Publications

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Communities of vertices within a giant network such as the World-Wide-Web are likely to be vastly smaller than the network itself. However, Fortunato and Barthelemy have proved that modularity maximization algorithms for community detection may fail to resolve communities with fewer than {radical} L/2 edges, where L is the number of edges in the entire network. This resolution limit leads modularity maximization algorithms to have notoriously poor accuracy on many real networks. Fortunato and Barthelemy's argument can be extended to networks with weighted edges as well, and we derive this corollary argument. We conclude that weighted modularity algorithms may fail to resolve communities with fewer than {radical} W{epsilon}/2 total edge weight, where W is the total edge weight in the network and {epsilon} is the maximum weight of an inter-community edge. If {epsilon} is small, then small communities can be resolved. Given a weighted or unweighted network, we describe how to derive new edge weights in order to achieve a low {epsilon}, we modify the 'CNM' community detection algorithm to maximize weighted modularity, and show that the resulting algorithm has greatly improved accuracy. In experiments with an emerging community standard benchmark, we find that our simple CNM variant is competitive with the most accurate community detection methods yet proposed.

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We have conducted a molecular dynamics (MD) simulation study of water confined between methyl-terminated and carboxyl-terminated alkylsilane self-assembled monolayers (SAMs) on amorphous silica substrates. In doing so, we have investigated the dynamic and structural behavior of the water molecules when compressed to loads ranging from 20 to 950 MPa for two different amounts of water (27 and 58 water molecules/nm{sup 2}). Within the studied range of loads, we observe that no water molecules penetrate the hydrophobic region of the carboxyl-terminated SAMs. However, we observe that at loads larger than 150 MPa water molecules penetrate the methyl-terminated SAMs and form hydrogen-bonded chains that connect to the bulk water. The diffusion coefficient of the water molecules decreases as the water film becomes thinner and pressure increases. When compared to bulk diffusion coefficients of water molecules at the various loads, we found that the diffusion coefficients for the systems with 27 water molecules/nm{sup 2} are reduced by a factor of 20 at low loads and by a factor of 40 at high loads, while the diffusion coefficients for the systems with 58 water molecules/nm{sup 2} are reduced by a factor of 25 at all loads.

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The computational work in many information retrieval and analysis algorithms is based on sparse linear algebra. Sparse matrix-vector multiplication is a common kernel in many of these computations. Thus, an important related combinatorial problem in parallel computing is how to distribute the matrix and the vectors among processors so as to minimize the communication cost. We focus on minimizing the total communication volume while keeping the computation balanced across processes. In [1], the first two authors presented a new 2D partitioning method, the nested dissection partitioning algorithm. In this paper, we improve on that algorithm and show that it is a good option for data partitioning in information retrieval. We also show partitioning time can be substantially reduced by using the SCOTCH software, and quality improves in some cases, too.

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The Heavy Ion Fusion Science Virtual National Laboratory has achieved 60-fold longitudinal pulse compression of ion beams on the Neutralized Drift Compression Experiment (NDCX) [P. K. Roy et al., Phys. Rev. Lett. 95, 234801 (2005)]. To focus a space-charge-dominated charge bunch to sufficiently high intensities for ion-beam-heated warm dense matter and inertial fusion energy studies, simultaneous transverse and longitudinal compression to a coincident focal plane is required. Optimizing the compression under the appropriate constraints can deliver higher intensity per unit length of accelerator to the target, thereby facilitating the creation of more compact and cost-effective ion beam drivers. The experiments utilized a drift region filled with high-density plasma in order to neutralize the space charge and current of an {approx}300 keV K{sup +} beam and have separately achieved transverse and longitudinal focusing to a radius <2 mm and pulse duration <5 ns, respectively. Simulation predictions and recent experiments demonstrate that a strong solenoid (B{sub Z} < 100 kG) placed near the end of the drift region can transversely focus the beam to the longitudinal focal plane. This paper reports on simulation predictions and experimental progress toward realizing simultaneous transverse and longitudinal charge bunch focusing. The proposed NDCX-II facility would capitalize on the insights gained from NDCX simulations and measurements in order to provide a higher-energy (>2 MeV) ion beam user-facility for warm dense matter and inertial fusion energy-relevant target physics experiments.