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Zhang P.,State University of New York at Stony Brook | Zhang N.,State University of New York at Stony Brook | Deng Y.,State University of New York at Stony Brook | Deng Y.,National Supercomputer Center in Jinan | Bluestein D.,State University of New York at Stony Brook
Journal of Computational Physics | Year: 2015

We developed a multiple time-stepping (MTS) algorithm for multiscale modeling of the dynamics of platelets flowing in viscous blood plasma. This MTS algorithm improves considerably the computational efficiency without significant loss of accuracy. This study of the dynamic properties of flowing platelets employs a combination of the dissipative particle dynamics (DPD) and the coarse-grained molecular dynamics (CGMD) methods to describe the dynamic microstructures of deformable platelets in response to extracellular flow-induced stresses. The disparate spatial scales between the two methods are handled by a hybrid force field interface. However, the disparity in temporal scales between the DPD and CGMD that requires time stepping at microseconds and nanoseconds respectively, represents a computational challenge that may become prohibitive. Classical MTS algorithms manage to improve computing efficiency by multi-stepping within DPD or CGMD for up to one order of magnitude of scale differential. In order to handle 3-4 orders of magnitude disparity in the temporal scales between DPD and CGMD, we introduce a new MTS scheme hybridizing DPD and CGMD by utilizing four different time stepping sizes. We advance the fluid system at the largest time step, the fluid-platelet interface at a middle timestep size, and the nonbonded and bonded potentials of the platelet structural system at two smallest timestep sizes. Additionally, we introduce parameters to study the relationship of accuracy versus computational complexities. The numerical experiments demonstrated 3000x reduction in computing time over standard MTS methods for solving the multiscale model. This MTS algorithm establishes a computationally feasible approach for solving a particle-based system at multiple scales for performing efficient multiscale simulations. © 2015.

Li W.,Institute of High Performance Computing of Singapore | Guo M.,National Supercomputer Center in Jinan | Zhang G.,Institute of High Performance Computing of Singapore | Zhang Y.-W.,Institute of High Performance Computing of Singapore
Physical Review B - Condensed Matter and Materials Physics | Year: 2014

MoS2, a member of transition metal dichalcogenides (TMDs), has recently emerged as an interesting two-dimensional material due to its unique mechanical, thermal, electronic and optical properties. Unlike graphene which possesses massless Dirac fermions with ultrahigh electron mobility, monolayer MoS2 is a direct band gap semiconductor. An interesting question arises: Can monolayer MoS2 also possess massless Dirac fermions with ultrahigh electron mobility? Here, using first-principles calculations, we show that a monolayer MoS2 allotrope, which consists of repeated square-octagon rings (abbreviated as so-MoS2 to distinguish it from the normal hexagonal lattice, h-MoS2) possesses both massless Dirac fermions and heavy fermions. Distinct from the p-orbital Dirac fermions of graphene, the Dirac fermions of so-MoS2 are d electrons and possess a Fermi velocity comparable to that of graphene. The Dirac cone structure in so-MoS2 demonstrated here greatly enriches our understanding on the physical properties of TMDs and opens up possibilities for developing high-performance electronic or spintronic devices. © 2014 American Physical Society.

Su X.,Northwest University, China | Su X.,Henan University of Science and Technology | Zhang R.,Northwest University, China | Guo C.,Northwest University, China | And 2 more authors.
Physical Chemistry Chemical Physics | Year: 2014

The possibility of forming quantum wells (QWs) in transition-metal dichalcogenide nanosheet assembled superlattices (SLs) was investigated by using the first principles calculations. The interfacial binding energies and electronic structures of MoS2/MX2 (MX2 = MoSe2, WS2, and WSe2) SLs were calculated. The interfacial binding energies show that all the SLs are stable, and the most stable atomic configuration is that where M atoms are located right above S atoms. By calculating the band offsets in the SLs, it was found that a QW with a depth of 0.17 eV can be formed in the MoS2 layer in MoS 2/WSe2 SLs. The calculated band structure shows that this SL has an indirect band gap due to the tensile strained state of the MoS 2 layer. The charge transfer between the two layers is very small, which is in favor of the QWs' formation. In particular, the depth of the QW in the SLs can be adjusted by strain engineering, which can be attributed to the different strain dependencies of the two materials' band gaps. These findings will guide the choice of future nanosheet assembled SLs to work on and suggest a new route to facilitate the design of QW based optoelectronic devices.

Wang J.,National Supercomputer Center in Jinan | Yang G.,National Supercomputer Center in Jinan
IET Conference Publications | Year: 2013

Over the past several years a lot of research has focused on privacy preserving of data. In this work we are interested in the following privacy-preserving problem in the domain of information security. A set of parties hold private lists of information security events and want to find and disclose the top-k security events without revealing any other information. We use secure homomorphic encryption techniques to solve this problem and design protocols, analyzing their efficiency.

Ma X.,Shandong University | Dai Y.,Shandong University | Guo M.,National Supercomputer Center in Jinan | Huang B.,Shandong University
Journal of Physical Chemistry C | Year: 2013

The general low quantum efficiency of semiconductor-based photocatalysts significantly limits their large-scale application. Here, we reveal the potential role that surface distortion can play in enhancing the photocatalytic quantum efficiency as well as the underlying mechanism by using TiO2 as a model photocatalyst. Specifically, proper surface distortion in a {101} surface can significantly promote the participation of electrons in photocatalytic reactions and further facilitate the transfer of photogenerated electrons in the bulk region to this surface. Moreover, surface distortion also prevents the photogenerated holes from transferring to the surface layer, thus separating the photogenerated holes from electrons and reducing the high recombination rate of carriers, which is believed to result in the generally low photocatalytic activities of the {101} surface. For the {001} surface, the distorted surface greatly promotes the transfer of electrons from the subsurface atomic layer (the initial electron trapping sites) to the outermost atomic layer (where photocatalytic reactions generally occur) by eliminating the original energy barrier, and the trapping of electrons on surface Ti 5c dz2 orbital cannot only facilitate their participation in the photocatalytic reactions but also significantly reduce the carrier recombination rate in the surface region. The results presented here can be used to account for the experimental results that surface distortion in TiO 2 can substantially improve the quantum efficiency of its intrinsic absorption. © 2013 American Chemical Society.

Li W.,Institute of High Performance Computing of Singapore | Zhang G.,Institute of High Performance Computing of Singapore | Guo M.,National Supercomputer Center in Jinan | Zhang Y.-W.,Institute of High Performance Computing of Singapore
Nano Research | Year: 2014

Using density functional theory calculations, we have investigated the mechanical properties and strain effects on the electronic structure and transport properties of molybdenum disulfide (MoS2) nanotubes. At a similar diameter, an armchair nanotube has a higher Young's modulus and Poisson ratio than its zigzag counterpart due to the different orientations of Mo-S bond topologies. An increase in axial tensile strain leads to a progressive decrease in the band gap for both armchair and zigzag nanotubes. For armchair nanotube, however, there is a semiconductor-to-metal transition at the tensile strain of about 8%. For both armchair and zigzag nanotubes, the effective mass of a hole is uniformly larger than its electron counterpart, and is more sensitive to strain. Based on deformation potential theory, we have calculated the carrier mobilities of MoS2 nanotubes. It is found that the hole mobility is higher than its electron counterpart for armchair (6, 6) nanotube while the electron mobility is higher than its hole counterpart for zigzag (10, 0) nanotube. Our results highlight the tunable electronic properties of MoS2 nanotubes, promising for interesting applications in nanodevices, such as opto-electronics, photoluminescence, electronic switch and nanoscale strain sensor. [Figure not available: see fulltext.] © 2014 Tsinghua University Press and Springer-Verlag Berlin Heidelberg.

Ma X.,Shandong University | Dai Y.,Shandong University | Guo M.,National Supercomputer Center in Jinan | Huang B.,Shandong University
Langmuir | Year: 2013

The photoredox ability of the TiO2 {100}, {101}, and {001} surfaces is investigated by examining the trapping energies, trapping sites, and relative oxidation and reduction potentials of simulated photogenerated holes and electrons in the form of more realistic polaronic states on the basis of density functional electronic structure calculations. Our results enable us to re-estimate their relative photooxidation ({100} > {101} > {001}) and photoreduction ({100} > {101} > {001}) activities, which rectify the conventional understanding. The dual functions of the surface under coordinated atoms acting as active adsorption sites for adsorbates and hindering the population of electrons to the outermost surface layer are identified, and the specific surface geometric structures also play an important role in trapping holes and electrons through the ease of lattice distortion. In addition, we attribute the commonly low photocatalytic performance of the {101} surface to the large and similar trapping energies and adjacent trapping sites for electrons and holes, which result in high electron-hole recombination rates. However, the large difference in trapping energies for electrons and holes on different surfaces allows us to spatially gather electrons and holes on different surfaces by artificially designing the exposing facets of nanocrystals without resorting to the energy band potential difference between surfaces, thus expanding the ideas to improve the photocatalytic properties of materials through the regulation of crystal facets. Our present work can provide a helpful message for the design of more reactive photocatalytic TiO2 nanocrystals and the fabrication of other reactive photocatalysts. © 2013 American Chemical Society.

Zhong Y.,CAS Institute of Computing Technology | Zhu X.,National Supercomputer Center in Jinan | Fang J.,CAS Institute of Computing Technology
Proceedings of the 1st ACM SIGSPATIAL International Workshop on Analytics for Big Geospatial Data, BigSpatial 2012 | Year: 2012

Geospatial applications have become prevalent in both scientific research and industry. Spatio-Temporal query processing is a fundamental issue for driving geospatial applications. However, the state-of-the-art spatio-temporal query processing methods are facing significant challenges as the data expand and concurrent users increase. In this paper we present a novel spatio-temporal querying scheme to provide efficient query processing over big geospatial data. The scheme improves query efficiency from three facets. Firstly, taking geographic proximity and storage locality into consideration, we propose a geospatial data organization approach to achieve high aggregate I/O throughput, and design a distributed indexing framework for efficient pruning of the search space. Furthermore, we design an indexing plus MapReduce query processing architecture to improve data retrieval efficiency and query computation efficiency. In addition, we design distributed caching model to accelerate the access response of hotspot spatial objects. We evaluate the effectiveness of our scheme with comprehensive experiments using real datasets and application scenarios. Copyright © 2012 ACM.

Liu J.,Shandong University | Cukier R.I.,Michigan State University | Bu Y.,Shandong University | Shang Y.,National Supercomputer Center in Jinan
Journal of Chemical Theory and Computation | Year: 2014

Ab initio molecular dynamics simulations reveal that an excess electron (EE) can be more efficiently localized as a cavity-shaped state in aqueous glucose solution (AGS) than in water. Compared with that (∼1.5 ps) in water, the localization time is shortened by ∼0.7-1.2 ps in three AGSs (0.56, 1.12, and 2.87 M). Although the radii of gyration of the solvated EEs are all close to 2.6 Å in the four solutions, the solvated EE cavities in the AGSs become more compact and can localize ∼80% of an EE, which is considerably larger than that (∼40-60% and occasionally ∼80%) in water. These observations are attributed to a modification of the hydrogen-bonded network by the introduction of glucose molecules into water. The water acts as a promoter and stabilizer, by forming voids around glucose molecules and, in this fashion, favoring the localization of an EE with high efficiency. This study provides important information about EEs in physiological AGSs and suggests a new strategy to efficiently localize an EE in a stable cavity for further exploration of biological function. © 2014 American Chemical Society.

Long R.,University College Dublin | Guo M.,National Supercomputer Center in Jinan | Ziletti A.,Boston University
Chemical Physics Letters | Year: 2014

Electronic structures and charge redistribution between P3HT and (10,2)/(6,5) carbon nanotubes (CNT) are investigated by density functional theory calculations. The simulations show that electron is transferred from flat P3HT to (10,2) CNT while hole is transferred from (6,5) CNT to wrapped P3HT due to the different work functions of these materials. The large built-in potential can compete to exciton binding energy, leading to efficient charge separation across the type-II photovoltaic heterojunctions. Electron transfer faster than hole is expected because the electron donor state is much more delocalization, creating larger donor-acceptor coupling, which provides critical insights of organic photovoltaic solar cells. © 2014 Elsevier B.V. All rights reserved.

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