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.

1 aG, Nitash, C1 aAdami, Christoph uhttps://www.sciencedirect.com/science/article/pii/S157106452100040301046nas a2200169 4500008004100000020001400041245011600055210006900171260001500240300001500255490000700270520047600277100002600753700002800779700002200807856004700829 2020 eng d a1572-976100aA hierarchical analysis of habitat area, connectivity, and quality on amphibian diversity across spatial scales0 ahierarchical analysis of habitat area connectivity and quality o c2020/02/01 a529 - -5440 v353 aHabitat 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.

1 aWright, Alexander, D.1 aGrant, Evan, H. Campbel1 aZipkin, Elise, F. uhttps://doi.org/10.1007/s10980-019-00963-z01517nas a2200577 4500008004100000245010300041210006900144260001200213490000800225100001500233700001500248700001900263700001900282700001400301700001800315700001500333700001700348700001500365700002200380700001300402700001500415700001500430700001300445700001500458700001400473700001700487700001900504700001400523700001400537700001500551700001300566700001600579700001600595700001900611700001600630700001600646700001600662700001500678700001400693700001400707700001400721700001400735700001500749700001600764700001900780700001800799700001600817700001500833700001900848856007200867 2014 eng d00aDetermining the rp-Process Flow through 56Ni: Resonances in 57Cu(p,g)58Zn Indentified with GRETINA0 aDetermining the rpProcess Flow through 56Ni Resonances in 57Cupg c07/20140 v1131 aLanger, C.1 aMontes, F.1 aAprahamian, A.1 aBardayan, D.W.1 aBazin, D.1 aBrown, B., A.1 aBrowne, J.1 aCrawford, H.1 aCyburt, R.1 aDomingo-Pardo, C.1 aGade, A.1 aGeorge, S.1 aHosmer, P.1 aKeek, L.1 aKontos, A.1 aLee, I.Y.1 aLemasson, A.1 aLunderberg, E.1 aMaeda, Y.1 aMatos, M.1 aMeisel, Z.1 aNoji, S.1 aNunes, F.M.1 aNystrom, A.1 aPerdikakis, G.1 aPereira, J.1 aQuinn, S.J.1 aRecchia, F.1 aSchatz, H.1 aScott, M.1 aSiegl, K.1 aSimon, A.1 aSmith, M.1 aSpyrou, A.1 aStevens, J.1 aStroberg, S.R.1 aWeisshaar, D.1 aWheeler, J.1 aWimmer, K.1 aZegers, R.G.T. uhttp://journals.aps.org/prl/abstract/10.1103/PhysRevLett.113.03250200748nas a2200241 4500008004100000245008800041210006900129260001200198490000700210100001800217700001800235700002000253700002500273700002200298700001800320700002100338700001700359700001600376700001600392700001700408700001300425856006800438 2014 eng d00aHigh-precision B(E2) Measurements of Semi-Magic 58,60,62,64Ni by Coulomb Excitation0 aHighprecision BE2 Measurements of SemiMagic 58606264Ni by Coulom c09/20140 v901 aAllmond, J.M.1 aBrown, B., A.1 aStuchbery, A.E.1 aGalindo-Uribarri, A.1 aPadilla-Rodal, E.1 aRadford, D.C.1 aBatchelder, J.C.1 aHoward, M.E.1 aLiang, J.F.1 aManning, B.1 aVarner, R.L.1 aYu, C.H. uhttp://journals.aps.org/prc/abstract/10.1103/PhysRevC.90.03430902323nas a2200133 4500008004100000245010700041210006900148260000900217520176600226653011701992100001302109700001302122856005402135 2014 eng d00aHost plant-specific remodeling of midgut physiology in the generalist insect herbivore Trichoplusia ni0 aHost plantspecific remodeling of midgut physiology in the genera c20143 aSpecies 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.

10aArabidopsis thaliana; Gut physiology; Herbivore; Jasmonate; Solanum lycopersicum; Transcriptome; Trichoplusia ni1 aM, Herde1 aGA, Howe uhttp://www.ncbi.nlm.nih.gov/pubmed/?term=2472701900727nas a2200181 4500008004100000245016300041210006900204260001200273490000700285100001400292700001800306700001900324700001600343700002200359700002300381700001600404856012500420 2014 eng d00aWRF Model Sensitivity to Land Surface Model and Cumulus Parameterization under Short-Term Climate Extremes over the Southern Great Plains of the United States0 aWRF Model Sensitivity to Land Surface Model and Cumulus Paramete c10/20140 v271 aPei, Lisi1 aMoore, Nathan1 aZhong, Shiyuan1 aLuo, Lifeng1 aHyndman, David, W1 aHeilman, Warren, E1 aGao, Zhiqiu uhttps://icer.msu.edu/research/publications/wrf-model-sensitivity-land-surface-model-cumulus-parameterization-under-short01651nas a2200553 4500008004100000245022000041210006900261260001200330653006000342100001500402700001500417700001500432700001200447700001400459700001300473700001200486700001300498700001600511700001700527700001300544700001700557700001500574700001500589700001800604700001800622700001200640700001500652700001300667700001400680700001900694700001800713700001500731700001800746700001200764700001500776700001500791700001500806700002000821700001400841700001400855700001200869700001800881700001600899700001400915700001500929700001300944700001400957856012600971 2012 eng d00aA 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~9.20 aCensus of StarForming Galaxies in the z910 Universe based on HST c11/201210aAstrophysics - Cosmology and Extragalactic Astrophysics1 aBouwens, R1 aBradley, L1 aZitrin, A.1 aCoe, D.1 aFranx, M.1 aZheng, W1 aSmit, R1 aHost, O.1 aPostman, M.1 aMoustakas, L1 aLabbe, I1 aCarrasco, M.1 aMolino, A.1 aDonahue, M1 aKelson, D., D1 aMeneghetti, M1 aJha, S.1 aBenitez, N1 aLemze, D1 aUmetsu, K1 aBroadhurst, T.1 aMoustakas, J.1 aRosati, P.1 aBartelmann, M1 aFord, H1 aGraves, G.1 aGrillo, C.1 aInfante, L1 aJiminez-Teja, Y1 aJouvel, S1 aLahav, O.1 aMaoz, D1 aMedezinski, E1 aMelchior, P1 aMerten, J1 aNonino, M.1 aOgaz, S.1 aSeitz, S. uhttps://icer.msu.edu/research/publications/census-star-forming-galaxies-z9-10-universe-based-hstspitzer-observations-over01350nas a2200457 4500008004100000245009300041210006900134260001200203490000800215653001600223653003200239653005400271653002800325653003400353100001500387700001800402700001500420700001200435700002200447700001600469700001100485700001300496700001700509700001600526700001900542700001200561700001300573700001400586700001800600700001800618700001500636700001500651700001500666700001500681700001300696700001800709700001500727700001500742700001300757856012200770 2012 eng d00aCLASH: Discovery of a Bright z ~= 6.2 Dwarf Galaxy Quadruply Lensed by MACS J0329.6-02110 aCLASH Discovery of a Bright z 62 Dwarf Galaxy Quadruply Lensed b c03/20120 v74710adark matter10agalaxies: clusters: general10agalaxies: clusters: individual: MACS J0329.6-021110aGalaxies: High-Redshift10agravitational lensing: strong1 aZitrin, A.1 aMoustakas, J.1 aBradley, L1 aCoe, D.1 aMoustakas, L., A.1 aPostman, M.1 aShu, X1 aZheng, W1 aBenítez, N.1 aBouwens, R.1 aBroadhurst, T.1 aFord, H1 aHost, O.1 aJouvel, S1 aKoekemoer, A.1 aMeneghetti, M1 aRosati, P.1 aDonahue, M1 aGrillo, C.1 aKelson, D.1 aLemze, D1 aMedezinski, E1 aMolino, A.1 aNonino, M.1 aOgaz, S. uhttps://icer.msu.edu/research/publications/clash-discovery-bright-z-62-dwarf-galaxy-quadruply-lensed-macs-j03296-021102193nas a2200733 4500008004100000245009800041210006900139260001200208490000800220653002800228653001600256653005400272653003400326653003200360100002000392700002300412700001800435700001900453700001600472700002000488700002000508700002300528700001900551700002200570700001300592700001800605700002100623700001900644700001700663700002200680700001900702700002100721700001800742700002200760700001800782700002000800700002000820700002100840700002000861700001800881700002200899700001900921700001800940700002200958700001400980700001700994700002001011700002401031700002401055700002501079700002201104700002101126700001901147700001801166700002701184700001901211700001601230700002001246700002001266700001501286700001801301700001501319856012501334 2012 eng d00aCLASH: Mass Distribution in and around MACS J1206.2-0847 from a Full Cluster Lensing Analysis0 aCLASH Mass Distribution in and around MACS J120620847 from a Ful c08/20120 v75510acosmology: observations10adark matter10agalaxies: clusters: individual: MACS J1206.2-084710agravitational lensing: strong10agravitational lensing: weak1 aUmetsu, Keiichi1 aMedezinski, Elinor1 aNonino, Mario1 aMerten, Julian1 aZitrin, Adi1 aMolino, Alberto1 aGrillo, Claudio1 aCarrasco, Mauricio1 aDonahue, Megan1 aMahdavi, Andisheh1 aCoe, Dan1 aPostman, Marc1 aKoekemoer, Anton1 aCzakon, Nicole1 aSayers, Jack1 aMroczkowski, Tony1 aGolwala, Sunil1 aKoch, Patrick, M1 aLin, Kai-Yang1 aMolnar, Sandor, M1 aRosati, Piero1 aBalestra, Italo1 aMercurio, Amata1 aScodeggio, Marco1 aBiviano, Andrea1 aAnguita, Timo1 aInfante, Leopoldo1 aSeidel, Gregor1 aSendra, Irene1 aJouvel, Stephanie1 aHost, Ole1 aLemze, Doron1 aBroadhurst, Tom1 aMeneghetti, Massimo1 aMoustakas, Leonidas1 aBartelmann, Matthias1 aBenítez, Narciso1 aBouwens, Rychard1 aBradley, Larry1 aFord, Holland1 aJiménez-Teja, Yolanda1 aKelson, Daniel1 aLahav, Ofer1 aMelchior, Peter1 aMoustakas, John1 aOgaz, Sara1 aSeitz, Stella1 aZheng, Wei uhttps://icer.msu.edu/research/publications/clash-mass-distribution-around-macs-j12062-0847-full-cluster-lensing-analysis01974nas a2200733 4500008004100000245008800041210006900129260001200198490000800210653001600218653003200234653005600266653002800322653003400350100001500384700001500399700001500414700001500429700001600444700001200460700001400472700001500486700001900501700001400520700001700534700001600551700001700567700001700584700001500601700001200616700001300628700002000641700001800661700001300679700001800692700001600710700001400726700001500740700001300755700001500768700001500783700001200798700001500810700001400825700001400839700001300853700001700866700001200883700001600895700001800911700001600929700001800945700001400963700001500977700002200992700001301014700001401027700001501041700001401056700001401070700001401084700002001098856012201118 2012 eng d00aCLASH: New Multiple Images Constraining the Inner Mass Profile of MACS J1206.2-08470 aCLASH New Multiple Images Constraining the Inner Mass Profile of c04/20120 v74910adark matter10agalaxies: clusters: general10agalaxies: clusters: individual: MACS J1206.2–084710aGalaxies: High-Redshift10agravitational lensing: strong1 aZitrin, A.1 aRosati, P.1 aNonino, M.1 aGrillo, C.1 aPostman, M.1 aCoe, D.1 aSeitz, S.1 aEichner, T1 aBroadhurst, T.1 aJouvel, S1 aBalestra, I.1 aMercurio, A1 aScodeggio, M1 aBenítez, N.1 aBradley, L1 aFord, H1 aHost, O.1 aJimenez-Teja, Y1 aKoekemoer, A.1 aZheng, W1 aBartelmann, M1 aBouwens, R.1 aCzoske, O1 aDonahue, M1 aGraur, O1 aGraves, G.1 aInfante, L1 aJha, S.1 aKelson, D.1 aLahav, O.1 aLazkoz, R1 aLemze, D1 aLombardi, M.1 aMaoz, D1 aMcCully, C.1 aMedezinski, E1 aMelchior, P1 aMeneghetti, M1 aMerten, J1 aMolino, A.1 aMoustakas, L., A.1 aOgaz, S.1 aPatel, B.1 aRegoes, E.1 aRiess, A.1 aRodney, S1 aUmetsu, K1 aVan der Wel, A. uhttps://icer.msu.edu/research/publications/clash-new-multiple-images-constraining-inner-mass-profile-macs-j12062-084701835nas a2200637 4500008004100000245007600041210006900117260001200186490000800198100001300206700002000219700001600239700001900255700002300274700001800297700002300315700001800338700002400356700002300380700002400403700002200427700001900449700002100468700001500489700001800504700002000522700002200542700001700564700002200581700001500603700002000618700001400638700001800652700002000670700001800690700002700708700002000735700002000755700001700775700002500792700002200817700002100839700001400860700002200874700001600896700002200912700001900934700002400953700001400977700002400991700001901015700001601034700001801050700001801068856011101086 2012 eng d00aCLASH: Precise New Constraints on the Mass Profile Galaxy Cluster A22610 aCLASH Precise New Constraints on the Mass Profile Galaxy Cluster c09/20120 v7571 aCoe, Dan1 aUmetsu, Keiichi1 aZitrin, Adi1 aDonahue, Megan1 aMedezinski, Elinor1 aPostman, Marc1 aCarrasco, Mauricio1 aAnguita, Timo1 aGeller, Margaret, J1 aRines, Kenneth, J.1 aDiaferio, Antonaldo1 aKurtz, Michael, J1 aBradley, Larry1 aKoekemoer, Anton1 aZheng, Wei1 aNonino, Mario1 aMolino, Alberto1 aMahdavi, Andisheh1 aLemze, Doron1 aInfante, Leopoldo1 aOgaz, Sara1 aMelchior, Peter1 aHost, Ole1 aFord, Holland1 aGrillo, Claudio1 aRosati, Piero1 aJiménez-Teja, Yolanda1 aMoustakas, John1 aAscaso, Begoña1 aLahav, Ofer;1 aBartelmann, Matthias1 aBenítez, Narciso1 aBouwens, Rychard1 aGraur, Or1 aGraves, Genevieve1 aJha, Saurab1 aJouvel, Stephanie1 aKelson, Daniel1 aMoustakas, Leonidas1 aMaoz, Dan1 aMeneghetti, Massimo1 aMerten, Julian1 aRiess, Adam1 aRodney, Steve1 aSeitz, Stella uhttps://icer.msu.edu/research/publications/clash-precise-new-constraints-mass-profile-galaxy-cluster-a226101554nas a2200529 4500008004100000245007700041210006900118260001200187490000800199100001500207700001800222700001600240700002000256700001600276700002200292700001500314700002000329700001900349700001300368700002700381700002300408700001800431700002200449700001800471700002200489700002100511700002100532700002300553700002500576700002000601700001900621700002000640700002200660700002000682700002300702700001600725700001700741700002000758700002400778700001900802700001800821700001500839700001800854700002000872700002300892856010900915 2012 eng d00aA magnified young galaxy from about 500 million years after the Big Bang0 amagnified young galaxy from about 500 million years after the Bi c09/20120 v4891 aZheng, Wei1 aPostman, Marc1 aZitrin, Adi1 aMoustakas, John1 aShu, Xinwen1 aJouvel, Stephanie1 aHøst, Ole1 aMolino, Alberto1 aBradley, Larry1 aCoe, Dan1 aMoustakas, Leonidas, A1 aCarrasco, Mauricio1 aFord, Holland1 aBenítez, Narciso1 aLauer, Tod, R1 aSeitz, Stella;, B1 aBouwens, Rychard1 aKoekemoer, Anton1 aMedezinski, Elinor1 aBartelmann, Matthias1 aBroadhurst, Tom1 aDonahue, Megan1 aGrillo, Claudio1 aInfante, Leopoldo1 aJha, Saurabh, W1 aKelson, Daniel, D.1 aLahav, Ofer1 aLemze, Doron1 aMelchior, Peter1 aMeneghetti, Massimo1 aMerten, Julian1 aNonino, Mario1 aOgaz, Sara1 aRosati, Piero1 aUmetsu, Keiichi1 avan der Wel, Arjen uhttps://icer.msu.edu/research/publications/magnified-young-galaxy-about-500-million-years-after-big-bang00643nas a2200157 4500008004100000245014700041210006900188260002200257300001200279490000800291100001400299700001800313700001400331700001800345856012200363 2011 eng d00aSelective pressures for accurate altruism targeting: evidence from digital evolution for difficult-to-test aspects of inclusive fitness theory0 aSelective pressures for accurate altruism targeting evidence fro bThe Royal Society a666-6740 v2781 aClune, J.1 aGoldsby, H.J.1 aOfria, C.1 aPennock, R.T. uhttps://icer.msu.edu/research/publications/selective-pressures-accurate-altruism-targeting-evidence-digital-evolution00594nas a2200145 4500008004100000245008500041210006900126653003900195100001900234700001600253700002000269700001900289700002400308856011600332 2011 eng d00aSignatures of minor mergers in Milky Way-like disc kinematics: Ringing revisited0 aSignatures of minor mergers in Milky Waylike disc kinematics Rin10aAstrophysics - Galaxy Astrophysics1 aGómez, F., A.1 aMinchev, I.1 aVillalobos, Á.1 aO'Shea, B., W.1 aWilliams, M., E. K. uhttps://icer.msu.edu/research/publications/signatures-minor-mergers-milky-way-disc-kinematics-ringing-revisited01232nas a2200121 4500008004100000245007800041210006900119260007200188520070000260100002000960700002000980856011001000 2010 eng d00aBeyond NomBank: A Study of Implicit Argumentation for Nominal Predicates0 aBeyond NomBank A Study of Implicit Argumentation for Nominal Pre aUppsala, SwedenbAssociation for Computational Linguisticsc07/20103 aDespite 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.

1 aGerber, Matthew1 aChai, Joyce, Y. uhttps://icer.msu.edu/research/publications/beyond-nombank-study-implicit-argumentation-nominal-predicates01129nas a2200157 4500008004100000245011900041210006900160260001200229300001000241490000800251520054300259100001800802700002200820700001700842856011200859 2010 eng d00aConformational Sampling of S- and R-Warfarin in Polar Solvents: Implications for Stereoselective Complex Formation0 aConformational Sampling of S and RWarfarin in Polar Solvents Imp c06/2010 a41-510 v9493 aMolecular 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.

1 aFeig, Michael1 aGebreyohannes, K.1 aMcGuffin, V. uhttps://icer.msu.edu/research/publications/conformational-sampling-s-r-warfarin-polar-solvents-implications01190nas a2200169 4500008004100000245011200041210006900153260001200222300001400234490000700248520055700255100002500812700002600837700001900863700001800882856012000900 2010 eng d00aPRIMO/PRIMONA: A coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy0 aPRIMOPRIMONA A coarsegrained model for proteins and nucleic acid c04/2010 a1266-12810 v783 aThe 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.

1 aGopal, Srinivasa, M.1 aMukherjee, Shayantani1 aCheng, Yi-Ming1 aFeig, Michael uhttps://icer.msu.edu/research/publications/primo-primona-coarse-grained-model-proteins-nucleic-acids-preserves-near00512nas a2200133 4500008004100000245008700041210006900128260001200197490000700209100000500216700001600221700001900237856012200256 2009 eng d00aAb Initio Coupled-Cluster and Configuration Interaction Calculations for O Using V0 aAb Initio CoupledCluster and Configuration Interaction Calculati c05/20090 v791 a1 aGour, J., R1 aPiecuch, Piotr uhttps://icer.msu.edu/research/publications/ab-initio-coupled-cluster-configuration-interaction-calculations-o-using-v01184nas a2200157 4500008004100000245009900041210006900140260001200209300001200221490000800233520062000241100000500861700002200866700001900888856011900907 2009 eng d00aCenter-of-Mass Problem in Truncated Configuration Interaction and Coupled-Cluster Calculations0 aCenterofMass Problem in Truncated Configuration Interaction and c08/2009 a334-3390 v6793 aThe 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.

1 a1 aGour, Jeffrey, R.1 aPiecuch, Piotr uhttps://icer.msu.edu/research/publications/center-mass-problem-truncated-configuration-interaction-coupled-cluster02843nas a2200157 4500008004100000245022400041210006900265260001200334300001400346490000800360520214900368100001902517700001602536700001402552856011902566 2009 eng d00aLeft-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 Approaches0 aLeftEigenstate Completely Renormalized Equationofmotion CoupledC c11/2009 a3268-33040 v1093 aThe 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

1 aPiecuch, Piotr1 aGour, J., R1 aWloch, M. uhttps://icer.msu.edu/research/publications/left-eigenstate-completely-renormalized-equation-motion-coupled-cluster01687nas a2200157 4500008004100000245009400041210006900135260001200204490000800216520112100224100001201345700001901357700001601376700001501392856012201407 2009 eng d00aLocal Correlation Calculations Using Standard and Renormalized Coupled-Cluster Approaches0 aLocal Correlation Calculations Using Standard and Renormalized C c09/20090 v1313 ahe 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.

1 aLi, Wei1 aPiecuch, Piotr1 aGour, J., R1 aLi, Shuhua uhttps://icer.msu.edu/research/publications/local-correlation-calculations-using-standard-renormalized-coupled-cluster02324nas a2200157 4500008004100000245021700041210007300258260001200331300001200343490000800355520162000363100001401983700001601997700001902013856013402032 2009 eng d00aLow-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 Methodologies0 aLowLying Valence Excited States of CNC C₂N N₃ and NCO Studied Us c04/2009 a871-8800 v1073 aLow-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.

1 aEhara, M.1 aGour, J., R1 aPiecuch, Piotr uhttps://icer.msu.edu/research/publications/low-lying-valence-excited-states-cnc-c%E2%82%82n-n%E2%82%83-nco-studied-using-electron01222nas a2200133 4500008004100000245005400041210005000095260007900145520072000224100002000944700002000964700001700984856008701001 2009 eng d00aThe Role of Implicit Argumentation in Nominal SRL0 aRole of Implicit Argumentation in Nominal SRL aBoulder, Colorado, USAbAssociation for Computational Linguisticsc06/20093 aNominals 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.

1 aGerber, Matthew1 aChai, Joyce, Y.1 aMeyers, Adam uhttps://icer.msu.edu/research/publications/role-implicit-argumentation-nominal-srl02100nas a2200181 4500008004100000245008800041210006900129300001000198490000800208520148500216100001401701700001601715700001501731700001401746700001901760700001801779856012101797 2008 eng d00aApplication of Renormalized Coupled- Cluster Methods to Potential Function of Water0 aApplication of Renormalized Coupled Cluster Methods to Potential a59-780 v1203 aThe 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.

1 aZheng, J.1 aGour, J., R1 aLutz, J.J.1 aWloch, M.1 aPiecuch, Piotr1 aTruhlar, D.G. uhttps://icer.msu.edu/research/publications/application-renormalized-coupled-cluster-methods-potential-function-water02156nas a2200181 4500008004100000245022700041210006900268260001200337490000800349520139600357100001401753700001601767700001501783700001401798700001901812700001801831856012501849 2008 eng d00aA 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 E0 aComparative Assessment of the Perturbative and Renormalized Coup c01/20080 v1283 aThe 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.

1 aZheng, J.1 aGour, J., R1 aLutz, J.J.1 aWloch, M.1 aPiecuch, Piotr1 aTruhlar, D.G. uhttps://icer.msu.edu/research/publications/comparative-assessment-perturbative-renormalized-coupled-cluster-theories-non02436nas a2200205 4500008004100000245012200041210006900163260001200232300001400244490000800258520172300266100001701989700001602006700001402022700001402036700001902050700001802069700001802087856012502105 2008 eng d00aStereoelectronic Effects on Molecular Geometries and State-Energy Splittings of Ligated Monocopper Diozygen Complexes0 aStereoelectronic Effects on Molecular Geometries and StateEnergy c03/2008 a3754-37670 v1123 aThe 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.

1 aCramer, C.J.1 aGour, J., R1 aKinal, A.1 aWloch, M.1 aPiecuch, Piotr1 aShahi, A.R.M.1 aGagliardi, L. uhttps://icer.msu.edu/research/publications/stereoelectronic-effects-molecular-geometries-state-energy-splittings-ligated02707nas a2200301 4500008004100000245017900041210006900220260001200289300001300301490000800314520164400322653003101966653003301997653002402030653001902054653001802073653001802091653001502109653002202124653002102146653003002167100001602197700001902213700001602232700001402248700001802262856012502280 2007 eng d00aActive-Space Symmetry-Adapted-Cluster Configuration-Interaction and Equation-of-Motion Cluster Methods for High Accuracy Calculations of Potential Energy Surfaces of Radicals0 aActiveSpace SymmetryAdaptedCluster ConfigurationInteraction and c04/2007 a28 pages0 v1263 aThe 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.

10aconfiguration interactions10acoupled cluster calculations10aelectron attachment10aexcited states10afree radicals10aground states10aionisation10aorganic compounds10aoxygen compounds10apotential energy surfaces1 aOhtsuka, Y.1 aPiecuch, Piotr1 aGour, J., R1 aEhara, M.1 aNakatsuji, H. uhttps://icer.msu.edu/active-space-symmetry-adapted-cluster-configuration-interaction-and-equation-motion-cluster-methods01936nas a2200157 4500008004100000245009100041210006900132260001200201300001200213490000800225520137300233100001101606700001701617700001901634856012501653 2007 eng d00aBreaking Bonds with the Left Eigenstate Completely Renormalized Coupled-Cluster Method0 aBreaking Bonds with the Left Eigenstate Completely Renormalized c11/2007 a6 pages0 v1273 aThe 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).

1 aGe, Y.1 aGordon, M.S.1 aPiecuch, Piotr uhttps://icer.msu.edu/research/publications/breaking-bonds-left-eigenstate-completely-renormalized-coupled-cluster-method01210nas a2200193 4500008004100000245008000041210006900121260001200190300001200202490000700214520059600221100001400817700001600831700001400847700002100861700001800882700001900900856009700919 2007 eng d00aCoupled-Cluster and Configuration-Interaction Calculations for Heavy Nuclei0 aCoupledCluster and ConfigurationInteraction Calculations for Hea c03/2007 a4 pages0 v983 aWe 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.

1 aHoroi, M.1 aGour, J., R1 aWloch, M.1 aLodriguito, M.D.1 aBrown, B., A.1 aPiecuch, Piotr uhttps://icer.msu.edu/coupled-cluster-and-configuration-interaction-calculations-heavy-nuclei01855nas a2200157 4500008004100000245017000041210006900211260001200280300001600292490000800308520120900316100001401525700001601539700001901555856012301574 2007 eng d00aExtension of the Renormalized Coupled-Cluster Methods Exploiting Left Eigenstates of the Similarity-Transformed Hamiltonian to Open- Shell Systems: A Benchmark Study0 aExtension of the Renormalized CoupledCluster Methods Exploiting c11/2007 a11359-113820 v1113 aThe 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.

1 aWloch, M.1 aGour, J., R1 aPiecuch, Piotr uhttps://icer.msu.edu/extension-renormalized-coupled-cluster-methods-exploiting-left-eigenstates-similarity-transformed01279nas a2200457 4500008004100000245014900041210006900190260001200259490000700271100001700278700001500295700001600310700001500326700001700341700001600358700001400374700001400388700001800402700001600420700001300436700001600449700001900465700001500484700001700499700001400516700001400530700001400544700001500558700001600573700001700589700001700606700001700623700001500640700001700655700001400672700001400686700001300700700001800713700001900731856007100750 2007 eng d00aShape and Structure of N = Z 64Ge: Electromagnetic Transition Rates from the Application ￼of the Recoil Distance Method to a Knockout Reaction0 aShape and Structure of N Z 64Ge Electromagnetic Transition Rates c07/20070 v991 aStarosta, K.1 aDewald, A.1 aDunomes, A.1 aAdrich, P.1 aAmthor, A.M.1 aBaumann, T.1 aBazin, D.1 aBowen, M.1 aBrown, B., A.1 aChester, A.1 aGade, A.1 aGalaviz, D.1 aGlasmacher, T.1 aGinter, T.1 aHausmann, M.1 aHoroi, M.1 aJolie, J.1 aMelon, B.1 aMiller, D.1 aMoeller, V.1 aNorris, R.P.1 aPissulla, T.1 aPortillo, M.1 aRother, W.1 aShimbara, Y.1 aStolz, A.1 aVaman, C.1 aVoss, P.1 aWeisshaar, D.1 aZelevinsky, V. uhttp://journals.aps.org/prl/abstract/10.1103/PhysRevLett.99.04250301096nas a2200385 4500008004100000245011100041210006900152260001200221490000700233100001400240700001700254700001400271700001800285700001800303700001900321700001600340700001500356700001600371700001300387700001600400700001900416700002600435700001400461700001500475700001600490700002000506700001700526700001700543700001400560700001600574700001400590700001900604700001600623856007100639 2007 eng d00aZ = 0 Shell Gap near 100Sn from Intermediate-Energy Coulomb Excitations ￼in Even-Mass 106-112Sn Isotopes0 aZ 0 Shell Gap near 100Sn from IntermediateEnergy Coulomb Excitat c10/20070 v991 aVaman, C.1 aAndreoiu, C.1 aBazin, D.1 aBeccerril, A.1 aBrown, B., A.1 aCampbell, C.M.1 aChester, A.1 aCook, J.M.1 aDinca, D.C.1 aGade, A.1 aGalaviz, D.1 aGlasmacher, T.1 aHjorth-Jensen}, M., {1 aHoroi, M.1 aMiller, D.1 aMoeller, V.1 aMueller, W., F.1 aSchiller, A.1 aStarosta, K.1 aStolz, A.1 aTerry, J.R.1 aVolya, A.1 aZelevinsky, V.1 aZwahlen, H. uhttp://journals.aps.org/prl/abstract/10.1103/PhysRevLett.99.16250101273nas a2200205 4500008004100000245008900041210006900130260001200199300001200211490000700223520060600230100001900836700001400855700001700869700001600886700002600902700001900928700001700947856010300964 2006 eng d00aAb Initio Coupled-Cluster Calculations for Nuclei Using Methods of Quantum Chemistry0 aAb Initio CoupledCluster Calculations for Nuclei Using Methods o c09/2005 a485-4880 v253 aWe 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.

1 aPiecuch, Piotr1 aWloch, M.1 aDean, D., J.1 aGour, J., R1 aHjorth-Jensen}, M., {1 aPapenbrock, T.1 aKowalski, K. uhttps://icer.msu.edu/ab-initio-coupled-cluster-calculations-nuclei-using-methods-quantum-chemistry00864nas a2200193 4500008004100000245003800041210003800079300001400117490000700131520031100138653006000449100001900509700001700528700001600545700001400561700002600575700001400601856005500615 2006 eng d00aCoupled Cluster Theory for Nuclei0 aCoupled Cluster Theory for Nuclei a5338-53450 v203 aThis 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.

10aNuclear structure; light nuclei; coupled-cluster theory1 aPapenbrock, T.1 aDean, D., J.1 aGour, J., R1 aHagen, G.1 aHjorth-Jensen}, M., {1 aWloch, M. uhttps://icer.msu.edu/coupled-cluster-theory-nuclei01833nas a2200181 4500008004100000245006500041210006400106260001100170300001300181490000700194520127600201100001901477700001601496700002601512700001401538700001701552856008201569 2006 eng d00aCoupled-Cluster Calculations for Valence Systems around 16 O0 aCoupledCluster Calculations for Valence Systems around 16 O c8/2006 a18 pages0 v743 aWe 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.

1 aPiecuch, Piotr1 aGour, J., R1 aHjorth-Jensen}, M., {1 aWloch, M.1 aDean, D., J. uhttps://icer.msu.edu/coupled-cluster-calculations-valence-systems-around-16-o01855nas a2200181 4500008004100000245006400041210006300105260001200168300001100180490000700191520130200198100001601500700001901516700002601535700001401561700001701575856008101592 2006 eng d00aCoupled-cluster calculations for valence systems around O160 aCoupledcluster calculations for valence systems around O16 c08/2006 a0243100 v743 aWe 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.

1 aGour, J., R1 aPiecuch, Piotr1 aHjorth-Jensen}, M., {1 aWloch, M.1 aDean, D., J. uhttps://icer.msu.edu/coupled-cluster-calculations-valence-systems-around-o1601911nas a2200193 4500008004100000245014700041210006900188260001200257300001300269490000800282520117900290653003301469653001801502653002201520653002201542100001601564700001901580856011801599 2006 eng d00aEfficient Formulation and Computer Implementation of the Active-Space Electron-Attached and Ionized Equation-of-Motion Coupled-Cluster Methods0 aEfficient Formulation and Computer Implementation of the ActiveS c12/2006 a17 pages0 v1253 aThe 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.

10acoupled cluster calculations10afree radicals10aorganic compounds10asulphur compounds1 aGour, J., R1 aPiecuch, Piotr uhttps://icer.msu.edu/efficient-formulation-and-computer-implementation-active-space-electron-attached-and-ionized01765nas a2200169 4500008004100000245014000041210006900181260001100250300001400261490000800275520098500283653015801268100001901426700001601445700001401461856012001475 2006 eng d00aExtension of the Active-Space Equation-of- Motion Coupled-Cluster Methods to Radical Systems: The EA-EOMCCSDt and IPEOMCCSDt Approaches0 aExtension of the ActiveSpace Equationof Motion CoupledCluster Me c7/2006 a2854-28740 v1063 aThe 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.

10aoupled-cluster theory;equation-of-a motion coupled-cluster method;active-space coupled-cluster approaches;electronic-attached and ionized states;radicals1 aPiecuch, Piotr1 aGour, J., R1 aWloch, M. uhttps://icer.msu.edu/extension-active-space-equation-motion-coupled-cluster-methods-radical-systems-ea-eomccsdt-and00503nas a2200145 4500008004100000245007200041210006900113300001100182490000700193100001900200700001400219700001900233700001600252856008900268 2006 eng d00aNon-iterative Coupled-Cluster Methods for Excited Electronic States0 aNoniterative CoupledCluster Methods for Excited Electronic State a45-1060 v151 aPiecuch, Piotr1 aWloch, M.1 aLodriguito, M.1 aGour, J., R uhttps://icer.msu.edu/non-iterative-coupled-cluster-methods-excited-electronic-states01338nas a2200169 4500008004100000245011100041210006900152260001200221300001400233490000800247520073400255100001900989700001401008700001601022700001401038856011601052 2006 eng d00aSingle-reference, size-extensive, non-iterative coupled-cluster approaches to bond breaking and biradicals0 aSinglereference sizeextensive noniterative coupledcluster approa c02/2006 a467–4740 v4183 aWe 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.

1 aPiecuch, Piotr1 aWloch, M.1 aGour, J., R1 aKinal, A. uhttps://icer.msu.edu/single-reference-size-extensive-non-iterative-coupled-cluster-approaches-bond-breaking-and01465nas a2200181 4500008004100000245010100041210006900142260001500211300001600226490000800242520084100250100001701091700001401108700001401122700001901136700001801155856011001173 2006 eng d00aTheoretical Characterization of End-on and Side-on Peroxide Coordination in Ligated Cu2O2 Models0 aTheoretical Characterization of Endon and Sideon Peroxide Coordi c09/15/2006 a11557-115680 v1103 aThe 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.

1 aCramer, C.J.1 aKinal, A.1 aWloch, M.1 aPiecuch, Piotr1 aGagliardi, L. uhttps://icer.msu.edu/theoretical-characterization-end-and-side-peroxide-coordination-ligated-cu2o2-models02131nas a2200181 4500008004100000245012100041210006900162260001200231300001600243490000800259520146800267100001701735700001401752700001901766700002401785700001801809856012201827 2006 eng d00aTheoretical Models on the Cu2O2 Torture Track. Mechanistic Implications for Oxytyrosinase and Small-molecule Analogs0 aTheoretical Models on the Cu2O2 Torture Track Mechanistic Implic c06/2007 a1991–20040 v1103 aAccurately 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.

1 aCramer, C.J.1 aWloch, M.1 aPiecuch, Piotr1 aPuzzarini, Cristina1 aGagliardi, L. uhttps://icer.msu.edu/theoretical-models-cu2o2-torture-track-mechanistic-implications-oxytyrosinase-and-small-molecule00614nas a2200157 4500008004100000245012500041210006900166260001100235300001400246490000800260100001900268700001400287700002100301700001600322856011800338 2006 eng d00aTwo New Classes of Non-Iterative Coupled-Cluster Methods Derived from the Method of Moments of Coupled-Cluster Equations0 aTwo New Classes of NonIterative CoupledCluster Methods Derived f c7/2006 a2149-21720 v1041 aPiecuch, Piotr1 aWloch, M.1 aLogriguito, M.D.1 aGour, J., R uhttps://icer.msu.edu/two-new-classes-non-iterative-coupled-cluster-methods-derived-method-moments-coupled-cluster01260nas a2200205 4500008004100000245004300041210004200084260001200126300001100138490000700149520068900156100001500845700001700860700001600877700002600893700001700919700001900936700001600955856008300971 2005 eng d00aAb Initio Coupled-Cluster Study of 16O0 aAb Initio CoupledCluster Study of 16O c06/2005 a2125010 v943 aWe 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.

1 aWłoch, M.1 aDean, D., J.1 aGour, J., R1 aHjorth-Jensen}, M., {1 aKowalski, K.1 aPapenbrock, T.1 aPiecuch, P. uhttps://icer.msu.edu/research/publications/ab-initio-coupled-cluster-study-16o01233nas a2200193 4500008004100000245004100041210004000082260001200122490000700134520068900141100001900830700001400849700001700863700001600880700002600896700001700922700001900939856008100958 2005 eng d00aAb Initio Coupled-Cluster Study of O0 aAb Initio CoupledCluster Study of O c06/20050 v943 aWe 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.

1 aPiecuch, Piotr1 aWloch, M.1 aDean, D., J.1 aGour, J., R1 aHjorth-Jensen}, M., {1 aKowalski, K.1 aPapenbrock, T. uhttps://icer.msu.edu/research/publications/ab-initio-coupled-cluster-study-o01392nas a2200181 4500008004100000245015300041210006900194300001600263490000800279520065800287653003300945653001800978653003200996100002201028700001901050700001701069856012401086 2005 eng d00aActive-space equation-of-motion coupled-cluster methods for excited states of radicals and other open-shell systems: {EA-EOMCCSDt} and {IP-EOMCCSDt}0 aActivespace equationofmotion coupledcluster methods for excited a134113–140 v1233 aThe 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.

10acoupled cluster calculations10afree radicals10amolecular electronic states1 aGour, Jeffrey, R.1 aPiecuch, Piotr1 aWloch, Marta uhttps://icer.msu.edu/research/publications/active-space-equation-motion-coupled-cluster-methods-excited-states-radicals00613nas a2200145 4500008004100000245014900041210006900190260001200259300001300271490000800284100001900292700001600311700001400327856012600341 2005 eng d00aActive-Space Equation-of=Motion Coupled-Cluster Methods for Excited States of Radicals and Other Open-Shell Systems: EA-EOMCCSDt and IP-EOMCCSDt0 aActiveSpace EquationofMotion CoupledCluster Methods for Excited c10/2005 a14 pages0 v1231 aPiecuch, Piotr1 aGour, J., R1 aWloch, M. uhttps://icer.msu.edu/research/publications/active-space-equation-ofmotion-coupled-cluster-methods-excited-states-radicals02028nas a2200193 4500008004100000245012400041210006900165260005600234300001000290490000800300520128900308100001901597700001401616700001601630700001701646700002601663700001901689856012601708 2005 eng d00aBridging Quantum Chemistry and Nuclear Structure Theory: Coupled-Cluster Calculations for Closed- and Open-Shell Nuclei0 aBridging Quantum Chemistry and Nuclear Structure Theory CoupledC aMelville, NYbAmerican Institute of Physicsc7/2005 a28-450 v7773 aWe 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

1 aPiecuch, Piotr1 aWloch, M.1 aGour, J., R1 aDean, D., J.1 aHjorth-Jensen}, M., {1 aPapenbrock, T. uhttps://icer.msu.edu/bridging-quantum-chemistry-and-nuclear-structure-theory-coupled-cluster-calculations-closed-and-open01156nas a2200157 4500008004100000245012800041210006900169260001200238490000800250520055100258100001900809700001400828700001600842700001700858856012300875 2005 eng d00aExtension of Renormalized Coupled-Cluster Methods Including Triple Excitations to Electronic States of Open-Shell Molecules0 aExtension of Renormalized CoupledCluster Methods Including Tripl c06/20050 v1223 aThe 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.

1 aPiecuch, Piotr1 aWloch, M.1 aGour, J., R1 aKowalski, K. uhttps://icer.msu.edu/research/publications/extension-renormalized-coupled-cluster-methods-including-triple-excitations01746nas a2200217 4500008004100000245008700041210006900128260001200197300001200209490000800221520103700229100001901266700001701285700001601302700001401318700002601332700001701358700001901375700001401394856012001408 2005 eng d00aNuclear Structure Calculations with Coupled-Cluster Methods from Quantum Chemistry0 aNuclear Structure Calculations with CoupledCluster Methods from c04/2005 a299-3080 v7523 aWe 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.

1 aPiecuch, Piotr1 aDean, D., J.1 aGour, J., R1 aHagen, G.1 aHjorth-Jensen}, M., {1 aKowalski, K.1 aPapenbrock, T.1 aWloch, M. uhttps://icer.msu.edu/research/publications/nuclear-structure-calculations-coupled-cluster-methods-quantum-chemistry01158nas a2200229 4500008004100000245007700041210006900118260001500187300001400202490000800216520046200224100001900686700001600705700001700721700001700738700001700755700001400772700001700786700002200803700001500825856008800840 2005 eng d00aWhere Does the Planar-to-Nonplanar Turnover Occur in Small Gold Clusters0 aWhere Does the PlanartoNonplanar Turnover Occur in Small Gold Cl c12/30/2004 a1049-10520 v1273 aSeveral 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.

1 aPiecuch, Piotr1 aOlson, R.M.1 aVarganov, S.1 aGordon, M.S.1 aChretien, S.1 aMetiu, H.1 aKowalski, K.1 aKucharski, S., A.1 aMusial, M. uhttps://icer.msu.edu/where-does-planar-nonplanar-turnover-occur-small-gold-clusters