How information is encoded in bio-molecular sequences is difficult to quantify since such an analysis usually requires sampling an exponentially large genetic space. Here we show how information theory reveals both robust and compressed encodings in the largest complete genotype-phenotype map (over 5 trillion sequences) obtained to date.

VL - 38 UR - https://www.sciencedirect.com/science/article/pii/S1571064521000403 ER - TY - JOUR T1 - A hierarchical analysis of habitat area, connectivity, and quality on amphibian diversity across spatial scales Y1 - 2020 A1 - Wright, Alexander D. A1 - Grant, Evan H. Campbell A1 - Zipkin, Elise F. AB -Habitat fragmentation can alter species distributions and lead to reduced diversity at multiple scales. Yet, the literature describing fragmentation effects on biodiversity patterns is contradictory, possibly because most studies fail to integrate spatial scale into experimental designs and statistical analyses. Thus, it is difficult to extrapolate the effects of fragmentation to large-scaled systems in which conservation management is of immediate importance.

VL - 35 SN - 1572-9761 UR - https://doi.org/10.1007/s10980-019-00963-z IS - 2 JO - Landscape Ecology ER - TY - JOUR T1 - Determining the rp-Process Flow through 56Ni: Resonances in 57Cu(p,g)58Zn Indentified with GRETINA JF - PHYSICAL REVIEW LETTERS Y1 - 2014 A1 - C. Langer A1 - F. Montes A1 - A. Aprahamian A1 - D.W. Bardayan A1 - D. Bazin A1 - B. A. Brown A1 - J. Browne A1 - H. Crawford A1 - R. Cyburt A1 - C. Domingo-Pardo A1 - A. Gade A1 - S. George A1 - P. Hosmer A1 - L. Keek A1 - A. Kontos A1 - I.Y. Lee A1 - A. Lemasson A1 - E. Lunderberg A1 - Y. Maeda A1 - M. Matos A1 - Z. Meisel A1 - S. Noji A1 - F.M. Nunes A1 - A. Nystrom A1 - G. Perdikakis A1 - J. Pereira A1 - S.J. Quinn A1 - F. Recchia A1 - H. Schatz A1 - M. Scott A1 - K. Siegl A1 - A. Simon A1 - M. Smith A1 - A. Spyrou A1 - J. Stevens A1 - S.R. Stroberg A1 - D. Weisshaar A1 - J. Wheeler A1 - K. Wimmer A1 - R.G.T. Zegers VL - 113 UR - http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.113.032502 ER - TY - JOUR T1 - High-precision B(E2) Measurements of Semi-Magic 58,60,62,64Ni by Coulomb Excitation JF - PHYSICAL REVIEW C Y1 - 2014 A1 - J.M. Allmond A1 - B. A. Brown A1 - A.E. Stuchbery A1 - A. Galindo-Uribarri A1 - E. Padilla-Rodal A1 - D.C. Radford A1 - J.C. Batchelder A1 - M.E. Howard A1 - J.F. Liang A1 - B. Manning A1 - R.L. Varner A1 - C.H. Yu VL - 90 UR - http://journals.aps.org/prc/abstract/10.1103/PhysRevC.90.034309 ER - TY - JOUR T1 - Host plant-specific remodeling of midgut physiology in the generalist insect herbivore Trichoplusia ni Y1 - 2014 A1 - Herde M A1 - Howe GA KW - Arabidopsis thaliana; Gut physiology; Herbivore; Jasmonate; Solanum lycopersicum; Transcriptome; Trichoplusia ni AB -Species diversity in terrestrial ecosystems is influenced by plant defense compounds that alter the behavior, physiology, and host preference of insect herbivores. Although it is established that insects evolved the ability to detoxify specific allelochemicals, the mechanisms by which polyphagous insects cope with toxic compounds in diverse host plants are not well understood. Here, we used defended and non-defended plant genotypes to study how variation in chemical defense affects midgut responses of the lepidopteran herbivore Trichoplusia ni, which is a pest of a wide variety of native and cultivated plants. The genome-wide midgut transcriptional response of T. ni larvae to glucosinolate-based defenses in the crucifer Arabidopsis thaliana was characterized by strong induction of genes encoding Phase I and II detoxification enzymes. In contrast, the response of T. ni to proteinase inhibitors and other jasmonate-regulated defenses in tomato (Solanum lycopersicum) was dominated by changes in the expression of digestive enzymes and, strikingly, concomitant repression of transcripts encoding detoxification enzymes. Unbiased proteomic analyses of T. ni feces demonstrated that tomato defenses remodel the complement of T.ni digestive enzymes, which was associated with increased amounts of serine proteases and decreased lipase protein abundance upon encountering tomato defense chemistry. These collective results indicate that T. ni adjusts its gut physiology to the presence of host plant-specific chemical defenses, and further suggest that plants may exploit this digestive flexibility as a defensive strategy to suppress the production of enzymes that detoxify allelochemicals. Copyright © 2014 Elsevier Ltd. All rights reserved.

UR - http://www.ncbi.nlm.nih.gov/pubmed/?term=24727019 ER - TY - JOUR T1 - WRF Model Sensitivity to Land Surface Model and Cumulus Parameterization under Short-Term Climate Extremes over the Southern Great Plains of the United States JF - Journal of Climate Y1 - 2014 A1 - Pei, Lisi A1 - Moore, Nathan A1 - Zhong, Shiyuan A1 - Luo, Lifeng A1 - Hyndman, David W A1 - Heilman, Warren E A1 - Gao, Zhiqiu VL - 27 IS - 20 ER - TY - JOUR T1 - 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 JF - Astrophysical Journal Y1 - 2012 A1 - Bouwens, R, A1 - Bradley, L A1 - Zitrin, A. A1 - Coe, D. A1 - Franx, M. A1 - Zheng, W A1 - Smit, R A1 - Host, O. A1 - Postman, M. A1 - Moustakas, L A1 - Labbe, I A1 - Carrasco, M. A1 - Molino, A. A1 - Donahue, M A1 - Kelson, D. D A1 - Meneghetti, M A1 - Jha, S. A1 - Benitez, N A1 - Lemze, D A1 - Umetsu, K A1 - Broadhurst, T. A1 - Moustakas, J. A1 - Rosati, P. A1 - Bartelmann, M A1 - Ford, H A1 - Graves, G. A1 - Grillo, C. A1 - Infante, L A1 - Jiminez-Teja, Y A1 - Jouvel, S A1 - Lahav, O. A1 - Maoz, D A1 - Medezinski, E A1 - Melchior, P A1 - Merten, J A1 - Nonino, M. A1 - Ogaz, S. A1 - Seitz, S. KW - Astrophysics - Cosmology and Extragalactic Astrophysics ER - TY - JOUR T1 - CLASH: Discovery of a Bright z ~= 6.2 Dwarf Galaxy Quadruply Lensed by MACS J0329.6-0211 JF - The Astrophysical Journal Letters Y1 - 2012 A1 - Zitrin, A. A1 - Moustakas, J. A1 - Bradley, L A1 - Coe, D. A1 - Moustakas, L. A. A1 - Postman, M. A1 - Shu, X A1 - Zheng, W A1 - Benítez, N. A1 - Bouwens, R. A1 - Broadhurst, T. A1 - Ford, H A1 - Host, O. A1 - Jouvel, S A1 - Koekemoer, A. A1 - Meneghetti, M A1 - Rosati, P. A1 - Donahue, M A1 - Grillo, C. A1 - Kelson, D. A1 - Lemze, D A1 - Medezinski, E A1 - Molino, A. A1 - Nonino, M. A1 - Ogaz, S. KW - dark matter KW - galaxies: clusters: general KW - galaxies: clusters: individual: MACS J0329.6-0211 KW - Galaxies: High-Redshift KW - gravitational lensing: strong VL - 747 IS - 1 ER - TY - JOUR T1 - CLASH: Mass Distribution in and around MACS J1206.2-0847 from a Full Cluster Lensing Analysis JF - The Astrophysical Journal Y1 - 2012 A1 - Umetsu, Keiichi A1 - Medezinski, Elinor A1 - Nonino, Mario A1 - Merten, Julian A1 - Zitrin, Adi A1 - Molino, Alberto A1 - Grillo, Claudio A1 - Carrasco, Mauricio A1 - Donahue, Megan A1 - Mahdavi, Andisheh A1 - Coe, Dan A1 - Postman, Marc A1 - Koekemoer, Anton A1 - Czakon, Nicole A1 - Sayers, Jack A1 - Mroczkowski, Tony A1 - Golwala, Sunil A1 - Koch, Patrick M A1 - Lin, Kai-Yang A1 - Molnar, Sandor M A1 - Rosati, Piero A1 - Balestra, Italo A1 - Mercurio, Amata A1 - Scodeggio, Marco A1 - Biviano, Andrea A1 - Anguita, Timo A1 - Infante, Leopoldo A1 - Seidel, Gregor A1 - Sendra, Irene A1 - Jouvel, Stephanie A1 - Host, Ole A1 - Lemze, Doron A1 - Broadhurst, Tom A1 - Meneghetti, Massimo A1 - Moustakas, Leonidas A1 - Bartelmann, Matthias A1 - Benítez, Narciso A1 - Bouwens, Rychard A1 - Bradley, Larry A1 - Ford, Holland A1 - Jiménez-Teja, Yolanda A1 - Kelson, Daniel A1 - Lahav, Ofer A1 - Melchior, Peter A1 - Moustakas, John A1 - Ogaz, Sara A1 - Seitz, Stella A1 - Zheng, Wei KW - cosmology: observations KW - dark matter KW - galaxies: clusters: individual: MACS J1206.2-0847 KW - gravitational lensing: strong KW - gravitational lensing: weak VL - 755 IS - 1 ER - TY - JOUR T1 - CLASH: New Multiple Images Constraining the Inner Mass Profile of MACS J1206.2-0847 JF - The Astrophysical Journal Y1 - 2012 A1 - Zitrin, A. A1 - Rosati, P. A1 - Nonino, M. A1 - Grillo, C. A1 - Postman, M. A1 - Coe, D. A1 - Seitz, S. A1 - Eichner, T A1 - Broadhurst, T. A1 - Jouvel, S A1 - Balestra, I. A1 - Mercurio, A A1 - Scodeggio, M A1 - Benítez, N. A1 - Bradley, L A1 - Ford, H A1 - Host, O. A1 - Jimenez-Teja, Y A1 - Koekemoer, A. A1 - Zheng, W A1 - Bartelmann, M A1 - Bouwens, R. A1 - Czoske, O A1 - Donahue, M A1 - Graur, O A1 - Graves, G. A1 - Infante, L A1 - Jha, S. A1 - Kelson, D. A1 - Lahav, O. A1 - Lazkoz, R A1 - Lemze, D A1 - Lombardi, M. A1 - Maoz, D A1 - McCully, C. A1 - Medezinski, E A1 - Melchior, P A1 - Meneghetti, M A1 - Merten, J A1 - Molino, A. A1 - Moustakas, L. A. A1 - Ogaz, S. A1 - Patel, B. A1 - Regoes, E. A1 - Riess, A. A1 - Rodney, S A1 - Umetsu, K A1 - Van der Wel, A. KW - dark matter KW - galaxies: clusters: general KW - galaxies: clusters: individual: MACS J1206.2–0847 KW - Galaxies: High-Redshift KW - gravitational lensing: strong VL - 749 IS - 2 ER - TY - JOUR T1 - CLASH: Precise New Constraints on the Mass Profile Galaxy Cluster A2261 JF - The Astrophysical Journal Y1 - 2012 A1 - Coe, Dan A1 - Umetsu, Keiichi A1 - Zitrin, Adi A1 - Donahue, Megan A1 - Medezinski, Elinor A1 - Postman, Marc A1 - Carrasco, Mauricio A1 - Anguita, Timo A1 - Geller, Margaret J A1 - Rines, Kenneth J. A1 - Diaferio, Antonaldo A1 - Kurtz, Michael J A1 - Bradley, Larry A1 - Koekemoer, Anton A1 - Zheng, Wei A1 - Nonino, Mario A1 - Molino, Alberto A1 - Mahdavi, Andisheh A1 - Lemze, Doron A1 - Infante, Leopoldo A1 - Ogaz, Sara A1 - Melchior, Peter A1 - Host, Ole A1 - Ford, Holland A1 - Grillo, Claudio A1 - Rosati, Piero A1 - Jiménez-Teja, Yolanda A1 - Moustakas, John A1 - Ascaso, Begoña A1 - Lahav, Ofer; A1 - Bartelmann, Matthias A1 - Benítez, Narciso A1 - Bouwens, Rychard A1 - Graur, Or A1 - Graves, Genevieve A1 - Jha, Saurab A1 - Jouvel, Stephanie A1 - Kelson, Daniel A1 - Moustakas, Leonidas A1 - Maoz, Dan A1 - Meneghetti, Massimo A1 - Merten, Julian A1 - Riess, Adam A1 - Rodney, Steve A1 - Seitz, Stella VL - 757 IS - 1 ER - TY - JOUR T1 - A magnified young galaxy from about 500 million years after the Big Bang JF - Nature Y1 - 2012 A1 - Zheng, Wei A1 - Postman, Marc A1 - Zitrin, Adi A1 - Moustakas, John A1 - Shu, Xinwen A1 - Jouvel, Stephanie A1 - Høst, Ole A1 - Molino, Alberto A1 - Bradley, Larry A1 - Coe, Dan A1 - Moustakas, Leonidas A A1 - Carrasco, Mauricio A1 - Ford, Holland A1 - Benítez, Narciso A1 - Lauer, Tod R A1 - Seitz, Stella; B A1 - Bouwens, Rychard A1 - Koekemoer, Anton A1 - Medezinski, Elinor A1 - Bartelmann, Matthias A1 - Broadhurst, Tom A1 - Donahue, Megan A1 - Grillo, Claudio A1 - Infante, Leopoldo A1 - Jha, Saurabh W A1 - Kelson, Daniel D. A1 - Lahav, Ofer A1 - Lemze, Doron A1 - Melchior, Peter A1 - Meneghetti, Massimo A1 - Merten, Julian A1 - Nonino, Mario A1 - Ogaz, Sara A1 - Rosati, Piero A1 - Umetsu, Keiichi A1 - van der Wel, Arjen VL - 489 IS - 7416 ER - TY - JOUR T1 - Selective pressures for accurate altruism targeting: evidence from digital evolution for difficult-to-test aspects of inclusive fitness theory JF - Proceedings of the Royal Society B: Biological Sciences Y1 - 2011 A1 - Clune, J. A1 - Goldsby, H.J. A1 - Ofria, C. A1 - Pennock, R.T. PB - The Royal Society VL - 278 ER - TY - JOUR T1 - Signatures of minor mergers in Milky Way-like disc kinematics: Ringing revisited JF - ArXiv e-prints Y1 - 2011 A1 - Gómez, F. A. A1 - Minchev, I. A1 - Villalobos, Á. A1 - O'Shea, B. W. A1 - Williams, M. E. K. KW - Astrophysics - Galaxy Astrophysics ER - TY - CONF T1 - Beyond NomBank: A Study of Implicit Argumentation for Nominal Predicates T2 - Association for Computational Linguistics Y1 - 2010 A1 - Matthew Gerber A1 - Joyce Y. Chai AB -Despite its substantial coverage, Nom- Bank does not account for all within- sentence arguments and ignores extra- sentential arguments altogether. These ar- guments, which we call implicit, are im- portant to semantic processing, and their recovery could potentially benefit many NLP applications. We present a study of implicit arguments for a select group of frequent nominal predicates. We show that implicit arguments are pervasive for these predicates, adding 65% to the coverage of NomBank. We demonstrate the feasibil- ity of recovering implicit arguments with a supervised classification model. Our re- sults and analyses provide a baseline for future work on this emerging task.

JF - Association for Computational Linguistics PB - Association for Computational Linguistics CY - Uppsala, Sweden ER - TY - JOUR T1 - Conformational Sampling of S- and R-Warfarin in Polar Solvents: Implications for Stereoselective Complex Formation JF - Journal of Molecular Structure (Theochem) Y1 - 2010 A1 - Michael Feig A1 - K. Gebreyohannes A1 - V. McGuffin AB -Molecular dynamics simulations of the open side chain conformation of ionic and neutral S- and R-warfarin in aqueous solvent and acetonitrile are described. In all cases, warfarin is found to sample a broad conformational ensemble with major and minor states due to torsional degrees of freedom associated with its side chain. Thermodynamics and kinetics of transitions between these states are analyzed from the simulations and interpreted in the context of stereoselective interactions in biological and non-biological complexes.

VL - 949 IS - 1-3 ER - TY - JOUR T1 - PRIMO/PRIMONA: A coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy JF - Proteins: Structure, Function, and Bioinformatics Y1 - 2010 A1 - Gopal, Srinivasa M. A1 - Mukherjee, Shayantani A1 - Cheng, Yi-Ming A1 - Michael Feig AB -The new coarse graining model PRIMO/PRIMONA for proteins and nucleic acids is proposed. This model combines one to several heavy atoms into coarse-grained sites that are chosen to allow an analytical, high-resolution reconstruction of all-atom models based on molecular bonding geometry constraints. The accuracy of proposed reconstruction method in terms of structure and energetics is tested and compared with other popular reconstruction methods for a variety of protein and nucleic acid test sets. Proteins 2010. © 2009 Wiley-Liss, Inc.

VL - 78 IS - 5 ER - TY - JOUR T1 - Ab Initio Coupled-Cluster and Configuration Interaction Calculations for O Using V JF - Physical Review C Y1 - 2009 A1 - R. Roth, A1 - J. R Gour A1 - Piotr Piecuch VL - 79 IS - 5 ER - TY - JOUR T1 - Center-of-Mass Problem in Truncated Configuration Interaction and Coupled-Cluster Calculations JF - Physical Letters B Y1 - 2009 A1 - R. Roth, A1 - Jeffrey R. Gour A1 - Piotr Piecuch AB -The 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.

VL - 679 IS - 4 ER - TY - JOUR T1 - 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 JF - International Journal of Quantum Chemistry Y1 - 2009 A1 - Piotr Piecuch A1 - J. R Gour A1 - M. Wloch AB -The 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

VL - 109 IS - 14 ER - TY - JOUR T1 - Local Correlation Calculations Using Standard and Renormalized Coupled-Cluster Approaches JF - The Journal of Chemical Physics Y1 - 2009 A1 - Wei Li A1 - Piotr Piecuch A1 - J. R Gour A1 - Shuhua Li AB -he 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.

VL - 131 IS - 11 ER - TY - JOUR T1 - 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 JF - Molecular Physics Y1 - 2009 A1 - M. Ehara A1 - J. R Gour A1 - Piotr Piecuch AB -Low-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.

VL - 107 IS - 8-12 ER - TY - CONF T1 - The Role of Implicit Argumentation in Nominal SRL T2 - North American Chapter of the Association for Computational Linguistics Y1 - 2009 A1 - Matthew Gerber A1 - Joyce Y. Chai A1 - Adam Meyers AB -Nominals frequently surface without overtly expressed arguments. In order to measure the potential benefit of nominal SRL for down- stream processes, such nominals must be ac- counted for. In this paper, we show that a state-of-the-art nominal SRL system with an overall argument F1 of 0.76 suffers a perfor- mance loss of more than 9% when nominals with implicit arguments are included in the evaluation. We then develop a system that takes implicit argumentation into account, im- proving overall performance by nearly 5%. Our results indicate that the degree of implicit argumentation varies widely across nominals, making automated detection of implicit argu- mentation an important step for nominal SRL.

JF - North American Chapter of the Association for Computational Linguistics PB - Association for Computational Linguistics CY - Boulder, Colorado, USA ER - TY - JOUR T1 - Application of Renormalized Coupled- Cluster Methods to Potential Function of Water JF - Theoretical Chemistry Accounts: Theory, Computation, and Modeling (THEORETICA CHIMICA ACTA) Y1 - 2008 A1 - J. Zheng A1 - J. R Gour A1 - J.J. Lutz A1 - M. Wloch A1 - Piotr Piecuch A1 - Truhlar, D.G. AB -The 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.

VL - 120 IS - 1-3 ER - TY - JOUR T1 - 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 JF - The Journal of Chemical Physics Y1 - 2008 A1 - J. Zheng A1 - J. R Gour A1 - J.J. Lutz A1 - M. Wloch A1 - Piotr Piecuch A1 - Truhlar, D.G. AB -The 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.

VL - 128 IS - 4 ER - TY - JOUR T1 - Stereoelectronic Effects on Molecular Geometries and State-Energy Splittings of Ligated Monocopper Diozygen Complexes JF - The Journal of Physical Chemistry Y1 - 2008 A1 - C.J. Cramer A1 - J. R Gour A1 - A. Kinal A1 - M. Wloch A1 - Piotr Piecuch A1 - A.R.M. Shahi A1 - L. Gagliardi AB -The 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.

VL - 112 IS - 16 ER - TY - JOUR T1 - Active-Space Symmetry-Adapted-Cluster Configuration-Interaction and Equation-of-Motion Cluster Methods for High Accuracy Calculations of Potential Energy Surfaces of Radicals JF - The Journal of Chemical Physics Y1 - 2007 A1 - Y. Ohtsuka A1 - Piotr Piecuch A1 - J. R Gour A1 - M. Ehara A1 - H. Nakatsuji KW - configuration interactions KW - coupled cluster calculations KW - electron attachment KW - excited states KW - free radicals KW - ground states KW - ionisation KW - organic compounds KW - oxygen compounds KW - potential energy surfaces AB -The 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.

VL - 126 IS - 16 ER - TY - JOUR T1 - Breaking Bonds with the Left Eigenstate Completely Renormalized Coupled-Cluster Method JF - The Journal of Chemical Physics Y1 - 2007 A1 - Y. Ge A1 - M.S. Gordon A1 - Piotr Piecuch AB -The 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).

VL - 127 IS - 17 ER - TY - JOUR T1 - Coupled-Cluster and Configuration-Interaction Calculations for Heavy Nuclei JF - Physical Review Lettters Y1 - 2007 A1 - M. Horoi A1 - J. R Gour A1 - M. Wloch A1 - M.D. Lodriguito A1 - B. A. Brown A1 - Piotr Piecuch AB -We 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.

VL - 98 IS - 11 ER - TY - JOUR T1 - Extension of the Renormalized Coupled-Cluster Methods Exploiting Left Eigenstates of the Similarity-Transformed Hamiltonian to Open- Shell Systems: A Benchmark Study JF - The Journal of Physical Chemistry A Y1 - 2007 A1 - M. Wloch A1 - J. R Gour A1 - Piotr Piecuch AB -The 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.

VL - 111 IS - 44 ER - TY - JOUR T1 - Shape and Structure of N = Z 64Ge: Electromagnetic Transition Rates from the Application ￼of the Recoil Distance Method to a Knockout Reaction JF - PHYSICAL REVIEW LETTERS Y1 - 2007 A1 - K. Starosta A1 - A. Dewald A1 - A. Dunomes A1 - P. Adrich A1 - A.M. Amthor A1 - T. Baumann A1 - D. Bazin A1 - M. Bowen A1 - B. A. Brown A1 - A. Chester A1 - A. Gade A1 - D. Galaviz A1 - T. Glasmacher A1 - T. Ginter A1 - M. Hausmann A1 - M. Horoi A1 - J. Jolie A1 - B. Melon A1 - D. Miller A1 - V. Moeller A1 - R.P. Norris A1 - T. Pissulla A1 - M. Portillo A1 - W. Rother A1 - Y. Shimbara A1 - A. Stolz A1 - C. Vaman A1 - P. Voss A1 - D. Weisshaar A1 - V. Zelevinsky VL - 99 UR - http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.99.042503 ER - TY - JOUR T1 - Z = 0 Shell Gap near 100Sn from Intermediate-Energy Coulomb Excitations ￼in Even-Mass 106-112Sn Isotopes JF - PHYSICAL REVIEW LETTERS Y1 - 2007 A1 - C. Vaman A1 - C. Andreoiu A1 - D. Bazin A1 - A. Beccerril A1 - B. A. Brown A1 - C.M. Campbell A1 - A. Chester A1 - J.M. Cook A1 - D.C. Dinca A1 - A. Gade A1 - D. Galaviz A1 - T. Glasmacher A1 - M. {Hjorth-Jensen} A1 - M. Horoi A1 - D. Miller A1 - V. Moeller A1 - W. F. Mueller A1 - A. Schiller A1 - K. Starosta A1 - A. Stolz A1 - J.R. Terry A1 - A. Volya A1 - V. Zelevinsky A1 - H. Zwahlen VL - 99 UR - http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.99.162501 ER - TY - JOUR T1 - Ab Initio Coupled-Cluster Calculations for Nuclei Using Methods of Quantum Chemistry JF - European Physics Journal A Y1 - 2006 A1 - Piotr Piecuch A1 - M. Wloch A1 - D. J. Dean A1 - J. R Gour A1 - M. {Hjorth-Jensen} A1 - T. Papenbrock A1 - K. Kowalski AB -We 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.

VL - 25 IS - 1 ER - TY - JOUR T1 - Coupled Cluster Theory for Nuclei JF - International Journal of Modern Physics B Y1 - 2006 A1 - T. Papenbrock A1 - D. J. Dean A1 - J. R Gour A1 - G. Hagen A1 - M. {Hjorth-Jensen} A1 - M. Wloch KW - Nuclear structure; light nuclei; coupled-cluster theory AB -This 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.

VL - 20 IS - 30-31 ER - TY - JOUR T1 - Coupled-Cluster Calculations for Valence Systems around 16 O JF - Physical Review C Y1 - 2006 A1 - Piotr Piecuch A1 - J. R Gour A1 - M. {Hjorth-Jensen} A1 - M. Wloch A1 - D. J. Dean AB -We 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.

VL - 74 IS - 2 ER - TY - JOUR T1 - Coupled-cluster calculations for valence systems around O16 JF - Physical Review C Y1 - 2006 A1 - J. R Gour A1 - Piotr Piecuch A1 - M. {Hjorth-Jensen} A1 - M. Wloch A1 - D. J. Dean AB -We 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.

VL - 74 N1 - Copyright {(C)} 2010 The American Physical Society; Please report any problems to prola@aps.org ER - TY - JOUR T1 - Efficient Formulation and Computer Implementation of the Active-Space Electron-Attached and Ionized Equation-of-Motion Coupled-Cluster Methods JF - Journal of Chemical Physics Y1 - 2006 A1 - J. R Gour A1 - Piotr Piecuch KW - coupled cluster calculations KW - free radicals KW - organic compounds KW - sulphur compounds AB -The 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.

VL - 125 IS - 23 ER - TY - JOUR T1 - Extension of the Active-Space Equation-of- Motion Coupled-Cluster Methods to Radical Systems: The EA-EOMCCSDt and IPEOMCCSDt Approaches JF - International Journal of Quantum Chemistry Y1 - 2006 A1 - Piotr Piecuch A1 - J. R Gour A1 - M. Wloch KW - oupled-cluster theory;equation-of-a motion coupled-cluster method;active-space coupled-cluster approaches;electronic-attached and ionized states;radicals AB -The 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.

VL - 106 IS - 14 ER - TY - CHAP T1 - Non-iterative Coupled-Cluster Methods for Excited Electronic States T2 - Progress in Theoretical Chemistry and Physics Y1 - 2006 A1 - Piotr Piecuch A1 - M. Wloch A1 - M. Lodriguito A1 - J. R Gour JF - Progress in Theoretical Chemistry and Physics VL - 15 ER - TY - JOUR T1 - Single-reference, size-extensive, non-iterative coupled-cluster approaches to bond breaking and biradicals JF - Chemical Physics Letters Y1 - 2006 A1 - Piotr Piecuch A1 - M. Wloch A1 - J. R Gour A1 - A. Kinal AB -We 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.

VL - 418 ER - TY - JOUR T1 - Theoretical Characterization of End-on and Side-on Peroxide Coordination in Ligated Cu2O2 Models JF - The Journal of Physical Chemistry A Y1 - 2006 A1 - C.J. Cramer A1 - A. Kinal A1 - M. Wloch A1 - Piotr Piecuch A1 - L. Gagliardi AB -The 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.

VL - 110 IS - 40 ER - TY - JOUR T1 - Theoretical Models on the Cu2O2 Torture Track. Mechanistic Implications for Oxytyrosinase and Small-molecule Analogs JF - The Journal of Physical Chemistry A Y1 - 2006 A1 - C.J. Cramer A1 - M. Wloch A1 - Piotr Piecuch A1 - Cristina Puzzarini A1 - L. Gagliardi AB -Accurately 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.

VL - 110 ER - TY - JOUR T1 - Two New Classes of Non-Iterative Coupled-Cluster Methods Derived from the Method of Moments of Coupled-Cluster Equations JF - Molecular Physics Y1 - 2006 A1 - Piotr Piecuch A1 - M. Wloch A1 - M.D. Logriguito A1 - J. R Gour VL - 104 IS - 13 & 14 ER - TY - JOUR T1 - Ab Initio Coupled-Cluster Study of 16O JF - Physical Review Letters Y1 - 2005 A1 - M. Włoch A1 - D. J. Dean A1 - J. R Gour A1 - M. {Hjorth-Jensen} A1 - K. Kowalski A1 - T. Papenbrock A1 - P. Piecuch AB -We 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.

VL - 94 IS - 21 ER - TY - JOUR T1 - Ab Initio Coupled-Cluster Study of O JF - Physical Review Letters Y1 - 2005 A1 - Piotr Piecuch A1 - M. Wloch A1 - D. J. Dean A1 - J. R Gour A1 - M. {Hjorth-Jensen} A1 - K. Kowalski A1 - T. Papenbrock AB -We 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.

VL - 94 ER - TY - JOUR T1 - Active-space equation-of-motion coupled-cluster methods for excited states of radicals and other open-shell systems: {EA-EOMCCSDt} and {IP-EOMCCSDt} JF - The Journal of Chemical Physics Y1 - 2005 A1 - Jeffrey R. Gour A1 - Piotr Piecuch A1 - Marta Wloch KW - coupled cluster calculations KW - free radicals KW - molecular electronic states AB -The 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.

VL - 123 IS - 13 ER - TY - JOUR T1 - Active-Space Equation-of=Motion Coupled-Cluster Methods for Excited States of Radicals and Other Open-Shell Systems: EA-EOMCCSDt and IP-EOMCCSDt JF - Journal of Chemical Physics Y1 - 2005 A1 - Piotr Piecuch A1 - J. R Gour A1 - M. Wloch VL - 123 IS - 13 ER - TY - Generic T1 - Bridging Quantum Chemistry and Nuclear Structure Theory: Coupled-Cluster Calculations for Closed- and Open-Shell Nuclei T2 - American Institute of Physics Y1 - 2005 A1 - Piotr Piecuch A1 - M. Wloch A1 - J. R Gour A1 - D. J. Dean A1 - M. {Hjorth-Jensen} A1 - T. Papenbrock AB -We 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

JF - American Institute of Physics T3 - NUCLEI AND MESOSCOPIC PHYSICS: Workshop on Nuclei and Mesoscopic Physics: WNMP 2004 PB - American Institute of Physics CY - Melville, NY VL - 777 ER - TY - JOUR T1 - Extension of Renormalized Coupled-Cluster Methods Including Triple Excitations to Electronic States of Open-Shell Molecules JF - The Journal of Chemical Physics Y1 - 2005 A1 - Piotr Piecuch A1 - M. Wloch A1 - J. R Gour A1 - K. Kowalski AB -The 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.

VL - 122 IS - 21 ER - TY - JOUR T1 - Nuclear Structure Calculations with Coupled-Cluster Methods from Quantum Chemistry JF - Nuclear Physics A Y1 - 2005 A1 - Piotr Piecuch A1 - D. J. Dean A1 - J. R Gour A1 - G. Hagen A1 - M. {Hjorth-Jensen} A1 - K. Kowalski A1 - T. Papenbrock A1 - M. Wloch AB -We 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.

VL - 752 ER - TY - JOUR T1 - Where Does the Planar-to-Nonplanar Turnover Occur in Small Gold Clusters JF - Journal of the American Chemical Society Y1 - 2005 A1 - Piotr Piecuch A1 - R.M. Olson A1 - S. Varganov A1 - M.S. Gordon A1 - S. Chretien A1 - H. Metiu A1 - K. Kowalski A1 - S. A. Kucharski A1 - M. Musial AB -Several 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.

VL - 127 IS - 3 ER -