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233. Advanced Simulation of Metal Clusters

Author

CLARK ATLANTA UNIV GA DEPT OF PHYSICS, Wang, Xiao-Qian, CLARK ATLANTA UNIV GA DEPT OF PHYSICS, and Wang, Xiao-Qian

Abstract

In an effort to develop efficient O(N) first-principles calculation algorithms, we devised the approach using wavelets as basis functions of electronic structure calculation. The theory of wavelets allows one to apply a multi-scale (multiresolution) analysis to problems that exhibit widely varying length scales. Furthermore, the dual localization property of the wavelet basis is useful for improving the existing (N) methods that are yet based solely on the real-space locality. Our application O this idea to the density-functional molecular dynamics method leads to a robust algorithm, which holds potential to extend the applicability of the current first-principles methods to systems an order of magnitude large. On the other hand, we have developed an approach to the development of reliable "pair-functional" interatomic potentials for monoatomic metals based on fitting to a large set of experimental and ab initio data. In connection with the construction of improved and accurate semi-empirical models, we have investigated the simulation tools such as hyper-Molecular Dynamics, generalized simulated annealing for global optimization, finite-difference method for calculating non-linear static third-order polarizabilities.

Published
1999

234. Advanced Simulation of Electronic Materials: A Paradigm for Distributive Computing and Simulations.

Author

CLARK ATLANTA UNIV GA, Wang, Xiao-Qian, CLARK ATLANTA UNIV GA, and Wang, Xiao-Qian

Abstract

The researchers have developed parallel and distributed algorithms for classical molecular dynamics and first-principles molecular dynamics methods for electronic structure calculations. An effective multivariable optimization scheme is employed for the construction of semi-empircal models. An innovative approach to apply the wavelet theory to electronic structure calculations is devised and implemented. A new iterative approach for solving quantum chemistry problems is discovered and tested for prototype atomic and molecular systems. In addition, a finite field method for calculating non-linear optical properties of molecules is developed and applied to the study of third-order polarizability of carbon-cage fullerenes. These developments in parallel and distributive algorithms have greatly enhanced the efficiency of simulating material properties. Moreover, under the support of the grant, three graduate students have completed their thesis, one for Ph.D, and two others for M.S.

Published
1999

238. Advanced Simulation of Electronic Materials: A Paradigm for Distributive Computing and Simulations.

Author

CLARK ATLANTA UNIV GA, Wang, Xiao-Qian, CLARK ATLANTA UNIV GA, and Wang, Xiao-Qian

Abstract

In this report we summarize the progress to date, including the implementation of Message Passing Interface (MPI) standard on local supercomputers (Cray and powerful workstations); the development of an integrated simulation environment based on distributive computing; the application of a parallel meolecular dynamics algorithm; the formation of the research team; and finally, a brief list of research performed in this four-month period.

Published
1996

248. A New Functional Site W115 in CdtA Is Critical for Aggregatibacter actinomycetemcomitans Cytolethal Distending Toxin.

Author

Li, Lu, Ding, Cheng, Duan, Jun-lan, Yang, Mi-fang, Sun, Ying, Wang, Xiao-qian, and Xu, Yan

Subjects
ACTINOBACILLUS actinomycetemcomitans, CYTOLOGY, GRAM-negative bacteria, CELL adhesion, PROTEIN-protein interactions, MICROBIAL mutation, MEDICAL microbiology
Abstract

Aggregatibacter actinomycetemcomitans, a specific pathogen of localized aggressive periodontitis, produces a cytolethal distending toxin (CDT) that arrests eukaryotic cells irreversibly in G0/G1 or G2/M phase of the cell cycle. Although structural studies show that the aromatic patch region of CdtA plays an important role in its biological activity, the functional sites of CdtA have not been firmly established. In this study, site-specific mutagenesis strategy was employed for cdtA point mutations construction so as to examine the contributions of individual amino acids to receptor binding and the biological activity of holotoxin. The binding ability was reduced in CdtAY181ABC holotoxin and the biological function of CDT was not weaken in CdtAY105ABC, CdtAY125ABC, CdtAF109ABC and CdtAS106NBC holotoxin suggesting that these sites were not critical to CDT. But the binding activity and cell cycle arrest ability of holotoxin complexes were inhibited in CdtAW115GBC. And this site did not affect the holotoxin assembly by size exclusion chromatography. Therefore, W115 might be a critical site of CdtA binding ability. These findings suggest that the functional sites of CdtA are not only in the aromatic patch region. W115, the new functional site is critical for receptor binding and cell cycle arrest, which provides potential targets for pharmacological disruption of CDT activity. [ABSTRACT FROM AUTHOR]

Published
2013
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