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At least 613 records · Page 34Linked to original sources
PubMed2004

Quantum statistical mechanics with Gaussians: equilibrium properties of van der Waals clusters.

The variational Gaussian wave-packet method for computation of equilibrium density matrices of quantum many-body systems is further developed. The density matrix is expressed in terms of Gaussian resolution, in which each Gaussian is propagated independently in imaginary time beta=(k(B)T)(-1) starting at the classical limit beta=0. For an N-particle system a Gaussian exp[(r-q)(T)G(r-q)+gamma] is represented by its center qinR(3N), the width matrix GinR(3Nx3N), and the scale gammainR, all treated as dynamical variables. Evaluation of observables is done by Monte Carlo sampling of the initial Gaussian positions. As demonstrated previously at not-very-low temperatures the method is surprisingly accurate for a range of model systems including the case of double-well potential. Ideally, a single Gaussian propagation requires numerical effort comparable to the propagation of a single classical trajectory for a system with 9(N(2)+N)/2 degrees of freedom. Furthermore, an approximation based on a direct product of single-particle Gaussians, rather than a fully coupled Gaussian, reduces the number of dynamical variables to 9N. The success of the methodology depends on whether various Gaussian integrals needed for calculation of, e.g., the potential matrix elements or pair correlation functions could be evaluated efficiently. We present techniques to accomplish these goals and apply the method to compute the heat capacity and radial pair correlation function of Ne(13) Lennard-Jones cluster. Our results agree very well with the available path-integral Monte Carlo calculations.

Journal Article↗
PubMed1999

Test of semiclassical amplitudes for quantum ray-splitting systems.

We compute semiclassically and numerically the weights of ray-splitting orbits in the density of states of a rectangular and an annular ray-splitting billiard. The agreement between the semiclassical and the numerical results is very good, confirming the necessity of including reflection and transmission coefficients of non-Newtonian ray-splitting orbits in semiclassical expressions for the density of states of ray-splitting systems.

Journal Article↗
PubMed2004

Reaction path potential for complex systems derived from combined ab initio quantum mechanical and molecular mechanical calculations.

Combined ab initio quantum mechanical and molecular mechanical calculations have been widely used for modeling chemical reactions in complex systems such as enzymes, with most applications being based on the determination of a minimum energy path connecting the reactant through the transition state to the product in the enzyme environment. However, statistical mechanics sampling and reaction dynamics calculations with a combined ab initio quantum mechanical (QM) and molecular mechanical (MM) potential are still not feasible because of the computational costs associated mainly with the ab initio quantum mechanical calculations for the QM subsystem. To address this issue, a reaction path potential energy surface is developed here for statistical mechanics and dynamics simulation of chemical reactions in enzymes and other complex systems. The reaction path potential follows the ideas from the reaction path Hamiltonian of Miller, Handy and Adams for gas phase chemical reactions but is designed specifically for large systems that are described with combined ab initio quantum mechanical and molecular mechanical methods. The reaction path potential is an analytical energy expression of the combined quantum mechanical and molecular mechanical potential energy along the minimum energy path. An expansion around the minimum energy path is made in both the nuclear and the electronic degrees of freedom for the QM subsystem internal energy, while the energy of the subsystem described with MM remains unchanged from that in the combined quantum mechanical and molecular mechanical expression and the electrostatic interaction between the QM and MM subsystems is described as the interaction of the MM charges with the QM charges. The QM charges are polarizable in response to the changes in both the MM and the QM degrees of freedom through a new response kernel developed in the present work. The input data for constructing the reaction path potential are energies, vibrational frequencies, and electron density response properties of the QM subsystem along the minimum energy path, all of which can be obtained from the combined quantum mechanical and molecular mechanical calculations. Once constructed, it costs much less for its evaluation. Thus, the reaction path potential provides a potential energy surface for rigorous statistical mechanics and reaction dynamics calculations of complex systems. As an example, the method is applied to the statistical mechanical calculations for the potential of mean force of the chemical reaction in triosephosphate isomerase.

Binding Sites↗
PubMed1998

A computational quantitative structure-activity relationship study of carbamate anticonvulsants using quantum pharmacological methods.

A pattern recognition quantitative structure-activity relationship (QSAR) study has been performed to determine the molecular features of carbamate anticonvulsants which influence biological activity. Although carbamates, such as felbamate, have been used to treat epilepsy, their mechanisms of efficacy and toxicity are not completely understood. Quantum and classical mechanics calculations have been exploited to describe 46 carbamate drugs. Employing a principal component analysis and multiple linear regression calculations, five crucial structural descriptors were identified which directly relate to the bioactivity of the carbamate family. With the resulting mathematical model, the biological activity of carbamate analogues can be predicted with 85-90% accuracy.

Anticonvulsants↗
PubMed2002

An atomistic approach to conduction between nanoelectrodes through a single molecule.

Capacitance and other properties of nanoelectrodes, finite-size metal clusters envisaged for use in complex molecular-electronic devices, are discussed. The applicability of classical electrostatics (Coulomb's and Gauss' law, Poisson's equation, etc.) to atomistic systems is investigated and the self-energy necessary to store a finite charge on an atom is found to be of central importance. In particular, the neglect of electron exchange is found to introduce severe limitations, with quantum calculations predicting fundamentally different electronic structures. Also, the well-known poor representation of the atomic self-energy inherent to modern DFT is discussed, along with its implications for molecular electronics calculations. An INDO/S method is introduced with new parameters for gold. This is the simplest approximate computational scheme that correctly includes quantum electrostatic, resonance, and spin effects, and is capable of describing arbitrary excited electronic states. Encouraging results are obtained for some trial problems. In particular, voltage differential between the electrodes in electrode-molecule-electrode conduction is obtained, not through an a priori prescription but rather by moving whole electrons between the electrodes and analyzing the response. The voltage drops across the molecule-electrode junctions and the central molecular region are then deduced. This alternative to the current Landauer-based 1-particle transmission equations for electrode-molecule-electrode conduction is discussed in terms of the use of the electronic states of the system. It provides a proper description not only of conduction via electrode-to-molecule charge or hole transfer but also of conduction via simultaneous charge and hole transfer via low-lying excited molecular electronic states, including the ability to account for electroluminescence and other chemical effects. In addition, various aspects of our research on the quantitative prediction of the I(V) curves for electrode-molecule-electrode conduction are reviewed, including demonstration of the equivalence of the formalisms generated by the Datta and the Mujica-Ratner groups, and the development of analytically solvable paradigms, including the conduction through a linear-chain Hückel wire.

Electric Capacitance↗
PubMed2005

Quantum wave packet ab initio molecular dynamics: an approach to study quantum dynamics in large systems.

A methodology to efficiently conduct simultaneous dynamics of electrons and nuclei is presented. The approach involves quantum wave packet dynamics using an accurate banded, sparse and Toeplitz representation for the discrete free propagator, in conjunction with ab initio molecular dynamics treatment of the electronic and classical nuclear degree of freedom. The latter may be achieved either by using atom-centered density-matrix propagation or by using Born-Oppenheimer dynamics. The two components of the methodology, namely, quantum dynamics and ab initio molecular dynamics, are harnessed together using a time-dependent self-consistent field-like coupling procedure. The quantum wave packet dynamics is made computationally robust by using adaptive grids to achieve optimized sampling. One notable feature of the approach is that important quantum dynamical effects including zero-point effects, tunneling, as well as over-barrier reflections are treated accurately. The electronic degrees of freedom are simultaneously handled at accurate levels of density functional theory, including hybrid or gradient corrected approximations. Benchmark calculations are provided for proton transfer systems and the dynamics results are compared with exact calculations to determine the accuracy of the approach.

Journal Article↗
PubMed1996

Progress toward chemical accuracy in the computer simulation of condensed phase reactions.

We describe a procedure for the generation of chemically accurate computer-simulation models to study chemical reactions in the condensed phase. The process involves (i) the use of a coupled semiempirical quantum and classical molecular mechanics method to represent solutes and solvent, respectively; (ii) the optimization of semiempirical quantum mechanics (QM) parameters to produce a computationally efficient and chemically accurate QM model; (iii) the calibration of a quantum/classical microsolvation model using ab initio quantum theory; and (iv) the use of statistical mechanical principles and methods to simulate, on massively parallel computers, the thermodynamic properties of chemical reactions in aqueous solution. The utility of this process is demonstrated by the calculation of the enthalpy of reaction in vacuum and free energy change in aqueous solution for a proton transfer involving methanol, methoxide, imidazole, and imidazolium, which are functional groups involved with proton transfers in many biochemical systems. An optimized semiempirical QM model is produced, which results in the calculation of heats of formation of the above chemical species to within 1.0 kcal/mol (1 kcal = 4.18 kJ) of experimental values. The use of the calibrated QM and microsolvation QM/MM (molecular mechanics) models for the simulation of a proton transfer in aqueous solution gives a calculated free energy that is within 1.0 kcal/mol (12.2 calculated vs. 12.8 experimental) of a value estimated from experimental pKa values of the reacting species.

Journal Article↗
PubMed2003

Quantum Andreev map: a paradigm of quantum chaos in superconductivity.

We introduce quantum maps with particle-hole conversion (Andreev reflection) and particle-hole symmetry, which exhibit the same excitation gap as quantum dots in the proximity to a superconductor. Computationally, the Andreev maps are much more efficient than billiard models of quantum dots. This makes it possible to test analytical predictions of random-matrix theory and semiclassical chaos that were previously out of reach of computer simulations. We have observed the universal distribution of the excitation gap for a large Lyapunov exponent and the logarithmic reduction of the gap when the Ehrenfest time becomes comparable to the quasiparticle dwell time.

Journal Article↗
PubMed2004

Two-electron integrations in the quantum theory of atoms in molecules.

A method to compute two-electron integrals over arbitrary regions of space is introduced and particularized to the basins appearing in the quantum theory of atoms in molecules. The procedure generalizes the conventional multipolar approach to account for overlapping densities. We show that the approach is always convergent and computationally efficient, scaling as N(4) in the worst, two-center case. Several numerical results supporting our claims are also presented.

Journal Article↗
PubMed2000

Image quality evaluation of a desktop computed radiography system.

The modulation transfer function (MTF), noise power spectrum (NPS), and detective quantum efficiency (DQE) of the Lumisys ACR-2000 desktop computed radiography (CR) reader were measured and compared to equivalent measurements acquired from a Fuji AC-3 CR system. The one-dimensional (1D) MTF was measured from an image of a sharp edge and the 1D NPS was derived from a 2D NPS measured from a uniform field exposure. The energy dependent ideal input signal to noise ratio of the incident x-ray beams was estimated using published x-ray spectra and attenuation coefficients. Measurements were acquired using Agfa, Fuji, and Kodak storage phosphor plates and it was concluded that use of the Fuji plates resulted in the highest system DQE for the ACR-2000. The DQE was measured using exposures of 0.10, 1.0, and 10.0 mR from 70 and 120 kVp x-ray beams filtered with aluminum. The DQE of the Lumisys ACR-2000 was lower than that of the Fuji AC-3.

Computers↗
PubMed1986

Computer simulations of organic reactions in solution.

Quantum and statistical mechanics have been used to determine energy profiles for the SN2 reaction of Cl- + CH3Cl in the gas phase, in aqueous solution, and in liquid DMF. The energy profile in the gas phase has the characteristic double-well form featuring unsymmetrical ion-dipole complexes as minima and a symmetrical transition state. Hydration causes the reaction surface to become almost unimodal and increases the barrier significantly. The reaction profile in DMF is intermediate between those for the gas phase and aqueous solution. The ion-dipole complexes are still free energy minima in DMF. Thus, the reaction in DMF involves initial formation of the complex before the rate-determining step. The computed results are shown to be in good accord with experimental free energies of activation. The same technique has been applied to the addition reaction of OH- + H2C = O in the gas phase and aqueous solution. Ab initio 6-31 + G* calculations indicate that the reaction proceeds essentially without activation in the gas phase. Hydration introduces a substantial energy barrier. The transition state in water has been located at a C-O separation of roughly 2 A. A key finding for both reactions is that the activation barriers induced by hydration result primarily from change in strengths rather than in numbers of solute-water hydrogen bonds along the reaction paths.

Chemical Phenomena↗
PubMed2002

Efficient classical simulation of continuous variable quantum information processes.

We obtain sufficient conditions for the efficient simulation of a continuous variable quantum algorithm or process on a classical computer. The resulting theorem is an extension of the Gottesman-Knill theorem to continuous variable quantum information. For a collection of harmonic oscillators, any quantum process that begins with unentangled Gaussian states, performs only transformations generated by Hamiltonians that are quadratic in the canonical operators, and involves only measurements of canonical operators (including finite losses) and suitable operations conditioned on these measurements can be simulated efficiently on a classical computer.

Journal Article↗
PubMed2005

Theoretical predictions of chemical degradation reaction mechanisms of RDX and other cyclic nitramines derived from their molecular structures.

Analysis of environmental degradation pathways of contaminants is aided by predictions of likely reaction mechanisms and intermediate products derived from computational models of molecular structure. Quantum mechanical methods and force-field molecular mechanics were used to characterize cyclic nitramines. Likely degradation mechanisms for hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) include hydroxylation utilizing addition of hydroxide ions to initiate proton abstraction via 2nd order rate elimination (E2) or via nucleophilic substitution of nitro groups, reductive chemical and biochemical degradation, and free radical oxidation. Due to structural similarities, it is predicted that, under homologous circumstances, certain RDX environmental degradation pathways should also be effective for octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) and similar cyclic nitramines. Computational models provided a theoretical framework whereby likely transformation mechanisms and transformation products of cyclic nitramines were predicted and used to elucidate in situ degradation pathways.

Azocines↗
PubMed1987

A quantitative method for the detection and localization of quantum-limited events from radionuclides in cells and tissue sections by computer-enhanced video microscopy.

Cellular dynamics often involve extremely low concentrations of biologically active substances, which can be radiolabeled and detected, localized and quantitated by autoradiography. The latter may require exposures from a few days to many months. The objective of this research was to demonstrate the feasibility of reducing this long period of data collection by one to two orders of magnitude, while maintaining or improving the spatial resolution and localization in tissues and the quantitative characteristics inherent in autoradiography. A mathematical model describing the complete system was generated using energy partition calculations to estimate photon production via scintillant per H3 beta particle emission and to estimate the subsequent photon capture based upon imaging system parameters and microscope geometry. Calculations showed that, typically, a single tritium beta particle produces a maximum of 5.8 X 10(3) photons. A photon-limited camera and microscope imaging system were selected and optimized in conjunction with a specially developed physical scintillation model. Results showed that the number of detected photoevents increases monotonically with both signal integration time and, independently, with the concentration of the radionuclide. Consequently, this work demonstrates that video microscopy imaging methods can spatially and temporally quantify very low concentrations of radiolabeled substances and can reduce data acquisition times.

Beta Particles↗
PubMed2001

From computation to black holes and space-time foam.

We show that quantum mechanics and general relativity limit the speed nu of a simple computer (such as a black hole) and its memory space I to I(nu2) less, similar(t(-2))P, where t(P) is the Planck time. We also show that the lifetime of a simple clock and its precision are similarly limited. These bounds and the holographic bound originate from the same physics that governs the quantum fluctuations of space-time. We further show that these physical bounds are realized for black holes, yielding the correct Hawking black hole lifetime, and that space-time undergoes much larger quantum fluctuations than conventional wisdom claims-almost within range of detection with modern gravitational-wave interferometers.

Journal Article↗
PubMed2001

Quantum backreaction through the Bohmian particle.

A novel solution to the quantum backreaction problem in a mixed quantum-classical simulation is provided using the Bohmian interpretation of quantum mechanics. The Bohmian backreaction is unique, computationally simple, features reaction channel branching, and easily gives the full classical limit. The Bohmian quantum-classical method is illustrated by application to a model of O2 interacting with a Pt surface.

Journal Article↗
PubMed1995

On the role of Glu-68 in alcohol dehydrogenase.

Theoretical computations (molecular dynamics and combined quantum chemical and molecular mechanical geometry optimizations) have been performed on horse liver alcohol dehydrogenase. The results provide evidence that Glu-68, a highly conserved residue located 0.47 nm from the catalytic zinc ion, may intermittently coordinate to the zinc ion. Structures with Glu-68 coordinated to the zinc ion are almost as stable as structures with Glu-68 at the crystal position and the barrier between the two configurations of Glu-68 is so low that it can readily be bypassed at room temperature. There is a cavity behind the zinc ion that seems to be tailored to allow such coordination of Glu-68 to the zinc ion. It is suggested that Glu-68 may facilitate the exchange of ligands in the substrate site by coordinating to the zinc ion when the old ligand dissociates.

Alcohol Dehydrogenase↗