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At least 1,117 records · Page 62Linked to original sources
PubMed1991

The implementation of ab initio quantum chemistry calculations on transporters.

The RHF and geometry optimization sections of the ab initio quantum chemistry code, GAMESS, have been optimized for a network of parallel microprocessors, Inmos T800-20 transputers, using both indirect and direct SCF techniques. The results indicate great scope for implementation of such codes on small parallel computer systems, very high efficiencies having been achieved, particularly in the cases of direct SCF and geometry optimization with large basis sets. The work, although performed upon one particular parallel system, the Meiko Computing Surface, is applicable to a wide range of parallel systems with both shared and distributed memory.

Computers↗
PubMed2002

Simulating the formation of cosmic structure.

A timely combination of new theoretical ideas and observational discoveries has brought about significant advances in our understanding of cosmic evolution. Computer simulations have played a key role in these developments by providing the means to interpret astronomical data in the context of physical and cosmological theory. In the current paradigm, our Universe has a flat geometry, is undergoing accelerated expansion and is gravitationally dominated by elementary particles that make up cold dark matter. Within this framework, it is possible to simulate in a computer the emergence of galaxies and other structures from small quantum fluctuations imprinted during an epoch of inflationary expansion shortly after the Big Bang. The simulations must take into account the evolution of the dark matter as well as the gaseous processes involved in the formation of stars and other visible components. Although many unresolved questions remain, a coherent picture for the formation of cosmic structure is now beginning to emerge.

Astronomy↗
PubMed2005

Zori 1.0: a parallel quantum Monte Carlo electronic structure package.

The Zori 1.0 package for electronic structure computations is described. Zori performs variational and diffusion Monte Carlo computations as well as correlated wave function optimization. This article presents an overview of the implemented methods and code capabilities.

Journal Article↗
PubMed2004

Energy conserving approximations to the quantum potential: dynamics with linearized quantum force.

Solution of the Schrodinger equation within the de Broglie-Bohm formulation is based on propagation of trajectories in the presence of a nonlocal quantum potential. We present a new strategy for defining approximate quantum potentials within a restricted trial function by performing the optimal fit to the log-derivatives of the wave function density. This procedure results in the energy-conserving dynamics for a closed system. For one particular form of the trial function leading to the linear quantum force, the optimization problem is solved analytically in terms of the first and second moments of the weighted trajectory distribution. This approach gives exact time-evolution of a correlated Gaussian wave function in a locally quadratic potential. The method is computationally cheap in many dimensions, conserves total energy and satisfies the criterion on the average quantum force. Expectation values are readily found by summing over trajectory weights. Efficient extraction of the phase-dependent quantities is discussed. We illustrate the efficiency and accuracy of the linear quantum force approximation by examining a one-dimensional scattering problem and by computing the wavepacket reaction probability for the hydrogen exchange reaction and the photodissociation spectrum of ICN in two dimensions.

Journal Article↗
PubMed2000

Hartree-fock approximation for inverse many-body problems

A new method is presented to reconstruct the potential of a quantum mechanical many-body system from observational data, combining a nonparametric Bayesian approach with a Hartree-Fock approximation. A priori information is implemented as a stochastic process, defined on the space of potentials. The method is computationally feasible and provides a general framework to treat inverse problems for quantum mechanical many-body systems.

Journal Article↗
PubMed2005

One-electron reduction potential for oxygen- and sulfur-centered organic radicals in protic and aprotic solvents.

We estimated one-electron reduction potentials of redox-active organic molecules for a spectrum of eight different functional groups (phenoxyl, p-benzoquinone, phenylthiyl, p-benzodithiyl, carboxyl, benzoyloxyl, carbthiyl, and benzoylthiyl) in protic (water) and aprotic (acetonitrile, N,N-dimethylacetamide) solvents. Electron affinities (EA) were evaluated in a vacuum with high level quantum chemical methods using Gaussian3-MP2 (G3MP2) and Becke 3 Lee, Yang, and Parr functional B3LYP with aug-cc-pVTZ basis set. To evaluate one-electron redox potentials, gas-phase free energies were combined with solvation energies obtained in a two-step computational approach. First, atomic partial charges were determined in a vacuum by the quantum chemical method B3LYP/6-31G(d,p). Second, solvation energies were determined, solving the Poisson equation with these atomic partial charges. Redox potentials computed this way, compared to experimental data for the 21 considered organic compounds in different solvents, yielded overall root-mean-square deviations of 0.058 and 0.131 V using G3MP2 or B3LYP to compute electronic energies, respectively, while B3LYP/6-31G(d,p) was used to compute solvation energies.

Journal Article↗
PubMedDate not supplied

Modeling large macromolecular structures using promolecular densities.

A procedure to easily construct fitted density functions is presented. This methodology, based on the promolecule approach, is able to handle large macromolecular systems, such as proteins. The usual procedure dealing with fitted densities has been improved by adding some restrictions, which allow faster calculations. As a main application example, molecular isodensity contours (MIDCOs) are constructed for two proteins, one of them composed of more than 50 000 atoms. MIDCOs, as a visual representation of the molecular density function, and thus an important descriptor of the molecular charge distribution, constitute a powerful tool in the understanding of molecular systems. MIDCOs are presented for both proteins, allowing exploration of their surfaces, as well as analysis of their shapes. Also, as a quantum mechanical calculation example, molecular quantum self-similarity measures are calculated for several proteins.

Computer Simulation↗
PubMed2005

"Smart dust": nanostructured devices in a grain of sand.

The term "smart dust" originally referred to miniature wireless semiconductor devices made using fabrication techniques derived from the microelectronics industry. These devices incorporate sensing, computing and communications in a centimetre-sized package. This article discusses the construction of much smaller silicon-based systems, using the tools of nanotechnology. The synthesis of millimetre- to micron-sized functional photonic crystals made from porous silicon is described. It is shown how the various optical, chemical, and mechanical properties can be harnessed to perform sensing, signal processing, communication and motive functions.

Electrochemistry↗
PubMed2003

Vibrational frequencies and structural determinations of tetraisocyanatosilane.

The normal mode frequencies and corresponding vibrational assignments of Si(NCO)(4) are examined theoretically using the GAUSSIAN 98 set of quantum chemistry codes. Each of the vibrational modes was assigned to one of six types of motion predicted by a group theoretical analysis (Si-N stretch, N-C-O symmetric stretch, N-C-O asymmetric stretch, N-C-O bend, Si-N-C bend, and N-Si-N bend) utilizing the T(d) symmetry of the molecule. Uniform scaling factors were derived for each type of motion. Predicted infrared and Raman intensities are reported.

Computational Biology↗
PubMed2006

Simulation of vibrational dephasing of I(2) in solid Kr using the semiclassical Liouville method.

In this paper, we present simulations of the decay of quantum coherence between vibrational states of I(2) in its ground (X) electronic state embedded in a cryogenic Kr matrix. We employ a numerical method based on the semiclassical limit of the quantum Liouville equation, which allows the simulation of the evolution and decay of quantum vibrational coherence using classical trajectories and ensemble averaging. The vibrational level-dependent interaction of the I(2)(X) oscillator with the rare-gas environment is modeled using a recently developed method for constructing state-dependent many-body potentials for quantum vibrations in a many-body classical environment [J. M. Riga, E. Fredj, and C. C. Martens, J. Chem. Phys. 122, 174107 (2005)]. The vibrational dephasing rates gamma(0n) for coherences prepared between the ground vibrational state mid R:0 and excited vibrational state mid R:n are calculated as a function of n and lattice temperature T. Excellent agreement with recent experiments performed by Karavitis et al. [Phys. Chem. Chem. Phys. 7, 791 (2005)] is obtained.

Algorithms↗
PubMed2000

Magnetic breakdown at high fields: semiclassical and quantum treatments

The effects of finite temperature and noninteracting spins on magnetic breakdown (MB) in a quasi-two-dimensional organic conductor have been determined by computing the field-dependent free energy using a realistic crystal structure with no adjustable parameters. The de Haas-van Alphen oscillation spectra, including the MB phenomena, are thereby obtained microscopically. Within the range of computed magnetic field, from 170 to 1400 T, we find remarkable agreement between the predictions of the semiclassical and quantum treatment. We also find that the Zeeman effect leads to splitting of a frequency corresponding to the fundamental orbit.

Journal Article↗
PubMed1995

QMView: a computational chemistry three-dimensional visualization tool at the interface between molecules and mankind.

QMView is designed to facilitate the visualization and interpretation of quantum mechanical data. Capabilities include display of chemical structure, animation of quantum mechanically determined vibrational modes, and depiction of electronic properties and three-dimensional molecular orbitals. QMView has a user-friendly interface that allows users to interactively manipulate many features of the molecular structure and/or property, including positioning and structure representation, via mouse-activated dialog boxes. Although the interface allows input from results of any of the popularly used quantum mechanical software, we have focused on GAMESS, a widely distributed quantum chemistry code. QMView has been designed with the special feature of working in distributed mode with GAMESS, the latter running on a supercomputer, the former running on a Silicon Graphics platform. Ancillary programs provide a method of obtaining output of graphic images in various media, including hardcopy, PostScript files, slide, and/or video. These and other original features discussed in this article provide a graphic interface that is unique compared to others that are currently available. Examples of images produced by QMView are presented.

Computer Graphics↗
PubMed2004

Critical evaluation of approximate quantum decoherence rates for an electronic transition in methanol solution.

We present a quantum molecular dynamics calculation of a semiclassical decoherence function to evaluate the accuracy of alternative short-time approximations for coherence loss in the dynamics of condensed phase electronically nonadiabatic processes. The semiclassical function from mixed quantum-classical molecular dynamics simulations and frozen Gaussian wave packets is computed for the electronic transition of an excited state excess electron to the ground state in liquid methanol. The decoherence function decays on a 10 fs time scale that is qualitatively similar to the aqueous case. We demonstrate that it is the motion of the hydrogen atom, and, in particular, the hydrogen rotation around the oxygen-methyl bond which is predominantly responsible for destroying the quantum correlations between alternative states. Multiple time scales due to the slower diffusive nuclear modes, which dominate the solvation response of methanol, do not contribute to the coherence loss. The choice of the coordinate representation is investigated in detail and concluded to be irrelevant to the decay. Changes in both nuclear momenta and positions on the two alternative potential surfaces are found to contribute to decoherence, the former dominating at short times (t < 5 fs), the latter controlling the decay at longer times. Various short-time approximations to the full dynamics for the decoherence function are tested for the first time. The present treatment rigorously develops the short-time description and establishes its range of validity. Whereas the lowest-order short-time approximation proves to be a very good approximation up to about 5 fs, we also find that it bounds the decay of the decoherence function. After 5 fs, the coherence decay in fact becomes faster than the single Gaussian predicted in the lowest-order short-time limit. This decay is well reflected by an enhanced low-order approximation, which is also easily computed from equilibrium classical forces.

Journal Article↗
PubMed2001

Real-space formulation of the quantum-mechanical electronic scattering under static n-fold axially symmetric electric and magnetic fields in a projection microscope.

A numerical technique is developed to compute electronic propagation in three-dimensional potential-energy and vector-potential distributions, as required for the quantum-mechanical modelization of scattering in static electric and magnetic fields in a projection microscope. The technique is implemented in a transfer-matrix and Green's functions general procedure to simulate field-emission and electronic projection microscopy. In particular, simulated observations of a transverse magnetic field confirms the occurrence of diffraction fringes that are oriented in the direction of the field. These diffraction fringes are mainly associated with the detection of a magnetic flux and tend to be more pronounced as this quantity increases. In the conditions of this paper, the smallest magnetic flux that was detected could be associated with a phase shift of around 2pi/8 rad.

Journal Article↗
PubMed2006

Direct computation of general chemical energy differences: Application to ionization potentials, excitation, and bond energies.

Chemists are mainly interested in energy differences. In contrast, most quantum chemical methods yield the total energy which is a large number compared to the difference and has therefore to be computed to a higher relative precision than would be necessary for the difference alone. Hence, it is desirable to compute energy differences directly, thereby avoiding the precision problem. Whenever it is possible to find a parameter which transforms smoothly from an initial to a final state, the energy difference can be obtained by integrating the energy derivative with respect to that parameter (cf. thermodynamic integration or adiabatic connection methods). If the dependence on the parameter is predominantly linear, accurate results can be obtained by single-point integration. In density functional theory and Hartree-Fock, we applied the formalism to ionization potentials, excitation energies, and chemical bond breaking. Example calculations for ionization potentials and excitation energies showed that accurate results could be obtained with a linear estimate. For breaking bonds, we introduce a nongeometrical parameter which gradually turns the interaction between two fragments of a molecule on. The interaction changes the potentials used to determine the orbitals as well as the constraint on the orbitals to be orthogonal.

Journal Article↗
PubMed2005

Entanglement of formation of bipartite quantum states.

We give an explicit tight lower bound for the entanglement of formation for arbitrary bipartite mixed states by using the convex hull construction of a certain function. This is achieved by revealing a novel connection among the entanglement of formation, the well-known Peres-Horodecki, and realignment criteria. The bound gives a quite simple and efficiently computable way to evaluate quantitatively the degree of entanglement for any bipartite quantum state.

Journal Article↗
PubMed2004

Bipolaron in different configuration of quantum confinement.

The authors used Landau-Pekar variational method to investigate a strong-coupling singlet optical bipolaron in different configuration of quantum confinement. Numerical and analytical results showed that when configuration changes from quantum dot and wire to well, confinement shows different effect on the formation of a bipolaron. In contrast to a bipolaron in a quantum dot or wire, the binding energy of a bipolaron in a quantum well increases with increasing confinement, indicating that confinement favors bipolaron formation in a quantum well.

Algorithms↗
PubMed2002

Digital and biological computing in organizations.

Michael Conrad unveiled many of the fundamental characteristics of biological computing. Underlying the behavioral variability and the adaptability of biological systems are these characteristics, including the ability of biological information processing to exploit quantum features at the atomic level, the powerful 3-D pattern recognition capabilities of macromolecules, the computational efficiency, and the ability to support biological function. Among many other things, Conrad formalized and explicated the underlying principles of biological adaptability, characterized the differences between biological and digital computing in terms of a fundamental tradeoff between adaptability and programmability of information processing, and discussed the challenges of interfacing digital computers and human society. This paper is about the encounter of biological and digital computing. The focus is on the nature of the biological information processing infrastructure of organizations and how it can be extended effectively with digital computing. In order to achieve this goal effectively, however, we need to embed properly digital computing into the information processing aspects of human and social behavior and intelligence, which are fundamentally biological. Conrad's legacy provides a firm, strong, and inspiring foundation for this endeavor.

Adaptation, Physiological↗