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PubMed2004

Higher order and infinite Trotter-number extrapolations in path integral Monte Carlo.

Improvements beyond the primitive approximation in the path integral Monte Carlo method are explored both in a model problem and in real systems. Two different strategies are studied: The Richardson extrapolation on top of the path integral Monte Carlo data and the Takahashi-Imada action. The Richardson extrapolation, mainly combined with the primitive action, always reduces the number-of-beads dependence, helps in determining the approach to the dominant power law behavior, and all without additional computational cost. The Takahashi-Imada action has been tested in two hard-core interacting quantum liquids at low temperature. The results obtained show that the fourth-order behavior near the asymptote is conserved, and that the use of this improved action reduces the computing time with respect to the primitive approximation.

Journal Article↗
PubMed1998

Design principles and applications of a cooled CCD camera for electron microscopy.

Cooled CCD cameras offer a number of advantages in recording electron microscope images with CCDs rather than film which include: immediate availability of the image in a digital format suitable for further computer processing, high dynamic range, excellent linearity and a high detective quantum efficiency for recording electrons. In one important respect however, film has superior properties: the spatial resolution of CCD detectors tested so far (in terms of point spread function or modulation transfer function) are inferior to film and a great deal of our effort has been spent in designing detectors with improved spatial resolution. Various instrumental contributions to spatial resolution have been analysed and in this paper we discuss the contribution of the phosphor-fibre optics system in this measurement. We have evaluated the performance of a number of detector components and parameters, e.g. different phosphors (and a scintillator), optical coupling with lens or fibre optics with various demagnification factors, to improve the detector performance. The camera described in this paper, which is based on this analysis, uses a tapered fibre optics coupling between the phosphor and the CCD and is installed on a Philips CM12 electron microscope equipped to perform cryo-microscopy. The main use of the camera so far has been in recording electron diffraction patterns from two dimensional crystals of bacteriorhodopsin--from wild type and from different trapped states during the photocycle. As one example of the type of data obtained with the CCD camera a two dimensional Fourier projection map from the trapped O-state is also included. With faster computers, it will soon be possible to undertake this type of work on an on-line basis. Also, with improvements in detector size and resolution, CCD detectors, already ideal for diffraction, will be able to compete with film in the recording of high resolution images.

Fiber Optic Technology↗
PubMed2005

Two-electron integrations in the quantum theory of atoms in molecules with correlated wave functions.

A recent method proposed to compute two-electron integrals over arbitrary regions of space [Martin Pendas, A. et al., J Chem Phys 2004, 120, 4581] is extended to deal with correlated wave functions. To that end, we use a monadic factorization of the second-order reduced density matrix originally proposed by E. R. Davidson [Chem Phys Lett 1995, 246, 209] that achieves a full separation of the interelectronic components into one-electron terms. The final computational effort is equivalent to that found in the integration of a one determinant wave function with as many orbitals as occupied functions in the correlated expansion. Similar strategies to extract the exchange and self-interaction contributions from the two-electron repulsion are also discussed, and several numerical results obtained in a few test systems are summarized.

Journal Article↗
PubMed2004

Computer simulation of solid and liquid benzene with an atomistic interaction potential derived from ab initio calculations.

Molecular dynamics atomistic simulations of solid and liquid benzene have been performed, employing a model intermolecular potential derived from quantum mechanical calculations. The ab initio database includes approximately 200 geometries of the benzene dimer with interaction energies computed at the MP2 level of theory. The accuracy of the modeled force field results is satisfactory. The thermodynamic and structural properties, calculated in the condensed phases, are compared with experimental data and previous simulation results. Single particle and collective dynamical properties are also investigated through the calculation of translational and rotational diffusion coefficients, reorientational dynamics, and viscosities. The agreement of these data with experimental measurements confirms the reliability of the proposed force field.

Journal Article↗
PubMed2005

Molecular structure of magnesium dibromide: an electron diffraction and quantum chemical study.

The molecular structure of magnesium dibromide was investigated by high-level computational techniques and gas-phase electron diffraction. The vapor consisted of about 88% monomeric and 12% dimeric species at the electron diffraction experimental conditions at 1065 K. The geometrical parameters and vibrational characteristics of monomeric, dimeric, and trimeric magnesium dibromide species were determined by computations. Very high level computations with extended basis sets and relativistic pseudopotentials on bromine were needed to reach an agreement between computed and estimated experimental equilibrium geometries for the monomer. For both the dimer and the trimer, different geometrical arrangements were tested. Their ground-state structures have halogen bridges with four-membered ring geometries and D2h and D2d symmetry, respectively. Thermodynamic parameters have also been calculated.

Journal Article↗
PubMed2004

The determinants of carboxyl pKa values in turkey ovomucoid third domain.

A computational methodology for protein pK(a) predictions, based on ab initio quantum mechanical treatment of part of the protein and linear Poisson-Boltzmann equation treatment of the bulk solvent, is presented. The method is used to predict and interpret the pK(a) values of the five carboxyl residues (Asp7, Glu10, Glu19, Asp27, and Glu43) in the serine protease inhibitor turkey ovomucoid third domain. All the predicted pK(a) values are within 0.5 pH units of experiment, with a root-mean-square deviation of 0.31 pH units. We show that the decreased pK(a) values observed for some of the residues are primarily due to hydrogen bonds to the carboxyl oxygens. Hydrogen bonds involving amide protons are shown to be particularly important, and the effect of hydrogen bonding is shown to be nonadditive. Hydrophobic effects are also shown to be important in raising the pK(a). Interactions with charged residues are shown to have relatively little effect on the carboxyl pK(a) values in this protein, in general agreement with experiment.

Animals↗
PubMed2006

Wet electron microscopy with quantum dots.

Wet electron microscopy (EM) is a new imaging method with the potential to allow higher spatial resolution of samples. In contrast to most EM methods, it requires little time to perform and does not require complicated equipment or difficult steps. We used this method on a common murine macrophage cell line, IC-21, in combination with various stains and preparations, to collect high resolution images of the actin cytoskeleton. Most importantly, we demonstrated the use of quantum dots in conjunction with this technique to perform light/electron correlation microscopy. We found that wet EM is a useful tool that fits into a niche between the simplicity of light microscopy and the high spatial resolution of EM.

Actins↗
PubMed2004

Combined Monte Carlo and quantum mechanics study of the hydration of the guanine-cytosine base pair.

We present a computer simulation study of the hydration of the guanine-cytosine (GC) hydrogen-bonded complex. Using first principles density-functional theory, with gradient-corrected exchange-correlation and Monte Carlo simulation, we include thermal contribution, structural effects, solvent polarization, and the water-water and water-GC hydrogen bond interaction to show that the GC interaction in an aqueous environment is weakened to about 70% of the value obtained for an isolated complex. We also analyze in detail the preferred hydration sites of the GC pair and show that on the average it makes around five hydrogen bonds with water.

Base Composition↗
PubMed1996

Neural networks as a tool for compact representation of ab initio molecular potential energy surfaces.

Ab initio quantum chemical calculations of molecular properties such as, e.g., torsional potential energies, require massive computational effort even for moderately sized molecules, if basis sets with a reasonable quality are employed. Using ab initio data on conformational properties of the cofactor (6R,1'R,2'S)-5,6,7,8-tetrahydrobiopterin, we demonstrate that error backpropagation networks can be established that efficiently approximate complicated functional relationships such as torsional potential energy surfaces of a flexible molecule. Our pilot simulations suggest that properly trained neural networks might provide an extremely compact storage medium for quantum chemically obtained information. Moreover, they are outstandingly comfortable tools when it comes to making use of the stored information. One possible application is demonstrated, namely, computation of relaxed torsional energy surfaces.

Biopterins↗
PubMed2005

Nondispersive two-electron wave packets in a helium atom.

We demonstrate the existence of stable nondispersing two-electron wave packets in the helium atom in combined magnetic and circularly polarized microwave fields. These packets follow circular orbits and we show that they can also exist in quantum dots. Classically the two electrons follow trajectories which resemble orbits discovered by Langmuir and which were used in attempts at a Bohr-like quantization of the helium atom. Eigenvalues of a generalized Hessian matrix are computed to investigate the classical stability of these states. Diffusion Monte Carlo simulations demonstrate the quantum stability of these two-electron wave packets in the helium atom and quantum-dot helium with an impurity center.

Journal Article↗
PubMed2004

Classical, semiclassical, and quantum investigations of the four-sphere scattering system.

A genuinely three-dimensional system, viz. the hyperbolic four-sphere scattering system, is investigated with classical, semiclassical, and quantum mechanical methods at various center-to-center separations of the spheres. The efficiency and scaling properties of the computations are discussed by comparisons to the two-dimensional three-disk system. While in systems with few degrees of freedom modern quantum calculations are, in general, numerically more efficient than semiclassical methods, this situation can be reversed with increasing dimension of the problem. For the four-sphere system with large separations between the spheres, we demonstrate the superiority of semiclassical versus quantum calculations, i.e., semiclassical resonances can easily be obtained even in energy regions which are unattainable with the currently available quantum techniques. The four-sphere system with touching spheres is a challenging problem for both quantum and semiclassical techniques. Here, semiclassical resonances are obtained via harmonic inversion of a cross-correlated periodic orbit signal.

Journal Article↗
PubMed1991

Medical informatics--an Australian perspective.

Computers, like the X-ray and stethoscope can be seen as clinical tools, that provide physicians with improved expertise in solving patient management problems. As tools they enable us to extend our clinical information base, and they also provide facilities that improve the delivery of the health care we provide. Automation (computerisation) in the health domain will cause the computer to become a more integral part of health care management and delivery before the start of the next century. To understand how the computer assists those who deliver and manage health care, it is important to be aware of its functional capabilities and how we can use them in medical practice. The rapid technological advances in computers over the last two decades has had both beneficial and counterproductive effects on the implementation of effective computer applications in the delivery of health care. For example, in the 1990s the computer hobbyist is able to make an investment of less than $10,000 on computer hardware that will match or exceed the technological capacities of machines of the 1960s. These rapid technological advances, which have produced a quantum leap in our ability to store and process information, have tended to make us overlook the need for effective computer programmes which will meet the needs of patient care. As the 1990s begin, those delivering health care (eg, physicians, nurses, pharmacists, administrators ...) need to become more involved in directing the effective implementation of computer applications that will provide the tools for improved information management, knowledge processing, and ultimately better patient care.

Australia↗
PubMed1993

13C n.m.r. isotopomer and computer-simulation studies of the non-oxidative pentose phosphate pathway of human erythrocytes.

13C double-quantum filtered correlation spectroscopy (DQF-COSY) provides a novel method for the detection of reactions involving carbon-bond scissions. We report the use of this technique to investigate isotopic exchange reactions of the non-oxidative pentose phosphate pathway in human erythrocytes. These exchange reactions resulted in the formation of a range of isotopic isomers (isotopomers) of glucose 6-phosphate after incubation of a mixture of universally 13C-labelled and unlabelled glucose 6-phosphate with fructose 1,6-bisphosphate and haemolysates. These isotopomers were detected in the coupling patterns of cross-peaks within the DQF-COSY spectrum of the deproteinized sample. A computer model which fully describes the reactions of the non-oxidative pentose phosphate pathway in human erythrocytes has previously been constructed and tested with 31P n.m.r. time-course data in our laboratory. This model was refined using 13C n.m.r. time-course data and extended to include the range of isotopomers which may be formed experimentally by the reactions of the non-oxidative pentose phosphate pathway. The isotopomer ratios obtained experimentally from the DQF-COSY spectrum were consistent with simulations generated by this model.

Carbon Isotopes↗
PubMed2003

Modelling inorganic solids and their interfaces: a combined approach of atomistic and electronic structure simulation techniques.

We are seeking to combine the reliability of the structures and energies obtained from quantum mechanical methods with the insights given by larger scale simulations, which are better able to search configurational space. We will discuss our recent work using quantum mechanical methods, based on DFT, which have been applied to the study of a number of solids. Al2O3, CeO2, MnO2 and CaCO3, and compare these with results using atomistic simulation where the forces between atoms are modelled using interatomic potentials. The results show that such quantum methods can be used successfully to screen the different potential models and where necessary, provide sufficient data to allow us to re-consider the potential models. In addition, we show examples where the quantum based methods can give further insights into the reactivity, particularly of surfaces. However, it still remains computationally expensive to search all possible configurations and by using the atomistic simulations to search through different configurations we can identify new structures which can be verified with the quantum based simulations.

Journal Article↗
PubMed2004

Spectral implementation of some quantum algorithms by one- and two-dimensional nuclear magnetic resonance.

Quantum information processing has been effectively demonstrated on a small number of qubits by nuclear magnetic resonance. An important subroutine in any computing is the readout of the output. "Spectral implementation" originally suggested by Z. L. Madi, R. Bruschweiler, and R. R. Ernst [J. Chem. Phys. 109, 10603 (1999)], provides an elegant method of readout with the use of an extra "observer" qubit. At the end of computation, detection of the observer qubit provides the output via the multiplet structure of its spectrum. In spectral implementation by two-dimensional experiment the observer qubit retains the memory of input state during computation, thereby providing correlated information on input and output, in the same spectrum. Spectral implementation of Grover's search algorithm, approximate quantum counting, a modified version of Berstein-Vazirani problem, and Hogg's algorithm are demonstrated here in three- and four-qubit systems.

Journal Article↗
PubMed1998

Solvent relaxation by uniformly magnetized solute spheres. The classical-quantal connection.

RATIONALE AND OBJECTIVES: Large magnetic entities, with diameters in the range of 4 nm to 4 microns, are becoming of increasing interest for magnetic resonance imaging (MRI). The smaller are iron oxide nanoparticles, used for the RE system, and the larger are deoxygenated blood cells, for functional MRI. It can be useful to model such systems as magnetized solute spheres in water. Classical computations of 1/T2 have been reported for the larger particles, in the micron range, where the computational complexities are simplified by Monte Carlo methods. For smaller particles, the quantum mechanical (quantal) expressions for outer sphere relaxation, for both 1/T1 and 1/T2, have been available for some time, and are particularly simple to apply at MRI fields. The questions that arise, and which the author addresses, are how to interrelate the classical and quantal approaches and when to use which. METHODS: The author compares published results of Monte Carlo calculations of 1/T2 for diamagnetic polystyrene solute spheres of various sizes in water, made paramagnetic by addition of dysprosium-(DTPA)2-, with quantum mechanical outer sphere theory applied to the same system. The latter includes the usual assumption of motional narrowing and yields both 1/T1 and 1/T2. RESULTS: For particles with diameters less than about 1 micron, both approaches give identical results for 1/T2. For larger particles, the conditions for motional narrowing breakdown, and quantal theory overestimates 1/T2. In addition, in the particular system studied, relaxation becomes so effective near solute that there is insufficient time for all water molecules to experience their maximal effect. Classical theory handles this well whereas quantal theory does not. CONCLUSIONS: In comparing the classical and quantal approaches, one balances computational complexity but broader applicability with more limited but far simpler mathematics. In addition, because the quantal approach shows that 1/T1 and 1/T2 are intimately related, the author suggests, by analogy, how to extend classical methods to computation of 1/T1.

Contrast Media↗