Symmetry To Improve Fpgaaccelerated Conjugate Gradient, Jason D. Bakos, Krishna K. Nagar
Exploiting Matrix Symmetry To Improve Fpgaaccelerated Conjugate Gradient, Jason D. Bakos, Krishna K. Nagar
Faculty Publications
In this paper we describe a new approach for accelerating the Conjugate Gradient (CG) method using an FPGA co-processor. As in previous approaches, our co-processor performs a double-precision sparse matrix-vector multiplication. However, our implementation doubles the amount of computation per unit of input data by exploiting the symmetry of the input matrix and computing the upper and lower triangle of the input matrix in parallel. Using a Virtex-2 Pro 100 FPGA, we have achieved an observed computational throughput of 1155 MFLOPS.
Agents And Service-Oriented Computing For Autonomic Computing: A Research Agenda, Frances M.T. Brazier, Jeffrey O. Kephart, H. Van Dyke Parunak, Michael N. Huhns
Agents And Service-Oriented Computing For Autonomic Computing: A Research Agenda, Frances M.T. Brazier, Jeffrey O. Kephart, H. Van Dyke Parunak, Michael N. Huhns
Faculty Publications
Autonomic computing is the solution proposed to cope with the complexity of today's computing environments. Self-management, an important element of autonomic computing, is also characteristic of single and multiagent systems, as well as systems based on service-oriented architectures. Combining these technologies can be profitable for all - in particular, for the development of autonomic computing systems.