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At least 847 records · Page 47Linked to original sources
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↗
PubMed2000

Computer experiments on xenon-containing molecules

Quantum chemical calculations have been performed on xenon-containing rare gas molecules. The novel HXeY molecules are best characterised as HXe+Y- where Y can be at least H, Cl, Br, I, CN, SH, OH or NCO. A good agreement of MP2/LJ18/6-311 + + G(2d,2p) results is obtained with respect to the trend in experimental data for the Xe-H stretching wavenumbers of the HXeY molecules. Predictions concerning compounds between Xe and carboxylic acids are made. It is shown that Xe can bind to the carboxy group of the side chains of amino acids, thus, allowing in principle Xe to bind to proteins.

Journal Article↗
PubMed2006

Optimal entanglement criterion for mixed quantum states.

We develop a strong and computationally simple entanglement criterion. The criterion is based on an elementary positive map Phi which operates on state spaces with even dimension N > or = 4. It is shown that Phi detects many entangled states with a positive partial transposition (PPT) and that it leads to a class of optimal entanglement witnesses. This implies that there are no other witnesses which can detect more entangled PPT states. The map Phi yields a systematic method for the explicit construction of high-dimensional manifolds of bound entangled states.

Journal Article↗
PubMed2005

Ab initio calculations for the Zn 2s and 2p core level binding energies in Zn oxo compounds and ZnO.

The Zn 2s and 2p core level binding energies of ZnO and a few Zn oxo compounds containing Zn in its oxidation state +2 were calculated by means of wave function based quantum chemical ab initio methods. The computations were performed at two levels of approximation. First, Hartree-Fock calculations were carried out for the ground state of the neutral systems yielding the "initial state" effects, i.e. the shifts of the core level binding energies due to the changes in the chemical environment of the Zn atom under consideration (Koopmans' theorem level, KT). In the second step, Hartree-Fock calculations were performed for the core ionized states in order to account for the relaxation effects after ionization, i.e. for the "final state" effects (DeltaSCF level). Scalar relativistic corrections and spin-orbit coupling were included in a "spin-orbit-coupling configuration interaction" (SOC-CI) treatment both at the KT and DeltaSCF levels. In all Zn oxo compounds (Zn(4)O(formate)(6), Zn(4)O(acetate)(6) and several ZnO cubanes) small negative initial state shifts between -1.0 and 0.0 eV (relative to the free Zn atom) were found which are caused by the negative charges at the surrounding O atoms. The relaxation effects vary between -1.0 and -0.5 eV, such that the calculated total shifts are moderately negative (-1.5 to -0.5 eV). Embedded ZnO clusters of increasing size, ranging from Zn(13)O(4) to Zn(69)O(38), were used as models for bulk ZnO, the Zn 2s and 2p core level shifts calculated for these clusters being extrapolated to infinite cluster size. The calculations show that bulk ZnO has a rather large negative initial state shift of -2.1 +/- 0.1 eV, due to the Madelung potential at the Zn atom, and a comparatively small relaxation contribution of -1.0 +/- 0.1 eV. This yields a total shift of -3.1 +/- 0.2 eV (both for 2s and 2p, relative to atomic Zn), which is in very good agreement with experiment, -2.9 +/- 0.2 eV. The surprising experimental observation that the Zn 2s and 2p XPS peak positions are nearly identical in Zn metal and ZnO is explained by the fact that the sum of initial and final state effects is accidentally the same for the two systems though the individual contributions differ quite significantly: the initial and final state shifts amount to +2.4 and -5.1 eV for Zn metal vs.-2.1 and -1.0 eV for ZnO.

Computer Simulation↗
PubMed2006

Diels-Alder reactions of cyclopentadiene and 9,10-dimethylanthracene with cyanoalkenes: the performance of density functional theory and Hartree-Fock calculations for the prediction of substituent effects.

The activation enthalpies for the reactions of cyclopentadiene with ethylene, acrylonitrile, fumaronitrile, maleonitrile, vinylidene cyanide, tricyanoethylene, and tetracyanoethylene have been computed with the Hartree-Fock quantum mechanical method and a variety of density functionals (B3LYP, BPW91, and MPW1K) and compared to classic experimental data obtained by Sauer, Wiest, and Mielert (Chem. Ber. 1964, 97, 3183). Some significant errors in B3LYP activation enthalpies involving cyano groups, especially 3 or 4 cyano groups, have been identified, whereas HF and MPW1K reproduce substituent effects quite accurately.

Alkenes↗
PubMed2003

Insights into the regioselectivity and RNA-binding affinity of HIV-1 nucleocapsid protein from linear-scaling quantum methods.

Human immunodeficiency virus type 1 (HIV-1) nucleocapsid protein (NC) plays several important roles in the viral life-cycle and presents an attractive target for rational drug design. Here, the macromolecular reactivity of NC and its binding to RNA is characterized through determination of electrostatic and chemical descriptors derived from linear-scaling quantum calculations in solution. The computational results offer a rationale for the experimentally observed susceptibility of the Cys49 thiolate toward small-molecule electrophilic agents, and support the recently proposed stepwise protonation mechanism of the C-terminal Zn-coordination complex. The distinctive binding mode of NC to SL2 and SL3 stem-loops of the HIV-1 genomic RNA packaging signal is studied on the basis of protein side-chain contributions to the electrostatic binding energies. These results indicate the importance of several basic residues in the 3(10) helical region and the N-terminal zinc finger, and rationalize the presence of several evolutionarily conserved residues in NC. The combined reactivity and RNA-binding study provides new insights that may contribute toward the structure-based design of anti-HIV therapies.

Cysteine↗
PubMed2004

Fluorinated imidazoles as proton carriers for water-free fuel cell membranes.

We propose an alternative new material (2,4,5-trifluoroimidazole impregnated Nafion) for use as a high-temperature, water-free membrane for proton-exchange membrane fuel cells. This material has been tested computationally using molecular dynamics and quantum mechanics techniques, leading to an estimated conductivity of approximately 0.06 S/cm at 177 degrees C. This material overcomes the weakness of the imidazole-impregnated membranes, i.e., the poisoning of the Pt electrode. We find that 2,4,5-trifluoroimidazole binds weakly to platinum surfaces, so poisoning is not expected.

Bioelectric Energy Sources↗
PubMed2001

Structural versatility of oxalamide-based compounds: a computational study on the isomerization of the oxalamide group and the structural preferences of the polyoxalamides.

The conformational properties of the oxalamide group and crystal structure of several polyoxalamides have been investigated by computational methods. First, a detailed quantum mechanical study of the conformational preferences of N,N'-dimethyloxalamide is reported. Results, which were obtained at the MP2/6-31G(d) level, provide not only the minimum energy conformations but also a description of the energetics and structural changes associated to the isomerization process of the oxalamide group. These quantum mechanical results together with those obtained from additional calculations have been used to develop a set of force-field parameters for the oxalamide group. Molecular mechanics calculations have been performed to test the parameters and to provide new information in terms of energy contributions about the isomerization of the oxalamide group. On the other hand, the new set of parameters has been used to investigate the structural preferences of polyoxalamides (-[NH-CO-CO-NH-(CH(2))(n)]-) by PCSP calculations. Results indicated that polyoxalamides with an even number of methylene groups adopt a structure with one hydrogen bonding direction, whereas polymers with an odd number of methylene groups prefer a structure with two hydrogen bonding directions. The latter crystal structure is completely different from that observed in conventional polyamides and has been investigated in detail through Monte Carlo simulations.

Crystallization↗
PubMed2006

Anharmonicity of amide modes.

The principal contributions to the anharmonic coupling of amide vibrations are explored with the objective of comparing recent experiments with density functional theory and evaluating simple models of mode coupling. Experimental information obtained by means of two-dimensional infrared spectroscopy (2D IR) is reasonably well predicted by the computed one- and two-quantum anharmonic modes of amide-A, -I, and -II types in mono-, di- and tripeptides. The expansion of the vibrational energy up to the cubic and quartic coupling of harmonic modes suggested criteria to assess how localized are the forces determining the anharmonicity. The off-diagonal anharmonicity between an amide-A and one other amide mode was shown to be mainly determined by forces involving only these two modes, whereas the off-diagonal anharmonicity of two amide-I modes in peptides depended significantly on forces due to motions other than those of the amide-I type. Both the diagonal and off-diagonal anharmonicities exhibit sensitivity to peptide structures. These results should prove useful in linking 2D IR experimental results to secondary structure. Further, the results are used to evaluate the vibrational exciton model for the mixed-mode anharmonicities of the amide-I transitions.

Amides↗