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- Taner Z. Sen, Andrzej Kloczkowski, +8 authors Drena Dobbs
- BMC Bioinformatics
- 2004

BACKGROUND
Protein-protein interactions play a critical role in protein function. Completion of many genomes is being followed rapidly by major efforts to identify interacting protein pairs experimentally in order to decipher the networks of interacting, coordinated-in-action proteins. Identification of protein-protein interaction sites and detection of… (More)

We propose three phases of H 2 O under ultrahigh pressure. Our structural search was performed using an adaptive genetic algorithm which allows an extensive exploration of crystal structure at density functional theory accuracy. The sequence of pressure-induced transitions beyond ice X at 0 K should be ice X → P bcm → P bca → P mc2 1 → P 2 1 → P 2 1 /c… (More)

Using a first-principles genetic algorithm we predict an Fe 2 P phase is the first post-pyrite phase of SiO 2 at low temperatures. This contrasts with a recently predicted cotunnite phase. Static enthalpy differences between these two phases are small near the transition pressure (0.69 TPa). While quasiharmonic free energy calculations predict an Fe 2… (More)

- Aaron Gilad Kusne, Tieren Gao, +8 authors Ichiro Takeuchi
- Scientific reports
- 2014

Advanced materials characterization techniques with ever-growing data acquisition speed and storage capabilities represent a challenge in modern materials science, and new procedures to quickly assess and analyze the data are needed. Machine learning approaches are effective in reducing the complexity of data and rapidly homing in on the underlying trend in… (More)

- Xiaofeng Qian, Ju Li, +5 authors Sidney Yip
- 2008

Wave functions obtained from plane-wave density-functional theory (DFT) calculations using norm-conserving pseudopotential, ultrasoft pseudopotential, or projector augmented-wave method are efficiently and robustly transformed into a set of spatially localized nonorthogonal quasiatomic orbitals (QOs) with pseudoangular momentum quantum numbers. We… (More)

- Tzu-Liang Chan, Cristian V Ciobanu, Feng-Chuan Chuang, Ning Lu, Cai-Zhuang Wang, Kai-Ming Ho
- Nano letters
- 2006

We report a genetic algorithm approach combined with ab initio calculations to determine the structure of hydrogenated 110 Si nanowires. As the number of atoms per length increases, we find that the cross section of the nanowire evolves from chains of six-atom rings to fused pairs of such chains to hexagons bounded by {001} and {111} facets. Our… (More)

- Ju Li, Cai-Zhuang Wang, Jin-Peng Chang, Wei Cai, Vasily V. Bulatov, Kai-Ming Ho
- 2004

Using a formulation based on anisotropic elasticity we determine the core energy and Peierls stress of the a 0 /2͓111͔ screw dislocation in bcc molybdenum at T = 0. We show that a proper definition of the core energy necessarily involves choosing a reference direction a ˆ and a reference radius r 0 in order to describe dislocation dipole rotation and… (More)

- Bei Liu, Zhong-Yi Lu, +4 authors Martin F. Jarrold
- 1998

We have performed a systematic ground state geometry search for the singly charged Si n cations in the medium-size range (nр20) using density functional theory in the local density approximation ͑LDA͒ and generalized gradient approximation ͑GGA͒. The structures resulting for nр18 generally follow the prolate ''stacked Si 9 tricapped trigonal prism'' pattern… (More)

This article may be used for research, teaching and private study purposes. Any substantial or systematic reproduction, redistribution , reselling , loan or sub-licensing, systematic supply or distribution in any form to anyone is expressly forbidden. The publisher does not give any warranty express or implied or make any representation that the contents… (More)

- Min Ji, Cai-Zhuang Wang, Kai-Ming Ho
- Physical chemistry chemical physics : PCCP
- 2010

In this work several crystal structure prediction problems which have been studied by first-principles evolutionary algorithms recently are revisited. We increased the system size to see how the search efficiency changes with respect to problem size. We find that the relative performance and underlying mechanism of genetic algorithms in crystal structure… (More)