The conformational sampling of monomeric, membrane-bound phospholamban is described from computer simulations. Phospholamban (PLB) plays a key role as a regulator of sarcoplasmic reticulum calcium ATPase. An implicit membrane model is used in conjunction with replica exchange molecular dynamics simulations to reach μs-ms timescales. The implicit membrane model was also used to study the effect of different membrane thicknesses by scaling the low-dielectric region. The conformational sampling with the membrane model mimicking dipalmitoylphosphatidylcholine bilayers is in good agreement overall with experimental measurements, but consists of a wide variety of different conformations including structures not described previously. The conformational ensemble shifts significantly in the presence of thinner or thicker membranes. This has implications for the structure and dynamics of PLB in physiological membranes and offers what we believe to be a new interpretation of previous experimental measurements of PLB in detergents and microsomal membrane.

VL - 98 IS - 5 ER - TY - JOUR T1 - Galaxy Cluster Radio Relics in Adaptive Mesh Refinement Cosmological Simulations: Relic Properties and Scaling Relationships JF - ArXiv e-prints Y1 - 2010 A1 - Skillman, S. W. A1 - undefined A1 - O'Shea, B. W. A1 - Burns, J. O. A1 - Smith, B. D. A1 - Turk, M. J. KW - Astrophysics - Cosmology and Extragalactic Astrophysics ER - TY - JOUR T1 - Constraints on the Density Dependence of the Symmetry Energy JF - Physical Review Letters Y1 - 2009 A1 - M. B. Tsang A1 - Yingxun Zhang A1 - P. Danielewicz A1 - M. Famiano A1 - Li, Z. A1 - W. G. Lynch A1 - A. W. Steiner AB -Collisions involving {112Sn} and {124Sn} nuclei have been simulated with the improved quantum molecular dynamics transport model. The results of the calculations reproduce isospin diffusion data from two different observables and the ratios of neutron and proton spectra. By comparing these data to calculations performed over a range of symmetry energies at saturation density and different representations of the density dependence of the symmetry energy, constraints on the density dependence of the symmetry energy at subnormal density are obtained. The results from the present work are compared to constraints put forward in other recent analyses.

VL - 102 N1 - Copyright {(C)} 2010 The American Physical Society; Please report any problems to prola@aps.org ER - TY - JOUR T1 - Dark Matter Annihilation and Primordial Star Formation JF - \apj Y1 - 2009 A1 - Natarajan, A. A1 - Tan, J. C. A1 - O'Shea, B. W. KW - cosmology: theory KW - dark matter KW - early universe KW - galaxies: formation KW - stars: formation VL - 692 ER - TY - JOUR T1 - The Formation of Population III Binaries from Cosmological Initial Conditions JF - Science Y1 - 2009 A1 - Turk, M. J. A1 - Abel, T. A1 - O'Shea, B. W. VL - 325 ER - TY - JOUR T1 - Scanning tunneling microscopy study of the CeTe3 charge density wave JF - Physical Review B Y1 - 2009 A1 - Tomic, A. A1 - Rak, Zs. A1 - Veazey, J. A1 - Malliakas, C. A1 - S. D. Mahanti A1 - Kanatzidis, M. A1 - Tessmer, S. VL - 79 IS - 8 ER - TY - JOUR T1 - Survey of Excited State Neutron Spectroscopic Factors for Z=8-28 Nuclei JF - Physical Review Letters Y1 - 2009 A1 - M. B. Tsang A1 - Jenny Lee A1 - S. C. Su A1 - J. Y. Dai A1 - M. Horoi A1 - H. Liu A1 - W. G. Lynch A1 - S. Warren AB -We have extracted 565 neutron spectroscopic factors of sd and fp shell nuclei by systematically analyzing more than 2000 measured (d, p) angular distributions. We are able to compare 125 of the extracted spectroscopic factors to values predicted by large-basis shell-model calculations and evaluate the accuracies of spectroscopic factors predicted by different shell-model interactions in these regions. We find that the spectroscopic factors predicted for most excited states of sd-shell nuclei using the latest {USDA} or {USDB} interactions agree with the experimental values. For fp shell nuclei, the inability of the current models to account for the core excitation and fragmentation of the states leads to considerable discrepancies. In particular, the agreement between data and shell-model predictions for Ni isotopes is not better than a factor of 2 using either the {GXPF1A} or the {XT} interaction.

VL - 102 N1 - Copyright {(C)} 2010 The American Physical Society; Please report any problems to prola@aps.org ER - TY - JOUR T1 - Thermochemical Kinetics for Multi-reference Systems: Addition Reactions of Ozone JF - Journal of Physical Chemistry A Y1 - 2009 A1 - Piotr Piecuch A1 - Zhao, Y. A1 - Truhlar, D.G. AB -The 1,3-dipolar cycloadditions of ozone to ethyne and ethene provide extreme examples of multireference singlet-state chemistry, and they are examined here to test the applicability of several approaches to thermochemical kinetics of systems with large static correlation. Four different multireference diagnostics are applied to measure the multireference characters of the reactants, products, and transition states; all diagnostics indicate significant multireference character in the reactant portion of the potential energy surfaces. We make a more complete estimation of the effect of quadruple excitations than was previously available, and we use this with CCSDT/CBS estimation of Wheeler et al. (Wheeler, S. E.; Ess, D. H.; Houk, K. N. J. Phys. Chem. A 2008, 112, 1798.) to make new best estimates of the van der Waals association energy, the barrier height, and the reaction energy to form the cycloadduct for both reactions. Comparing with these best estimates, we present comprehensive mean unsigned errors for a variety of coupled cluster, multilevel, and density functional methods. Several computational aspects of multireference reactions are considered: (i) the applicability of multilevel theory, (ii) the convergence of coupled cluster theory for reaction barrier heights, (iii) the applicability of completely renormalized coupled cluster methods to multireference systems, (iv) the treatment by density functional theory, (v) the multireference perturbation theory for multireference reactions, and (vi) the relative accuracy of scaling-type multilevel methods as compared with additive ones. It is found that scaling-type multilevel methods do not perform better than the additive-type multilevel methods. Among the 48 tested density functionals, only M05 reproduces the best estimates within their uncertainty. Multireference perturbation theory based on the complete-active-space reference wave functions constructed using a small number of reaction-specific active orbitals gives accurate forward barrier heights; however, it significantly underestimates reaction energies.

VL - 113 IS - 19 ER - TY - JOUR T1 - Three Modes of Metal-Enriched Star Formation in the Early Universe JF - \apj Y1 - 2009 A1 - Smith, B. D. A1 - Turk, M. J. A1 - Sigurdsson, S. A1 - O'Shea, B. W. A1 - Norman, M. L. KW - early universe KW - stars: formation VL - 691 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 - The influence of cluster emission and the symmetry energy on neutron-proton spectral double ratios JF - Physics Letters B Y1 - 2008 A1 - Yingxun Zhang A1 - P. Danielewicz A1 - M. Famiano A1 - Li, Z. A1 - W. G. Lynch A1 - M. B. Tsang AB -The emissions of neutrons, protons and bound clusters from central {124Sn} + {124Sn} and {112Sn} + {112Sn} collisions are simulated using the Improved Quantum Molecular Dynamics model for two different density-dependent symmetry-energy functions. The calculated neutron-proton spectral double ratios for these two systems are sensitive to the density dependence of the symmetry energy, consistent with previous work. Cluster emission increases the double ratios in the low energy region relative to values calculated in a coalescence-invariant approach. To circumvent uncertainties in cluster production and secondary decays, it is important to have more accurate measurements of the neutron-proton ratios at higher energies in the center of mass system, where the influence of such effects is reduced.

VL - 664 ER - TY - JOUR T1 - Transport Model Simulations of Projectile Fragmentation Reactions at 140 {MeV/nucleon} JF - Physical Review C Y1 - 2008 A1 - M. Mocko A1 - M. B. Tsang A1 - D. Lacroix A1 - A. Ono A1 - P. Danielewicz A1 - W. G. Lynch A1 - R. J Charity KW - Nuclear Experiment KW - Nuclear Theory AB -The collisions in four different reaction systems using {\$ˆ{40,48}\$Ca} and {\$ˆ{58,64}\$Ni} isotope beams and a Be target have been simulated using the Heavy Ion Phase Space Exploration and the Antisymmetrized Molecular Dynamics models. The present study mainly focuses on the model predictions for the excitation energies of the hot fragments and the cross sections of the final fragments produced in these reactions. The effects of various factors influencing the final fragment cross sections, such as the choice of the statistical decay code and its parameters have been explored. The predicted fragment cross sections are compared to the projectile fragmentation cross sections measured with the A1900 mass separator. At {\$E/A=140\$} {MeV,} reaction dynamics can significantly modify the detection efficiencies for the fragments and make them different from the efficiencies applied to the measured data reported in the previous work. The effects of efficiency corrections on the validation of event generator codes are discussed in the context of the two models.

VL - 78 IS - 2 N1 - {Phys.Rev.C78:024612,2008} 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 - Experimental and Theoretical UV Characterizations of Acetyloacetone and its Isomers JF - The Journal of Physical Chemistry A Y1 - 2006 A1 - Piotr Piecuch A1 - S. Coussan A1 - Y. Ferro A1 - A. Trivella A1 - P. Roubin A1 - R. Wieczorek A1 - C. Manca A1 - K. Kowalski A1 - M. Wloch A1 - S. Kucharski A1 - M. Musial AB -Cryogenic matrix isolation experiments have allowed the measurement of the UV absorption spectra of the high-energy non-chelated isomers of acetylacetone, these isomers being produced by UV irradiation of the stable chelated form. Their identification has been done by coupling selective UV-induced isomerization, infrared spectroscopy, and harmonic vibrational frequency calculations using density functional theory. The relative energies of the chelated and non-chelated forms of acetylacetone in the S0 state have been obtained using density functional theory and coupled-cluster methods. For each isomer of acetylacetone, we have calculated the UV transition energies and dipole oscillator strengths using the excited-state coupled-cluster methods, including EOMCCSD (equation-of-motion coupled-cluster method with singles and doubles) and CR-EOMCCSD(T) (the completely renormalized EOMCC approach with singles, doubles, and non-iterative triples). For dipole-allowed transition energies, there is a very good agreement between experiment and theory. In particular, the CR-EOMCCSD(T) approach explains the blue shift in the electronic spectrum due to the formation of the non-chelated species after the UV irradiation of the chelated form of acetylacetone. Both experiment and CR-EOMCCSD(T) theory identify two among the seven non-chelated forms to be characterized by red-shifted UV transitions relative to the remaining five non-chelated isomers.

VL - 110 IS - 11 ER - TY - JOUR T1 - Half-life and spin of 60Mng JF - Physical Review C Y1 - 2006 A1 - S. N. Liddick A1 - P. F. Mantica A1 - B. A. Brown A1 - M. P. Carpenter A1 - A. D. Davies A1 - M. Horoi A1 - R. V. F. Janssens A1 - A. C. Morton A1 - W. F. Mueller A1 - J. Pavan A1 - H. Schatz A1 - A. Stolz A1 - S. L. Tabor A1 - B. E. Tomlin A1 - M. Wiedeking AB -A value of 0.28±0.02 s has been deduced for the half-life of the ground state of {60Mn,} in sharp contrast to the previously adopted value of 51±6 s. Access to the low-spin {60Mn} ground state was accomplished via β decay of the 0+ {60Cr} parent nuclide. New low-energy states in {60Mn} have been identified from β-delayed γ-ray spectroscopy. The new, shorter half-life of {60Mng} is not suggestive of isospin-forbidden β decay, and new spin and parity assignments of 1+ and 4+ have been adopted for the ground and isomeric β-decaying states, respectively, of {60Mn.}

VL - 73 IS - 4 N1 - Copyright {(C)} 2010 The American Physical Society; Please report any problems to prola@aps.org ER - TY - JOUR T1 - Half-life and spin of 60Mng JF - PHYSICAL REVIEW C Y1 - 2006 A1 - S. N. Liddick A1 - P. F. Mantica A1 - B. A. Brown A1 - M. P. Carpenter A1 - A. D. Davies A1 - M. Horoi A1 - R. V. F. Janssens A1 - A. C. Morton A1 - W. F. Mueller A1 - J. Pavan A1 - H. Schatz A1 - A. Stolz A1 - S. L. Tabor A1 - B. E. Tomlin A1 - M. Wiedeking VL - 73 UR - http://journals.aps.org/prc/abstract/10.1103/PhysRevC.73.044322 IS - 4 ER - TY - JOUR T1 - Molecular Dynamics Simulations of Large Integral Membrane Proteins with an Implicit Membrane Model JF - The Journal of Physical Chemistry B Y1 - 2006 A1 - Seiichiro Tanizaki A1 - Michael Feig AB -The heterogeneous dielectric generalized Born {(HDGB)} methodology is an the extension of the {GBMV} model for the simulation of integral membrane proteins with an implicit membrane environment. Three large integral membrane proteins, the bacteriorhodopsin monomer and trimer and the {BtuCD} protein, were simulated with the {HDGB} model in order to evaluate how well thermodynamic and dynamic properties are reproduced. Effects of the truncation of electrostatic interactions were examined. For all proteins, the {HDGB} model was able to generate stable trajectories that remained close to the starting experimental structures, in excellent agreement with explicit membrane simulations. Dynamic properties evaluated through a comparison of B-factors are also in good agreement with experiment and explicit membrane simulations. However, overall flexibility was slightly underestimated with the {HDGB} model unless a very large electrostatic cutoff is employed. Results with the {HDGB} model are further compared with equivalent simulations in implicit aqueous solvent, demonstrating that the membrane environment leads to more realistic simulations.

VL - 110 ER - TY - JOUR T1 - Can a Single-Reference Approach Provide a Balanced Description of Ground and Excited States? A Comparison of the Completely Renormalized Equation-of-the-Motion Coupled-Cluster Method with Multi-Reference Quasi-Degenerate Perturbation Theory Near a Conical JF - Journal of Chemical Physics A Y1 - 2005 A1 - Piotr Piecuch A1 - S. Nangia A1 - Truhlar, D.G. A1 - M. J. {McGuire} AB -We calculated the two lowest electronically adiabatic potential energy surfaces of ammonia in the region of the conical intersection and at a sequence of geometries along which one of the N-H bonds is broken. We employed both a multireference (MR) method and a single-reference (SR) method. The MR calculations are based on multiconfiguration quasidegenerate perturbation theory (MC-QDPT) with a 6-311+G(3df,3pd) basis set. The SR calculations, carried out with the same basis, employ the completely renormalized equation-ofmotion coupled-cluster method with singles and doubles, and a noniterative treatment of triples, denoted CR-EOMCCSD(T). At 91 geometries used for comparison, including geometries near a conical intersection, the surfaces agree to 7% on average.

VL - 109 IS - 51 ER - TY - JOUR T1 - Comparison of Low-Order Multireference Many-Body Perturbation Theories JF - Journal of Chemical Physics Y1 - 2005 A1 - Piotr Piecuch A1 - R.K. Chaudhuri A1 - K.F. Freed A1 - G. Hose A1 - K. Kowalski A1 - M. Wloch A1 - S. Chattopadhyay A1 - D. Mukherjee A1 - R. Rolik A1 - A. Szabados A1 - G. Toth A1 - P.R. Surjan AB -Tests have been made to benchmark and assess the relative accuracies of low-order multireference perturbation theories as compared to coupled cluster (CC) and full configuration interaction (FCI) methods. Test calculations include the ground and some excited states of the Be, H(2), BeH(2), CH(2), and SiH(2) systems. Comparisons with FCI and CC calculations show that in most cases the effective valence shell Hamiltonian (H(v)) method is more accurate than other low-order multireference perturbation theories, although none of the perturbative methods is as accurate as the CC approximations. We also briefly discuss some of the basic differences among the multireference perturbation theories considered in this work.

VL - 122 IS - 13 ER -