Biomedical subjects

Takeshi Yanai

Publications and source records attributed to Takeshi Yanai.

7 recordsLinked to original sources

PubMed2004

Multiresolution quantum chemistry: basic theory and initial applications.

We describe a multiresolution solver for the all-electron local density approximation Kohn-Sham equations for general polyatomic molecules. The resulting solutions are obtained to a user-specified precision and the computational cost of applying all operators scales linearly with the number of parameters. The construction and use of separated forms for operators (here, the Green's functions for the Poisson and bound-state Helmholtz equations) enable practical computation in three and higher dimensions. Initial applications include the alkali-earth atoms down to strontium and the water and benzene molecules.

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PubMed2004

Multiresolution quantum chemistry in multiwavelet bases: Hartree-Fock exchange.

In a previous study we reported an efficient, accurate multiresolution solver for the Kohn-Sham self-consisitent field (KS-SCF) method for general polyatomic molecules. This study presents an efficient numerical algorithm to evalute Hartree-Fock (HF) exchange in the multiresolution SCF method to solve the HF equations. The algorithm employs fast integral convolution with the Poission kernel in the nonstandard form, screening the sparse multiwavelet representation to compute results of the integral operator only where required by the nonlocal exchange operator. Localized molecular obitals are used to attain near linear scaling. Results for atoms and molecules demonstrate reliable precision and speed. Calculations for small water clusters demonstrate a total cost to compute the HF exchange potential for all n(occ) occpuied MOs scaling as O(n(occ) (1.5)).

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PubMed2004

Multiresolution quantum chemistry in multiwavelet bases: Analytic derivatives for Hartree-Fock and density functional theory.

An efficient and accurate analytic gradient method is presented for Hartree-Fock and density functional calculations using multiresolution analysis in multiwavelet bases. The derivative is efficiently computed as an inner product between compressed forms of the density and the differentiated nuclear potential through the Hellmann-Feynman theorem. A smoothed nuclear potential is directly differentiated, and the smoothing parameter required for a given accuracy is empirically determined from calculations on six homonuclear diatomic molecules. The derivatives of N2 molecule are shown using multiresolution calculation for various accuracies with comparison to correlation consistent Gaussian-type basis sets. The optimized geometries of several molecules are presented using Hartree-Fock and density functional theory. A highly precise Hartree-Fock optimization for the H2O molecule produced six digits for the geometric parameters.

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PubMed2004

A long-range-corrected time-dependent density functional theory.

We apply the long-range correction (LC) scheme for exchange functionals of density functional theory to time-dependent density functional theory (TDDFT) and examine its efficiency in dealing with the serious problems of TDDFT, i.e., the underestimations of Rydberg excitation energies, oscillator strengths, and charge-transfer excitation energies. By calculating vertical excitation energies of typical molecules, it was found that LC-TDDFT gives accurate excitation energies, within an error of 0.5 eV, and reasonable oscillator strengths, while TDDFT employing a pure functional provides 1.5 eV lower excitation energies and two orders of magnitude lower oscillator strengths for the Rydberg excitations. It was also found that LC-TDDFT clearly reproduces the correct asymptotic behavior of the charge-transfer excitation energy of ethylene-tetrafluoroethylene dimer for the long intramolecular distance, unlike a conventional far-nucleus asymptotic correction scheme. It is, therefore, presumed that poor TDDFT results for pure functionals may be due to their lack of a long-range orbital-orbital interaction.

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PubMed2004

Third-order Douglas-Kroll relativistic coupled-cluster theory through connected single, double, triple, and quadruple substitutions: applications to diatomic and triatomic hydrides.

Coupled-cluster methods including through and up to the connected single, double, triple, and quadruple substitutions have been derived and implemented automatically for sequential and parallel executions by an algebraic and symbolic manipulation program TCE (TENSOR CONTRACTION ENGINE) for use in conjunction with a one-component third-order Douglas-Kroll approximation for relativistic corrections. A combination of the converging electron-correlation methods, the accurate relativistic reference wave functions, and the use of systematic basis sets tailored to the relativistic approximation has been shown to predict the experimental singlet-triplet separations within 0.02 eV (0.5 kcal/mol) for five triatomic hydrides (CH2, NH2+, SiH2, PH2+, and AsH2+), the experimental bond lengths (re or r0) within 0.002 angstroms, rotational constants (Be or B0) within 0.02 cm(-1), vibration-rotation constants (alphae) within 0.01 cm(-1), centrifugal distortion constants (De) within 2%, harmonic vibration frequencies (omegae) within 8 cm(-1) (0.4%), anharmonic vibrational constants (xomegae) within 2 cm(-1), and dissociation energies (D0(0)) within 0.02 eV (0.4 kcal/mol) for twenty diatomic hydrides (BH, CH, NH, OH, FH, AlH, SiH, PH, SH, ClH, GaH, GeH, AsH, SeH, BrH, InH, SnH, SbH, TeH, and IH) containing main-group elements across the second through fifth rows of the periodic table. In these calculations, spin-orbit effects on dissociation energies, which were assumed to be additive, were estimated from the measured spin-orbit coupling constants of atoms and diatomic molecules, and an electronic energy in the complete-basis-set, complete-electron-correlation limit has been extrapolated in two ways to verify the robustness of the results: One assuming Gaussian-exponential dependence of total energies on double through quadruple zeta basis sets and the other assuming n(-3) dependence of correlation energies on double through quintuple zeta basis sets.

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PubMed2002

Relativistic electronic structure theory.

The theoretical and technical foundations are presented for the efficient relativistic electronic structure theories to treat heavy-atomic molecular systems. This review contains two surveys of four-component and two-component quasi-relativistic approaches. First, we review our highly efficient computational scheme for four-component relativistic ab initio molecular orbital (MO) methods over generally contracted spherical harmonic Gaussian-type spinors (GTSs). Illustrative calculations, which are performed with a new four-component relativistic ab initio molecular orbital program package REL4D, clearly show the efficiency of our computational scheme by the Dirac-Hartree-Fock (DHF) and Dirac-Hartree-Fock (DKS) methods. Next, in the two-component quasi-relativistic framework, two relativistic Hamiltonians, RESC and higher order Douglas-Kroll (DK) Hamiltonians, are introduced, and several illustrative calculations are shown. Numerical results for several systems show that good accuracy can be obtained with our third-order DK (DK3) Hamiltonian.

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PubMed2002

Identification of a BMP-responsive element in Id1, the gene for inhibition of myogenesis.

BACKGROUND: Bone morphogenetic protein-2 (BMP-2) stimulates osteoblast differentiation, but inhibits myogenic differentiation in C2C12 myoblasts. BMP-2 induces transcription of Id1, an inhibitor for myogenesis, within 1 h in the cells. To examine the molecular mechanism of the action of BMP-2, we analysed a BMP-2-responsive element (BRE) in the 5' flanking region of the human Id1 gene. RESULTS: A GC-rich region between -985 bp and -957 bp of the human Id1 gene was identified as a BRE. The BRE containing promoter activity was stimulated by BMP-2 or by constitutively active BMP receptors (BMPR-IA and BMPR-IB). The stimulation was blocked by co-transfecting with dominant negative BMPR-IA or Smad7. A unique DNA-protein complex was induced in response to BMP-2 on the BRE. The complex induced by BMP-2 contained Smad1 and Smad4, possibly as a complex of both Smads. BMP-2 failed to stimulate the expression of Id1 mRNA in Smad4-deficient cells. Over-expression of Smad4, but not Smad1, stimulated the Id1 reporter activity and the expression of endogenous Id1 mRNA in Smad4-deficient cells. CONCLUSION: Signalling of BMP-2 to stimulate the expression of Id1 would be transduced by BMPR-IA and mediated by Smad1 and Smad4, both of which form a complex on the 29 bp GC-rich element.

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