Influenza fusion peptide is critical for mediating the fusion of viral and host cell membranes during viral entry. The interaction of monomeric influenza fusion peptide with membranes is studied with replica exchange molecular dynamics simulations using a new implicit membrane model to effectively reach microsecond to millisecond time scales. The conformational sampling of the fusion peptide was studied as a function of different N- and C-termini, including an experimental construct with an additional C-terminal tag, as well as a function of protonation of acidic residues. It is found that the influenza fusion peptide mostly adopts helical structures with a pronounced kink at residues 11−13 with both N-terminal and C-terminal helices oriented mostly parallel to the membrane surface. A charged C-terminus and the presence of a charge C-terminal tag significantly alters the conformational sampling of the fusion peptide and results in more diverse conformational ensembles that include obliquely inserted N-terminal peptide structures. Protonation of acidic residues also affects the conformational sampling, however, based on pKa shift estimates the overall effect of pH = 5 on the conformational sampling of the influenza fusion peptide appears to be only minor.

%B Journal of Physical Chemistry B %V 114 %P 1407-1416 %8 12/2009 %G eng %9 Journal Article %0 Journal Article %J Journal of Molecular Structure (Theochem) %D 2010 %T Conformational Sampling of S- and R-Warfarin in Polar Solvents: Implications for Stereoselective Complex Formation %A Michael Feig %A K. Gebreyohannes %A V. McGuffin %XMolecular 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.

%B Journal of Molecular Structure (Theochem) %V 949 %P 41-51 %8 06/2010 %G eng %N 1-3 %0 Journal Article %J Physical Letters B %D 2009 %T Center-of-Mass Problem in Truncated Configuration Interaction and Coupled-Cluster Calculations %A R. Roth, %A Jeffrey R. Gour %A Piotr Piecuch %XThe problem of center-of-mass (CM) contaminations in ab initio nuclear structure calculations using configuration interaction (CI) and coupled-cluster (CC) approaches is analyzed. A rigorous and quantitative scheme for diagnosing the CM contamination of intrinsic observables is proposed and applied to ground-state calculations for 4He and 16O. The CI and CC calculations for 16O based on model spaces defined via a truncation of the single-particle basis lead to sizable CM contaminations, while the importance-truncated no-core shell model based on the NmaxΩ space is virtually free of CM contaminations.

%B Physical Letters B %V 679 %P 334-339 %8 08/2009 %G eng %N 4 %0 Journal Article %J Physical Review Letters %D 2009 %T Constraints on the Density Dependence of the Symmetry Energy %A M. B. Tsang %A Yingxun Zhang %A P. Danielewicz %A M. Famiano %A Li, Z. %A W. G. Lynch %A A. W. Steiner %XCollisions 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.

%B Physical Review Letters %V 102 %P 122701 %8 03/2009 %G eng %0 Journal Article %J The Journal of Chemical Physics %D 2008 %T A Comparative Assessment of the Perturbative and Renormalized Coupled Cluster Theories with a Non-iterative Treatment of Triple Excitations for Thermochemical Kinetics, Including a Study of Basis Set and Core Correlation E %A J. Zheng %A J. R Gour %A J.J. Lutz %A M. Wloch %A Piotr Piecuch %A Truhlar, D.G. %XThe CCSD, CCSD(T), and CR-CC(2,3) coupled cluster methods, combined with five triple-zeta basis sets, namely, MG3S, aug-cc-pVTZ, aug-cc-pV(T+d)Z, aug-cc-pCVTZ, and aug-cc-pCV(T+d)Z, are tested against the DBH24 database of diverse reaction barrier heights. The calculations confirm that the inclusion of connected triple excitations is essential to achieving high accuracy for thermochemical kinetics. They show that various noniterative ways of incorporating connected triple excitations in coupled cluster theory, including the CCSD(T) approach, the full CR-CC(2,3) method, and approximate variants of CR-CC(2,3) similar to the triples corrections of the CCSD(2) approaches, are all about equally accurate for describing the effects of connected triply excited clusters in studies of activation barriers. The effect of freezing core electrons on the results of the CCSD, CCSD(T), and CR-CC(2,3) calculations for barrier heights is also examined. It is demonstrated that to include core correlation most reliably, a basis set including functions that correlate the core and that can treat core-valence correlation is required. On the other hand, the frozen-core approximation using valence-optimized basis sets that lead to relatively small computational costs of CCSD(T) and CR-CC(2,3) calculations can achieve almost as high accuracy as the analogous fully correlated calculations.

%B The Journal of Chemical Physics %V 128 %8 01/2008 %G eng %N 4 %0 Journal Article %J \apj %D 2008 %T Cosmological Shocks in Adaptive Mesh Refinement Simulations and the Acceleration of Cosmic Rays %A Skillman, S. W. %A O'Shea, B. W. %A Hallman, E. J. %A Burns, J. O. %A Norman, M. L. %K cosmology: theory %K hydrodynamics %K ISM: Cosmic Rays %K methods: numerical %B \apj %V 689 %P 1063-1077 %G eng %0 Journal Article %J Journal of Physical Chemistry A %D 2007 %T Computational Investigation of the Conrotatory and Disrotatory Isomerization Channels of Bicyclo[1.1.0]butane to Buta-1,3-diene: A Completely Renormalized Coupled-Cluster Study %A A. Kinal %A Piotr Piecuch %XThe conrotatory and disrotatory mechanisms of the isomerization of bicyclo[1.1.0]butane to trans-buta-1,3-diene have been computationally investigated with the CASSCF, MCQDPT2, (U)B3LYP, CCSD(T), CR-CCSD(T), and CR-CC(2,3) approaches. The coupled-cluster (CC) methods, including the CC approach with singles, doubles, and noniterative triples (CCSD(T)), and its completely renormalized (CR) extensions called CR-CCSD(T) and CR-CC(2,3), and the density functional theory B3LYP approach do an excellent job of correctly predicting the activation barrier for the conrotatory pathway, which corresponds to a weakly biradical transition state (TS), producing values within experimental error bars. In particular, the recently developed CR-CC(2,3) method gives 40.8 or 41.1 kcal/mol, in perfect agreement with the experimental value of 40.6 ± 2.5 kcal/mol. The complete-active-space self-consistent-field (CASSCF) approach and the second-order multireference perturbation theory (MCQDPT2) are less accurate in describing the conrotatory barrier than CR-CC(2,3). The higher energy disrotatory pathway, which has not been characterized experimentally and which involves a strongly biradical TS, poses a great challenge for many methods. CCSD(T) fails, predicting the activation barrier for the disrotatory pathway significantly below the conrotatory barrier, contradicting the experimental result that the conrotatory pathway describes the mechanism. The strongly biradical character of the disrotatory TS, spin contamination, and the proximity of singlet and triplet potential energy surfaces cause difficulties for B3LYP, which does not link this TS with gauche-buta-1,3-diene. No such difficulties occur in the CASSCF calculations, which offer a proper description of the structure of the disrotatory TS that links it with the reactant and product molecules. The CR-CC(2,3) approach, which accurately balances dynamical and nondynamical correlations in systems containing closed-shell and biradical structures, predicts the activation enthalpy for the disrotatory mechanism of 66 kcal/mol. CR-CCSD(T) gives 69 kcal/mol. In agreement with experiment and earlier multireference configuration interaction calculations of Nguyen and Gordon, CR-CCSD(T) and CR-CC(2,3) favor the conrotatory mechanism. The CASSCF, MCQDPT2, and B3LYP methods correctly place the disrotatory barrier above the conrotatory one, but, on the basis of a comparison with the accurate CR-CC(2,3) results, they underestimate the activation energy for the disrotatory pathway. All CC approaches employed in this study produce very good estimates of the enthalpy of isomerization of bicyclo[1.1.0]butane into buta-1,3-diene, the experimental value of which is −25.9 ± 0.4 kcal/mol, giving about −28 kcal/mol, when trans-buta-1,3-diene is used as a product, and −25 kcal/mol, when the nearly isoenergetic gauche-buta-1,3-diene rotamer is used as a product. The CC reaction enthalpies are more accurate than those obtained with CASSCF, MCQDPT2, and B3LYP.

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

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

%B Physical Review C %V 76 %P 11 pages %8 09/2007 %G eng %N 3 %0 Journal Article %J International Journal of Modern Physics B %D 2006 %T Coupled Cluster Theory for Nuclei %A T. Papenbrock %A D. J. Dean %A J. R Gour %A G. Hagen %A M. {Hjorth-Jensen} %A M. Wloch %K Nuclear structure; light nuclei; coupled-cluster theory %XThis presentation focuses on some of the recent developments in low-energy nuclear structure theory, with emphasis on applications of coupled-cluster theory. We report on results for ground and excited states in 4He and 16O, and about extensions of coupled-cluster theory to treat three-body forces.

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

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

%B Physical Review C %V 74 %P 024310 %8 08/2006 %G eng %0 Book %B Condensed Matter Theories %D 2006 %T Coupled-Cluster Theory for Nuclei %B Condensed Matter Theories %I Nova Publishers %V 20 %@ 1-59454-989-3 %G eng %0 Journal Article %J Journal of Chemical Physics A %D 2005 %T Can a Single-Reference Approach Provide a Balanced Description of Ground and Excited States? A Comparison of the Completely Renormalized Equation-of-the-Motion Coupled-Cluster Method with Multi-Reference Quasi-Degenerate Perturbation Theory Near a Conical %A Piotr Piecuch %A S. Nangia %A Truhlar, D.G. %A M. J. {McGuire} %XWe calculated the two lowest electronically adiabatic potential energy surfaces of ammonia in the region of the conical intersection and at a sequence of geometries along which one of the N-H bonds is broken. We employed both a multireference (MR) method and a single-reference (SR) method. The MR calculations are based on multiconfiguration quasidegenerate perturbation theory (MC-QDPT) with a 6-311+G(3df,3pd) basis set. The SR calculations, carried out with the same basis, employ the completely renormalized equation-ofmotion coupled-cluster method with singles and doubles, and a noniterative treatment of triples, denoted CR-EOMCCSD(T). At 91 geometries used for comparison, including geometries near a conical intersection, the surfaces agree to 7% on average.

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

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

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

%B Key Topics in Nuclear Structure, Proceedings of the 8th International Spring Seminar on Nuclear Physics %C Paestum, Italy %8 2005 %G eng %0 Journal Article %J Journal of Physics G: Nuclear and Particle Physics %D 2005 %T Coupled-Cluster Calculations for Ground and Excited States of Closed- and Open-Shell Nuclei Using Methods of Quantum Chemistry %XWe discuss large-scale ab initio calculations of ground and excited states of 16O and preliminary calculations for 15O 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 are able to obtain the virtually converged results for 16O and promising results for 15O and 17O at the level of two-body interactions. The calculated properties other than binding and excitation energies include 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 seven or eight major oscillator shells, for which nontruncated shell-model calculations for nuclei with A = 15–17 active particles are presently not possible.

%B Journal of Physics G: Nuclear and Particle Physics %V 31 %8 7/2005 %G eng %N 8