Winter circulation exerts a strong control on the release and timing of nutrients and contaminants from bays into the adjoining lakes. To estimate winter residence times of solutes in the presence of ice cover, we used an ice model coupled to hydrodynamic, thermal and solute transport models of Saginaw Bay and Lake Huron for two low (2010 and 2013) and two high (2009 and 2014) ice years. The models were tested using temperature data from thermistor chains and current data from ADCP moorings deployed during the winter- time. Simulated water temperatures compared favorably to lake-wide average surface temperatures derived from NOAA’s AVHRR satellite imagery. Simulated results of ice cover are in agreement with observed data from the Great Lakes Ice Atlas. Our results indicate that ice cover significantly dampens water movement producing almost stagnant conditions around February. Estimates of residence times for Saginaw Bay (defined as the e-folding flushing time based on vertically integrated dye concentrations) show that the mean resi- dence times in a low ice year (2013) are 2.2 months for the inner bay, and 3.5 months for the entire bay. The corresponding numbers for a high ice year (2014) are 4.9 and 5.3 months, respectively. Considering the entire bay, solutes stored in the bay can be expected to be released into the lake between March (low ice year) and April (high ice year). These results are expected to aid in understanding the behavior of contami- nants in the Great Lakes during the winter months and in early spring.

%B Limnology and Oceanography %V 62 %G eng %U http://www.egr.msu.edu/~phani/lno10431.pdf %N 1 %& 376-393 %0 Conference Paper %B In proceedings of 2013 XSEDE Conference %D 2013 %T The Institute for Cyber-Enabled Research: Regional Organization to Promote Computation in Science %A Dirk Colbry %A Punch, William %A Bauer, Wolfgang %XThe Institute for Cyber-Enabled Research (iCER) at Michigan State University (MSU) was established in 2009 to coordinate and support multidisciplinary resources for computation and computational sciences. iCER is the home of MSU's centralized High Performance Computing resources, which include a heterogeneous compute cluster with various hardware designed to meet the needs of different scientists. The goal of iCER is not to maximize Flops, but instead to maximize the amount of quality science being accomplished. This paper outlines many of the initiatives that iCER has taken to support researchers at MSU and throughout Michigan; describes the structure and evolution of iCER and its relationship with XSEDE and offers insights for other institutions interested in putting together a similar computational organization.

%B In proceedings of 2013 XSEDE Conference %C San Diego, California %G eng %0 Journal Article %J Soil Biology and Biochemistry %D 2013 %T Intra-aggregate pore structures are related to total C distribution within soil macro-aggregates %A K. Ananyeva %A W. Wang %A A.J.M. Smucker %A M.L. Rivers %A A.N. Kravchenko %B Soil Biology and Biochemistry %V 57 %P 686-875 %G eng %0 Journal Article %J J. Chem. Phys. %D 2012 %T Interfacial friction between semiflexible polymers and crystalline surfaces %A Nikolai V. Priezjev %B J. Chem. Phys. %V 136 %G eng %0 Journal Article %J Soil Sci. Soc Am J. %D 2012 %T Intra-aggregate pore characteristics: X-ray computed microtomography analysis %A W. Wang %A A.N. Kravchenko %A A.J.M. Smucker %A M.L. Rivers %B Soil Sci. Soc Am J. %V 76 %P 1159-1171 %G eng %0 Journal Article %J Journal of Scientific Computing %D 2011 %T Implicit Parallel Time Integrators %A Andrew Christlieb %A Benjamin Ong %B Journal of Scientific Computing %V 49 %P 167 - 179 %8 11/2011 %G eng %N 2 %0 Journal Article %J Artificial Life %D 2011 %T Information Content of Colored Motifs in Complex Networks %A Adami, Christoph %A Qian, Jifeng %A Rupp, Matthew %A Hintze, Arend %XWe study complex networks in which the nodes are tagged with different colors depending on their function (colored graphs), using information theory applied to the distribution of motifs in such networks. We find that colored motifs can be viewed as the building blocks of the networks (much more than the uncolored structural motifs can be) and that the relative frequency with which these motifs appear in the network can be used to define its information content. This information is defined in such a way that a network with random coloration (but keeping the relative number of nodes with different colors the same) has zero color information content. Thus, colored motif information captures the exceptionality of coloring in the motifs that is maintained via selection. We study the motif information content of the C. elegans brain as well as the evolution of colored motif information in networks that reflect the interaction between instructions in genomes of digital life organisms. While we find that colored motif information appears to capture essential functionality in the C. elegans brain (where the color assignment of nodes is straightforward), it is not obvious whether the colored motif information content always increases during evolution, as would be expected from a measure that captures network complexity. For a single choice of color assignment of instructions in the digital life form Avida, we find rather that colored motif information content increases or decreases during evolution, depending on how the genomes are organized, and therefore could be an interesting tool to dissect genomic rearrangements.

%B Artificial Life %V 17 %P 375–390 %G eng %U http://dx.doi.org/10.1162/artl_a_00045 %0 Journal Article %J Journal of Scientific Computing %D 2010 %T Implicit Parallel Time Integrators %A Andrew Christlieb %A Benjamin Ong %XIn this work, we discuss a family of parallel implicit time integrators for multicore and potentially multi-node or multi-gpgpu systems. The method is an extension of Revisionist Integral Deferred Correction (RIDC) by Christlieb, Macdonald and Ong (SISC- 2010) which constructed parallel explicit time integrators. The key idea is to re-write the defect correction framework so that, after initial startup costs, each correction loop can be lagged behind the previous correction loop in a manner that facilitates running the predictor and correctors in parallel. In this paper, we show that RIDC provides a framework to use p cores to generate a pth-order implicit solution to an initial value problem (IVP) in approximately the same wall clock time as a single core, backward Euler implementation (p ≤ 12). The construction, convergence and stability of the schemes are presented, along with supporting numerical evidence.

%B Journal of Scientific Computing %V 46 %8 12/2010 %G eng %N 1 %0 Conference Paper %B Proceedings of the Genetic and Evolutionary Computation Conference %D 2010 %T Investigating whether HyperNEAT produces modular neural networks %A Clune, J. %A Beckmann, B.E. %A McKinley, P.K. %A Ofria, C. %B Proceedings of the Genetic and Evolutionary Computation Conference %I ACM %P 635–642 %G eng %0 Journal Article %J Physics Letters B %D 2008 %T The influence of cluster emission and the symmetry energy on neutron-proton spectral double ratios %A Yingxun Zhang %A P. Danielewicz %A M. Famiano %A Li, Z. %A W. G. Lynch %A M. B. Tsang %XThe emissions of neutrons, protons and bound clusters from central {124Sn} + {124Sn} and {112Sn} + {112Sn} collisions are simulated using the Improved Quantum Molecular Dynamics model for two different density-dependent symmetry-energy functions. The calculated neutron-proton spectral double ratios for these two systems are sensitive to the density dependence of the symmetry energy, consistent with previous work. Cluster emission increases the double ratios in the low energy region relative to values calculated in a coalescence-invariant approach. To circumvent uncertainties in cluster production and secondary decays, it is important to have more accurate measurements of the neutron-proton ratios at higher energies in the center of mass system, where the influence of such effects is reduced.

%B Physics Letters B %V 664 %P 145–148 %8 02/2008 %G eng %0 Journal Article %J Journal of Molecular Structure: THEOCHEM %D 2006 %T Intriguing Accuracies of the Exponential Wave Function Expansions Exploiting Finite Two-Body Correlation Operators in Calculations for Many-Electron Systems %A P.-D. Fan %A P. Piecuch %K xact many-electron wave functions; Generalized coupled-cluster methods; Two-body correlation operators; Nooijen's conjecture; Variational calculations; Multi-determinantal reference states; Excited states %XFollowing the ideas laid down by Nooijen and Nakatsuji, several authors have considered an intriguing possibility of representing the exact many-electron wave functions by the exponential cluster expansions involving two-body correlation operators. In particular, inspired by the symmetric form of the Horn–Weinstein exact energy formula, and exploiting the variational principle and numerical analysis, we have demonstrated that one can obtain nearly exact ground-state wave functions for a few many-electron systems using the exponential cluster expansion involving a finite two-body operator acting on the Hartree–Fock determinant [P. Piecuch et al., Phys. Rev. Lett. 90 (2003) 113001]. After summarizing these earlier findings and making some additional comments on the nature of the exponential cluster expansions involving two-body correlation operators, we examine the following issues: (i) the improvements in the accuracy and convergence toward the full configuration interaction (CI) limit offered by cluster operators containing two-body as well as one-body components, (ii) the improvements in the accuracy resulting from the use of multi-determinantal reference states, and (iii) the potential accuracy of the exponential wave function expansions involving finite one- and two-body cluster operators in excited-state calculations. All calculations are performed for an eight electron model system, which is simple enough to allow for the exact, full CI, and other electronic structure calculations, which has fewer independent parameters in the Hamiltonian than the dimension of the corresponding full CI problem, and which enables one to examine ground and excited states with a varying degree of configurational quasi-degeneracy by simple changes in the corresponding nuclear geometry.

%B Journal of Molecular Structure: THEOCHEM %V 768 %P 3-16 %8 08/31/2006 %G eng %N 1-3