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Quantum statistical calculations and symplectic corrector algorithms.

The quantum partition function at finite temperature requires computing the trace of the imaginary time propagator. For numerical and Monte Carlo calculations, the propagator is usually split into its kinetic and potential parts. A higher-order splitting will result in a higher-order convergent algorithm. At imaginary time, the kinetic energy propagator is usually the diffusion Green's function. Since diffusion cannot be simulated backward in time, the splitting must maintain the positivity of all intermediate time steps. However, since the trace is invariant under similarity transformations of the propagator, one can use this freedom to "correct" the split propagator to higher order. This use of similarity transforms classically gives rise to symplectic corrector algorithms. The split propagator is the symplectic kernel and the similarity transformation is the corrector. This work proves a generalization of the Sheng-Suzuki theorem: no positive time step propagators with only kinetic and potential operators can be corrected beyond second order. Second-order forward propagators can have fourth-order traces only with the inclusion of an additional commutator. We give detailed derivations of four forward correctable second-order propagators and their minimal correctors.

Journal Article↗

Cutoff anti-de Sitter space/conformal-field-theory duality and the quest for braneworld black holes.

Significant evidence is presented in favor of the holographic conjecture that "4D black holes localized on the brane found by solving the classical bulk equations in AdS5 are quantum corrected black holes and not classical ones." The quantum correction to the Newtonian potential is computed using a numerical computation of in Schwarzschild spacetime for matter fields in the zero-temperature Boulware vacuum state. For the conformally invariant scalar field the leading order term is equivalent to that previously obtained in the weak-field approximation using Feynman diagrams and which has been shown to be equivalent, via the anti-de Sitter space/conformal-field-theory (AdS/CFT) duality, to the analogous calculation in Randall-Sundrum braneworlds. The 4D backreaction equations are used to make a prediction about the existence and the possible spacetime structure of macroscopic static braneworld black holes.

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↗

Management of liver disease in thalassemia: main drug targets for a correct therapy.

Liver disease is the second cause of mortality in thalassemia major. We present a review on the hepatic damage in thalassemic patients aimed at a knowledge of current preventive, diagnostic and therapeutic approaches, useful to guide in clinical judgment and treatment decisions. Transfusion related iron overload and hepatitis are the causes of liver damage in thalassemic patients. We examined means of primary prevention, anti-hepatitis vaccinations, blood donors screening; diagnostic tests for secondary prevention (computed tomography, magnetic resonance imaging, super conducting quantum interference device and biopsy) were also discussed about. A survey of treatment methods and strategies ( chelation therapy, antiviral treatments and liver and bone marrow transplantation) follows.

Antiviral Agents↗

Hydrogen tunnelling in enzyme-catalysed H-transfer reactions: flavoprotein and quinoprotein systems.

It is now widely accepted that enzyme-catalysed C-H bond breakage occurs by quantum mechanical tunnelling. This paradigm shift in the conceptual framework for these reactions away from semi-classical transition state theory (TST, i.e. including zero-point energy, but with no tunnelling correction) has been driven over the recent years by experimental studies of the temperature dependence of kinetic isotope effects (KIEs) for these reactions in a range of enzymes, including the tryptophan tryptophylquinone-dependent enzymes such as methylamine dehydrogenase and aromatic amine dehydrogenase, and the flavoenzymes such as morphinone reductase and pentaerythritol tetranitrate reductase, which produced observations that are also inconsistent with the simple Bell-correction model of tunnelling. However, these data-especially, the strong temperature dependence of reaction rates and the variable temperature dependence of KIEs-are consistent with other tunnelling models (termed full tunnelling models), in which protein and/or substrate fluctuations generate a configuration compatible with tunnelling. These models accommodate substrate/protein (environment) fluctuations required to attain a configuration with degenerate nuclear quantum states and, when necessary, motion required to increase the probability of tunnelling in these states. Furthermore, tunnelling mechanisms in enzymes are supported by atomistic computational studies performed within the framework of modern TST, which incorporates quantum nuclear effects.

Computer Simulation↗

Determining the geometry of hydrogen bonds in solids with picometer accuracy by quantum-chemical calculations and NMR spectroscopy.

The structure of multiply hydrogen-bonded systems is determined with picometer accuracy by a combined solid-state NMR and quantum-chemical approach. On the experimental side, advanced 1H-15N dipolar recoupling NMR techniques are capable of providing proton-nitrogen distances of up to about 250 pm with an accuracy level of +/-1 pm for short distances (i.e., around 100 pm) and +/-5 pm for longer ones (i.e., 180 to 250 pm). The experiments were performed under fast magic-angle spinning, which ensures sufficient dipolar decoupling and spectral resolution of the 1H resonance lines. On the quantum-chemical side, the structures of the hydrogen-bonded systems were computationally optimised, yielding complete sets of nitrogen-proton and proton-proton distances, which are essential for correctly interpreting the experimental NMR data. In this way, nitrogen-proton distances were determined with picometer accuracy, so that vibrational averaging effects on dipole-dipole couplings need to be considered. The obtained structures were finally confirmed by the complete agreement of computed and experimental 'H and '5N chemical shifts. This demonstrates that solid-state NMR and quantum-chemical methods ideally complement each other and, in a combined manner, represent a powerful approach for reliable, high-precision structure determination whenever scattering techniques are inapplicable.

Chemistry, Physical↗

Quantum mechanical methods for enzyme kinetics.

This review discusses methods for the incorporation of quantum mechanical effects into enzyme kinetics simulations in which the enzyme is an explicit part of the model. We emphasize three aspects: (a) use of quantum mechanical electronic structure methods such as molecular orbital theory and density functional theory, usually in conjunction with molecular mechanics; (b) treating vibrational motions quantum mechanically, either in an instantaneous harmonic approximation, or by path integrals, or by a three-dimensional wave function coupled to classical nuclear motion; (c) incorporation of multidimensional tunneling approximations into reaction rate calculations.

Computer Simulation↗

Nonlinear polychromatic and noise artifacts in x-ray computed tomography images.

The variance of the image noise in computed X-ray transmission tomography (CT) due to quantum noise is in a first approximation a nonlinear function of X-ray attenuation. Beam hardening in CT is also a nonlinear function of attenuation. We present a theoretical study of both phenomena. Computer simulations and numerical results show that both nonlinear dependencies have quite similar effects on image quality. We also show how the two-dimensional distribution of the noise variance in a CT image is a weighted superposition of images obtained by backprojecting integer powers of the noiseless projection data corresponding to the scanned object. The streak-like pattern in the image noise due to the anisotropic nature of the noise cross-correlation function is discussed. We also discuss how these nonlinear phenomena affect noise filtering and tissue characterization using statistical parameters.

Electronics, Medical↗

Improved QSARs for predictive toxicology of halogenated hydrocarbons.

In our continuing efforts to provide a predictive toxicology capability, we seek to improve QSARs (quantitative structure-activity relationships) for chemicals of interest. Currently, although semi-empirical molecular orbital methods are hardly the state of the art for studying small molecules, AM1 calculations appear to be the method of choice when calculating quantum-chemical descriptors. However, with the advent of modern computational capabilities and the development of fast algorithms, ab initio molecular orbital and first principles density functional methods can be expeditiously applied in current QSAR studies. We present a study on halogenated alkanes to assess whether more accurate quantum methods result in QSARs that correlate better with experimental data. Furthermore, improved QSARs can also be obtained through development of new descriptors with explicit physical interpretations that should lead to better understanding of the mechanisms involved in the toxic response. We show that descriptors calculated from chemical intermediates may be useful in future QSARs.

Computer Simulation↗

A test of the continuous configuration time-dependent self-consistent field (CC-TDSCF) method on the H + CH4 reaction.

The continuous configuration time-dependent self-consistent field (CC-TDSCF) method is employed to calculate the flux-flux autocorrelation functions for the H + CH4 reaction on the potential energy surface recently developed by Manthe and co-workers. We include up to 10 out of the total 12 degrees of freedom in our calculations, only with the doubly degenerate bending modes involving the motion of the hydrogens in nonreacting CH3 group excluded. Comparison of flux-flux autocorrelation functions obtained by using the exact dynamics method and the CC-TDSCF method shows that the CC-TDSCF method is capable of producing very accurate results. Our calculations clearly reveal that the CC-TDSCF method is a powerful approximation quantum dynamics method. It allows us to partition a big problem into several smaller ones. By changing partition systematically, one can investigate the correlations between different degrees of freedom. By grouping modes with strong correlations together as a cluster, one can systematically improve accuracy of the result.

Computer Simulation↗

[Basic principles of computational chemistry for medical biologists].

The lecture describes the basic principles of computational chemistry underlying the methods of molecular modelling used in bioinformatics area. The basic positions, methods of molecular and quantum mechanics and combined approaches are considered. This lecture is from theoretical cycle "Bioinformatics and Computer-Aided Drug Design" for fourth year students of Medico-Biological Department of Russian State Medical University (specialty--biochemistry, biophysics and medical cybernetics). It can also be advised for all students and post-graduate students of medico-biological specialties.

Computational Biology↗

Efficient approximation of the dynamics of one-dimensional quantum spin systems.

In this Letter we show that an arbitrarily good approximation to the propagator e(itH) for a 1D lattice of n quantum spins with Hamiltonian H may be obtained with polynomial computational resources in n and the error epsilon and exponential resources in |t|. Our proof makes use of the finitely correlated state or matrix product state formalism exploited by numerical renormalization group algorithms like the density matrix renormalization group. There are two immediate consequences of this result. The first is that Vidal's time-dependent density matrix renormalization group will require only polynomial resources to simulate 1D quantum spin systems for logarithmic |t|. The second consequence is that continuous-time 1D quantum circuits with logarithmic |t| can be simulated efficiently on a classical computer, despite the fact that, after discretization, such circuits are of polynomial depth.

Journal Article↗

Estimation of fractal dimension in radiographs.

In the last decade, the fractal dimension has become a popular parameter to characterize image textures. Also in radiographs, various procedures have been used to estimate the fractal dimension. However, certain characteristics of the radiographic process, e.g., noise and blurring, interfere with the straightforward application of these estimation methods. In this study, the influence of quantum noise and image blur on several estimation methods was quantified by simulating the effect of quantum noise and the effect of modulation transfer functions, corresponding with different screen-film combinations, on computer generated fractal images. The results are extrapolated to explain the effect of film-grain noise on fractal dimension estimation. The effect of noise is that, irrespective of the noise source, the fractal dimension is overestimated, especially for lower fractal dimensions. On the other hand, blurring results in an underestimation of the dimensions. The effect of blurring is dependent on the estimation method used; the dimension estimates by the power spectrum method are lowered with a constant value, whereas the underestimation by the methods working in the spatial domain is dependent on the given dimension. The influence of the MTF and noise on fractal dimension estimation seriously limits the comparability of fractal dimensions estimated from radiographs which differ in noise content or MTF. Only when the power spectrum method is used, it is possible to correct for the influence of different MTFs of screen-film combinations. It is concluded that only when using the same object-focus distance, the same exposure conditions, the same digitizer at the same resolution, can fractal dimensions as estimated in radiographs be reliably compared.

Biophysical Phenomena↗

Excitations in photoactive molecules from quantum Monte Carlo.

Despite significant advances in electronic structure methods for the treatment of excited states, attaining an accurate description of the photoinduced processes in photoactive biomolecules is proving very difficult. For the prototypical photosensitive molecules, formaldimine, formaldehyde, and a minimal protonated Schiff base model of the retinal chromophore, we investigate the performance of various approaches generally considered promising for the computation of excited potential energy surfaces. We show that quantum Monte Carlo can accurately estimate the excitation energies of the studied systems if one constructs carefully the trial wave function, including in most cases the reoptimization of its determinantal part within quantum Monte Carlo. While time-dependent density functional theory and quantum Monte Carlo are generally in reasonable agreement, they yield a qualitatively different description of the isomerization of the Schiff base model. Finally, we find that the restricted open shell Kohn-Sham method is at variance with quantum Monte Carlo in estimating the lowest-singlet excited state potential energy surface for low-symmetry molecular structures.

Journal Article↗

Semiclassical nonadiabatic dynamics based on quantum trajectories for the O(3P,1D) + H2 system.

The O(3P,1D) + H2 --> OH + H reaction is studied using trajectory dynamics within the approximate quantum potential approach. Calculations of the wave-packet reaction probabilities are performed for four coupled electronic states for total angular momentum J = 0 using a mixed coordinate/polar representation of the wave function. Semiclassical dynamics is based on a single set of trajectories evolving on an effective potential-energy surface and in the presence of the approximate quantum potential. Population functions associated with each trajectory are computed for each electronic state. The effective surface is a linear combination of the electronic states with the contributions of individual components defined by their time-dependent average populations. The wave-packet reaction probabilities are in good agreement with the quantum-mechanical results. Intersystem crossing is found to have negligible effect on reaction probabilities summed over final electronic states.

Journal Article↗

Vibrationally inelastic collisions in H+ +CO system: comparing quantum calculations with experiments.

State-resolved cross beam experiments [H. Udseth et al., J. Chem. Phys. 60, 3051 (1974); J. Krutein and F. Linder, J. Chem. Phys. 71, 599 (1979); G. Niedner-Schatteburg and J. P. Toennies, Adv. Chem. Phys. LXXXII, 553 (1992)], coupled with proton energy loss spectroscopy for the inelastic scattering of H(+) from CO in the collision range of 10-30 eV show very low vibrational excitation of the target molecule. Stimulated by the experimentally observed low vibrational inelasticity in the system the ground and the first two low-lying excited electronic potential-energy surfaces have been computed using the ab initio multireference configuration interaction method. Quantum dynamics has been performed on the ground potential energy surface in the framework of vibrational close-coupling rotational infinite-order sudden approximation. The various computed dynamical attributes such as differential and integral cross sections, and average vibrational energy transfer are analyzed in detail, and compared successfully with the available experimental results.

Journal Article↗

Evaluation of nonlinear quantum time correlation functions within the centroid dynamics formulation.

A method to evaluate nonlinear centroid correlation functions is presented that is amenable to simple numerical computation. It can be implemented with the centroid molecular dynamics method for approximate quantum dynamics with no additional assumptions. Two nonlinear correlation functions are evaluated for a model potential using this scheme and compared with results from exact quantum calculations.

Models, Molecular↗

Subunits in quantal transmission at the mouse neuromuscular junction: tests of peak intervals in amplitude distributions.

The regular spacing of peaks throughout the amplitude distribution of miniature end-plate potentials, quantal evoked end-plate potentials and quantal currents was demonstrated using autocorrelations and power density spectra calculated from the number of events in the successive bins of the histograms built by Matteson et al. (1979), Kriebel & Florey (1983) and Erxleben & Kriebel (1984). At the same mouse neuromuscular junction, the calculated interpeak was constant for evoked and spontaneous quantal releases, throughout sequential sampling and after change of bin size. The presence of regular peak intervals supports the hypothesis that quantal potentials are composed of potential subunits the size of the smallest subminiature potential. Challenging the hypothesis of an acetylcholine quantum composed of acetylcholine subunits, a postsynaptic origin of the subunit is proposed on the basis of the spatial arrangement in rows of the ACh receptors. The ACh-saturating patch evoked by a quantum release (Land et al., 1980, 1981) activates 10-20 rows of receptors, which is roughly the number of subunits composing a quantal event. Therefore the position of the ACh patch or the continuous variations in its size might cause stepwise variations in the total number of ACh receptors activated by an ACh quantum.

Acetylcholine↗