Search PubMed⌕ Search

Biomedical subjects

Robert J Harrison

Publications and source records attributed to Robert J Harrison.

8 recordsLinked to original sources

Complexation of the carbonate, nitrate, and acetate anions with the uranyl dication: density functional studies with relativistic effective core potentials.

The structures and vibrational frequencies of uranyl carbonates, [UO2(CO3)n](2-2n) and [(UO2)3(CO3)6]6-, uranyl nitrates, [UO2(NO3)n](2-n), and uranyl acetates, [UO2(CH3COO)n](2-n) (n = 1,2,3) have been calculated by using local density functional theory (LDFT). Only bidentate ligand coordination modes to the uranyl dication have been modeled. The calculated structures and frequencies are compared to available experimental data, including IR, Raman, X-ray diffraction, and EXAFS solution and crystal structure data. The energetics of ligand binding have been calculated using the B3LYP hybrid functional. In general, the structural and vibrational results at the LDFT level are in good agreement with experimental results and provide realistic pictures of solution phase and solid-state behavior. For the [UO2(CO3)3]6- anion, calculations suggest that complexity in the CO3(2-) stretching signature upon complexation is due to the formation of C=O and C-O domains, the latter of which can split by as much as 300 cm(-1). Assessment of the binding energies indicate that the [UO2(CO3)2]2- anion is more stable than the [UO2(CO3)3]4- anion due to the accumulation of excess charge, whereas the tri-ligand species are the most stable in the nitrate and acetate anions.

Journal Article↗

Persistent activation of select forebrain regions in aggressive, adolescent cocaine-treated hamsters.

Hamsters repeatedly exposed to cocaine throughout adolescence display highly escalated offensive aggression compared to saline-treated littermates. The current study investigated whether adolescent cocaine exposure activated neurons in areas of hamster forebrain implicated in aggressive behavior by examining the expression of FOS, i.e., the protein product of the immediate early gene c-fos shown to be a reliably sensitive marker of neuronal activation. Adolescent cocaine-treated hamsters and saline-treated littermates were scored for offensive aggression and then sacrificed 1 day later and examined for the number of FOS immunoreactive (FOS-ir) cells in regions of the hamster forebrain important for aggression control. When compared with non-aggressive, saline-treated controls, aggressive cocaine-treated hamsters showed persistent increases in the number of FOS-ir cells in several aggression regions, including the anterior hypothalamus, nucleus circularis, lateral hypothalamus (i.e., the hypothalamic attack area), lateral septum, and medial and corticomedial amygdaloid nuclei. Conversely, aggressive cocaine-treated hamsters showed a significant decrease in FOS-ir cells in the medial supraoptic nucleus, bed nucleus of the stria terminalis, and central amygdala when compared with controls. However, no differences in FOS-ir cells were found in other areas implicated in aggression such as the paraventricular hypothalamic nucleus, or in a number of non-aggression areas. These results suggest that adolescent cocaine exposure may constitutively activate neurons in select forebrain areas critical for the regulation of aggression in hamsters. A model for how persistent activation of neurons in one of these brain regions (i.e., the hypothalamus) may facilitate the development of the aggressive phenotype in adolescent cocaine-exposed animals is presented.

Adolescent↗

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↗

Quantitative analysis of electronic properties of carbon nanotubes by scanning probe microscopy: from atomic to mesoscopic length scales.

A new multiscale approach to the quantitative interpretation of scanning probe microscopy data in terms of the local electronic properties of 1D systems such as carbon nanotubes is presented. The interactions between a probe and the system are treated using a combination of first-principles density functional calculations and continuum electrostatics modeling. Realistic tip size effects are included using an image charge model. It is shown that the local potential at a nanotube on a substrate due to a probe can be calculated quantitatively, allowing experimental data to be analyzed in terms of the electronic structure of defects.

Journal Article↗

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↗

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↗

Krylov subspace accelerated inexact Newton method for linear and nonlinear equations.

A Krylov subspace accelerated inexact Newton (KAIN) method for solving linear and nonlinear equations is described, and its relationship to the popular direct inversion in the iterative subspace method [DIIS; Pulay, P., Chem Phys Lett 1980, 393, 73] is analyzed. The two methods are compared with application to simple test equations and the location of the minimum energy crossing point of potential energy surfaces. KAIN is no more complicated to implement than DIIS, but can accommodate a wider variety of preconditioning and performs substantially better with poor preconditioning. With perfect preconditioning, KAIN is shown to be very similar to DIIS. For these reasons, KAIN is recommended as a replacement for DIIS.

Journal Article↗

Promise and challenge of high-performance computing, with examples from molecular modelling.

Computational modelling is one of the most significant developments in the practice of scientific inquiry in the 20th century. During the past decade, advances in computing technologies have increased the speed of computers by a factor of 100; an increase of a factor of 1000 can be expected in the next decade. These advances have, however, come at a price, namely, radical change(s) in computer architecture. Will computational scientists and engineers be able to harness the power offered by these high-performance computers to solve the most critical problems in science and engineering? In this paper, we discuss the challenges that must be addressed if we are to realize the benefits offered by high-performance computing. The task will not be easy; it will require revision or replacement of much of the software developed for vector supercomputers as well as advances in a number of key theoretical areas. Because of the pace of computing advances, these challenges must be met by close collaboration between computational scientists, computer scientists and applied mathematicians. The effectiveness of such a multidisciplinary approach is illustrated in a brief review of NWCHEM, a general-purpose computational chemistry code designed for parallel supercomputers.

Algorithms↗