Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

“Bioinformatics” 특집을 내면서

Recent years have seen a renewed interest in the harvesting and conversion of solar energy. Among various technologies, the direct conversion of solar to chemical energy using photocatalysts has received significant attention. Although heterogeneous photocatalysts are almost exclusively semiconductors, it has been demonstrated recently that plasmonic nanostructures of noble metals (mainly silver and gold) also show significant promise. Here we review recent progress in using plasmonic metallic nanostructures in the field of photocatalysis. We focus on plasmon-enhanced water splitting on composite photocatalysts containing semiconductor and plasmonic-metal building blocks, and recently reported plasmon-mediated photocatalytic reactions on plasmonic nanostructures of noble metals. We also discuss the areas where major advancements are needed to move the field of plasmon-mediated photocatalysis forward.

Plasmonic-metal nanostructures for efficient conversion of solar to chemical energy

Catalysis plays a critical role in chemical conversion, energy production and pollution mitigation. High activation barriers associated with rate-limiting elementary steps require most commercial heterogeneous catalytic reactions to be run at relatively high temperatures, which compromises energy efficiency and the long-term stability of the catalyst. Here we show that plasmonic nanostructures of silver can concurrently use low-intensity visible light (on the order of solar intensity) and thermal energy to drive catalytic oxidation reactions--such as ethylene epoxidation, CO oxidation, and NH₃ oxidation--at lower temperatures than their conventional counterparts that use only thermal stimulus. Based on kinetic isotope experiments and density functional calculations, we postulate that excited plasmons on the silver surface act to populate O₂ antibonding orbitals and so form a transient negative-ion state, which thereby facilitates the rate-limiting O₂-dissociation reaction. The results could assist the design of catalytic processes that are more energy efficient and robust than current processes.

Visible-light-enhanced catalytic oxidation reactions on plasmonic silver nanostructures

Eukaryotic genomes are packaged into nucleosome particles that occlude the DNA from interacting with most DNA binding proteins. Nucleosomes have higher affinity for particular DNA sequences, reflecting the ability of the sequence to bend sharply, as required by the nucleosome structure. However, it is not known whether these sequence preferences have a significant influence on nucleosome position in vivo, and thus regulate the access of other proteins to DNA. Here we isolated nucleosome-bound sequences at high resolution from yeast and used these sequences in a new computational approach to construct and validate experimentally a nucleosome–DNA interaction model, and to predict the genome-wide organization of nucleosomes. Our results demonstrate that genomes encode an intrinsic nucleosome organization and that this intrinsic organization can explain ∼50% of the in vivo nucleosome positions. This nucleosome positioning code may facilitate specific chromosome functions including transcription factor binding, transcription initiation, and even remodelling of the nucleosomes themselves.

http://absimage.aps.org/image/MAR08/MWS_MAR08-2008-020581.pdf

The Genomic Code for Nucleosome Positioning

A Pt(111) surface saturated with molecular oxygen was irradiated by UV light from a mercury arc lamp with various cutoff filters. High‐resolution electron energy‐loss spectroscopy (HREELS) and temperature programmed desorption mass spectroscopy (TPD) were used to characterize the products retained on the surface. Upon UV irradiation at 95 K, chemisorbed O2 (peroxo) undergoes dissociation, desorption and rearrangement. Different wavelength dependences were observed for the three processes: dissociation was not observed at wavelengths longer than 295 nm, in agreement with gas phase photodissociation of the O–O bond in hydrogen peroxide; desorption and rearrangement became negligible at wavelengths longer than 420 nm, in agreement with the photolysis of an organometallic peroxoplatinum complex. For wavelengths between 230 and 315 nm, the average cross sections of dissociation and desorption were estimated to be 5.7×10−20 and 1.2×10−19 cm2 , respectively. The possible origins of the three processes are discussed.

Surface photochemistry. II. Wavelength dependences of photoinduced dissociation, desorption, and rearrangement of O2 on Pt(111)

A novel calcium-binding peptide from Antarctic krill protein hydrolysates and identification of binding sites of calcium-peptide complex.

standard normal mode analysis (nma) method is able to calculate vibrational entropy of proteins, but it is computationally intensive, especially for large proteins. to evaluate vibrational entropy efficiently and accurately, we, here, propose computation schemes based on coarse-grained nma methods. this can be achieved by rescaling coarse-grained results with a specific factor that is derived on the basis of the linear correlation of protein vibrational entropy between standard nma and coarse-grained nma. our coarse-grained nma computation schemes can repeat correctly and efficiently the results of standard nma for large proteins. (c) 2011 wiley periodicals, inc. j comput chem 32: 3188-3193, 2011

Xiao Zhu

Papers

Surface photochemistry. II. Wavelength dependences of photoinduced dissociation, desorption, and rearrangement of O2 on Pt(111)

A novel calcium-binding peptide from Antarctic krill protein hydrolysates and identification of binding sites of calcium-peptide complex.

Fast and Accurate Computation Schemes for Evaluating Vibrational Entropy of Proteins

Photoinduced pathways to dissociation and desorption of dioxygen on silver (110) and platinum (111)

A molecular dynamics simulation study on the conformational stability of amylose-linoleic acid complex in water.