Computer simulations and edge-state analysis of the Hall effect in two-dimensional quantum-dot arrays connected to phase-randomizing reservoirs.
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Journal Article↗
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Results for “quantum computing”
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Understanding the role of stereoelectronic effects in determining collagen stability. 2. A quantum mechanical/molecular mechanical study of (Proline-Proline-Glycine)(n) polypeptides.
The importance of vicinal and long-range interresidue effects in determining the stability of the collagen triple helix has been investigated by quantum mechanical (QM) and molecular mechanical (MM) computations on suitable model polypeptides, taking into account solvent effects by the polarizable continuum model (PCM). At the QM level, the PII conformation corresponds to an energy minimum for pentapeptide analogues incorporating the sequence Gly-Pro-Pro-Gly, irrespective of the down or up puckering of the pyrrolidine ring. However, our computations indicate that the alternation of down and up prolines characterizing collagen and collagen-like peptides is not due to an intrinsic preference of the Pro-Pro-Gly sequence. This result is confirmed by MM computations of longer polypeptides. Next, MM computations on model triple helices show that a better packing is obtained for specific values of backbone dihedrals, which, in turn, favor the alternation of down and up prolines along each chain.
Collagen↗
Elucidating the nature of enzyme catalysis utilizing a new twist on an old methodology: quantum mechanical-free energy calculations on chemical reactions in enzymes and in aqueous solution.
How do enzymes achieve very large rate enhancements compared to corresponding uncatalyzed reactions in solution? We present a computational approach which combines high-level ab initio quantum mechanical calculations with classical free energy calculations to address this question. Our calculations lead to accurate estimates of DeltaG for both trypsin and catechol O-methyltransferase-catalyzed and reference uncatalyzed reactions and give new insights into the nature of enzyme catalysis. The same methodology applied to steps in the catalytic mechanism of citrate synthase further supports the conclusion that one need not invoke special concepts such as "low-barrier hydrogen bonds" or "pK(a) matching" to explain enzyme catalysis.
Catalysis↗
The Military Health System Computer-based Patient Record.
The Composite Health Care System II (CHCS II) is the Military's electronic Computer-based Patient Record, a clinical information system that will generate, maintain, and provide secure online access to a comprehensive and legible health record. In moving to CHCS II, the Department of Defense (DoD) is making the quantum leap from paper based medical records to computer based patient record (CPR). The CPR will enable DoD health care to meet its strategic goals for the 21st century and is paramount to providing comprehensive patient-focused information.
Humans↗
A study of homonuclear dipolar recoupling pulse sequences in solid-state nuclear magnetic resonance.
Dipolar recoupling pulse sequences are of great importance in magic angle spinning solid-state NMR. Recoupling sequences are used for excitation of double-quantum coherence, which, in turn, is employed in experiments to estimate internuclear distances and molecular torsion angles. Much effort is spent on the design of recoupling sequences that are able to produce double-quantum coherence with high efficiency in demanding spin systems, i.e., spin systems with small dipole-dipole couplings and large chemical-shift anisotropies (CSAs). The sequence should perform robustly under a variety of experimental conditions. This paper presents experiments and computer calculations that extend the theory of double-quantum coherence preparation from the strong coupling/small CSA limit to the weak coupling limit. The performance of several popular dipole-dipole recoupling sequences-DRAWS, POST-C7, SPC-5, R1, and R2-are compared. It is found that the optimum performance for several of these sequences, in the weak coupling/large CSA limit, varies dramatically, with respect to the sample spinning speed, the magnitude and orientation of the CSAs, and the magnitude of dipole-dipole couplings. It is found that the efficiency of double-quantum coherence preparation by gamma-encoded sequences departs from the predictions of first-order theory. The discussion is supported by density-matrix calculations.
Alanine↗
Future in biomolecular computation.
Large-scale computations for biomolecules are dominated by three levels of theory: rigorous quantum mechanical calculations for molecules with up to about 30 atoms, semi-empirical quantum mechanical calculations for systems with up to several hundred atoms, and force-field molecular dynamics studies of biomacromolecules with 10,000 atoms and more including surrounding solvent molecules. It can be anticipated that increased computational power will allow the treatment of larger systems of ever growing complexity. Due to the scaling of the computational requirements with increasing number of atoms, the force-field approaches will benefit the most from increased computational power. On the other hand, progress in methodologies such as density functional theory will enable us to treat larger systems on a fully quantum mechanical level and a combination of molecular dynamics and quantum mechanics can be envisioned. One of the greatest challenges in biomolecular computation is the protein folding problem. It is unclear at this point, if an approach with current methodologies will lead to a satisfactory answer or if unconventional, new approaches will be necessary. In any event, due to the complexity of biomolecular systems, a hierarchy of approaches will have to be established and used in order to capture the wide ranges of length-scales and time-scales involved in biological processes. In terms of hardware development, speed and power of computers will increase while the price/performance ratio will become more and more favorable. Parallelism can be anticipated to become an integral architectural feature in a range of computers.(ABSTRACT TRUNCATED AT 250 WORDS)
Chemical Phenomena↗
The role of solvent interaction in quantum pharmacological studies.
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Chemical Phenomena↗
Efficient classical simulation of optical quantum information circuits.
We identify a broad class of physical processes in an optical quantum circuit that can be efficiently simulated on a classical computer: this class includes unitary transformations, amplification, noise, and measurements. This simulatability result places powerful constraints on the capability to realize exponential quantum speedups as well as on inducing an optical nonlinear transformation via linear optics, photodetection-based measurement, and classical feedforward of measurement results, optimal cloning, and a wide range of other processes.
Journal Article↗
Noise analysis of a digital radiography system.
The sources of noise in a digital video subtraction angiography system were identified and analyzed. Signal-to-noise ratios of digital radiography systems were measured using the digital image data recorded in the computer. The major sources of noise include quantum noise, TV camera electronic noise, quantization noise from the analog-to-digital converter, time jitter, structure noise in the image intensifier, and video recorder electronic noise. A new noise source was identified, which results from the interplay of fixed pattern noise and the lack of image registration. This type of noise may result from image-intensifier structure noise in combination with TV camera time jitter or recorder time jitter. A similar noise source is generated from the interplay of patient absorption inhomogeneities and patient motion or image re-registration. Signal-to-noise ratios were measured for a variety of experimental conditions using subtracted digital images. The measured signal-to-noise ratios were found to fluctuate on repeat trials with about a 10% standard deviation. Averaging of video frames was found to reduce the noise level by the expected square root N relation, where N is the number of frames averaged. Image-intensifier structure noise was shown to be a dominant noise source in unsubtracted images at medium to high radiation exposure levels. A total-system signal-to-noise ratio (SNR) of 750:1 was measured for an input exposure of 1 mR/frame at the image intensifier input. The effect of scattered radiation on subtracted image SNR was found to be greater than previously reported. The detail SNR was found to vary approximately as one plus the scatter degradation factor. Quantization error noise with 8-bit image processors (signal-to-noise ratio of 890:1) was shown to be of increased importance after recent improvements in TV cameras. The results of the analysis are useful both in the design of future digital radiography systems and the selection of optimum clinical techniques.
Angiography↗
Strategies to improve the signal and noise performance of active matrix, flat-panel imagers for diagnostic x-ray applications.
A theoretical investigation of factors limiting the detective quantum efficiency (DQE) of active matrix flat-panel imagers (AMFPIs), and of methods to overcome these limitations, is reported. At the higher exposure levels associated with radiography, the present generation of AMFPIs is capable of exhibiting DQE performance equivalent, or superior, to that of existing film-screen and computed radiography systems. However, at exposure levels commonly encountered in fluoroscopy, AMFPIs exhibit significantly reduced DQE and this problem is accentuated at higher spatial frequencies. The problem applies both to AMFPIs that rely on indirect detection as well as direct detection of the incident radiation. This reduced performance derives from the relatively large magnitude of the square of the total additive noise compared to the system gain for existing AMFPIs. In order to circumvent these restrictions, a variety of strategies to decrease additive noise and enhance system gain are proposed. Additive noise could be reduced through improved preamplifier, pixel and array design, including the incorporation of compensation lines to sample external line noise. System gain could be enhanced through the use of continuous photodiodes, pixel amplifiers, or higher gain x-ray converters such as lead iodide. The feasibility of these and other strategies is discussed and potential improvements to DQE performance are quantified through a theoretical investigation of a variety of hypothetical 200 microm pitch designs. At low exposures, such improvements could greatly increase the magnitude of the low spatial frequency component of the DQE, rendering it practically independent of exposure while simultaneously reducing the falloff in DQE at higher spatial frequencies. Furthermore, such noise reduction and gain enhancement could lead to the development of AMFPIs with high DQE performance which are capable of providing both high resolution radiographic images, at approximately 100 microm pixel resolution, as well as variable resolution fluoroscopic images at 30 fps.
Feasibility Studies↗
Fast and stable method for simulating quantum electron dynamics
A fast and stable method is formulated to compute the time evolution of a wave function by numerically solving the time-dependent Schrodinger equation. This method is a real-space-real-time evolution method implemented by several computational techniques such as Suzuki's exponential product, Cayley's form, the finite differential method, and an operator named adhesive operator. This method conserves the norm of the wave function, manages periodic conditions and adaptive mesh refinement technique, and is suitable for vector- and parallel-type supercomputers. Applying this method to some simple electron dynamics, we confirmed the efficiency and accuracy of the method for simulating fast time-dependent quantum phenomena.
Journal Article↗
Imaging of quantum array structures with coherent and partially coherent diffraction.
Recent achievements in experimental and computational methods open the possibility of measuring and inverting the diffraction pattern from a finite object of submicrometer size. In this paper the possibilities of such experiments for two-dimensional arrays of quantum dots are discussed. The diffraction pattern corresponding to coherent and partial coherent illumination of a sample was generated. Test calculations based on the iterative algorithms were applied to reconstruct the shape of the individual islands in such a quantum structure directly from its diffraction pattern. It is demonstrated that, in the case of coherent illumination, the correct shape and orientation of an individual island can be obtained. In the case of partially coherent illumination, the correct shape of the particle can be obtained only when the coherence of the incoming beam is reduced to match the size of the island.
Algorithms↗
Reactivity and binding energies of transition metal halide ions with benzene.
We have generated novel halogen-ligated transition metal ions MX(n)+ (M = Sc, Ti, V, and Fe, X = Cl, Br and I, n = 1-3). We have explored their reactions with benzene, a typical aromatic hydrocarbon. Attachment of one benzene molecule is usually rapid, whereas attachment of a second benzene molecule is generally much slower. The kinetics were analyzed to estimate binding energies, modeling the attachment reaction as a radiative association process. In all cases the Standard Hydrocarbon semiquantitative estimation approach was employed, and in some cases the more accurate variational transition state (VTST) kinetic modeling approach was also applied. Density functional (DFT) quantum calculations were also performed to give computed binding energies for some of the complexes. Taking previously determined binding energies for halogen-ligated alkaline-earth ions as benchmarks, it is concluded that binding of the first benzene molecule to the transition-metal species is strongly enhanced by specific chemical interactions, while binding of the second benzene molecule is more nearly electrostatic. The binding energies are not strongly dependent on the identity of the transition metal ion, and the metal-ion dependences can be rationalized in terms of valence-orbital occupations of the metals. The binding energies are nearly independent of the identity of the halogen ligands.
Journal Article↗
Stability of complexes of aromatic amides with bromide anion: quantitative structure--property relationships
Most of the theoretical studies published to-date on the structural and electronic properties of supramolecules have been devoted to the neutral or cationic complexes, while little is known about anionic systems. A detailed theoretical study of the interaction between simple aromatic amides and the bromide anion has recently been published (Cajan, M.; Stibor, I.; Koca, J. J. Phys. Chem. A 1999, 103, 3778). The present work focuses on the structural and physicochemical parameters of simple aromatic amides related to their ability to form the 1:1 complex with a bromide anion. A quantitative structure-property relationships (QSPR) model for the prediction of association constants is proposed. The model based on 22 complexes and nine molecular descriptors explained 96% (84% cross-validated) of the variance in association constants. The descriptors employed in this model included parameters for the characterization of conformational behavior and the 3D structure of amide molecules, distribution of electron density on the amidic functional group, and parameters for substitution on aromatic units. The quantitative structure-property relationship approach predicted the association constants with comparable quality, but significantly lower computational demand, than molecular modeling or standard quantum chemistry calculations.
Journal Article↗
On the possibility of detecting low barrier hydrogen bonds with kinetic measurements.
Recent experimental evidence has pointed to the possible presence of a short, strong hydrogen bond in the enzyme-substrate transition states in some biochemical reactions. To date, most experimental measures of these short, strong hydrogen bonds have monitored their equilibrium properties. In this work we show that kinetic measurements can also be used to detect the presence of short, strong hydrogen bonds. In particular, we find nontrivial differences among rate constant ratios of protonated to deuterated hydrogen bonds between strong and weak hydrogen bonds for proton transfer between donor-acceptor sites. We quantify this kinetic isotope effect by performing dynamical calculations of these rate constants by computing reactive flux through a dividing surface. This reactive flux is computed by evolving trajectories on an effective quantum mechanical potential energy surface.
Journal Article↗
Factors governing the protonation state of Zn-bound histidine in proteins: a DFT/CDM study.
We have performed systematic theoretical studies to elucidate the factors governing the His protonation/deprotonation state in Zn-binding sites, especially those containing the ubiquitous Zn-His-Asp/Glu triad. Specifically, we have addressed the following three questions: (1) How does the transfer of the Zn-bound His imidazole proton to the second-shell Asp/Glu carboxylate oxygen depend on the composition of the other first-shell ligands and the solvent accessibility of the metal-binding site? (2) Can any second-shell ligand with a proton acceptor group such as the backbone carbonyl oxygen also act as a proton acceptor? (3) What is the effect of the Asp/Glu in the Zn-His-Asp/Glu triad on the Zn-bound water protonation state? To address these questions, we used a combination of quantum mechanical and continuum dielectric methods to compute the free energies for deprotonating a Zn-bound imidazole/water in various Zn complexes. The calculations show that whether the Zn-bound His is protonated or deprotonated depends on (1) the solvent accessibility of the metal-binding site, and (2) the Lewis acid ability of Zn, which is indirectly determined by both the first- and the second-shell Zn ligands. The calculations also show that the effect of the Zn-His-Asp/Glu interaction on the nucleophilicity of the Zn-bound water depends on the solvent accessibility of the catalytic Zn site. Furthermore, they show that the Asp/Glu side chain in the Zn-His-Asp/Glu triad can increase the negative charge of its partner, His, and create an anionic hole that may stabilize a cation in buried cavities, provided that the Zn complex is cationic/neutral. The findings of this work are in accord with available experimental data.
Binding Sites↗
Path-integral study of positronium decay in xenon.
We use path-integral Monte Carlo to study the properties of a quantum particle equilibrated in a classical Lennard-Jones fluid. By choosing 2m(e) for its mass, and potential parameters corresponding to xenon, we are able to model the behavior of thermalized positronium above the xenon critical temperature. We carefully study the local distortion of the fluid in the neighborhood of the quantum particle, and use this information to compute the annihilation rate as a function of density on two isotherms. The results compare favorably with experiment below the critical point density. Contrary to accepted views, we demonstrate that positronium remains in a self-trapped state at over twice the critical point density.
Journal Article↗
Principal component elimination method for the improvement of S/N in evoked neuromagnetic field measurements.
In the study of magnetoencephalography, it is important to obtain evoked fields with good signal-to-noise ratios (S/N) and with a small number of epochs in averaging. The noises are considered to be mainly spontaneous neuromagnetic fields. In the present study, we propose a method to improve the S/N. The basic principle of this method is the elimination of a principal component (PC) of multichannel-recorded neuromagnetic fields, utilizing the synchronized characteristics of spontaneous rhythmic activities dominating the fields. The proposed method is, therefore, called the principal component elimination method (PCEM). PCEM was applied to neuromagnetic fields measured by a 37-channel superconducting quantum interference device system, on which computer-generated evoked fields were superposed, in order to examine possible improvement in S/N. It was found that elimination of the first PC could improve the S/N of the evoked fields. The improvement in S/N with elimination of the first PC, compared to conventional simple averaging, increased with increases in the number of epochs and reached more than 50% after averaging over 128 epochs. PCEM also reduced the number of epochs needed in averaging to about half of that needed in conventional simple averaging.
Adult↗