Free Energy Approach to the Formation of an Icosahedral Structure during the Freezing of Gold Nanoclusters

The freezing of metal nanoclusters such as gold, silver, and copper exhibits a novel structural evolution. The formation of the icosahedral (Ih) structure is dominant despite its energetic metastability. This important phenomenon, hitherto not understood, is studied by calculating free energies of gold nanoclusters. The structural transition barriers have been determined by using the umbrella sampling technique combined with molecular dynamics simulations. Our calculations show that the formation of Ih gold nanoclusters is attributed to the lower free energy barrier from the liquid to the Ih phases compared to the barrier from the liquid to the face-centered-cubic crystal phases

Formation of an Icosahedral Structure during the Freezing of Gold Nanoclusters: Surface-Induced Mechanism

The freezing behavior of gold nanoclusters was studied by employing molecular dynamics simulations based on a semi-empirical embedded-atom method. Investigations of the gold nanoclusters revealed that, just after freezing, ordered nano-surfaces with a fivefold symmetry were formed with interior atoms remaining in the disordered state. Further lowering of temperatures induced nano-crystallization of the interior atoms that proceeded from the surface towards the core region, finally leading to an icosahedral structure. These dynamic processes explain why the icosahedral cluster structure is dominantly formed in spite of its energetic metastability.Comment: 9 pages, 4 figures(including 14 eps-files

Parallel progressive multiple sequence alignment on reconfigurable meshes

<p>Abstract</p> <p>Background</p> <p>One of the most fundamental and challenging tasks in bio-informatics is to identify related sequences and their hidden biological significance. The most popular and proven best practice method to accomplish this task is aligning multiple sequences together. However, multiple sequence alignment is a computing extensive task. In addition, the advancement in DNA/RNA and Protein sequencing techniques has created a vast amount of sequences to be analyzed that exceeding the capability of traditional computing models. Therefore, an effective parallel multiple sequence alignment model capable of resolving these issues is in a great demand.</p> <p>Results</p> <p>We design <it>O</it>(1) run-time solutions for both local and global dynamic programming pair-wise alignment algorithms on reconfigurable mesh computing model. To align <it>m </it>sequences with max length <it>n</it>, we combining the parallel pair-wise dynamic programming solutions with newly designed parallel components. We successfully reduce the progressive multiple sequence alignment algorithm's run-time complexity from <it>O</it>(<it>m </it>× <it>n</it>⁴) to <it>O</it>(<it>m</it>) using <it>O</it>(<it>m </it>× <it>n</it>³) processing units for scoring schemes that use three distinct values for match/mismatch/gap-extension. The general solution to multiple sequence alignment algorithm takes <it>O</it>(<it>m </it>× <it>n</it>⁴) processing units and completes in <it>O</it>(<it>m</it>) time.</p> <p>Conclusions</p> <p>To our knowledge, this is the first time the progressive multiple sequence alignment algorithm is completely parallelized with <it>O</it>(<it>m</it>) run-time. We also provide a new parallel algorithm for the Longest Common Subsequence (LCS) with <it>O</it>(1) run-time using <it>O</it>(<it>n</it>³) processing units. This is a big improvement over the current best constant-time algorithm that uses <it>O</it>(<it>n</it>⁴) processing units.</p

The electronic structure of iridium oxide electrodes active in water splitting

Iridium oxide based electrodes are among the most promising candidates for electrocatalyzing the oxygen evolution reaction, making it imperative to understand their chemical/electronic structure. However, the complexity of iridium oxide's electronic structure makes it particularly difficult to experimentally determine the chemical state of the active surface species. To achieve an accurate understanding of the electronic structure of iridium oxide surfaces, we have combined synchrotron-based X-ray photoemission and absorption spectroscopies with ab initio calculations. Our investigation reveals a pre-edge feature in the O K-edge of highly catalytically active X-ray amorphous iridium oxides that we have identified as O 2p hole states forming in conjunction with IrIII. These electronic defects in the near-surface region of the anionic and cationic framework are likely critical for the enhanced activity of amorphous iridium oxides relative to their crystalline counterparts