Biomedical subjects

Tucker Carrington

Publications and source records attributed to Tucker Carrington.

8 recordsLinked to original sources

PubMed2005

Theoretical and experimental studies of the infrared rovibrational spectrum of He2-N2O.

Rovibrational spectra of the He(2)-N(2)O complex in the nu(1) fundamental band of N(2)O (2224 cm(-1)) have been observed using a tunable infrared laser to probe a pulsed supersonic jet expansion, and calculated using five coordinates that specify the positions of the He atoms with respect to the NNO molecule, a product basis, and a Lanczos eigensolver. Vibrational dynamics of the complex are dominated by the torsional motion of the two He atoms on a ring encircling the N(2)O molecule. The resulting torsional states could be readily identified, and they are relatively uncoupled to other He motions up to at least upsilon(t) = 7. Good agreement between experiment and theory was obtained with only one adjustable parameter, the band origin. The calculated results were crucial in assigning many weaker observed transitions because the effective rotational constants depend strongly on the torsional state. The observed spectra had effective temperatures around 0.7 K and involved transitions with J < or =3, with upsilon(t) = 0 and 1, and (with one possible exception) with Deltaupsilon(t)=0. Mixing of the torsion-rotation states is small but significant: some transitions with Deltaupsilon(t) not equal 0 were predicted to have appreciable intensity even assuming that the dipole transition moment coincides perfectly with the NNO axis. One such transition was tentatively assigned in the observed spectra, but confirmation will require further work.

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PubMed2005

Computing resonance energies, widths, and wave functions using a Lanczos method in real arithmetic.

We introduce new ideas for calculating resonance energies and widths. It is shown that a non-Hermitian-Lanczos approach can be used to compute eigenvalues of H+W, where H is the Hamiltonian and W is a complex absorbing potential (CAP), without evaluating complex matrix-vector products. This is done by exploiting the link between a CAP-modified Hamiltonian matrix and a real but nonsymmetric matrix U suggested by Mandelshtam and Neumaier [J. Theor. Comput. Chem. 1, 1 (2002)] and using a coupled-two-term Lanczos procedure. We use approximate resonance eigenvectors obtained from the non-Hermitian-Lanczos algorithm and a very good CAP to obtain very accurate energies and widths without solving eigenvalue problems for many values of the CAP strength parameter and searching for cusps. The method is applied to the resonances of HCO. We compare properties of the method with those of established approaches.

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PubMed2005

How to choose one-dimensional basis functions so that a very efficient multidimensional basis may be extracted from a direct product of the one-dimensional functions: energy levels of coupled systems with as many as 16 coordinates.

In this paper we propose a scheme for choosing basis functions for quantum dynamics calculations. Direct product bases are frequently used. The number of direct product functions required to converge a spectrum, compute a rate constant, etc., is so large that direct product calculations are impossible for molecules or reacting systems with more than four atoms. It is common to extract a smaller working basis from a huge direct product basis by removing some of the product functions. We advocate a build and prune strategy of this type. The one-dimensional (1D) functions from which we build the direct product basis are chosen to satisfy two conditions: (1) they nearly diagonalize the full Hamiltonian matrix; (2) they minimize off-diagonal matrix elements that couple basis functions with diagonal elements close to those of the energy levels we wish to compute. By imposing these conditions we increase the number of product functions that can be removed from the multidimensional basis without degrading the accuracy of computed energy levels. Two basic types of 1D basis functions are in common use: eigenfunctions of 1D Hamiltonians and discrete variable representation (DVR) functions. Both have advantages and disadvantages. The 1D functions we propose are intermediate between the 1D eigenfunction functions and the DVR functions. If the coupling is very weak, they are very nearly 1D eigenfunction functions. As the strength of the coupling is increased they resemble more closely DVR functions. We assess the usefulness of our basis by applying it to model 6D, 8D, and 16D Hamiltonians with various coupling strengths. We find approximately linear scaling.

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PubMed2005

Calculating intensities using effective Hamiltonians in terms of Coriolis-adapted normal modes.

The calculation of rovibrational transition energies and intensities is often hampered by the fact that vibrational states are strongly coupled by Coriolis terms. Because it invalidates the use of perturbation theory for the purpose of decoupling these states, the coupling makes it difficult to analyze spectra and to extract information from them. One either ignores the problem and hopes that the effect of the coupling is minimal or one is forced to diagonalize effective rovibrational matrices (rather than diagonalizing effective rotational matrices). In this paper we apply a procedure, based on a quantum mechanical canonical transformation for deriving decoupled effective rotational Hamiltonians. In previous papers we have used this technique to compute energy levels. In this paper we show that it can also be applied to determine intensities. The ideas are applied to the ethylene molecule.

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PubMed2004

Using preconditioned adaptive step size Runge-Kutta methods for solving the time-dependent Schrödinger equation.

If the Hamiltonian is time dependent it is common to solve the time-dependent Schrödinger equation by dividing the propagation interval into slices and using an (e.g., split operator, Chebyshev, Lanczos) approximate matrix exponential within each slice. We show that a preconditioned adaptive step size Runge-Kutta method can be much more efficient. For a chirped laser pulse designed to favor the dissociation of HF the preconditioned adaptive step size Runge-Kutta method is about an order of magnitude more efficient than the time sliced method.

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PubMed2004

Contracted basis Lanczos methods for computing numerically exact rovibrational levels of methane.

We present a numerically exact calculation of rovibrational levels of a five-atom molecule. Two contracted basis Lanczos strategies are proposed. The first and preferred strategy is a two-stage contraction. Products of eigenfunctions of a four-dimensional (4D) stretch problem and eigenfunctions of 5D bend-rotation problems, one for each K, are used as basis functions for computing eigenfunctions and eigenvalues (for each K) of the Hamiltonian without the Coriolis coupling term, denoted H0. Finally, energy levels of the full Hamiltonian are calculated in a basis of the eigenfunctions of H0. The second strategy is a one-stage contraction in which energy levels of the full Hamiltonian are computed in the product contracted basis (without first computing eigenfunctions of H0). The two-stage contraction strategy, albeit more complicated, has the crucial advantage that it is trivial to parallelize the calculation so that the CPU and memory costs are independent of J. For the one-stage contraction strategy the CPU and memory costs of the difficult part of the calculation scale linearly with J. We use the polar coordinates associated with orthogonal Radau vectors and spherical harmonic type rovibrational basis functions. A parity-adapted rovibrational basis suitable for a five-atom molecule is proposed and employed to obtain bend-rotation eigenfunctions in the first step of both contraction methods. The effectiveness of the two methods is demonstrated by calculating a large number of converged J = 1 rovibrational levels of methane using a global potential energy surface.

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PubMed2004

A multidimensional discrete variable representation basis obtained by simultaneous diagonalization.

Direct product basis functions are frequently used in quantum dynamics calculations, but they are poor in the sense that many such functions are required to converge a spectrum, compute a rate constant, etc. Much better, contracted, basis functions, that account for coupling between coordinates, can be obtained by diagonalizing reduced dimension Hamiltonians. If a direct product basis is used, it is advantageous to use discrete variable representation (DVR) basis functions because matrix representations of functions of coordinates are diagonal in the DVR. By diagonalizing matrices representing coordinates it is straightforward to obtain the DVR that corresponds to any direct product basis. Because contracted basis functions are eigenfunctions of reduced dimension Hamiltonians that include coupling terms they are not direct product functions. The advantages of contracted basis functions and the advantages of the DVR therefore appear to be mutually exclusive. A DVR that corresponds to contracted functions is unknown. In this paper we propose such a DVR. It spans the same space as a contracted basis, but in it matrix representations of coordinates are diagonal. The DVR basis functions are chosen to achieve maximal diagonality of coordinate matrices. We assess the accuracy of this DVR by applying it to model four-dimensional problems.

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PubMed2002

Comment on "Spectral filters in quantum mechanics: a measurement theory perspective".

We criticize a paper by Vijay and Wyatt [Phys. Rev. E 63, 4351 (2000)], in which the authors suggest that energy levels computed, from the same set of matrix-vector products, with the filter diagonalization method (FDM) and the Fourier spectral analysis using the same Chebyshev correlation function are of comparable accuracy. We explain why the FDM is superior and demonstrate it numerically, using the same test matrix as that employed in the above paper. We also compare the FDM with the Lanczos method, another commonly used iterative technique for computing eigenvalues. We find that eigenvalues in a low-density region near the middle of the spectrum converge more quickly with the FDM, but that the Lanczos method requires fewer matrix-vector products to converge all the eigenvalues.

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