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 Journal Article %J Journal of Hydrology %D 2017 %T Manifold methods for assimilating geophysical and meteorological data in Earth system models and their components %A Ammar Safaie %A Chinh Dang %A Han Qiu %A Hayder Radha %A Phanikumar, M.S. %XA novel manifold method of reconstructing dynamically evolving spatial fields is presented for assimilating data from sensor networks in integrated land surface – subsurface, oceanic/lake models. The method was developed based on the assumption that data can be mapped onto an underlying differential manifold. In this study, the proposed method was used to reconstruct meteorological forcing over Lake Michigan, the bathymetry of an inland lake (Gull Lake), and precipitation over the Grand River watershed in Michigan. In the first case study, hourly meteorological forcing data were reconstructed and used to run a three-dimensional hydrodynamic model of Lake Michigan and to quantify the improvement that results from the use of the new method. In the second example, the bathymetry of Gull Lake was reconstructed from measured scatter point data using the manifold technique. A hydrodynamic model of Gull Lake was developed and refined using the improved bathymetry. In the last case study, improved daily participation data for a six-year period over the Grand River watershed were used as input to an integrated, distributed hydrologic model. All three examples illustrate the superior performance of the manifold method over standard methods in terms of accuracy and computational efficiency. Our results also indicate that using the cross-validation technique to evaluate the performance of data reconstruction methods can lead to misleading conclusions about their relative performance.

%B Journal of Hydrology %V 544 %8 11/2016 %G eng %U http://hydrology1.weebly.com/uploads/6/6/2/1/66216077/jh_safaie.pdf %& 383 %0 Journal Article %J PHYSICAL REVIEW LETTERS %D 2014 %T Determining the rp-Process Flow through 56Ni: Resonances in 57Cu(p,g)58Zn Indentified with GRETINA %A C. Langer %A F. Montes %A A. Aprahamian %A D.W. Bardayan %A D. Bazin %A B. A. Brown %A J. Browne %A H. Crawford %A R. Cyburt %A C. Domingo-Pardo %A A. Gade %A S. George %A P. Hosmer %A L. Keek %A A. Kontos %A I.Y. Lee %A A. Lemasson %A E. Lunderberg %A Y. Maeda %A M. Matos %A Z. Meisel %A S. Noji %A F.M. Nunes %A A. Nystrom %A G. Perdikakis %A J. Pereira %A S.J. Quinn %A F. Recchia %A H. Schatz %A M. Scott %A K. Siegl %A A. Simon %A M. Smith %A A. Spyrou %A J. Stevens %A S.R. Stroberg %A D. Weisshaar %A J. Wheeler %A K. Wimmer %A R.G.T. Zegers %B PHYSICAL REVIEW LETTERS %V 113 %8 07/2014 %G eng %U http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.113.032502 %0 Journal Article %J PNAS %D 2014 %T Gill bacteria enable a novel digestive strategy in a wood-feeding mollusk %A Roberta M O'Connor %A Jennifer M Fung %A Koty H Sharp %A Jack S Benner %A Colleen McClung %A Shelley Cushing %A Elizabeth R Lamkin %A Alexey I Fomenkov %A Bernard Henrissat %A Yuri Y Londer %A Matthew B Scholz %A Janos Posfai %A Stephanie Malfatti %A Susannah G Tringe %A Tanja Woyke %A Rex R Malmstrom %A Devin Coleman-Derr %A Marvin A Altamia %A Sandra Dedrick %A Stefan T Kaluziak %A Margo G Haywood %A Daniel L Distel %B PNAS %V 111 %8 11/2014 %G eng %U http://www.pnas.org/content/111/47/E5096.full %N 47 %& E5096–E5104 %0 Journal Article %J PHYSICAL REVIEW C %D 2014 %T High-precision B(E2) Measurements of Semi-Magic 58,60,62,64Ni by Coulomb Excitation %A J.M. Allmond %A B. A. Brown %A A.E. Stuchbery %A A. Galindo-Uribarri %A E. Padilla-Rodal %A D.C. Radford %A J.C. Batchelder %A M.E. Howard %A J.F. Liang %A B. Manning %A R.L. Varner %A C.H. Yu %B PHYSICAL REVIEW C %V 90 %8 09/2014 %G eng %U http://journals.aps.org/prc/abstract/10.1103/PhysRevC.90.034309 %0 Journal Article %J THE EUROPEAN PHYSICAL JOURNAL A %D 2014 %T High-resolution two-proton stripping to 2p-1h 7/2− states via the 59Co(3He,nγ)61Cu reaction %A P. Papka %A J.F. Sharpey-Schafer %A B. A. Brown %A T.S. Dinoko %A E.A.M.A Khaleel %A E.A. Lawrie %A J.J. Lawrie %A K.C.W. Li %A S.N.T. Majola %A W.A. Richter %A O. Shirinda %A M.A. Stankiewicz %A P. Vymers %A M. Wiedeking %B THE EUROPEAN PHYSICAL JOURNAL A %V 50 %8 10/2014 %G eng %U https://people.nscl.msu.edu/~brown/brown-all-papers/541-2014-epja50.158.pdf %0 Journal Article %J PHYSICAL REVIEW C %D 2014 %T Shell and Shape Evolution at N=28: The 40Mg Ground State %A H.L. Crawford %A P. Fallon %A A.O. Macchiavelli %A R.M. Clark %A B. A. Brown %A J.A. Tostevin %A D. Bazin %A N. Aoi %A P. Doornenbal %A M. Matsushita %A H. Scheit %A D. Steppenbeck %A S. Takeuchi %A H. Baba %A C.M. Campbell %A M. Cromaz %A E. Ideguchi %A N. Kobayashi %A Y. Kondo %A G. Lee %A I.Y. Lee %A J. Lee %A K. Li %A S. Michimasa %A T. Motobayashi %A T. Nakamura %A S. Ota %A S. Paschalis %A M. Petri %A T. Sako %A H. Sakurai %A S. Shimoura %A M. Takechi %A Y. Togano %A H. Wang %A K. Yoneda %B PHYSICAL REVIEW C %V 80 %8 04/2014 %G eng %U http://journals.aps.org/prc/abstract/10.1103/PhysRevC.89.041303 %0 Journal Article %J Journal of Applied Physics %D 2014 %T Untangling the contributions of image charge and laser profile for optimal photoemission of high-brightness electron beams %A J. Portman %A H. Zhang %A K. Makino %A C.Y. Ruan %A M. Berz %A P. M. Duxbury %B Journal of Applied Physics %V 116 %8 2014 %G eng %U http://scitation.aip.org/content/aip/journal/jap/116/17/10.1063/1.4900582 %0 Journal Article %J Journal of Climate %D 2014 %T WRF Model Sensitivity to Land Surface Model and Cumulus Parameterization under Short-Term Climate Extremes over the Southern Great Plains of the United States %A Pei, Lisi %A Moore, Nathan %A Zhong, Shiyuan %A Luo, Lifeng %A Hyndman, David W %A Heilman, Warren E %A Gao, Zhiqiu %B Journal of Climate %V 27 %8 10/2014 %G eng %N 20 %& 7703–7724 %0 Journal Article %J The Astrophysical Journal Letters %D 2013 %T CLASH: The Enhanced Lensing Efficiency of the Highly Elongated Merging Cluster MACS J0416.1-2403 %A Zitrin, A. %A Meneghetti, M %A Umetsu, K %A Broadhurst, T. %A Bartelmann, M %A Bouwens, R. %A Bradley, L %A Carrasco, M. %A Coe, D. %A Ford, H %A Kelson, D. %A Koekemoer, A. M %A Medezinski, E %A Moustakas, J. %A Moustakas, L. A. %A Nonino, M. %A Postman, M. %A Rosati, P. %A Seidel, G %A Seitz, S. %A Sendra, I %A Shu, X %A Vega, J %A Zheng, W %K dark matter %K galaxies: clusters: general %K galaxies: clusters: individual: MACS J0416.1–2403 %K Galaxies: High-Redshift %K gravitational lensing: strong %B The Astrophysical Journal Letters %V 762 %8 01/2013 %G eng %N 2 %0 Journal Article %J The Astrophysical Journal Letters %D 2013 %T CLASH: The Enhanced Lensing Efficiency of the Highly Elongated Merging Cluster MACS J0416.1-2403 %A Zitrin, A. %A Meneghetti, M %A Umetsu, K %A Broadhurst, T. %A Bartelmann, M %A Bouwens, R. %A Bradley, L %A Carrasco, M. %A Coe, D. %A Ford, H %A Kelson, D. %A Koekemoer, A. M %A Medezinski, E %A Moustakas, J. %A Moustakas, L. A. %A Nonino, M. %A Postman, M. %A Rosati, P. %A Seidel, G %A Seitz, S. %A Sendra, I %A Shu, X %A Vega, J %A Zheng, W %K dark matter %K galaxies: clusters: general %K galaxies: clusters: individual: MACS J0416.1–2403 %K Galaxies: High-Redshift %K gravitational lensing: strong %B The Astrophysical Journal Letters %V 762 %8 01/2013 %G eng %& 6 %0 Journal Article %J The Astrophysical Journal %D 2013 %T CLASH: Three Strongly Lensed Images of a Candidate z 11 Galaxy %A Coe, Dan %A Zitrin, Adi %A Carrasco, Mauricio %A Shu, Xinwen %A Zheng, Wei %A Postman, Marc %A Bradley, Larry %A Koekemoer, Anton %A Bouwens, Rychard %A Broadhurst, Tom %A Monna, Anna %A Host, Ole %A Moustakas, Leonidas A %A Ford, Holland %A Moustakas, John %A van der Wel, Arjen %A Donahue, Megan %A Rodney, Steven A %A Ben{\'ıtez, Narciso %A Jouvel, Stephanie %A Seitz, Stella %A Kelson, Daniel D. %A Rosati, Piero %K clusters %K distances and redshifts %K early universe %K galaxies %K individual %B The Astrophysical Journal %V 762 %8 01/2013 %G eng %& 32 %0 Journal Article %J The Astrophysical Journal %D 2013 %T CLASH: Three Strongly Lensed Images of a Candidate z~11 Galaxy %A Coe, Dan %A Zitrin, Adi %A Carrasco, Mauricio %A Shu, Xinwen %A Zheng, Wei %A Postman, Marc %A Bradley, Larry %A Koekemoer, Anton %A Bouwens, Rychard %A Broadhurst, Tom %A Monna, Anna %A Host, Ole %A Moustakas, Leonidas A %A Ford, Holland %A Moustakas, John %A van der Wel, Arjen %A Donahue, Megan %A Rodney, Steven A %A Benítez, Narciso %A Jouvel, Stephanie %A Seitz, Stella %A Kelson, Daniel D. %A Rosati, Piero %K clusters %K distances and redshifts %K early universe %K galaxies %K individual %B The Astrophysical Journal %V 762 %8 01/2013 %G eng %N 1 %0 Journal Article %J Journal of Great Lakes Research %D 2013 %T Estimating wounding of lake trout by sea lamprey in the upper Great Lakes: Allowing for changing size-specific patterns %A Carson G. Prichard %A James R. Bence %K AD Model Builder %B Journal of Great Lakes Research %P - %G eng %0 Journal Article %J Physical Review E %D 2013 %T Heterogeneous relaxation dynamics in amorphous materials under cyclic loading %A Nikolai V. Priezjev %B Physical Review E %I IEEE %C Tampa, Florida %V 87 %G eng %N 5 %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 Microfluidics and Nanofluidics %D 2013 %T Molecular dynamics simulations of oscillatory Couette flows with slip boundary conditions %A N. V Priezjev %B Microfluidics and Nanofluidics %V 14 %G eng %N 1-2 %0 Journal Article %J Evolution %D 2012 %T ALTITUDINAL CLINAL VARIATION IN WING SIZE AND SHAPE IN AFRICAN DROSOPHILA MELANOGASTER: ONE CLINE OR MANY? %A Pitchers, William %A Pool, John E %A Dworkin, Ian %B Evolution %V 67 %P 438–452 %G eng %0 Journal Article %J Astrophysical Journal %D 2012 %T A Census of Star-Forming Galaxies in the z~9-10 Universe based on HST+Spitzer Observations Over 19 CLASH clusters: Three Candidate z~9-10 Galaxies and Improved Constraints on the Star Formation Rate Density at z~9.2 %A Bouwens, R, %A Bradley, L %A Zitrin, A. %A Coe, D. %A Franx, M. %A Zheng, W %A Smit, R %A Host, O. %A Postman, M. %A Moustakas, L %A Labbe, I %A Carrasco, M. %A Molino, A. %A Donahue, M %A Kelson, D. D %A Meneghetti, M %A Jha, S. %A Benitez, N %A Lemze, D %A Umetsu, K %A Broadhurst, T. %A Moustakas, J. %A Rosati, P. %A Bartelmann, M %A Ford, H %A Graves, G. %A Grillo, C. %A Infante, L %A Jiminez-Teja, Y %A Jouvel, S %A Lahav, O. %A Maoz, D %A Medezinski, E %A Melchior, P %A Merten, J %A Nonino, M. %A Ogaz, S. %A Seitz, S. %K Astrophysics - Cosmology and Extragalactic Astrophysics %B Astrophysical Journal %8 11/2012 %G eng %0 Journal Article %J The Astrophysical Journal Letters %D 2012 %T CLASH: Discovery of a Bright z ~= 6.2 Dwarf Galaxy Quadruply Lensed by MACS J0329.6-0211 %A Zitrin, A. %A Moustakas, J. %A Bradley, L %A Coe, D. %A Moustakas, L. A. %A Postman, M. %A Shu, X %A Zheng, W %A Benítez, N. %A Bouwens, R. %A Broadhurst, T. %A Ford, H %A Host, O. %A Jouvel, S %A Koekemoer, A. %A Meneghetti, M %A Rosati, P. %A Donahue, M %A Grillo, C. %A Kelson, D. %A Lemze, D %A Medezinski, E %A Molino, A. %A Nonino, M. %A Ogaz, S. %K dark matter %K galaxies: clusters: general %K galaxies: clusters: individual: MACS J0329.6-0211 %K Galaxies: High-Redshift %K gravitational lensing: strong %B The Astrophysical Journal Letters %V 747 %8 03/2012 %G eng %N 1 %0 Journal Article %J The Astrophysical Journal %D 2012 %T CLASH: Mass Distribution in and around MACS J1206.2-0847 from a Full Cluster Lensing Analysis %A Umetsu, Keiichi %A Medezinski, Elinor %A Nonino, Mario %A Merten, Julian %A Zitrin, Adi %A Molino, Alberto %A Grillo, Claudio %A Carrasco, Mauricio %A Donahue, Megan %A Mahdavi, Andisheh %A Coe, Dan %A Postman, Marc %A Koekemoer, Anton %A Czakon, Nicole %A Sayers, Jack %A Mroczkowski, Tony %A Golwala, Sunil %A Koch, Patrick M %A Lin, Kai-Yang %A Molnar, Sandor M %A Rosati, Piero %A Balestra, Italo %A Mercurio, Amata %A Scodeggio, Marco %A Biviano, Andrea %A Anguita, Timo %A Infante, Leopoldo %A Seidel, Gregor %A Sendra, Irene %A Jouvel, Stephanie %A Host, Ole %A Lemze, Doron %A Broadhurst, Tom %A Meneghetti, Massimo %A Moustakas, Leonidas %A Bartelmann, Matthias %A Benítez, Narciso %A Bouwens, Rychard %A Bradley, Larry %A Ford, Holland %A Jiménez-Teja, Yolanda %A Kelson, Daniel %A Lahav, Ofer %A Melchior, Peter %A Moustakas, John %A Ogaz, Sara %A Seitz, Stella %A Zheng, Wei %K cosmology: observations %K dark matter %K galaxies: clusters: individual: MACS J1206.2-0847 %K gravitational lensing: strong %K gravitational lensing: weak %B The Astrophysical Journal %V 755 %8 08/2012 %G eng %N 1 %0 Journal Article %J The Astrophysical Journal %D 2012 %T CLASH: New Multiple Images Constraining the Inner Mass Profile of MACS J1206.2-0847 %A Zitrin, A. %A Rosati, P. %A Nonino, M. %A Grillo, C. %A Postman, M. %A Coe, D. %A Seitz, S. %A Eichner, T %A Broadhurst, T. %A Jouvel, S %A Balestra, I. %A Mercurio, A %A Scodeggio, M %A Benítez, N. %A Bradley, L %A Ford, H %A Host, O. %A Jimenez-Teja, Y %A Koekemoer, A. %A Zheng, W %A Bartelmann, M %A Bouwens, R. %A Czoske, O %A Donahue, M %A Graur, O %A Graves, G. %A Infante, L %A Jha, S. %A Kelson, D. %A Lahav, O. %A Lazkoz, R %A Lemze, D %A Lombardi, M. %A Maoz, D %A McCully, C. %A Medezinski, E %A Melchior, P %A Meneghetti, M %A Merten, J %A Molino, A. %A Moustakas, L. A. %A Ogaz, S. %A Patel, B. %A Regoes, E. %A Riess, A. %A Rodney, S %A Umetsu, K %A Van der Wel, A. %K dark matter %K galaxies: clusters: general %K galaxies: clusters: individual: MACS J1206.2–0847 %K Galaxies: High-Redshift %K gravitational lensing: strong %B The Astrophysical Journal %V 749 %8 04/2012 %G eng %N 2 %0 Journal Article %J The Astrophysical Journal %D 2012 %T CLASH: Precise New Constraints on the Mass Profile Galaxy Cluster A2261 %A Coe, Dan %A Umetsu, Keiichi %A Zitrin, Adi %A Donahue, Megan %A Medezinski, Elinor %A Postman, Marc %A Carrasco, Mauricio %A Anguita, Timo %A Geller, Margaret J %A Rines, Kenneth J. %A Diaferio, Antonaldo %A Kurtz, Michael J %A Bradley, Larry %A Koekemoer, Anton %A Zheng, Wei %A Nonino, Mario %A Molino, Alberto %A Mahdavi, Andisheh %A Lemze, Doron %A Infante, Leopoldo %A Ogaz, Sara %A Melchior, Peter %A Host, Ole %A Ford, Holland %A Grillo, Claudio %A Rosati, Piero %A Jiménez-Teja, Yolanda %A Moustakas, John %A Ascaso, Begoña %A Lahav, Ofer; %A Bartelmann, Matthias %A Benítez, Narciso %A Bouwens, Rychard %A Graur, Or %A Graves, Genevieve %A Jha, Saurab %A Jouvel, Stephanie %A Kelson, Daniel %A Moustakas, Leonidas %A Maoz, Dan %A Meneghetti, Massimo %A Merten, Julian %A Riess, Adam %A Rodney, Steve %A Seitz, Stella %B The Astrophysical Journal %V 757 %8 09/2012 %G eng %N 1 %0 Journal Article %J Phys. Rev. Lett. %D 2012 %T Designing Electrical Contacts to ${\mathrm{MoS}}_{2}$ Monolayers: A Computational Study %A Popov, Igor %A Seifert, Gotthard %A David Tománek %B Phys. Rev. Lett. %I American Physical Society %V 108 %P 156802 %8 Apr %G eng %0 Journal Article %J Journal of Management Studies %D 2012 %T Dynamics of Performing and Remembering Organizational Routines %A Miller, K. D. %A Pentland, B. T. %A Choi, S. %B Journal of Management Studies %V 49 %P 1536-1558 %G eng %N 8 %0 Journal Article %J Journal of Membrane Science %D 2012 %T Effects of crossflow velocity and transmembrane pressure on microfiltration of oil-in-water emulsions %A Tohid Darvishzadeh %A Nikolai V. Priezjev %B Journal of Membrane Science %V 423 %8 10/2012 %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 Nature %D 2012 %T A magnified young galaxy from about 500 million years after the Big Bang %A Zheng, Wei %A Postman, Marc %A Zitrin, Adi %A Moustakas, John %A Shu, Xinwen %A Jouvel, Stephanie %A Høst, Ole %A Molino, Alberto %A Bradley, Larry %A Coe, Dan %A Moustakas, Leonidas A %A Carrasco, Mauricio %A Ford, Holland %A Benítez, Narciso %A Lauer, Tod R %A Seitz, Stella; B %A Bouwens, Rychard %A Koekemoer, Anton %A Medezinski, Elinor %A Bartelmann, Matthias %A Broadhurst, Tom %A Donahue, Megan %A Grillo, Claudio %A Infante, Leopoldo %A Jha, Saurabh W %A Kelson, Daniel D. %A Lahav, Ofer %A Lemze, Doron %A Melchior, Peter %A Meneghetti, Massimo %A Merten, Julian %A Nonino, Mario %A Ogaz, Sara %A Rosati, Piero %A Umetsu, Keiichi %A van der Wel, Arjen %B Nature %V 489 %8 09/2012 %G eng %N 7416 %0 Journal Article %J Database, doi: 10.1093/database/bar053. %D 2011 %T The Comprehensive Phytopathogen Genomics Resource: An electronic resource for data-mining plant pathogen genomes %A Hamilton, J. P. %A Neeno-Eckwall, E. %A Adhikari, B. %A Perna, N. %A Tisserat, N. %A Leach, J.E. %A Lévesque, C. A. %A C. R. Buell %B Database, doi: 10.1093/database/bar053. %G eng %0 Journal Article %J Climatic Change %D 2011 %T East African Food Security as Influenced by Future Climate Change and Land Use Change at Local to Regional Scales %A Moore, Nathan %A Alagarswamy, Gopal %A Pijanowski, Bryan %A Thornton, Phil %A Lofgren, Brent %A Olson, Jennifer %A Yanda, Pius %A Qi, Jiaguo %B Climatic Change %V 107 %G eng %0 Journal Article %J Earth Interactions %D 2011 %T Evaluating error propagation in coupled land-atmosphere models %A Pijanowski, Bryan %A Moore, Nathan %A Mauree, Desaraden %A Niyogi, Dev %B Earth Interactions %V 15 %G eng %0 Journal Article %J J. Chem. Phys. %D 2011 %T Molecular diffusion and slip boundary conditions at smooth surfaces with periodic and random nanoscale textures %A N. V Priezjev %B J. Chem. Phys. %V 135 %G eng %0 Journal Article %J IEEE Transactions on Evolutionary Computation %D 2011 %T On the Performance of Indirect Encoding Across the Continuum of Regularity %A Clune, J. %A Stanley, K.O. %A Pennock, R.T. %A Ofria, C. %B IEEE Transactions on Evolutionary Computation %G eng %0 Journal Article %J Proceedings of the Royal Society B: Biological Sciences %D 2011 %T Selective pressures for accurate altruism targeting: evidence from digital evolution for difficult-to-test aspects of inclusive fitness theory %A Clune, J. %A Goldsby, H.J. %A Ofria, C. %A Pennock, R.T. %B Proceedings of the Royal Society B: Biological Sciences %I The Royal Society %V 278 %P 666-674 %G eng %0 Journal Article %J International Journal of Climatology %D 2010 %T Adapting MODIS-derived LAI and fractional cover into the RAMS model for East Africa %A Moore, Nathan %A Torbick, Nathan %A Pijanowski, Bryan %A Lofrgren, Brent %A Wang, Jing %A Kim, Dong-Yun %A Andresen, Jeffrey %A Olson, Jennifer %B International Journal of Climatology %V 30 %G eng %N 13 %0 Journal Article %J Journal of Physical Chemistry B %D 2010 %T Conformational Sampling of Influenza Fusion Peptide in Membrane Bilayers as a Function of Termini and Protonation States %A Panahi, Afra %A Michael Feig %XInfluenza fusion peptide is critical for mediating the fusion of viral and host cell membranes during viral entry. The interaction of monomeric influenza fusion peptide with membranes is studied with replica exchange molecular dynamics simulations using a new implicit membrane model to effectively reach microsecond to millisecond time scales. The conformational sampling of the fusion peptide was studied as a function of different N- and C-termini, including an experimental construct with an additional C-terminal tag, as well as a function of protonation of acidic residues. It is found that the influenza fusion peptide mostly adopts helical structures with a pronounced kink at residues 11−13 with both N-terminal and C-terminal helices oriented mostly parallel to the membrane surface. A charged C-terminus and the presence of a charge C-terminal tag significantly alters the conformational sampling of the fusion peptide and results in more diverse conformational ensembles that include obliquely inserted N-terminal peptide structures. Protonation of acidic residues also affects the conformational sampling, however, based on pKa shift estimates the overall effect of pH = 5 on the conformational sampling of the influenza fusion peptide appears to be only minor.

%B Journal of Physical Chemistry B %V 114 %P 1407-1416 %8 12/2009 %G eng %9 Journal Article %0 Journal Article %J Physical Review E %D 2010 %T Modeling the combined effect of surface roughness and shear rate on slip flow of simple fluids %A A. Niavarani %A N. V Priezjev %XMolecular dynamics (MD) and continuum simulations are carried out to investigate the influence of shear rate and surface roughness on slip flow of a Newtonian fluid. For weak wall-fluid interaction energy, the nonlinear shear-rate dependence of the intrinsic slip length in the flow over an atomically flat surface is computed by MD simulations. We describe laminar flow away from a curved boundary by means of the effective slip length defined with respect to the mean height of the surface roughness. Both the magnitude of the effective slip length and the slope of its rate dependence are significantly reduced in the presence of periodic surface roughness. We then numerically solve the Navier-Stokes equation for the flow over the rough surface using the rate-dependent intrinsic slip length as a local boundary condition. Continuum simulations reproduce the behavior of the effective slip length obtained from MD simulations at low shear rates. The slight discrepancy between MD and continuum results at high shear rates is explained by examination of the local velocity profiles and the pressure distribution along the wavy surface. We found that in the region where the curved boundary faces the mainstream flow, the local slip is suppressed due to the increase in pressure. The results of the comparative analysis can potentially lead to the development of an efficient algorithm for modeling rate-dependent slip flows over rough surfaces.

%B Physical Review E %V 81 %8 01/2010 %G eng %N 1 %9 Physics %0 Journal Article %J Journal of Physical Chemistry A %D 2010 %T Multi-level Extension of the Cluster-In-Molecule Local Correlation Methodology: Merging Coupled-Cluster and Moller-Plesset Perturbation Theories %A Wei Li %A Piotr Piecuch %XA multilevel extension of the local correlation “cluster-in-molecule” (CIM) framework, which enables one to combine different quantum chemistry methods to treat different regions in a large molecular system without splitting it into ad hoc fragments and saturating dangling bonds, is proposed. The resulting schemes combine higher-level methods, such as the completely renormalized coupled-cluster (CC) approach with singles, doubles, and noniterative triples, termed CR-CC(2,3), to treat the reactive part of a large molecular system, and lower-order methods, such as the second-order Møller−Plesset perturbation theory (MP2), to handle the chemically inactive regions. The multilevel CIM-CC/MP2 approaches preserve the key features of all CIM methods, such as the use of orthonormal localized orbitals and coarse-grain parallelism, while substantially reducing the already relatively low costs of the single-level CIM-CC calculations. Illustrative calculations include bond breaking in dodecane and the reactions of the bis(2,4,4-trimethylpentyl)dithiophosphinic acid with one and two water molecules.

%B Journal of Physical Chemistry A %V 114 %P 6721-6727 %8 05/2010 %G eng %N 24 %0 Journal Article %J Advances in Water Resources %D 2010 %T A Process-Based, Distributed Hydrologic Model Based on a Large-Scale Method for Surface - Subsurface Coupling, Advances in Water Resources %A Shen, Chaopeng %A M. Phanikumar %XProcess-based watershed models are useful tools for understanding the impacts of natural and anthropogenic influences on water resources and for predicting water and solute fluxes exported from watersheds to receiving water bodies. The applicability of process-based hydrologic models has been previously limited to small catchments and short time frames. Computational demands, especially the solution to the three-dimensional subsurface flow domain, continue to pose significant constraints. This paper documents the mathematical development, numerical testing and the initial application of a new distributed hydrologic model PAWS (Process-based Adaptive Watershed Simulator). The model solves the governing equations for the major hydrologic processes efficiently so that large scale applications become relevant. PAWS evaluates the integrated hydrologic response of the surface–subsurface system using a novel non-iterative method that couples runoff and groundwater flow to vadose zone processes approximating the 3D Richards equation. The method is computationally efficient and produces physically consistent solutions. All flow components have been independently verified using analytical solutions and experimental data where applicable. The model is applied to a medium-sized watershed in Michigan (1169 km2) achieving high performance metrics in terms of streamflow prediction at two gages during the calibration and verification periods. PAWS uses public databases as input and possesses full capability to interact with GIS datasets. Future papers will describe applications to other watersheds and the development and application of fate and transport modules.

%B Advances in Water Resources %V 33 %8 09/2010 %G eng %0 Journal Article %J Physical Review E %D 2010 %T Relationship between induced fluid structure and boundary slip in nanoscale polymer films %A N. V Priezjev %B Physical Review E %V 82 %G eng %0 Journal Article %J Physical Review C %D 2009 %T Ab Initio Coupled-Cluster and Configuration Interaction Calculations for O Using V %A R. Roth, %A J. R Gour %A Piotr Piecuch %B Physical Review C %V 79 %8 05/2009 %G eng %N 5 %0 Journal Article %J Physical Letters B %D 2009 %T Center-of-Mass Problem in Truncated Configuration Interaction and Coupled-Cluster Calculations %A R. Roth, %A Jeffrey R. Gour %A Piotr Piecuch %XThe problem of center-of-mass (CM) contaminations in ab initio nuclear structure calculations using configuration interaction (CI) and coupled-cluster (CC) approaches is analyzed. A rigorous and quantitative scheme for diagnosing the CM contamination of intrinsic observables is proposed and applied to ground-state calculations for 4He and 16O. The CI and CC calculations for 16O based on model spaces defined via a truncation of the single-particle basis lead to sizable CM contaminations, while the importance-truncated no-core shell model based on the NmaxΩ space is virtually free of CM contaminations.

%B Physical Letters B %V 679 %P 334-339 %8 08/2009 %G eng %N 4 %0 Journal Article %J Physics of Fluids %D 2009 %T The effective slip length and vortex formation in laminar flow over a rough surface %A A. Niavarani %A N. V Priezjev %K external flows %K laminar flow %K Navier-Stokes equations %K rough surfaces %K shear flow %K slip flow %K vortices %XThe flow of viscous incompressible fluid over a periodically corrugated surface is investigated numerically by solving the Navier–Stokes equation with the local slip and no-slip boundary conditions. We consider the effective slip length which is defined with respect to the level of the mean height of the surface roughness. With increasing corrugation amplitude the effective no-slip boundary plane is shifted toward the bulk of the fluid, which implies a negative effective slip length. The analysis of the wall shear stress indicates that a flow circulation is developed in the grooves of the rough surface provided that the local boundary condition is no-slip. By applying a local slip boundary condition, the center of the vortex is displaced toward the bottom of the grooves and the effective slip length increases. When the intrinsic slip length is larger than the corrugation amplitude, the flow streamlines near the surface are deformed to follow the boundary curvature, the vortex vanishes, and the effective slip length saturates to a constant value. Inertial effects promote vortex flow formation in the grooves and reduce the effective slip length.

%B Physics of Fluids %V 21 %8 05/2009 %G eng %N 5 %0 Conference Paper %B Proceedings of the IEEE Congress on Evolutionary Computation %D 2009 %T Evolving coordinated quadruped gaits with the HyperNEAT generative encoding %A Clune, J. %A Beckmann, B.E. %A Ofria, C. %A Pennock, R.T. %B Proceedings of the IEEE Congress on Evolutionary Computation %P 2764-2771 %G eng %0 Conference Paper %B Proceedings of the European Conference on Artificial Life %D 2009 %T HybrID: A Hybridization of Indirect and Direct Encodings for Evolutionary Computation %A Clune, J. %A Beckmann, B.E. %A Pennock, R.T. %A Ofria, C. %B Proceedings of the European Conference on Artificial Life %G eng %0 Journal Article %J International Journal of Quantum Chemistry %D 2009 %T Left-Eigenstate Completely Renormalized Equation-of-motion Coupled-Cluster Methods: Review of Key Concepts, Extension to Excited States of Open-Shell Systems, and Comparison with Electron-Attached and ionized Approaches %A Piotr Piecuch %A J. R Gour %A M. Wloch %XThe recently proposed left-eigenstate completely renormalized (CR) coupled-cluster (CC) method with singles, doubles, and noniterative triples, termed CR-CC(2,3) Piecuch and Włoch, J Chem Phys, 2005, 123, 224105; Piecuch et al. Chem Phys Lett, 2006, 418, 467 and the companion CR-EOMCC(2,3) methodology, which has been previously applied to singlet excited states of closed-shell molecular systems Włoch et al. Mol Phys, 2006, 104, 2149 and in which relatively inexpensive noniterative corrections due to triple excitations derived from the biorthogonal method of moments of CC equations (MMCC) are added to the CC singles and doubles (CCSD) or equation-of-motion (EOM) CCSD energies, have been extended to excited states of open-shell species. The resulting highly efficient computer codes for the open-shell CR-EOMCC(2,3) approach exploiting the recursively generated intermediates and fast matrix multiplication routines have been developed and interfaced with the GAMESS package, enabling CR-EOMCC(2,3) calculations for singlet as well as nonsinglet ground and excited states of closed- and open-shell systems using the restricted Hartree–Fock or restricted open-shell Hartree–Fock references. A number of important mathematical and algorithmic details related to formal aspects and computer implementation of the CR-EOMCC(2,3) method have been discussed, in addition to overviewing the key concepts behind the CR-EOMCC(2,3) and biorthogonal MMCC methodologies for ground and excited states, and the numerical results involving low-lying states of the CH, CNC, C2N, N3, and NCO species, including states dominated by two-electron transitions, have been presented. The results of the CR-EOMCC(2,3) calculations have been compared with other CC/EOMCC approaches, including the EOMCCSD and EOMCC singles, doubles, and triples methods, and their full and active-space valence counterparts based on the electron-attached and ionized EOMCC methodologies, and the predecessor of CR-EOMCC(2,3) termed CR-EOMCCSD(T) Kowalski and Piecuch, J Chem Phys, 2004, 120, 1715. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009

%B International Journal of Quantum Chemistry %V 109 %P 3268-3304 %8 11/2009 %G eng %N 14 %0 Journal Article %J The Journal of Chemical Physics %D 2009 %T Local Correlation Calculations Using Standard and Renormalized Coupled-Cluster Approaches %A Wei Li %A Piotr Piecuch %A J. R Gour %A Shuhua Li %Xhe linear scaling local correlation approach, termed “cluster-in-molecule” (CIM), is extended to the coupled-cluster (CC) theory with singles and doubles (CCSD) and CC methods with singles, doubles, and noniterative triples, including CCSD(T) and the completely renormalized CR-CC(2,3) approach. The resulting CIM-CCSD, CIM-CCSD(T), and CIM-CR-CC(2,3) methods are characterized by (i) the linear scaling of the CPU time with the system size, (ii) the use of orthonormal orbitals in the CC subsystem calculations, (iii) the natural parallelism, (iv) the high computational efficiency, enabling calculations for much larger systems and at higher levels of CC theory than previously possible, and (v) the purely noniterative character of local triples corrections. By comparing the results of the canonical and CIM-CC calculations for normal alkanes and water clusters, it is shown that the CIM-CCSD, CIM-CCSD(T), and CIM-CR-CC(2,3) approaches accurately reproduce the corresponding canonical CC correlation and relative energies, while offering savings in the computer effort by orders of magnitude.

%B The Journal of Chemical Physics %V 131 %8 09/2009 %G eng %N 11 %0 Journal Article %J Molecular Physics %D 2009 %T Low-Lying Valence Excited States of CNC, C₂N, N₃ and NCO Studied Using the Electron-Attached and Ionized Symmetry-Adapted Cluster Configuration-Interaction and Equation-of-Motion Coupled-Cluster Methodologies %A M. Ehara %A J. R Gour %A Piotr Piecuch %XLow-lying valence excited states of four open-shell triatomic molecules, CNC, C2N, N3, and NCO, are investigated using the electron-attached (EA) and ionized (IP) symmetry-adapted-cluster configuration-interaction (SAC-CI) general-R as well as the full and active-space EA and IP equation-of-motion coupled-cluster (EOMCC) methods. A comparison is made with experiment and with the results of the completely renormalized (CR) CC calculations with singles, doubles, and non-iterative triples defining the CR-CC(2,3) approach. Adiabatic excitation energies of the calculated states are in reasonable agreement with the experimental values, provided that the 3-particle-2-hole (3p-2h) components in the electron attaching operator, as in the EA SAC-CI SDT-R and EA EOMCCSD(3p-2h) approaches, are included in the calculations for the excited states of C2N and CNC which have a predominantly two-electron character. The results also reveal that the active-space EA/IP EOMCC schemes with up to 3p-2h/3h-2p excitations are able to accurately reproduce the results of their much more expensive parent methods while requiring significantly less computational effort. Furthermore, the more 'black-box' CR-CC(2,3) approach calculates the lowest state of each symmetry with the same accuracy as that obtained with the EA/IP SAC-CI SDT-R and EA/IP EOMCCSD(3p-2h/3h-2p) methods, confirming the significance of higher-order correlation effects in obtaining an accurate description of excited states of radicals, particularly the valence excited states of the CNC and C2N species dominated by two-electron processes.

%B Molecular Physics %V 107 %P 871-880 %8 04/2009 %G eng %N 8-12 %0 Journal Article %J Molecular Physics %D 2009 %T Method of Moments for the Continuous Transition Between the Brillouin-Wigner-Type and Rayleigh-Schrodinger-Type Multireference Coupled Cluster Theories %A J. Pittner %A Piotr Piecuch %XWe apply the method of moments to the multireference (MR) coupled cluster (CC) formalism representing the continuous transition between the Brillouin-Wigner-type and Rayleigh-Schr\"{o}dinger-type theories based on the Jeziorski-Monkhorst wave function ansatz and derive the formula for the noniterative energy corrections to the corresponding MRCC energies that recover the exact, full configuration interaction energies in the general model space case, including complete and incomplete model spaces. We also extend the relationship between the generalized moments of the state-universal (SU) MRCC equations within the Jeziorski-Monkhorst and Kucharski-Bartlett formulations of the SUMRCC theory to the general model space case. Finally, we argue that in the complete model space case, the relationship between moments of the SUMRCC equations corresponding to the Jeziorski-Monkhorst and Kucharski-Bartlett formulations of the SUMRCC theory, derived in this work, implies an equivalence of these two formulations of the SUMRCC approach, provided that the disconnected linked terms are included in the Kucharski-Bartlett formulation, and verify this statement numerically.

%B Molecular Physics %V 107 %P 1209-1221 %8 01/2009 %G eng %N 08-12 %0 Journal Article %J PNAS %D 2009 %T Protecting the Amazon with Protected Areas %A Robert Walker %A Moore, Nathan %A Arima, Eugenio %A Perz, Stephen %A Simmons, Cynthia %A Caldas, Marcellus %A Vergara, Dante %A Bohrer, Claudio %B PNAS %V 106 %8 08/2009 %G eng %0 Conference Paper %B Proceedings of the Genetic and Evolutionary Computation Conference %D 2009 %T The sensitivity of HyperNEAT to different geometric representations of a problem %A Clune, J. %A Ofria, C. %A Pennock, R.T. %B Proceedings of the Genetic and Evolutionary Computation Conference %P 675–682 %G eng %0 Journal Article %J Phys. Rev. E %D 2009 %T Shear rate threshold for the boundary slip in dense polymer films %A N. V Priezjev %XThe shear rate dependence of the slip length in thin polymer films confined between atomically flat surfaces is investigated by molecular dynamics simulations. The polymer melt is described by the bead-spring model of linear flexible chains. We found that at low shear rates the velocity profiles acquire a pronounced curvature near the wall and the absolute value of the negative slip length is approximately equal to the thickness of the viscous interfacial layer. At higher shear rates, the velocity profiles become linear and the slip length increases rapidly as a function of shear rate. The gradual transition from no-slip to steady-state slip flow is associated with faster relaxation of the polymer chains near the wall evaluated from decay of the time autocorrelation function of the first normal mode. We also show that at high melt densities the friction coefficient at the interface between the polymer melt and the solid wall follows a power-law decay as a function of the slip velocity. At large slip velocities the friction coefficient is determined by the product of the surface-induced peak in the structure factor, the temperature, and the contact density of the first fluid layer near the solid wall.

%B Phys. Rev. E %V 80 %P 11 Pages %8 09/2009 %G eng %N 3 %0 Journal Article %J Journal of Physical Chemistry A %D 2009 %T Thermochemical Kinetics for Multi-reference Systems: Addition Reactions of Ozone %A Piotr Piecuch %A Zhao, Y. %A Truhlar, D.G. %XThe 1,3-dipolar cycloadditions of ozone to ethyne and ethene provide extreme examples of multireference singlet-state chemistry, and they are examined here to test the applicability of several approaches to thermochemical kinetics of systems with large static correlation. Four different multireference diagnostics are applied to measure the multireference characters of the reactants, products, and transition states; all diagnostics indicate significant multireference character in the reactant portion of the potential energy surfaces. We make a more complete estimation of the effect of quadruple excitations than was previously available, and we use this with CCSDT/CBS estimation of Wheeler et al. (Wheeler, S. E.; Ess, D. H.; Houk, K. N. J. Phys. Chem. A 2008, 112, 1798.) to make new best estimates of the van der Waals association energy, the barrier height, and the reaction energy to form the cycloadduct for both reactions. Comparing with these best estimates, we present comprehensive mean unsigned errors for a variety of coupled cluster, multilevel, and density functional methods. Several computational aspects of multireference reactions are considered: (i) the applicability of multilevel theory, (ii) the convergence of coupled cluster theory for reaction barrier heights, (iii) the applicability of completely renormalized coupled cluster methods to multireference systems, (iv) the treatment by density functional theory, (v) the multireference perturbation theory for multireference reactions, and (vi) the relative accuracy of scaling-type multilevel methods as compared with additive ones. It is found that scaling-type multilevel methods do not perform better than the additive-type multilevel methods. Among the 48 tested density functionals, only M05 reproduces the best estimates within their uncertainty. Multireference perturbation theory based on the complete-active-space reference wave functions constructed using a small number of reaction-specific active orbitals gives accurate forward barrier heights; however, it significantly underestimates reaction energies.

%B Journal of Physical Chemistry A %V 113 %P 5786-5799 %8 04/2009 %G eng %N 19 %0 Journal Article %J Theoretical Chemistry Accounts: Theory, Computation, and Modeling (THEORETICA CHIMICA ACTA) %D 2008 %T Application of Renormalized Coupled- Cluster Methods to Potential Function of Water %A J. Zheng %A J. R Gour %A J.J. Lutz %A M. Wloch %A Piotr Piecuch %A Truhlar, D.G. %XThe goal of this paper is to examine the performance of the conventional and renormalized single-reference coupled-cluster (CC) methods in calculations of the potential energy surface of the water molecule. A comparison with the results of the internally contracted multi-reference configuration interaction calculations including the quasi-degenerate Davidson correction (MRCI(Q)) and the spectroscopically accurate potential energy surface of water resulting from the use of the energy switching (ES) approach indicates that the relatively inexpensive completely renormalized (CR) CC methods with singles (S), doubles (D), and a non-iterative treatment of triples (T) or triples and quadruples (TQ), such as CR-CCSD(T), CR-CCSD(TQ), and the recently developed rigorously size extensive extension of CR-CCSD(T), termed CR-CC(2,3), provide substantial improvements in the results of conventional CCSD(T) and CCSD(TQ) calculations at larger internuclear separations. It is shown that the CR-CC(2,3) results corrected for the effect of quadruply excited clusters through the CR-CC(2,3)+Q approach can compete with the highly accurate MRCI(Q) data. The excellent agreement between the CR-CC(2,3)+Q and MRCI(Q) results suggests ways of improving the global potential energy surface of water resulting from the use of the ES approach in the regions of intermediate bond stretches and intermediate energies connecting the region of the global minimum with the asymptotic regions.

%B Theoretical Chemistry Accounts: Theory, Computation, and Modeling (THEORETICA CHIMICA ACTA) %V 120 %P 59-78 %G eng %N 1-3 %0 Journal Article %J The Journal of Chemical Physics %D 2008 %T A Comparative Assessment of the Perturbative and Renormalized Coupled Cluster Theories with a Non-iterative Treatment of Triple Excitations for Thermochemical Kinetics, Including a Study of Basis Set and Core Correlation E %A J. Zheng %A J. R Gour %A J.J. Lutz %A M. Wloch %A Piotr Piecuch %A Truhlar, D.G. %XThe CCSD, CCSD(T), and CR-CC(2,3) coupled cluster methods, combined with five triple-zeta basis sets, namely, MG3S, aug-cc-pVTZ, aug-cc-pV(T+d)Z, aug-cc-pCVTZ, and aug-cc-pCV(T+d)Z, are tested against the DBH24 database of diverse reaction barrier heights. The calculations confirm that the inclusion of connected triple excitations is essential to achieving high accuracy for thermochemical kinetics. They show that various noniterative ways of incorporating connected triple excitations in coupled cluster theory, including the CCSD(T) approach, the full CR-CC(2,3) method, and approximate variants of CR-CC(2,3) similar to the triples corrections of the CCSD(2) approaches, are all about equally accurate for describing the effects of connected triply excited clusters in studies of activation barriers. The effect of freezing core electrons on the results of the CCSD, CCSD(T), and CR-CC(2,3) calculations for barrier heights is also examined. It is demonstrated that to include core correlation most reliably, a basis set including functions that correlate the core and that can treat core-valence correlation is required. On the other hand, the frozen-core approximation using valence-optimized basis sets that lead to relatively small computational costs of CCSD(T) and CR-CC(2,3) calculations can achieve almost as high accuracy as the analogous fully correlated calculations.

%B The Journal of Chemical Physics %V 128 %8 01/2008 %G eng %N 4 %0 Conference Paper %B Parallel Problem Solving from Nature %D 2008 %T How a generative encoding fares as problem-regularity decreases %A Clune, J. %A Ofria, C. %A Pennock, R.T. %B Parallel Problem Solving from Nature %I Springer %P 358–367 %G eng %0 Journal Article %J Journal of Chemical Physics %D 2008 %T Rheological study of polymer flow past rough surfaces with slip boundary conditions %A A. Niavarani %A N. V Priezjev %K liquid films %K molecular dynamics method %K polymer melts %K rheology %K shear flow %K slip flow %K surface roughness %XThe slip phenomena in thin polymer films confined by either flat or periodically corrugated surfaces are investigated by molecular dynamics and continuum simulations. For atomically flat surfaces and weak wall-fluid interactions, the shear rate dependence of the slip length has a distinct local minimum which is followed by a rapid increase at higher shear rates. For corrugated surfaces with wavelength larger than the radius of gyration of polymer chains, the effective slip length decays monotonically with increasing corrugation amplitude. At small amplitudes, this decay is reproduced accurately by the numerical solution of the Stokes equation with constant and rate-dependent local slip length. When the corrugation wavelength is comparable to the radius of gyration, the continuum predictions overestimate the effective slip length obtained from molecular dynamics simulations. The analysis of the conformational properties indicates that polymer chains tend to stretch in the direction of shear flow above the crests of the wavy surface.

%B Journal of Chemical Physics %V 129 %8 10/2008 %G eng %N 14 %0 Journal Article %J Physical Review E %D 2008 %T Slip boundary conditions for shear flow of polymer melts past atomically flat surfaces %A A. Niavarani %A N. V Priezjev %K molecular dynamics %K shear rate %K slip length %K slip velocity %K smooth thermal surfaces %XMolecular dynamics simulations are carried out to investigate the dynamic behavior of the slip length in thin polymer films confined between atomically smooth thermal surfaces. For weak wall-fluid interactions, the shear rate dependence of the slip length acquires a distinct local minimum followed by a rapid growth at higher shear rates. With increasing fluid density, the position of the local minimum is shifted to lower shear rates. We found that the ratio of the shear viscosity to the slip length, which defines the friction coefficient at the liquid/solid interface, undergoes a transition from a nearly constant value to power law decay as a function of the slip velocity. In a wide range of shear rates and fluid densities, the friction coefficient is determined by the product of the value of the surface-induced peak in the structure factor and the contact density of the first fluid layer near the solid wall.

%B Physical Review E %V 77 %8 04/2008 %G eng %N 4 %0 Journal Article %J The Journal of Physical Chemistry %D 2008 %T Stereoelectronic Effects on Molecular Geometries and State-Energy Splittings of Ligated Monocopper Diozygen Complexes %A C.J. Cramer %A J. R Gour %A A. Kinal %A M. Wloch %A Piotr Piecuch %A A.R.M. Shahi %A L. Gagliardi %XThe relative energies of side-on versus end-on binding of molecular oxygen to a supported Cu(I) species, and the singlet versus triplet nature of the ground electronic state, are sensitive to the nature of the supporting ligands and, in particular, depend upon their geometric arrangement relative to the O2 binding site. Highly correlated ab initio and density functional theory electronic structure calculations demonstrate that optimal overlap (and oxidative charge transfer) occurs for the side-on geometry, and this is promoted by ligands that raise the energy, thereby enhancing resonance, of the filled Cu dxz orbital that hybridizes with the in-plane π* orbital of O2. Conversely, ligands that raise the energy of the filled Cu dz2 orbital foster a preference for end-on binding as this is the only mode that permits good overlap with the in-plane O2 π*. Because the overlap of Cu dz2 with O2 π* is reduced as compared to the overlap of Cu dxz with the same O2 orbital, the resonance is also reduced, leading to generally more stable triplet states relative to singlets in the end-on geometry as compared to the side-on geometry, where singlet ground states become more easily accessible once ligands are stronger donors. Biradical Cu(II)-O2 superoxide character in the electronic structure of the supported complexes leads to significant challenges for accurate quantum chemical calculations that are best addressed by exploiting the spin-purified M06L local density functional, single-reference completely renormalized coupled-cluster theory, or multireference second-order perturbation theory, all of which provide predictions that are qualitatively and quantitatively consistent with one another.

%B The Journal of Physical Chemistry %V 112 %P 3754-3767 %8 03/2008 %G eng %N 16 %0 Journal Article %J The Journal of Chemical Physics %D 2007 %T Active-Space Symmetry-Adapted-Cluster Configuration-Interaction and Equation-of-Motion Cluster Methods for High Accuracy Calculations of Potential Energy Surfaces of Radicals %A Y. Ohtsuka %A Piotr Piecuch %A J. R Gour %A M. Ehara %A H. Nakatsuji %K configuration interactions %K coupled cluster calculations %K electron attachment %K excited states %K free radicals %K ground states %K ionisation %K organic compounds %K oxygen compounds %K potential energy surfaces %XThe electron-attached (EA) and ionized (IP) symmetry-adapted-cluster configuration-interaction (SAC-CI) methods and their equation-of-motion coupled-cluster (EOMCC) analogs provide an elegant framework for studying open-shell systems. As shown in this study, these schemes require the presence of higher-order excitations, such as the four-particle-three-hole (4p-3h) or four-hole–three-particle (4h-3p) terms, in the electron attaching or ionizing operator R in order to produce accurate ground- and excited-state potential energy surfaces of radicals along bond breaking coordinates. The full inclusion of the 4p-3h/4h-3p excitations in the EA/IP SAC-CI and EOMCC methods leads to schemes which are far too expensive for calculations involving larger radicals and realistic basis sets. In order to reduce the large costs of such schemes without sacrificing accuracy, the active-space EA/IP EOMCC methodology [ J. R. Gour et al., J. Chem. Phys. 123, 134113 (2005) ] is extended to the EA/IP SAC-CI approaches with 4p-3h/4h-3p excitations. The resulting methods, which use a physically motivated set of active orbitals to pick out the most important 3p-2h/3h-2p and 4p-3h/4h-3p excitations, represent practical computational approaches for high-accuracy calculations of potential energy surfaces of radicals. To illustrate the potential offered by the active-space EA/IP SAC-CI approaches with up to 4p-3h/4h-3p excitations, the results of benchmark calculations for the potential energy surfaces of the low-lying doublet states of CH and OH are presented and compared with other SAC-CI and EOMCC methods, and full CI results.

%B The Journal of Chemical Physics %V 126 %P 28 pages %8 04/2007 %G eng %N 16 %0 Journal Article %J The Journal of Chemical Physics %D 2007 %T Breaking Bonds with the Left Eigenstate Completely Renormalized Coupled-Cluster Method %A Y. Ge %A M.S. Gordon %A Piotr Piecuch %XThe recently developed [ P. Piecuch and M. Wloch, J. Chem. Phys. 123, 224105 (2005) ] size-extensive left eigenstate completely renormalized (CR) coupled-cluster (CC) singles (S), doubles (D), and noniterative triples (T) approach, termed CR-CC(2,3) and abbreviated in this paper as CCL, is compared with the full configuration interaction (FCI) method for all possible types of single bond-breaking reactions between C, H, Si, and Cl (except H2) and the H2SiSiH2 double bond-breaking reaction. The CCL method is in excellent agreement with FCI in the entire region R = 1–3Re for all of the studied single bond-breaking reactions, where R and Re are the bond distance and the equilibrium bond length, respectively. The CCL method recovers the FCI results to within approximately 1 mhartree in the region R = 1–3Re of the H–SiH3, H–Cl, H3Si–SiH3, Cl–CH3, H–CH3, and H3C–SiH3 bonds. The maximum errors are −2.1, 1.6, and 1.6 mhartree in the R = 1–3Re region of the H3C–CH3, Cl–Cl, and H3Si–Cl bonds, respectively, while the discrepancy for the H2SiSiH2 double bond-breaking reaction is 6.6 (8.5) mhartree at R = 2(3)Re. CCL also predicts more accurate relative energies than the conventional CCSD and CCSD(T) approaches, and the predecessor of CR-CC(2,3) termed CR-CCSD(T).

%B The Journal of Chemical Physics %V 127 %P 6 pages %8 11/2007 %G eng %N 17 %0 Journal Article %J Journal of Physical Chemistry A %D 2007 %T Computational Investigation of the Conrotatory and Disrotatory Isomerization Channels of Bicyclo[1.1.0]butane to Buta-1,3-diene: A Completely Renormalized Coupled-Cluster Study %A A. Kinal %A Piotr Piecuch %XThe conrotatory and disrotatory mechanisms of the isomerization of bicyclo[1.1.0]butane to trans-buta-1,3-diene have been computationally investigated with the CASSCF, MCQDPT2, (U)B3LYP, CCSD(T), CR-CCSD(T), and CR-CC(2,3) approaches. The coupled-cluster (CC) methods, including the CC approach with singles, doubles, and noniterative triples (CCSD(T)), and its completely renormalized (CR) extensions called CR-CCSD(T) and CR-CC(2,3), and the density functional theory B3LYP approach do an excellent job of correctly predicting the activation barrier for the conrotatory pathway, which corresponds to a weakly biradical transition state (TS), producing values within experimental error bars. In particular, the recently developed CR-CC(2,3) method gives 40.8 or 41.1 kcal/mol, in perfect agreement with the experimental value of 40.6 ± 2.5 kcal/mol. The complete-active-space self-consistent-field (CASSCF) approach and the second-order multireference perturbation theory (MCQDPT2) are less accurate in describing the conrotatory barrier than CR-CC(2,3). The higher energy disrotatory pathway, which has not been characterized experimentally and which involves a strongly biradical TS, poses a great challenge for many methods. CCSD(T) fails, predicting the activation barrier for the disrotatory pathway significantly below the conrotatory barrier, contradicting the experimental result that the conrotatory pathway describes the mechanism. The strongly biradical character of the disrotatory TS, spin contamination, and the proximity of singlet and triplet potential energy surfaces cause difficulties for B3LYP, which does not link this TS with gauche-buta-1,3-diene. No such difficulties occur in the CASSCF calculations, which offer a proper description of the structure of the disrotatory TS that links it with the reactant and product molecules. The CR-CC(2,3) approach, which accurately balances dynamical and nondynamical correlations in systems containing closed-shell and biradical structures, predicts the activation enthalpy for the disrotatory mechanism of 66 kcal/mol. CR-CCSD(T) gives 69 kcal/mol. In agreement with experiment and earlier multireference configuration interaction calculations of Nguyen and Gordon, CR-CCSD(T) and CR-CC(2,3) favor the conrotatory mechanism. The CASSCF, MCQDPT2, and B3LYP methods correctly place the disrotatory barrier above the conrotatory one, but, on the basis of a comparison with the accurate CR-CC(2,3) results, they underestimate the activation energy for the disrotatory pathway. All CC approaches employed in this study produce very good estimates of the enthalpy of isomerization of bicyclo[1.1.0]butane into buta-1,3-diene, the experimental value of which is −25.9 ± 0.4 kcal/mol, giving about −28 kcal/mol, when trans-buta-1,3-diene is used as a product, and −25 kcal/mol, when the nearly isoenergetic gauche-buta-1,3-diene rotamer is used as a product. The CC reaction enthalpies are more accurate than those obtained with CASSCF, MCQDPT2, and B3LYP.

%B Journal of Physical Chemistry A %V 111 %P 734-742 %8 01/2007 %G eng %N 4 %0 Journal Article %J Physical Review Lettters %D 2007 %T Coupled-Cluster and Configuration-Interaction Calculations for Heavy Nuclei %A M. Horoi %A J. R Gour %A M. Wloch %A M.D. Lodriguito %A B. A. Brown %A Piotr Piecuch %XWe compare coupled-cluster (CC) and configuration-interaction (CI) results for 56Ni obtained in the pf-shell basis, focusing on practical CC approximations that can be applied to systems with dozens or hundreds of correlated fermions. The weight of the reference state and the strength of correlation effects are controlled by the gap between the f7/2 orbit and the f5/2, p3/2, p1/2 orbits. Independent of the gap, the CC method with 1p-1h and 2p-2h clusters and a noniterative treatment of 3p-3h clusters is as accurate as the more demanding CI approach truncated at the 4p-4h level.

%B Physical Review Lettters %V 98 %P 4 pages %8 03/2007 %G eng %N 11 %0 Journal Article %J Physical Review C %D 2007 %T Coupled-Cluster Theory for Three-Body Hamiltonians %A G. Hagen %A T. Papenbrock %A D. J. Dean %A A. Schwenk %A A. NHogga %A M. Wloch %A Piotr Piecuch %XWe derive coupled-cluster equations for three-body Hamiltonians. The equations for the one- and two-body cluster amplitudes are presented in a factorized form that leads to an efficient numerical implementation. We employ low-momentum two- and three-nucleon interactions and calculate the binding energy of 4He. The results show that the main contribution of the three-nucleon interaction stems from its density-dependent zero-, one-, and two-body terms that result from the normal ordering of the Hamiltonian in coupled-cluster theory. The residual three-body terms that remain after normal ordering can be neglected.

%B Physical Review C %V 76 %P 11 pages %8 09/2007 %G eng %N 3 %0 Journal Article %J The Journal of Chemical Physics %D 2007 %T Effect of surface roughness on rate-dependent slip in simple fluids %A N. V Priezjev %K elastic constants %K interface roughness %K liquid films %K molecular dynamics method %K slip %K surface roughness %K thin films %XMolecular dynamics simulations are used to investigate the influence of molecular-scale surface roughness on the slip behavior in thin liquid films. The slip length increases almost linearly with the shear rate for atomically smooth rigid walls and incommensurate structures of the liquid/solid interface. The thermal fluctuations of the wall atoms lead to an effective surface roughness, which makes the slip length weakly dependent on the shear rate. With increasing the elastic stiffness of the wall, the surface roughness smoothes out and the strong rate dependence is restored again. Both periodically and randomly corrugated rigid surfaces reduce the slip length and its shear rate dependence.

%B The Journal of Chemical Physics %V 127 %P 144708 %8 10/2007 %G eng %N 14 %0 Journal Article %J The Journal of Physical Chemistry A %D 2007 %T Extension of the Renormalized Coupled-Cluster Methods Exploiting Left Eigenstates of the Similarity-Transformed Hamiltonian to Open- Shell Systems: A Benchmark Study %A M. Wloch %A J. R Gour %A Piotr Piecuch %XThe recently formulated completely renormalized coupled-cluster method with singles, doubles, and noniterative triples, exploiting the biorthogonal form of the method of moments of coupled-cluster equations (Piecuch, P.; Włoch, M. J. Chem. Phys. 2005, 123, 224105; Piecuch, P.; Włoch, M.; Gour, J. R.; Kinal, A. Chem. Phys. Lett. 2006, 418, 467), termed CR-CC(2,3), is extended to open-shell systems. Test calculations for bond breaking in the OH radical and the ion and singlet−triplet gaps in the CH2, HHeH, and (HFH)- biradical systems indicate that the CR-CC(2,3) approach employing the restricted open-shell Hartree−Fock (ROHF) reference is significantly more accurate than the widely used CCSD(T) method and other noniterative triples coupled-cluster approximations without making the calculations substantially more expensive. A few molecular examples, including the activation energies of the C2H4 + H → C2H5 forward and reverse reactions and the triplet states of the CH2 and H2Si2O2 biradicals, are used to show that the dependence of the ROHF-based CR-CC(2,3) energies on the method of canonicalization of the ROHF orbitals is, for all practical purposes, negligible.

%B The Journal of Physical Chemistry A %V 111 %P 11359-11382 %8 11/2007 %G eng %N 44 %0 Book Section %B Electron Correlation Methodology %D 2007 %T New Alternatives for Accurate Electronic Structure Calculations of Potential Energy Surfaces Involving Bond Breaking %A Piotr Piecuch %A I. S. O. Pimienta %A P.-D. Fan %A K. Kowalski %XThe method of moments of coupled-cluster equations (MMCC) is extended to potential energy surfaces involving multiple bond breaking by developing the quasi-variational (QV) and quadratic (Q) variants of the MMCC theory. The QVMMCC and QMMCC methods are related to the extended CC (ECC) theory, in which products involving cluster operators and their deexcitation counterparts mimic the effects of higher-order clusters. The test calculations for N2 show that the QMMCC and ECC methods can provide spectacular improvements in the description of multiple bond breaking by the standard CC approaches.

%B Electron Correlation Methodology %S ACS Symposium Series %I American Chemical Sociegy %C Washington, DC %V 958 %@ ISBN13: 9780841238435 %G eng %0 Journal Article %J Physical Review E %D 2007 %T Rate-dependent slip boundary conditions for simple fluids %A N. V Priezjev %XThe dynamic behavior of the slip length in a fluid flow confined between atomically smooth surfaces is investigated using molecular dynamics simulations. At weak wall-fluid interactions, the slip length increases nonlinearly with the shear rate provided that the liquid/solid interface forms incommensurable structures. A gradual transition to the linear rate dependence is observed upon increasing the wall-fluid interaction. We found that the slip length can be well described by a function of a single variable that in turn depends on the in-plane structure factor, contact density, and temperature of the first fluid layer near the solid wall. Extensive simulations show that this formula is valid in a wide range of shear rates and wall-fluid interactions.

%B Physical Review E %V 75 %P 51605 %8 05/2007 %G eng %N 5 %0 Book Section %B Progress in Theoretical Chemistry and Physics %D 2007 %T Renormalized Coupled-Cluster Methods: Theoretical Foundations and Application to Potential Function of Water %A Piotr Piecuch %A M. Wloch %A A.J.C. Verandas %XConventional single-reference methods fail when bond breaking and other situations characterized by larger non-dynamical correlation effects are examined. In consequence, the adequate treatment of molecular potential energy surfaces involving signiﬁcant bond rearrangements has been the domain of expert multi-reference methods. The question arises if one can develop practical single-reference procedures that could be applied to at least some of the most frequent multi-reference situations, such as single and double bond dissociations. This question is addressed in the present paper by examining the performance of the conventional and renormalized coupled-cluster (CC) methods in calculations of the potential enery surface of the water molecule. A comparison with the results of the highly accurate internally contracted multi-reference conﬁguration interaction calculations including the quasi-degenerate Davidson correction (MRCI(Q)) and the spectroscopically accurate potential energy surface of water resulting from the use of the energy switching (ES) approach indicates that the relatively inexpensive completely renormalized (CR) CC methods with singles (S), doubles (D), and a non-iterative treatment of triples (T) or triples and quadruples (TQ), such as CR-CCSD(T), CR-CCSD(TQ), and the recently developed rigorously size extensive extension of the CR-CCSD(T), termed CR-CC(2,3), provide considerable improvements in the results of conventional CCSD(T) and CCSD(TQ) calculations at larger internuclear separations. It is shown that the CR-CC(2,3) results a posteriori corrected for the effect of quadruply excited clusters (the CR-CC(2,3)+Q approach) can compete with the highly accurate MRCI(Q) data. The excellent agreement between the CR-CC(2,3)+Q and MRCI(Q) results suggests ways of improving the global potential energy surface of water resulting from the use of the ES approach in the regions of intermediate bond stretches and intermediate and higher energies connecting the region of the global minimum with the asymptotic regions. In addition to the examination of the performance of the CR-CCSD(T), CR-CCSD(TQ), CR-CC(2,3), and CR-CC(2,3)+Q approaches, we provide a thorough review of the method of moments of CC equations (MMCC), as applied to ground electronic states, including the most recent biorthogonal formulation of MMCC theory employing the left eigenstates of the similarity-transformed Hamiltonian, and other mathematical and physical concepts that lie behind all renormalized CC approximations. In particular, we discuss the similarities and differences between the older CR-CCSD(T) and CR-CCSD(TQ) approximations and the recently formulated size extensive renormalized CC methods, such as CR-CC(2,3), and open questions that emerge in the process of designing higher-order schemes based on the biorthogonalMMCC formalism, such as CR-CC(2,4), which describe the combined effect of triples (already present in CR-CC(2,3) calculations) and quadruples in a proper manner.

%B Progress in Theoretical Chemistry and Physics %V 16 %P 63-121 %G eng %N Part 1 %0 Journal Article %J PHYSICAL REVIEW LETTERS %D 2007 %T Shape and Structure of N = Z 64Ge: Electromagnetic Transition Rates from the Application ￼of the Recoil Distance Method to a Knockout Reaction %A K. Starosta %A A. Dewald %A A. Dunomes %A P. Adrich %A A.M. Amthor %A T. Baumann %A D. Bazin %A M. Bowen %A B. A. Brown %A A. Chester %A A. Gade %A D. Galaviz %A T. Glasmacher %A T. Ginter %A M. Hausmann %A M. Horoi %A J. Jolie %A B. Melon %A D. Miller %A V. Moeller %A R.P. Norris %A T. Pissulla %A M. Portillo %A W. Rother %A Y. Shimbara %A A. Stolz %A C. Vaman %A P. Voss %A D. Weisshaar %A V. Zelevinsky %B PHYSICAL REVIEW LETTERS %V 99 %8 07/2007 %G eng %U http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.99.042503 %0 Journal Article %J European Physics Journal A %D 2006 %T Ab Initio Coupled-Cluster Calculations for Nuclei Using Methods of Quantum Chemistry %A Piotr Piecuch %A M. Wloch %A D. J. Dean %A J. R Gour %A M. {Hjorth-Jensen} %A T. Papenbrock %A K. Kowalski %XWe report preliminary large scale ab initio calculations of ground and excited states of 16O using quantum chemistry inspired coupled cluster methods and realistic two-body interactions. By using the renormalized Hamiltonians obtained with a no-core G-matrix approach, we obtain the virtually converged results at the level of two-body interactions. Due to the polynomial scaling with the system size that characterizes coupled cluster methods, we can probe large model spaces with up to seven major oscillator shells, for which standard non-truncated shell-model calculations are not possible.

%B European Physics Journal A %V 25 %P 485-488 %8 09/2005 %G eng %N 1 %0 Journal Article %J Nature %D 2006 %T Ab initio determination of solid-state nanostructure %A P. Juhás %A D. M. Cherba %A P. M. Duxbury %A W. F. Punch %A S. J. L. Billinge %XAdvances in materials science and molecular biology followed rapidly from the ability to characterize atomic structure using single crystals1, 2, 3, 4. Structure determination is more difficult if single crystals are not available5. Many complex inorganic materials that are of interest in nanotechnology have no periodic long-range order and so their structures cannot be solved using crystallographic methods6. Here we demonstrate that ab initio structure solution of these nanostructured materials is feasible using diffraction data in combination with distance geometry methods. Precise, sub-ångström resolution distance data are experimentally available from the atomic pair distribution function (PDF)6, 7. Current PDF analysis consists of structure refinement from reasonable initial structure guesses6, 7 and it is not clear, a priori, that sufficient information exists in the PDF to obtain a unique structural solution. Here we present and validate two algorithms for structure reconstruction from precise unassigned interatomic distances for a range of clusters. We then apply the algorithms to find a unique, ab initio, structural solution for C60 from PDF data alone. This opens the door to sub-ångström resolution structure solution of nanomaterials, even when crystallographic methods fail.

%B Nature %V 440 %P 655–658 %8 07/2005 %G eng %0 Journal Article %J International Journal of Quantum Chemistry %D 2006 %T Automated derivation and parallel computer implementation of renormalized and active-space coupled-cluster methods %A Piotr Piecuch %A So Hirata %A K. Kowalski %A P.-D. Fan %A Theresa L. Windus %XOur recent efforts that have led to an automated derivation and computer implementation of the renormalized and active-space coupled-cluster {(CC)} methods with Tensor Contraction Engine {(TCE)} are summarized. The {TCE-generated} renormalized and active-space {CC} computer codes are parallel and applicable to closed- and open-shell references, enabling accurate calculations of potential energy surfaces along bond-breaking coordinates and excited states displaying a significant multi-reference character. The effectiveness of the new codes in describing electronic quasi-degeneracies is illustrated by the renormalized {CC} calculations of the potential energy curve of {HCl} and the active-space {CC} calculations for the low-lying excited states of the Be3 system. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006

%B International Journal of Quantum Chemistry %V 106 %P 79–97 %8 08/2005 %G eng %N 1 %0 Journal Article %J International Journal of Modern Physics B %D 2006 %T Coupled Cluster Theory for Nuclei %A T. Papenbrock %A D. J. Dean %A J. R Gour %A G. Hagen %A M. {Hjorth-Jensen} %A M. Wloch %K Nuclear structure; light nuclei; coupled-cluster theory %XThis presentation focuses on some of the recent developments in low-energy nuclear structure theory, with emphasis on applications of coupled-cluster theory. We report on results for ground and excited states in 4He and 16O, and about extensions of coupled-cluster theory to treat three-body forces.

%B International Journal of Modern Physics B %V 20 %P 5338-5345 %G eng %N 30-31 %0 Journal Article %J Physical Review C %D 2006 %T Coupled-Cluster Calculations for Valence Systems around 16 O %A Piotr Piecuch %A J. R Gour %A M. {Hjorth-Jensen} %A M. Wloch %A D. J. Dean %XWe study the ground and low-lying excited states of 15O, 17O, 15N, and 17F using modern two-body nucleon-nucleon interactions and the suitably designed variants of the ab initio equation-of-motion coupled-cluster theory aimed at an accurate description of systems with valence particles and holes. A number of properties of 15O, 17O, 15N, and 17F, including ways the energies of ground and excited states of valence systems around 16O change as functions of the number of nucleons, are correctly reproduced by the equation-of-motion coupled-cluster calculations performed in up to eight major-oscillator shells. Certain disagreements with experiment are in part because of the degrees of freedom such as three-body interactions not accounted for in our effective two-body Hamiltonians. In particular, the calculated binding energies of 15O/15N and 17O/17F enable us to rationalize the discrepancy between the experimental and recently published [Phys. Rev. Lett. 94, 212501 (2005)] equation-of-motion coupled-cluster excitation energies for the Jπ=3- state of 16O. Our calculations demonstrate the feasibility of the equation-of-motion coupled-cluster methods to deal with valence systems around closed-shell nuclei and to provide results for systems beyond A=16.

%B Physical Review C %V 74 %P 18 pages %8 8/2006 %G eng %N 2 %0 Journal Article %J Physical Review C %D 2006 %T Coupled-cluster calculations for valence systems around O16 %A J. R Gour %A Piotr Piecuch %A M. {Hjorth-Jensen} %A M. Wloch %A D. J. Dean %XWe study the ground and low-lying excited states of {15O,} {17O,} {15N,} and {17F} using modern two-body nucleon-nucleon interactions and the suitably designed variants of the ab initio equation-of-motion coupled-cluster theory aimed at an accurate description of systems with valence particles and holes. A number of properties of {15O,} {17O,} {15N,} and {17F,} including ways the energies of ground and excited states of valence systems around {16O} change as functions of the number of nucleons, are correctly reproduced by the equation-of-motion coupled-cluster calculations performed in up to eight major-oscillator shells. Certain disagreements with experiment are in part because of the degrees of freedom such as three-body interactions not accounted for in our effective two-body Hamiltonians. In particular, the calculated binding energies of {15O/15N} and {17O/17F} enable us to rationalize the discrepancy between the experimental and recently published {[Phys.} Rev. Lett. 94, 212501 (2005)] equation-of-motion coupled-cluster excitation energies for the Jπ=3- state of {16O.} Our calculations demonstrate the feasibility of the equation-of-motion coupled-cluster methods to deal with valence systems around closed-shell nuclei and to provide results for systems beyond A=16.

%B Physical Review C %V 74 %P 024310 %8 08/2006 %G eng %0 Journal Article %J Journal of Chemical Physics %D 2006 %T Efficient Formulation and Computer Implementation of the Active-Space Electron-Attached and Ionized Equation-of-Motion Coupled-Cluster Methods %A J. R Gour %A Piotr Piecuch %K coupled cluster calculations %K free radicals %K organic compounds %K sulphur compounds %XThe efficient, general-purpose implementations of the active-space electron-attached (EA) and ionized (IP) equation-of-motion coupled-cluster (EOMCC) methods including up to 3p-2h and 3h-2p excitations, called EA-EOMCCSDt and IP-EOMCCSDt, respectively, are discussed. The details of the algorithm that enables one to achieve a high degree of code vectorization for the active-space methods and the factorized forms of the EA- and IP-EOMCCSDt equations that maximize the benefits of using active orbitals in the process of selecting the dominant 3p-2h and 3h-2p excitations are presented. The results of benchmark calculations for the low-lying doublet and quartet states of the CH and SH radicals reveal that the active-space EA-EOMCCSDt and IP-EOMCCSDt methods are capable of producing results for the electronic excitations in open-shell systems that match the high accuracy of EA- and IP-EOMCC calculations with a full treatment of 3p-2h and 3h-2p excitations, even when the excited states of interest display a manifestly multideterminantal nature, with the costs that can be on the same order of those characterizing the basic EOMCC singles and doubles approach.

%B Journal of Chemical Physics %V 125 %P 17 pages %8 12/2006 %G eng %N 23 %0 Journal Article %J The Journal of Physical Chemistry A %D 2006 %T Experimental and Theoretical UV Characterizations of Acetyloacetone and its Isomers %A Piotr Piecuch %A S. Coussan %A Y. Ferro %A A. Trivella %A P. Roubin %A R. Wieczorek %A C. Manca %A K. Kowalski %A M. Wloch %A S. Kucharski %A M. Musial %XCryogenic matrix isolation experiments have allowed the measurement of the UV absorption spectra of the high-energy non-chelated isomers of acetylacetone, these isomers being produced by UV irradiation of the stable chelated form. Their identification has been done by coupling selective UV-induced isomerization, infrared spectroscopy, and harmonic vibrational frequency calculations using density functional theory. The relative energies of the chelated and non-chelated forms of acetylacetone in the S0 state have been obtained using density functional theory and coupled-cluster methods. For each isomer of acetylacetone, we have calculated the UV transition energies and dipole oscillator strengths using the excited-state coupled-cluster methods, including EOMCCSD (equation-of-motion coupled-cluster method with singles and doubles) and CR-EOMCCSD(T) (the completely renormalized EOMCC approach with singles, doubles, and non-iterative triples). For dipole-allowed transition energies, there is a very good agreement between experiment and theory. In particular, the CR-EOMCCSD(T) approach explains the blue shift in the electronic spectrum due to the formation of the non-chelated species after the UV irradiation of the chelated form of acetylacetone. Both experiment and CR-EOMCCSD(T) theory identify two among the seven non-chelated forms to be characterized by red-shifted UV transitions relative to the remaining five non-chelated isomers.

%B The Journal of Physical Chemistry A %V 110 %P 3920-3926 %8 2/2006 %G eng %N 11 %0 Journal Article %J International Journal of Quantum Chemistry %D 2006 %T Extension of the Active-Space Equation-of- Motion Coupled-Cluster Methods to Radical Systems: The EA-EOMCCSDt and IPEOMCCSDt Approaches %A Piotr Piecuch %A J. R Gour %A M. Wloch %K oupled-cluster theory;equation-of-a motion coupled-cluster method;active-space coupled-cluster approaches;electronic-attached and ionized states;radicals %XThe development of the active-space variants of the electron-attached (EA) and ionized (IP) equation-of-motion coupled-cluster (EOMCC) methods, in which higher-than-doubly excited components of the cluster operator T and higher than 2p-1h or 2h-1p components of the electron attaching and ionizing operators R are defined through the use of active orbitals, is discussed. As shown by preliminary test calculations of adiabatic excitation energies and potential energy curves for the low-lying states of the CH and OH radicals, the basic active-space EA-EOMCC and IP-EOMCC methods, referred to as the EA-EOMCCSDt and IP-EOMCCSDt approaches, are capable of accuratelydescribing the ground and excited states of open-shell systems, even at the moderately stretched nuclear geometries and even for states with a strong multi-determinantal or doubly excited character, at the low costs that are on the order of those characterizing the standard EOMCC singles and doubles method.

%B International Journal of Quantum Chemistry %V 106 %P 2854-2874 %8 7/2006 %G eng %N 14 %0 Journal Article %J Chemical Physics Letters %D 2006 %T Extrapolating Potential Energy Surfaces by Scaling Electron Correlation at a Single Geometry %A A.J.C. Varandas %A Piotr Piecuch %XIt is shown that the molecular potential energy surface corresponding to a high level of ab initio theory can be accurately predicted by performing calculations with smaller basis sets and then scaling the electron correlation at a single point calculated with the larger target basis set.

%B Chemical Physics Letters %V 430 %P 448-453 %8 10/30/2006 %G eng %N 4-6 %0 Journal Article %J Physical Review C %D 2006 %T Half-life and spin of 60Mng %A S. N. Liddick %A P. F. Mantica %A B. A. Brown %A M. P. Carpenter %A A. D. Davies %A M. Horoi %A R. V. F. Janssens %A A. C. Morton %A W. F. Mueller %A J. Pavan %A H. Schatz %A A. Stolz %A S. L. Tabor %A B. E. Tomlin %A M. Wiedeking %XA value of 0.28±0.02 s has been deduced for the half-life of the ground state of {60Mn,} in sharp contrast to the previously adopted value of 51±6 s. Access to the low-spin {60Mn} ground state was accomplished via β decay of the 0+ {60Cr} parent nuclide. New low-energy states in {60Mn} have been identified from β-delayed γ-ray spectroscopy. The new, shorter half-life of {60Mng} is not suggestive of isospin-forbidden β decay, and new spin and parity assignments of 1+ and 4+ have been adopted for the ground and isomeric β-decaying states, respectively, of {60Mn.}

%B Physical Review C %V 73 %P 044322 %8 04/2006 %G eng %N 4 %0 Journal Article %J PHYSICAL REVIEW C %D 2006 %T Half-life and spin of 60Mng %A S. N. Liddick %A P. F. Mantica %A B. A. Brown %A M. P. Carpenter %A A. D. Davies %A M. Horoi %A R. V. F. Janssens %A A. C. Morton %A W. F. Mueller %A J. Pavan %A H. Schatz %A A. Stolz %A S. L. Tabor %A B. E. Tomlin %A M. Wiedeking %B PHYSICAL REVIEW C %V 73 %8 04/2006 %G eng %U http://journals.aps.org/prc/abstract/10.1103/PhysRevC.73.044322 %N 4 %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 %0 Journal Article %J The Journal of Physical Chemistry %D 2006 %T Is the Mechanism of the [2+2] Cycloaddition of Cyclopentyne to Ethylene Concerted or Biradical? A Completely Renormalized Coupled Cluster Study %A Piotr Piecuch %A A. Kinal %XThe mechanism of the [2+2] cycloaddition reaction of cyclopentyne to ethylene has been studied using the completely renormalized coupled cluster method with singles, doubles, and noniterative triples (CR−CCSD(T)). In agreement with the experimentally observed stereochemistry, the CR−CCSD(T) method favors the concerted pathway involving a [2+1] transition state, whereas the popular CCSD(T) method, which is often regarded as the “gold standard” of electronic structure theory, and low-order multireference methods support the less probable biradical mechanism. In addition, the CCSD(T) approach produces an erroneous description of some transition states and intermediates, particularly those which have a significant biradical character. The CR−CCSD(T) calculations indicate that the reaction is a highly exothermic (Δ = −68 kcal/mol), predominantly concerted process with a relatively low activation barrier on the order of 13−16 kcal/mol which permits its thermal occurrence.

%B The Journal of Physical Chemistry %V 110 %P 367-378 %8 6/2005 %G eng %N 2 %0 Journal Article %J Journal of Molecular Structure: THEOCHEM %D 2006 %T Non-Iterative Coupled- Cluster Methods Employing Multi-Reference Perturbation Theory Wave Functions %A Piotr Piecuch %A M.D. Lodriguito %A K. Kowalski %A M. Wloch %K Coupled-cluster theory; Equation-of-motion coupled-cluster methods; Method of moments of coupled-cluster equations; Multi-reference perturbation theory; Non-iterative coupled-cluster methods %XA new class of non-iterative coupled-cluster (CC) methods, which improve the results of standard CC and equation-of-motion (EOM) CC calculations for ground and excited-state potential energy surfaces along bond breaking coordinates and for excited states dominated by two-electron transitions, is explored. The proposed approaches combine the method of moments of coupled-cluster equations (MMCC), in which the a posteriori corrections due to higher-order correlations are added to standard CC/EOMCC energies, with the multi-reference many-body perturbation theory (MRMBPT), which provides information about the most essential non-dynamic and dynamic correlation effects that are relevant to electronic quasi-degeneracies. The performance of the basic MRMBPT-corrected MMCC approximation, in which inexpensive non-iterative corrections due to triple excitations are added to ground- and excited-state energies obtained with the CC/EOMCC singles and doubles approach, is illustrated by the results of a few test calculations, including bond breaking in HF and H2O, and excited states of CH+.

%B Journal of Molecular Structure: THEOCHEM %V 771 %P 89-104 %8 10/2006 %G eng %N 1-3 %0 Book Section %B Progress in Theoretical Chemistry and Physics %D 2006 %T Non-iterative Coupled-Cluster Methods for Excited Electronic States %A Piotr Piecuch %A M. Wloch %A M. Lodriguito %A J. R Gour %B Progress in Theoretical Chemistry and Physics %V 15 %P 45-106 %G eng %0 Journal Article %J Chemical Physics Letters %D 2006 %T Single-reference, size-extensive, non-iterative coupled-cluster approaches to bond breaking and biradicals %A Piotr Piecuch %A M. Wloch %A J. R Gour %A A. Kinal %XWe propose the non-iterative, completely renormalized (CR) coupled-cluster (CC) approaches, including the CR-CC(2, 3) method which offers considerable improvements over the CCSD(T) approach without a significant increase in the computer effort. The CR-CC(2, 3) method, in which the CCSD (CC singles and doubles) energy is corrected for the effect of triples, is size extensive, competitive with CCSD(T) in calculations for non-degenerate states, and as accurate as the expensive CC approach with singles, doubles, and triples in the bond-breaking region. Calculations of the activation enthalpy for the thermal isomerizations of cyclopropane involving trimethylene suggest that CR-CC(2, 3) may be applicable to biradicals.

%B Chemical Physics Letters %V 418 %P 467–474 %8 02/2006 %G eng %0 Journal Article %J The Journal of Physical Chemistry A %D 2006 %T Theoretical Characterization of End-on and Side-on Peroxide Coordination in Ligated Cu2O2 Models %A C.J. Cramer %A A. Kinal %A M. Wloch %A Piotr Piecuch %A L. Gagliardi %XThe relative energetics of μ-η1:η1 (trans end-on) and μ-η2:η2 (side-on) peroxo isomers of Cu2O2 fragments supported by 0, 2, 4, and 6 ammonia ligands have been computed with various density functional, coupled-cluster, and multiconfigurational protocols. There is substantial disagreement between the different levels for most cases, although completely renormalized coupled-cluster methods appear to offer the most reliable predictions. The significant biradical character of the end-on peroxo isomer proves problematic for the density functionals, while the demands on active space size and the need to account for interactions between different states in second-order perturbation theory prove challenging for the multireference treatments. In the latter case, it proved impossible to achieve any convincing convergence.

%B The Journal of Physical Chemistry A %V 110 %P 11557-11568 %8 09/15/2006 %G eng %N 40 %0 Journal Article %J The Journal of Physical Chemistry A %D 2006 %T Theoretical Models on the Cu2O2 Torture Track. Mechanistic Implications for Oxytyrosinase and Small-molecule Analogs %A C.J. Cramer %A M. Wloch %A Piotr Piecuch %A Cristina Puzzarini %A L. Gagliardi %XAccurately describing the relative energetics of alternative bis(mu-oxo) and mu-eta2:eta2 peroxo isomers of Cu2O2 cores supported by 0, 2, 4, and 6 ammonia ligands is remarkably challenging for a wide variety of theoretical models, primarily owing to the difficulty of maintaining a balanced description of rapidly changing dynamical and nondynamical electron correlation effects and a varying degree of biradical character along the isomerization coordinate. The completely renormalized coupled-cluster level of theory including triple excitations and extremely efficient pure density functional levels of theory quantitatively agree with one another and also agree qualitatively with experimental results for Cu2O2 cores supported by analogous but larger ligands. Standard coupled-cluster methods, such as CCSD(T), are in most cases considerably less accurate and exhibit poor convergence in predicted relative energies. Hybrid density functionals significantly underestimate the stability of the bis(mu-oxo) form, with the magnitude of the error being directly proportional to the percentage Hartree-Fock exchange in the functional. Single-root CASPT2 multireference second-order perturbation theory, by contrast, significantly overestimates the stability of bis(mu-oxo) isomers. Implications of these results for modeling the mechanism of C-H bond activation by supported Cu2O2 cores, like that found in the active site of oxytyrosinase, are discussed.

%B The Journal of Physical Chemistry A %V 110 %P 1991–2004 %8 06/2007 %G eng %0 Journal Article %J Molecular Physics %D 2006 %T Two New Classes of Non-Iterative Coupled-Cluster Methods Derived from the Method of Moments of Coupled-Cluster Equations %A Piotr Piecuch %A M. Wloch %A M.D. Logriguito %A J. R Gour %B Molecular Physics %V 104 %P 2149-2172 %8 7/2006 %G eng %N 13 & 14 %0 Journal Article %J Advances in Quantum Chemistry %D 2006 %T The Usefulness of Exponential Wave Function Expansions Employing One- and Two-Body Cluster Operators in Electronic Structure Theory: The Extended and Generalized Coupled-Cluster Methods %A P.-D. Fan %A Piotr Piecuch %XIn this paper, the applicability of exponential cluster expansions involving one- and two-body operators in high accuracy ab initio electronic structure calculations is examined. First, the extended coupled-cluster method with singles and doubles (ECCSD) is tested in the demanding studies of systems with strong quasi-degeneracies, including potential energy surfaces involving multiple bond breaking. The numerical results show that the single-reference ECCSD method is capable of providing a qualitatively correct description of quasi-degenerate electronic states and potential energy surfaces involving bond breaking, eliminating, in particular, the failures and the unphysical behavior of standard coupled-cluster methods in similar cases. It is also demonstrated that one can obtain entire potential energy surfaces with millihartree accuracies by combining the ECCSD theory with the non-iterative a posteriori corrections obtained by using the generalized variant of the method of moments of coupled-cluster equations. This is one of the first instances where the relatively simple single-reference formalism, employing only one- and two-body clusters in the design of the relevant energy expressions, provides a highly accurate description of the dynamic and significant non-dynamic correlation effects characterizing quasi-degenerate and multiply bonded systems. Second, an evidence is presented that one may be able to represent the virtually exact ground- and excited-state wave functions of many-electron systems by exponential cluster expansions employing general two-body or one- and two-body operators. Calculations for small many-electron model systems indicate the existence of finite two-body parameters that produce the numerically exact wave functions for ground and excited states. This finding may have a significant impact on future quantum calculations for many-electron systems, since normally one needs triply excited, quadruply excited, and other higher-than-doubly excited Slater determinants, in addition to all singly and doubly excited determinants, to obtain the exact or virtually exact wave functions.

%B Advances in Quantum Chemistry %V 51 %P 1-57 %8 12/2006 %G eng %0 Journal Article %J Physical Review Letters %D 2005 %T Ab Initio Coupled-Cluster Study of 16O %A M. Włoch %A D. J. Dean %A J. R Gour %A M. {Hjorth-Jensen} %A K. Kowalski %A T. Papenbrock %A P. Piecuch %XWe report converged results for the ground and excited states and matter density of 16O using realistic two-body nucleon-nucleon interactions and coupled-cluster methods and algorithms developed in quantum chemistry. Most of the binding is obtained with the coupled-cluster singles and doubles approach. Additional binding due to three-body clusters (triples) is minimal. The coupled-cluster method with singles and doubles provides a good description of the matter density, charge radius, charge form factor, and excited states of a one-particle, one-hole nature, but it cannot describe the first-excited 0+ state. Incorporation of triples has no effect on the latter finding.

%B Physical Review Letters %V 94 %P 212501 %8 06/2005 %G eng %N 21 %0 Journal Article %J Physical Review Letters %D 2005 %T Ab Initio Coupled-Cluster Study of O %A Piotr Piecuch %A M. Wloch %A D. J. Dean %A J. R Gour %A M. {Hjorth-Jensen} %A K. Kowalski %A T. Papenbrock %XWe report converged results for the ground and excited states and matter density of 16O using realistic two-body nucleon-nucleon interactions and coupled-cluster methods and algorithms developed in quantum chemistry. Most of the binding is obtained with the coupled-cluster singles and doubles approach. Additional binding due to three-body clusters (triples) is minimal. The coupled-cluster method with singles and doubles provides a good description of the matter density, charge radius, charge form factor, and excited states of a one-particle, one-hole nature, but it cannot describe the first-excited 0+ state. Incorporation of triples has no effect on the latter finding.

%B Physical Review Letters %V 94 %8 06/2005 %G eng %0 Journal Article %J The Journal of Chemical Physics %D 2005 %T Active-Space Coupled-Cluster Study of Electronic States of Be 3 %A Piotr Piecuch %A K. Kowalski %A S. Hirata %A M. Wloch %A T.L. Windus %XThe active-space coupled-cluster (CC) and equation-of-motion (EOM) CC methods with all single and double excitations with triple excitations defined via active orbitals (CCSDt, EOMCCSDt), as implemented with TENSOR CONTRACTION ENGINE, are applied to the challenging Be3 system, which is characterized by a large number of low-lying excited states dominated by two-electron transitions and significant high-order correlation effects in the ground electronic state. It is demonstrated that the CCSDt and EOMCCSDt methods provide an excellent description of complicated electronic quasidegeneracies present in the Be3 cluster. Different strategies for defining triple excitations within the CCSDt∕EOMCCSDt approach are discussed.

%B The Journal of Chemical Physics %V 123 %P 6 pages %8 08/2005 %G eng %N 7 %0 Journal Article %J Journal of Chemical Physics %D 2005 %T Active-Space Equation-of=Motion Coupled-Cluster Methods for Excited States of Radicals and Other Open-Shell Systems: EA-EOMCCSDt and IP-EOMCCSDt %A Piotr Piecuch %A J. R Gour %A M. Wloch %B Journal of Chemical Physics %V 123 %P 14 pages %8 10/2005 %G eng %N 13 %0 Journal Article %J The Journal of Chemical Physics %D 2005 %T Active-space equation-of-motion coupled-cluster methods for excited states of radicals and other open-shell systems: {EA-EOMCCSDt} and {IP-EOMCCSDt} %A Jeffrey R. Gour %A Piotr Piecuch %A Marta Wloch %K coupled cluster calculations %K free radicals %K molecular electronic states %XThe previously developed active-space coupled-cluster (CC) and equation-of-motion (EOM) CC methods are extended to radicals and other open-shell systems by combining them with the electron attached (EA) and ionized (IP) EOMCC approaches. As illustrated by the calculations for the CH and OH radicals, the resulting EA-EOMCCSDt and IP-EOMCCSDt theories are capable of providing a highly accurate description of the electronic spectra of radical systems, including excited states displaying a manifestly multideterminantal nature, with the low costs that are not much greater that those characterizing the standard EOMCC singles and doubles method.

%B The Journal of Chemical Physics %V 123 %P 134113–14 %G eng %N 13 %0 Journal Article %J Journal of the American Chemical Society %D 2005 %T Balancing Dynamic and Non-Dynamic Correlation for Diradical and Aromatic Transition States: A Renormalized Coupled-Cluster Study of the Cope Rearrangement of 1,5-Hexadiene %A Piotr Piecuch %A M. J. {McGuire} %XSingle-reference coupled-cluster calculations employing the completely renormalized CCSD(T) (CR-CCSD(T)) approach have been used to examine the mechanism of the Cope rearrangement of 1,5-hexadiene. In agreement with multireference perturbation theory, the CR-CCSD(T) method favors the concerted mechanism of the Cope rearrangement involving an aromatic transition state. The CCSD(T) approach, which is often regarded as the “gold standard” of electronic structure theory, seems to fail in this case, favoring pathways through diradical structures.

%B Journal of the American Chemical Society %V 127 %P 2608-2614 %8 02/05/2005 %G eng %N 8 %0 Conference Proceedings %B American Institute of Physics %D 2005 %T Bridging Quantum Chemistry and Nuclear Structure Theory: Coupled-Cluster Calculations for Closed- and Open-Shell Nuclei %A Piotr Piecuch %A M. Wloch %A J. R Gour %A D. J. Dean %A M. {Hjorth-Jensen} %A T. Papenbrock %XWe review basic elements of the single-reference coupled-cluster theory and discuss large scale ab initio calculations of ground and excited states of 15O, 16O, and 17O using coupled-cluster methods and algorithms developed in quantum chemistry. By using realistic two-body interactions and the renormalized form of the Hamiltonian obtained with a no-core G-matrix approach, we obtain the converged results for 16O and promising preliminary results for 15O and 17O at the level of two-body interactions. The calculated properties other than energies include matter density, charge radius, and charge form factor. The relatively low costs of coupled-cluster calculations, which are characterized by the low-order polynomial scaling with the system size, enable us to probe large model spaces with up to 7 or 8 major oscillator shells, for which non-truncated shell-model calculations for nuclei with A = 15 17 active particles are presently not possible. We argue that the use of coupled-cluster methods and computer algorithms developed by quantum chemists to calculate properties of nuclei is an important step toward the development of accurate and affordable many-body theories that cross the boundaries of various physical sciences. ©2005 American Institute of Physics

%B American Institute of Physics %S NUCLEI AND MESOSCOPIC PHYSICS: Workshop on Nuclei and Mesoscopic Physics: WNMP 2004 %I American Institute of Physics %C Melville, NY %V 777 %P 28-45 %8 7/2005 %G eng %0 Journal Article %J Journal of Chemical Physics A %D 2005 %T Can a Single-Reference Approach Provide a Balanced Description of Ground and Excited States? A Comparison of the Completely Renormalized Equation-of-the-Motion Coupled-Cluster Method with Multi-Reference Quasi-Degenerate Perturbation Theory Near a Conical %A Piotr Piecuch %A S. Nangia %A Truhlar, D.G. %A M. J. {McGuire} %XWe calculated the two lowest electronically adiabatic potential energy surfaces of ammonia in the region of the conical intersection and at a sequence of geometries along which one of the N-H bonds is broken. We employed both a multireference (MR) method and a single-reference (SR) method. The MR calculations are based on multiconfiguration quasidegenerate perturbation theory (MC-QDPT) with a 6-311+G(3df,3pd) basis set. The SR calculations, carried out with the same basis, employ the completely renormalized equation-ofmotion coupled-cluster method with singles and doubles, and a noniterative treatment of triples, denoted CR-EOMCCSD(T). At 91 geometries used for comparison, including geometries near a conical intersection, the surfaces agree to 7% on average.

%B Journal of Chemical Physics A %V 109 %P 11643-11646 %8 11/2005 %G eng %N 51 %0 Journal Article %J Journal of Chemical Physics %D 2005 %T Comparison of Low-Order Multireference Many-Body Perturbation Theories %A Piotr Piecuch %A R.K. Chaudhuri %A K.F. Freed %A G. Hose %A K. Kowalski %A M. Wloch %A S. Chattopadhyay %A D. Mukherjee %A R. Rolik %A A. Szabados %A G. Toth %A P.R. Surjan %XTests have been made to benchmark and assess the relative accuracies of low-order multireference perturbation theories as compared to coupled cluster (CC) and full configuration interaction (FCI) methods. Test calculations include the ground and some excited states of the Be, H(2), BeH(2), CH(2), and SiH(2) systems. Comparisons with FCI and CC calculations show that in most cases the effective valence shell Hamiltonian (H(v)) method is more accurate than other low-order multireference perturbation theories, although none of the perturbative methods is as accurate as the CC approximations. We also briefly discuss some of the basic differences among the multireference perturbation theories considered in this work.

%B Journal of Chemical Physics %V 122 %P 9 pages %8 04/01/2005 %G eng %N 13 %0 Journal Article %J Journal of Chemical Physics %D 2005 %T A Comparison of Renormalized Coupled-Cluster and Multireference Methods with Full Configuration Interaction Benchmarks %A Piotr Piecuch %A C.D. Sherrill %XUnusual bonding and electronic near degeneracies make the lowest-lying singlet states of the C2 molecule particularly challenging for electronic structure theory. Here we compare two alternative approaches to modeling bond-breaking reactions and excited states: sophisticated multireference configuration interaction and multireference perturbation theory methods, and a more "black box," single-reference approach, the completely renormalized coupled-cluster method. These approximate methods are assessed in light of their ability to reproduce the full configuration interaction potential energy curves for the X1Sigmag+, B1Deltag, and B' 1Sigmag+ states of C2, which are numerically exact solutions of the electronic Schrodinger equation within the space spanned by a 6-31G* basis set. Both the multireference methods and the completely renormalized coupled-cluster approach provide dramatic improvements over the standard single-reference methods. The multireference methods are nearly as reliable for this challenging test case as for simpler reactions which break only single bonds. The completely renormalized coupled-cluster approach has difficulty for large internuclear separations R in this case, but over the wide range of R=1.0-2.0 A, it compares favorably with the more complicated multireference methods.

%B Journal of Chemical Physics %V 122 %8 3/22/2005 %G eng %N 12 %0 Conference Proceedings %B Key Topics in Nuclear Structure, Proceedings of the 8th International Spring Seminar on Nuclear Physics %D 2005 %T Coupled Cluster Approaches to Nuclei, Ground States and Excited States %A Piotr Piecuch %A D. J. Dean %A M. Jhorth-Jensen %A K. Kowalski %A T. Papenbrock %A M. Wloch %XWe present recent coupled-cluster studies of nuclei, with an emphasis on ground state and excited states of closed shell nuclei. Perspectives for future studies are delineated.

%B Key Topics in Nuclear Structure, Proceedings of the 8th International Spring Seminar on Nuclear Physics %C Paestum, Italy %8 2005 %G eng %0 Journal Article %J The Journal of Chemical Physics %D 2005 %T Extension of Renormalized Coupled-Cluster Methods Including Triple Excitations to Electronic States of Open-Shell Molecules %A Piotr Piecuch %A M. Wloch %A J. R Gour %A K. Kowalski %XThe general-purpose open-shell implementation of the completely renormalized equation-of-motion coupled-cluster approach with singles, doubles, and noniterative triples [CR-EOMCCSD(T)] is reported. Benchmark calculations for the low-lying doublet and quartet states of the CH radical show that the CR-EOMCCSD(T) method is capable of providing a highly accurate description of ground and excited states of open-shell molecules. This includes states with strong double excitation character, for which the conventional EOMCCSD approach fails.

%B The Journal of Chemical Physics %V 122 %8 06/2005 %G eng %N 21 %0 Journal Article %J The Journal of Chemical Physics %D 2005 %T Extensive Generalization of Renormalized Coupled-Cluster Methods %A Piotr Piecuch %A K. Kowalski %XThe recently developed completely renormalized (CR) coupled-cluster (CC) methods with singles, doubles, and noniterative triples or triples and quadruples [CR-CCSD(T) or CR-CCSD(TQ), respectively], which are based on the method of moments of CC equations (MMCC) [K. Kowalski and P. Piecuch, J. Chem. Phys. 113, 18 (2000)], eliminate the failures of the standard CCSD(T) and CCSD(TQ) methods at larger internuclear separations, but they are not rigorously size extensive. Although the departure from strict size extensivity of the CR-CCSD(T) and CR-CCSD(TQ) methods is small, it is important to examine the possibility of formulating the improved CR-CC methods, which are as effective in breaking chemical bonds as the existing CR-CCSD(T) and CR-CCSD(TQ) approaches, which are as easy to use as the CR-CCSD(T) and CR-CCSD(TQ) methods, and which can be made rigorously size extensive. This may be particularly useful for the applications of CR-CC methods and other MMCC approaches in calculations of potential energy surfaces of large many-electron systems and van der Waals molecules, where the additive separability of energies in the noninteracting limit is very important. In this paper, we propose different types of CR-CC approximations, termed the locally renormalized (LR) CCSD(T) and CCSD(TQ) methods, which become rigorously size extensive if the orbitals are localized on nointeracting fragments. The LR-CCSD(T) and LR-CCSD(TQ) methods rely on the form of the energy expression in terms of the generalized moments of CC equations, derived in this work, termed the numerator-denominator-connected MMCC expansion. The size extensivity and excellent performance of the LR-CCSD(T) and LR-CCSD(TQ) methods are illustrated numerically by showing the results for the dimers of stretched HF and LiH molecules and bond breaking in HF and H2O.

%B The Journal of Chemical Physics %V 122 %8 02/09/2005 %G eng %N 7 %0 Journal Article %J Molecular Physics %D 2005 %T Noniterative Corrections to Extended Coupled-Cluster Energies Employing the Generalized Method of Moments of Coupled-Cluster Equations %A Piotr Piecuch %A {P.-D.} Fan %A K. Kowalski %XIt is shown that the extended coupled-cluster method with singles and doubles (ECCSD) does not suffer from the non-variational collapse observed in the standard CCSD calculations when multiple bond breaking is examined. This interesting feature of the single-reference ECCSD theory is used to design the non-iterative CC methods with singles, doubles and non-iterative triples and quadruples, which provide a highly accurate and variational description of potential energy surfaces involving multiple bond breaking with computational steps that scale as with the system size. This is accomplished with the help of the generalized version of the method of moments of coupled-cluster equations (GMMCC), which can be used to correct the results of non-standard CC calculations, such as ECCSD. The theoretical considerations are illustrated by the preliminary results of the ECCSD-based GMMCC calculations for triple bond breaking in N2. Keywords: Coupled-cluster theory; Extended coupled-cluster method; Method of moments of coupled-cluster equations; Non-iterative coupled-cluster approaches; Bond breaking

%B Molecular Physics %V 103 %P 2191-2213 %8 08/2005 %G eng %N 15 & 16 %0 Journal Article %J Nuclear Physics A %D 2005 %T Nuclear Structure Calculations with Coupled-Cluster Methods from Quantum Chemistry %A Piotr Piecuch %A D. J. Dean %A J. R Gour %A G. Hagen %A M. {Hjorth-Jensen} %A K. Kowalski %A T. Papenbrock %A M. Wloch %XWe present several coupled-cluster calculations of ground and excited states of 4He and 16O employing methods from quantum chemistry. A comparison of coupled cluster results with the results of exact diagonalization of the hamiltonian in the same model space and other truncated shell-model calculations shows that the quantum chemistry inspired coupled cluster approximations provide an excellent description of ground and excited states of nuclei, with much less computational effort than traditional large-scale shell-model approaches. Unless truncations are made, for nuclei like 16O, full-fledged shell-model calculations with four or more major shells are not possible. However, these and even larger systems can be studied with the coupled cluster methods due to the polynomial rather than factorial scaling inherent in standard shell-model studies. This makes the coupled cluster approaches, developed in quantum chemistry, viable methods for describing weakly bound systems of interest for future nuclear facilities.

%B Nuclear Physics A %V 752 %P 299-308 %8 04/2005 %G eng %0 Journal Article %J The Journal of Chemical Physics %D 2005 %T Renormalized coupled-cluster methods exploiting left eigenstates of the similarity-transformed Hamiltonian %A Piotr Piecuch %A Marta Wloch %K bonds (chemical) %K configuration interactions %K coupled cluster calculations %K enthalpy %K excited states %K fluorine %K ground states %K heat of reaction %K hydrogen compounds %K isomerisation %K method of moments %K organic compounds %K reaction kinetics theory %K water %XCompletely renormalized (CR) coupled-cluster (CC) approaches, such as CR-CCSD(T), in which one corrects the standard CC singles and doubles (CCSD) energy for the effects of triply (T) and other higher-than-doubly excited clusters [ K. Kowalski and P. Piecuch, J. Chem. Phys. 113, 18 (2000) ], are reformulated in terms of the left eigenstates 〈Φ∣L of the similarity-transformed Hamiltonian of CC theory. The resulting CR-CCSD(T)L or CR-CC(2,3) and other CR-CCL methods are derived from the new biorthogonal form of the method of moments of CC equations (MMCC) in which, in analogy to the original MMCC theory, one focuses on the noniterative corrections to standard CC energies that recover the exact, full configuration-interaction energies. One of the advantages of the biorthogonal MMCC theory, which will be further analyzed and extended to excited states in a separate paper, is a rigorous size extensivity of the basic ground-state CR-CCL approximations that result from it, which was slightly violated by the original CR-CCSD(T) and CR-CCSD(TQ) approaches. This includes the CR-CCSD(T)L or CR-CC(2,3) method discussed in this paper, in which one corrects the CCSD energy by the relatively inexpensive noniterative correction due to triples. Test calculations for bond breaking in HF, F2, and H2O indicate that the noniterative CR-CCSD(T)L or CR-CC(2,3) approximation is very competitive with the standard CCSD(T) theory for nondegenerate closed-shell states, while being practically as accurate as the full CC approach with singles, doubles, and triples in the bond-breaking region. Calculations of the activation enthalpy for the thermal isomerizations of cyclopropane involving the trimethylene biradical as a transition state show that the noniterative CR-CCSD(T)L approximation is capable of providing activation enthalpies which perfectly agree with experiment.

%B The Journal of Chemical Physics %V 123 %P 224105–10 %8 12/2005 %G eng %N 22 %0 Journal Article %J Journal of the American Chemical Society %D 2005 %T Where Does the Planar-to-Nonplanar Turnover Occur in Small Gold Clusters %A Piotr Piecuch %A R.M. Olson %A S. Varganov %A M.S. Gordon %A S. Chretien %A H. Metiu %A K. Kowalski %A S. A. Kucharski %A M. Musial %XSeveral levels of theory, including both Gaussian-based and plane wave density functional theory (DFT), second-order perturbation theory (MP2), and coupled cluster methods (CCSD(T)), are employed to study Au6 and Au8 clusters. All methods predict that the lowest energy isomer of Au6 is planar. For Au8, both DFT methods predict that the two lowest isomers are planar. In contrast, both MP2 and CCSD(T) predict the lowest Au8 isomers to be nonplanar.

%B Journal of the American Chemical Society %V 127 %P 1049-1052 %8 12/30/2004 %G eng %N 3 %0 Journal Article %J Theoretical Chemistry Accounts: Theory, Computation, and Modeling %D 2004 %T Method of moments of coupled-cluster equations: a new formalism for designing accurate electronic structure methods for ground and excited states %A Piotr Piecuch %A K. Kowalski %A I. S. O. Pimienta %A P.-D. Fan %A M.D. Lodriguito %A M. J. {McGuire} %A S. A. Kucharski %A T. Kuś %A M. Musial %K Coupled-cluster theory - Method of moments of coupled-cluster equations - Renormalized coupled-cluster methods - extended coupled cluster theory - Potential energy surfaces %XThe method of moments of coupled-cluster equations {(MMCC),} which provides a systematic way of improving the results of the standard coupled-cluster {(CC)} and equation-of-motion {CC} {(EOMCC)} calculations for the ground- and excited-state energies of atomic and molecular systems, is described. The {MMCC} theory and its generalized {MMCC} {(GMMCC)} extension that enables one to use the cluster operators resulting from the standard as well as nonstandard {CC} calculations, including those obtained with the extended {CC} {(ECC)} approaches, are based on rigorous mathematical relationships that define the many-body structure of the differences between the full configuration interaction {(CI)} and {CC} or {EOMCC} energies. These relationships can be used to design the noniterative corrections to the {CC/EOMCC} energies that work for chemical bond breaking and potential energy surfaces of excited electronic states, including excited states dominated by double excitations, where the standard single-reference {CC/EOMCC} methods fail. Several {MMCC} and {GMMCC} approximations are discussed, including the renormalized and completely renormalized {CC/EOMCC} methods for closed- and open-shell states, the quadratic {MMCC} approaches, the {CI-corrected} {MMCC} methods, and the {GMMCC} approaches for multiple bond breaking based on the {ECC} cluster amplitudes.

%B Theoretical Chemistry Accounts: Theory, Computation, and Modeling %V 112 %P 349–393 %8 07/2004 %G eng