Equation for the direct determination of the density matrix: Time-dependent density equation and perturbation theory

The density equation proposed previously for the direct determination of the density matrix, i.e. for the wave mechanics without wave, is extended to a time-dependent case. The time-dependent density equation has been shown to be equivalent to the time-dependent Schr?dinger equation so long as the density matrix, included as a self-contained variable, is N-representable. Formally, it is obtainable from the previous time-independent equation by replacing the energy E with . The perturbation theory formulas for the density equation have also been given for both the time-dependent and time-independent cases. Received: 16 June 1998 / Accepted: 2 September 1998 / Published online: 8 February 1999     

Reduced density matrix hybrid approach: an efficient and accurate method for adiabatic and non-adiabatic quantum dynamics

We present a new approach to calculate real-time quantum dynamics in complex systems. The formalism is based on the partitioning of a system's environment into "core" and "reservoir" modes with the former to be treated quantum mechanically and the latter classically. The presented method only requires the calculation of the system's reduced density matrix averaged over the quantum core degrees of freedom which is then coupled to a classically evolved reservoir to treat the remaining modes. We demonstrate our approach by applying it to the spin-boson problem using the noninteracting blip approximation to treat the system and core, and Ehrenfest dynamics to treat the reservoir. The resulting hybrid methodology is accurate for both fast and slow baths, since it naturally reduces to its composite methods in their respective regimes of validity. In addition, our combined method is shown to yield good results in intermediate regimes where neither approximation alone is accurate and to perform equally well for both strong and weak system-bath coupling. Our approach therefore provides an accurate and efficient methodology for calculating quantum dynamics in complex systems.     

Time-dependent density-functional theory/localized density matrix method for dynamic hyperpolarizability

Time-dependent density-functional theory/localized density matrix method (TDDFT/LDM) was developed to calculate the excited state energy, absorption spectrum and dynamic polarizability. In the present work we generalize it to calculate the dynamic hyperpolarizabilities in both time and frequency domains. We show that in the frequency domain the 2n+1 rule can be derived readily and the dynamic hyperpolarizabilities are thus calculated efficiently. Although the time-domain TDDFT/LDM is time consuming, its implementation is straightforward because the evaluation of the derivatives of exchange-correlation potential with respect to electron density is avoided. Moreover, the time-domain method can be used to simulate higher order response which is very difficult to be calculated with the frequency-domain method.     

An efficient linear scaling procedure for constructing localized orbitals of large molecules based on the one-particle density matrix

We have developed a linear-scaling algorithm for obtaining the Boys localized molecular orbitals from the one-particle density matrix. The algorithm is made up of two steps: the Cholesky decomposition of the density matrix to obtain Cholesky molecular orbitals and the subsequent Boys localization process. Linear-scaling algorithms have been proposed to achieve linear-scaling calculations of these two steps, based on the sparse matrix technique and the locality of the Cholesky molecular orbitals. The present algorithm has been applied to compute the Boys localized orbitals in a number of systems including α-helix peptides, water clusters, and protein molecules. Illustrative calculations demonstrate that the computational time of obtaining Boys localized orbitals with the present algorithm is asymptotically linear with increasing the system size.     

Time-dependent density functional theory based upon the fragment molecular orbital method

Time-dependent density functional theory (TDDFT) was combined with the two-body fragment molecular orbital method (FMO2). In this FMO2-TDDFT scheme, the system is divided into fragments, and the electron density for fragments is determined self-consistently. Consequently, only one main fragment of interest and several fragment pairs including it are calculated by TDDFT. To demonstrate the accuracy of FMO2-TDDFT, we computed several low-lying singlet and triplet excited states of solvated phenol and polyalanine using our method and the standard TDDFT for the full system. The BLYP functional with the long-range correction (LC-BLYP) was employed with the 6-31G(*) basis set (some tests were also performed with 6-311G(*), as well as with B3LYP and time-dependent Hartree-Fock). Typically, FMO2-TDDFT reproduced the full TDDFT excitation energies within 0.1 eV, and for one excited state the error was about 0.2 eV. Beside the accurate reproduction of the TDDFT excitation energies, we also automatically get an excitation energy decomposition analysis, which provides the contributions of individual fragments. Finally, the efficiency of our approach was exemplified on the LC-BLYP6-31G(*) calculation of the lowest singlet excitation of the photoactive yellow protein which consists of 1931 atoms, and the obtained value of 3.1 eV is in agreement with the experimental value of 2.8 eV.     

Spin-adapted density matrix renormalization group algorithms for quantum chemistry

We extend the spin-adapted density matrix renormalization group (DMRG) algorithm of McCulloch and Gulacsi [Europhys. Lett. 57, 852 (2002)] to quantum chemical Hamiltonians. This involves using a quasi-density matrix, to ensure that the renormalized DMRG states are eigenfunctions of S?(2), and the Wigner-Eckart theorem, to reduce overall storage and computational costs. We argue that the spin-adapted DMRG algorithm is most advantageous for low spin states. Consequently, we also implement a singlet-embedding strategy due to Tatsuaki [Phys. Rev. E 61, 3199 (2000)] where we target high spin states as a component of a larger fictitious singlet system. Finally, we present an efficient algorithm to calculate one- and two-body reduced density matrices from the spin-adapted wavefunctions. We evaluate our developments with benchmark calculations on transition metal system active space models. These include the Fe(2)S(2), [Fe(2)S(2)(SCH(3))(4)](2-), and Cr(2) systems. In the case of Fe(2)S(2), the spin-ladder spacing is on the microHartree scale, and here we show that we can target such very closely spaced states. In [Fe(2)S(2)(SCH(3))(4)](2-), we calculate particle and spin correlation functions, to examine the role of sulfur bridging orbitals in the electronic structure. In Cr(2) we demonstrate that spin-adaptation with the Wigner-Eckart theorem and using singlet embedding can yield up to an order of magnitude increase in computational efficiency. Overall, these calculations demonstrate the potential of using spin-adaptation to extend the range of DMRG calculations in complex transition metal problems.     

Infinite-order quasirelativistic density functional method based on the exact matrix quasirelativistic theory

The exact one-electron matrix quasirelativistic theory [Kutzelnigg and Liu, J. Chem. Phys. 123, 241102 (2005)] is extended to the effective one-particle Kohn-Sham scheme of density functional theory. Several variants of the resultant theory are discussed. Although they are in principle equivalent, consideration of computational efficiency strongly favors the one (F(+)) in which the effective potential remains untransformed. Further combined with the atomic approximation for the matrix X relating the small and large components of the Dirac spinors as well as a simple ansatz for correcting the two-electron picture change errors, a very elegant, accurate, and efficient infinite-order quasirelativistic approach is obtained, which is far simpler than all existing quasirelativistic theories and must hence be regarded as a breakthrough in relativistic quantum chemistry. In passing, it is also shown that the Dirac-Kohn-Sham scheme can be made as efficient as two-component approaches without compromising the accuracy. To demonstrate the performance of the new methods, atomic calculations on Hg and E117 are first carried out. The spectroscopic constants (bond length, vibrational frequency, and dissociation energy) of E117(2) are then reported. All the results are in excellent agreement with those of the Dirac-Kohn-Sham calculations.     

Time-dependent density functional theory scheme for efficient calculations of dynamic (hyper)polarizabilities

The authors present an efficient perturbative method to obtain both static and dynamic polarizabilities and hyperpolarizabilities of complex electronic systems. This approach is based on the solution of a frequency-dependent Sternheimer equation, within the formalism of time-dependent density functional theory, and allows the calculation of the response both in resonance and out of resonance. Furthermore, the excellent scaling with the number of atoms opens the way to the investigation of response properties of very large molecular systems. To demonstrate the capabilities of this method, they implemented it in a real-space (basis-set-free) code and applied it to benchmark molecules, namely, CO, H2O, and para-nitroaniline. Their results are in agreement with experimental and previous theoretical studies and fully validate their approach.     

An efficient method for the calculation of quantum mechanics/molecular mechanics free energies

The combination of quantum mechanics (QM) with molecular mechanics (MM) offers a route to improved accuracy in the study of biological systems, and there is now significant research effort being spent to develop QM/MM methods that can be applied to the calculation of relative free energies. Currently, the computational expense of the QM part of the calculation means that there is no single method that achieves both efficiency and rigor; either the QM/MM free energy method is rigorous and computationally expensive, or the method introduces efficiency-led assumptions that can lead to errors in the result, or a lack of generality of application. In this paper we demonstrate a combined approach to form a single, efficient, and, in principle, exact QM/MM free energy method. We demonstrate the application of this method by using it to explore the difference in hydration of water and methane. We demonstrate that it is possible to calculate highly converged QM/MM relative free energies at the MP2/aug-cc-pVDZ/OPLS level within just two days of computation, using commodity processors, and show how the method allows consistent, high-quality sampling of complex solvent configurational change, both when perturbing hydrophilic water into hydrophobic methane, and also when moving from a MM Hamiltonian to a QM/MM Hamiltonian. The results demonstrate the validity and power of this methodology, and raise important questions regarding the compatibility of MM and QM/MM forcefields, and offer a potential route to improved compatibility.     

Communication: Partial linearized density matrix dynamics for dissipative, non-adiabatic quantum evolution

An approach for treating dissipative, non-adiabatic quantum dynamics in general model systems at finite temperature based on linearizing the density matrix evolution in the forward-backward path difference for the environment degrees of freedom is presented. We demonstrate that the approach can capture both short time coherent quantum dynamics and long time thermal equilibration in an application to excitation energy transfer in a model photosynthetic light harvesting complex. Results are also presented for some nonadiabatic scattering models which indicate that, even though the method is based on a "mean trajectory" like scheme, it can accurately capture electronic population branching through multiple avoided crossing regions and that the approach offers a robust and reliable way to treat quantum dynamical phenomena in a wide range of condensed phase applications.     

Critical comparison of electrode models in density functional theory based quantum transport calculations

We study the performance of two different electrode models in quantum transport calculations based on density functional theory: parametrized Bethe lattices and quasi-one-dimensional wires or nanowires. A detailed account of implementation details in both the cases is given. From the systematic study of nanocontacts made of representative metallic elements, we can conclude that the parametrized electrode models represent an excellent compromise between computational cost and electronic structure definition as long as the aim is to compare with experiments where the precise atomic structure of the electrodes is not relevant or defined with precision. The results obtained using parametrized Bethe lattices are essentially similar to the ones obtained with quasi-one-dimensional electrodes for large enough cross-sections of these, adding a natural smearing to the transmission curves that mimics the true nature of polycrystalline electrodes. The latter are more demanding from the computational point of view, but present the advantage of expanding the range of applicability of transport calculations to situations where the electrodes have a well-defined atomic structure, as is the case for carbon nanotubes, graphene nanoribbons, or semiconducting nanowires. All the analysis is done with the help of codes developed by the authors which can be found in the quantum transport toolbox ALACANT and are publicly available.     

Time-dependent Fourier grid Hamiltonian method for modelling real-time quantum dynamics: Theoretical models and applications

A local grid method for modelling real-time quantum dynamical events is formulated. The formulation is straightforward for 1-D systems. For more than one dimension, appeal has to be made to mean-field approximation of the appropriate kind. The simplest mean-field model results in time-dependent Hartree-Fourier grid method. The relationship of the proposed method with some other methods available in the literature is examined. A few examples of numerical applications dealing with (i) the dynamics of dissociation and ionization processes in diatoms and atoms respectively and (ii) tunnelling dynamics in the intramolecular H-atom transfer phenomenon are presented.     

An efficient first-order CASSCF method based on the renormalized Fock-operator technique

Summary A new efficient first-order CASSCF method (multiconfiguration SCF (self consistent field) in a complete active space) is described. Its main characteristics are (i) use of the generalized Brillouin theorem (Fock-operator method), (ii) renormalization of single excitations, (iii) fast microiterations containing only two-index transformations, i.e. M ³N² steps. Convergence is generally reached in eight to twelve macroiterations. The method is applied to several examples (LiH, N₂, AlO) and compared to other MCSCF (multiconfiguration SCF) methods.     

Lagrange multiplier based transport theory for quantum wires

We discuss how the Lagrange multiplier method of nonequilibrium steady state statistical mechanics can be applied to describe the electronic transport in a quantum wire. We describe the theoretical scheme using a tight-binding model. The Hamiltonian of the wire is extended via a Lagrange multiplier to "open" the quantum system and to drive current through it. The diagonalization of the extended Hamiltonian yields the transport properties of wire. We show that the Lagrange multiplier method is equivalent to the Landauer approach within the considered model.     

An efficient method for recovery of target ssDNA based on amino-modified silica-coated magnetic nanoparticles

In this paper, an improved recovery method for target ssDNA using amino-modified silica-coated magnetic nanoparticles (ASMNPs) is reported. This method takes advantages of the amino-modified silica-coated magnetic nanoparticles prepared using water-in-oil microemulsion technique, which employs amino-modified silica as the shell and iron oxide as the core of the magnetic nanoparticles. The nanoparticles have a silica surface with amino groups and can be conjugated with any desired bio-molecules through many existing amino group chemistry. In this research, a linear DNA probe was immobilized onto nanoparticles through streptavidin conjugation using covalent bonds. A target ssDNA(I) (5′-TMR-CGCATAGGGCCTCGTGATAC-3′) has been successfully recovered from a crude sample under a magnet field through their special recognition and hybridization. A designed ssDNA fragment of severe acute respiratory syndrome (SARS) virus at a much lower concentration than the target ssDNA(I) was also recovered with high efficiency and good selectivity.     

Reduced density matrix quantum approach for particle trapping and sticking on corrugated moving surfaces

A short time propagation algorithm for the reduced density matrix is derived to model the interaction of a quantum particle with a moving corrugated surface. The algorithm includes dissipative terms, which can be derived directly from the full Hamiltonian. The scattering of He from a corrugated Cu surface is examined as a function of incident energy and angle and the temperature of the substrate, with a focus on the nature of trapping. It is found that corrugation can make a significant contribution to trapping, even on a metal surface. Energy exchange with the phonons is shown to significantly modify the nature of diffraction mediated selective adsorption.     

Local hybrid functionals based on density matrix products

We present a novel similarity metric comparing exact and semilocal density functional theory (DFT) exchange holes in real space. This metric is obtained from the product of the one-particle density matrix and the uniform electron gas model density matrix. The metric is bound between 0 and 1, 1 in the uniform electron gas, 0 in regions asymptotically far from finite systems, and can detect delocalization of the exact exchange hole and effective fractional occupations. We also present a parameter-free local hybrid functional that uses this similarity metric to locally mix exact and semilocal DFT exchange energy densities. The resulting functional gives better thermochemistry and reaction barrier heights than our original local hybrids [Jaramillo et al., J. Chem. Phys. 118, 1068 (2003)], while retaining moderate accuracy for symmetric radical cation dimers.     

Computational method for the quantum Hamilton-Jacobi equation: bound states in one dimension

An accurate computational method for the one-dimensional quantum Hamilton-Jacobi equation is presented. The Mobius propagation scheme, which can accurately pass through singularities, is used to numerically integrate the quantum Hamilton-Jacobi equation for the quantum momentum function. Bound state wave functions are then synthesized from the phase integral using the antithetic cancellation technique. Through this procedure, not only the quantum momentum functions but also the wave functions are accurately obtained. This computational approach is demonstrated through two solvable examples: the harmonic oscillator and the Morse potential. The excellent agreement between the computational and the exact analytical results shows that the method proposed here may be useful for solving similar quantum mechanical problems.