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.

1 aNguyen, Tuan, D.1 aHawley, Nathan1 aPhanikumar, Mantha, S. uhttp://www.egr.msu.edu/~phani/lno10431.pdf01392nas a2200133 4500008004100000245010200041210006900143260002600212520084200238100001701080700001901097700002001116856012201136 2013 eng d00aThe Institute for Cyber-Enabled Research: Regional Organization to Promote Computation in Science0 aInstitute for CyberEnabled Research Regional Organization to Pro aSan Diego, California3 aThe 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.

1 aColbry, Dirk1 aPunch, William1 aBauer, Wolfgang uhttps://icer.msu.edu/research/publications/institute-cyber-enabled-research-regional-organization-promote-computation00600nas a2200157 4500008004100000245010100041210006900142300001200211490000700223100001700230700001300247700002000260700001700280700002100297856012400318 2013 eng d00aIntra-aggregate pore structures are related to total C distribution within soil macro-aggregates0 aIntraaggregate pore structures are related to total C distributi a686-8750 v571 aAnanyeva, K.1 aWang, W.1 aSmucker, A.J.M.1 aRivers, M.L.1 aKravchenko, A.N. uhttps://icer.msu.edu/research/publications/intra-aggregate-pore-structures-are-related-total-c-distribution-within-soil00441nas a2200097 4500008004100000245008000041210006900121490000800190100002600198856011900224 2012 eng d00aInterfacial friction between semiflexible polymers and crystalline surfaces0 aInterfacial friction between semiflexible polymers and crystalli0 v1361 aPriezjev, Nikolai, V. uhttps://icer.msu.edu/research/publications/interfacial-friction-between-semiflexible-polymers-crystalline-surfaces00554nas a2200145 4500008004100000245008200041210006900123300001400192490000700206100001300213700002100226700002000247700001700267856012400284 2012 eng d00aIntra-aggregate pore characteristics: X-ray computed microtomography analysis0 aIntraaggregate pore characteristics Xray computed microtomograph a1159-11710 v761 aWang, W.1 aKravchenko, A.N.1 aSmucker, A.J.M.1 aRivers, M.L. uhttps://icer.msu.edu/research/publications/intra-aggregate-pore-characteristics-x-ray-computed-microtomography-analysis00411nas a2200133 4500008004100000245003900041210003900080260001200119300001400131490000700145100002300152700001800175856008400193 2011 eng d00aImplicit Parallel Time Integrators0 aImplicit Parallel Time Integrators c11/2011 a167 - 1790 v491 aChristlieb, Andrew1 aOng, Benjamin uhttps://icer.msu.edu/research/publications/implicit-parallel-time-integrators-002110nas a2200157 4500008004100000245006200041210006200103300001400165490000700179520164900186100002101835700001701856700001801873700001801891856004301909 2011 eng d00aInformation Content of Colored Motifs in Complex Networks0 aInformation Content of Colored Motifs in Complex Networks a375–3900 v173 aWe 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.

1 aAdami, Christoph1 aQian, Jifeng1 aRupp, Matthew1 aHintze, Arend uhttp://dx.doi.org/10.1162/artl_a_0004501333nas a2200133 4500008004100000245003900041210003900080260001200119490000700131520093800138100002301076700001801099856008201117 2010 eng d00aImplicit Parallel Time Integrators0 aImplicit Parallel Time Integrators c12/20100 v463 aIn 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.

1 aChristlieb, Andrew1 aOng, Benjamin uhttps://icer.msu.edu/research/publications/implicit-parallel-time-integrators00525nas a2200145 4500008004100000245006900041210006900110260000800179300001400187100001400201700001900215700001900234700001400253856011200267 2010 eng d00aInvestigating whether HyperNEAT produces modular neural networks0 aInvestigating whether HyperNEAT produces modular neural networks bACM a635–6421 aClune, J.1 aBeckmann, B.E.1 aMcKinley, P.K.1 aOfria, C. uhttps://icer.msu.edu/research/publications/investigating-whether-hyperneat-produces-modular-neural-networks01478nas a2200193 4500008004100000245010300041210006900144260001200213300001400225490000800239520081400247100001901061700002001080700001601100700001101116700001801127700001801145856012101163 2008 eng d00aThe influence of cluster emission and the symmetry energy on neutron-proton spectral double ratios0 ainfluence of cluster emission and the symmetry energy on neutron c02/2008 a145–1480 v6643 aThe 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.

1 aZhang, Yingxun1 aDanielewicz, P.1 aFamiano, M.1 aLi, Z.1 aLynch, W., G.1 aTsang, M., B. uhttps://icer.msu.edu/research/publications/influence-cluster-emission-symmetry-energy-neutron-proton-spectral-double02648nas a2200157 4500008004100000245016100041210006900202260001500271300000900286490000800295520182400303653020902127100001502336700001602351856012302367 2006 eng d00aIntriguing Accuracies of the Exponential Wave Function Expansions Exploiting Finite Two-Body Correlation Operators in Calculations for Many-Electron Systems0 aIntriguing Accuracies of the Exponential Wave Function Expansion c08/31/2006 a3-160 v7683 aFollowing 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.

10axact many-electron wave functions; Generalized coupled-cluster methods; Two-body correlation operators; Nooijen's conjecture; Variational calculations; Multi-determinantal reference states; Excited states1 aFan, P.-D.1 aPiecuch, P. uhttps://icer.msu.edu/intriguing-accuracies-exponential-wave-function-expansions-exploiting-finite-two-body-correlation