Biomedical subjects

Gregory Beylkin

Publications and source records attributed to Gregory Beylkin.

5 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.

Journal Article↗

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)).

Journal Article↗

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.

Journal Article↗

PubMed2002

Numerical operator calculus in higher dimensions.

When an algorithm in dimension one is extended to dimension d, in nearly every case its computational cost is taken to the power d. This fundamental difficulty is the single greatest impediment to solving many important problems and has been dubbed the curse of dimensionality. For numerical analysis in dimension d, we propose to use a representation for vectors and matrices that generalizes separation of variables while allowing controlled accuracy. Basic linear algebra operations can be performed in this representation using one-dimensional operations, thus bypassing the exponential scaling with respect to the dimension. Although not all operators and algorithms may be compatible with this representation, we believe that many of the most important ones are. We prove that the multiparticle Schrödinger operator, as well as the inverse Laplacian, can be represented very efficiently in this form. We give numerical evidence to support the conjecture that eigenfunctions inherit this property by computing the ground-state eigenfunction for a simplified Schrödinger operator with 30 particles. We conjecture and provide numerical evidence that functions of operators inherit this property, in which case numerical operator calculus in higher dimensions becomes feasible.

Journal Article↗

PubMedDate not supplied

A fast reconstruction algorithm for electron microscope tomography.

We have implemented a Fast Fourier Summation algorithm for tomographic reconstruction of three-dimensional biological data sets obtained via transmission electron microscopy. We designed the fast algorithm to reproduce results obtained by the direct summation algorithm (also known as filtered or R-weighted backprojection). For two-dimensional images, the new algorithm scales as O(N(theta)M log M)+O(MN log N) operations, where N(theta) is the number of projection angles and M x N is the size of the reconstructed image. Three-dimensional reconstructions are constructed from sequences of two-dimensional reconstructions. We demonstrate the algorithm on real data sets. For typical sizes of data sets, the new algorithm is 1.5-2.5 times faster than using direct summation in the space domain. The speed advantage is even greater as the size of the data sets grows. The new algorithm allows us to use higher order spline interpolation of the data without additional computational cost. The algorithm has been incorporated into a commonly used package for tomographic reconstruction.

Algorithms↗