Biomedical subjects

Karol Kowalski

Publications and source records attributed to Karol Kowalski.

11 recordsLinked to original sources

PubMed2006

Asymptotic extrapolation scheme for large-scale calculations with hybrid coupled cluster and molecular dynamics simulations.

In this paper we discuss a simple extrapolation scheme based on the asymptotic behavior of the electronic energies considered as functions of cutoff factor for orbital energies corresponding to virtual orbitals. The performance of this approach is illustrated in the context of large-scale dynamic simulations for excitation energies of the cytosine molecule in its native DNA environment. We demonstrate that the extrapolation errors are significantly smaller than the excitation-energy fluctuations, due to the fluctuating environment.

Journal Article↗

PubMed2006

Hybrid coupled cluster and molecular dynamics approach: application to the excitation spectrum of cytosine in the native DNA environment.

Evolution of the excited state energies of cytosine base in the native DNA environment was investigated using a hybrid coupled cluster and classical molecular dynamics approach. The time averaged excitation energies obtained with the variant of the completely renormalized equation-of-motion with singles, doubles, and non-iterative triples approach that includes a bulk of the correlation effects for excited states, are compared with the analogous calculations in the gas phase. Significant blue shifts for the two lowest singlet excitation energies can be observed as a result of the interaction of the quantum system with the surrounding environment.

Cluster Analysis↗

PubMed2006

Excitation energies through the locally renormalized equation-of-motion formalism: singles and doubles model.

The stationary conditions obtained from approximate coupled-cluster functional derived from the numerator-denominator connected expansion (NDC) [K. Kowalski and P. Piecuch, J. Chem. Phys. 122, 074107 (2005)] are employed to calculate the linear response of cluster amplitudes. A simple scheme that involves singly and doubly excited amplitudes, termed locally renormalized equation-of-motion approach with singles and doubles (LR-EOMCCSD), is compared with other excited-state methods that include up to two-body operators in the wave function expansion. In particular, the impact of the local denominators on the excitation energies is discussed in detail. Several benchmark calculations on the CH(+), C(2), N(2), O(3), and ClOCl molecules are presented to illustrate the performance of the LR-EOMCCSD approach.

Journal Article↗

PubMed2005

Active-space coupled-cluster study of electronic states of Be3.

The active-space coupled-cluster (CC) and equation-of-motion (EOM) CC methods with all single and double excitations with triple excitations defined via active orbitals (CCSDt, EOMCCSDt), as implemented with TENSOR CONTRACTION ENGINE, are applied to the challenging Be3 system, which is characterized by a large number of low-lying excited states dominated by two-electron transitions and significant high-order correlation effects in the ground electronic state. It is demonstrated that the CCSDt and EOMCCSDt methods provide an excellent description of complicated electronic quasidegeneracies present in the Be3 cluster. Different strategies for defining triple excitations within the CCSDtEOMCCSDt approach are discussed.

Journal Article↗

PubMed2005

Implementation of the locally renormalized CCSD(T) approaches for arbitrary reference function.

Several new variants of the locally-renormalized coupled-cluster (CC) approaches that account for the effect of triples (LR-CCSD(T)) have been formulated and implemented for arbitrary reference states using the TENSOR CONTRACTION ENGINE functionality, enabling the automatic generation of an efficient parallel code. Deeply rooted in the recently derived numerator-denominator-connected (NDC) expansion for the ground-state energy [K. Kowalski and P. Piecuch, J. Chem. Phys. 122, 074107 (2005)], LR-CCSD(T) approximations use, in analogy to the completely renormalized CCSD(T) (CR-CCSD(T)) approach, the three-body moments in constructing the noniterative corrections to the energies obtained in CC calculations with singles and doubles (CCSD). In contrast to the CR-CCSD(T) method, the LR-CCSD(T) approaches discussed in this paper employ local denominators, which assure the additive separability of the energies in the noninteracting system limit when the localized occupied spin-orbitals are employed in the CCSD and LR-CCSD(T) calculations. As clearly demonstrated on several challenging examples, including breaking the bonds of the F2, N2, and CN molecules, the LR-CCSD(T) approaches are capable of providing a highly accurate description of the entire potential-energy surface (PES), while maintaining the characteristic N(7) scaling of the ubiquitous CCSD(T) approach. Moreover, as illustrated numerically for the ozone molecule, the LR-CCSD(T) approaches yield highly competitive values for a number of equilibrium properties including bond lengths, angles, and harmonic frequencies.

Journal Article↗

PubMed2005

Extension of renormalized coupled-cluster methods including triple excitations to excited electronic states of open-shell molecules.

The general-purpose open-shell implementation of the completely renormalized equation-of-motion coupled-cluster approach with singles, doubles, and noniterative triples [CR-EOMCCSD(T)] is reported. Benchmark calculations for the low-lying doublet and quartet states of the CH radical show that the CR-EOMCCSD(T) method is capable of providing a highly accurate description of ground and excited states of open-shell molecules. This includes states with strong double excitation character, for which the conventional EOMCCSD approach fails.

Journal Article↗

PubMed2005

Comparison of low-order multireference many-body perturbation theories.

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.

Journal Article↗

PubMed2005

Extensive generalization of renormalized coupled-cluster methods.

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

Journal Article↗

PubMed2005

Where does the planar-to-nonplanar turnover occur in small gold clusters?

Several levels of theory, including both Gaussian-based and plane wave density functional theory (DFT), second-order perturbation theory (MP2), and coupled cluster methods (CCSD(T)), are employed to study Au6 and Au8 clusters. All methods predict that the lowest energy isomer of Au6 is planar. For Au8, both DFT methods predict that the two lowest isomers are planar. In contrast, both MP2 and CCSD(T) predict the lowest Au8 isomers to be nonplanar.

Journal Article↗

PubMed2004

New coupled-cluster methods with singles, doubles, and noniterative triples for high accuracy calculations of excited electronic states.

The single-reference ab initio methods for high accuracy calculations of potential energy surfaces (PESs) of excited electronic states, termed the completely renormalized equation-of-motion coupled-cluster approaches with singles, doubles, and noniterative triples [CR-EOMCCSD(T)], are developed. In the CR-EOMCCSD(T) methods, which are based on the formalism of the method of moments of coupled-cluster equations, the suitably designed corrections due to triple excitations are added, in a state-selective manner, to the excited-state energies obtained in the standard equation-of-motion coupled-cluster calculations with singles and doubles (EOMCCSD). It is demonstrated that the CR-EOMCCSD(T) approaches, which can be regarded as the excited-state analogs of the ground-state CR-CCSD(T) theory, provide a highly accurate description of excited states dominated by double excitations, excited states displaying a manifestly multireference character, and PESs of excited states along bond breaking coordinates with the ease of the ground-state CCSD(T) or CR-CCSD(T) calculations. The performance of the CR-EOMCCSD(T) methods is illustrated by the results of calculations for the excited states of CH+, HF, N2, C2, and ozone.

Journal Article↗

PubMed2003

Exactness of two-body cluster expansions in many-body quantum theory.

The Horn-Weinstein formula and the variational principle, combined with numerical results for a few many-electron systems, are used to provide support for a conjecture that the exact ground-state wave function for a Hamiltonian system containing up to two-body terms may be represented by an exponential cluster expansion employing a finite two-body operator.

Journal Article↗