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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↗

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↗

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↗

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↗

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↗

Stochastic particle formulation of the vesicle hypothesis. Relevance to short-term phenomena.

Based on the vesicle hypothesis, the modes of elementary quantum-vesicle interactions have been formulated in terms of probabilities of induced and spontaneous interstate quanta transitions and generalized within the framework of the previously developed theory of the double barrier synapse. Among the three allowed states for a quantum, the transition state is a novel formulation for the fraction of immediately available quanta governed by both vesicle and presynaptic membranes. The parameters of the model were determined by fitting solutions to the experimental curves representing effects of single pulse and short train activation on transmitter release at the frog neuromuscular junction. Qualitative differences in particle physics of transmitter release found under low quantal outputs on one hand and normal transmission on the other allowed the formulation of the uncertainty hypothesis and the quantum condition of synaptic homeostasis.

Computer Simulation↗

Interactive computer simulations of knee-replacement surgery.

OBJECTIVE: Current surgical training programs in the United States are based on an apprenticeship model. This model is outdated because it does not provide conceptual scaffolding, promote collaborative learning, or offer constructive reinforcement. Our objective was to create a more useful approach by preparing students and residents for operative cases using interactive computer simulations of surgery. Total-knee-replacement surgery (TKR) is an ideal procedure to model on the computer because there is a systematic protocol for the procedure. Also, this protocol is difficult to learn by the apprenticeship model because of the multiple instruments that must be used in a specific order. We designed an interactive computer tutorial to teach medical students and residents how to perform knee-replacement surgery. We also aimed to reinforce the specific protocol of the operative procedure. Our final goal was to provide immediate, constructive feedback. DESCRIPTION: We created a computer tutorial by generating three-dimensional wire-frame models of the surgical instruments. Next, we applied a surface to the wire-frame models using three-dimensional modeling. Finally, the three-dimensional models were animated to simulate the motions of an actual TKR. The tutorial is a step-by-step tutorial that teaches and tests the correct sequence of steps in a TKR. The student or resident must select the correct instruments in the correct order. The learner is encouraged to learn the stepwise surgical protocol through repetitive use of the computer simulation. Constructive feedback is acquired through a grading system, which rates the student's or resident's ability to perform the task in the correct order. The grading system also accounts for the time required to perform the simulated procedure. We evaluated the efficacy of this teaching technique by testing medical students who learned by the computer simulation and those who learned by reading the surgical protocol manual. Both groups then performed TKR on manufactured bone models using real instruments. Their technique was graded with the standard protocol. The students who learned on the computer simulation performed the task in a shorter time and with fewer errors than the control group. They were also more engaged in the learning process. DISCUSSION: Surgical training programs generally lack a consistent approach to preoperative education related to surgical procedures. This interactive computer tutorial has allowed us to make a quantum leap in medical student and resident teaching in our orthopedic department because the students actually participate in the entire process. Our technique provides a linear, sequential method of skill acquisition and direct feedback, which is ideally suited for learning stepwise surgical protocols. Since our initial evaluation has shown the efficacy of this program, we have implemented this teaching tool into our orthopedic curriculum. Our plans for future work with this simulator include modeling procedures involving other anatomic areas of interest, such as the hip and shoulder.

Arthroplasty, Replacement, Knee↗

[Clinical method of newborn's maturity evaluation according to R. Klimek's index].

The object of the study was to evaluate R. Klimek's new simple clinical method of computing newborn's maturity index (K) without having to use the computer-aided method or understand the basics of the quantum mechanics or theory of relativity, which gave rise to the modern definition of maturity. The study was based on the material of 1000 successive newborns delivered in the Clinic of Gynecology and Obstetrics of the Jagiellonian University. Their maturity was determined routinely in BK scale, and confirmed by means of computer-aided method of birth term prognosis. Posture, angle of the elbow, pulling an elbow to the middle line of the body, breast appearance, presence of lanugo and plantar creases were evaluated by means of K index with points from 0 to 2. Newborns' maturity index K was 9.2 +/- 1.9 points (range 2-12). 2.6% newborns were immature and one third of them (0.8%) were born with the gestational age < 37 weeks, 28 of which (77%) had correct K index > or = 6 points. There is a high, statistically significant correlation between maturity assessed in Ballard-Klimek scale and K index (r = 0.61, t = 24.78).

Electronic Data Processing↗

Magnetocardiographic localization of arrhythmia substrates: a methodology study with accessory pathway ablation as reference.

In magnetocardiographic (MCG) localization of arrhythmia substrates, a model of the thorax as volume conductor is a crucial component of the calculations. In this study, we investigated different models of the thorax, to determine the most suitable to use in the computations. Our methods and results are as follows. We studied 11 patients with overt Wolff-Parkinson-White syndrome, scheduled for catheter ablation. The MCG registrations were made with a 37-channel "superconducting quantum interference device" system. The underlying equivalent current dipole was computed for the delta-wave. Three models of the thorax were used: the infinite halfspace, a sphere and a box. For anatomical correlation and to define the suitable sphere and box, magnetic resonance images were obtained. As reference we used the position of the tip of the catheter, at successful radio-frequency-ablation, documented by cine-fluoroscopy. Nine patients could be evaluated. The mean errors (range) when using the infinite halfspace, the sphere and the box were 96 (49-125), 21 (5-39), and 36 mm (20-58 mm), respectively (p < 0.0001). In conclusion, the sphere was significantly better suited than the other models tested in this study, but even with this model the accuracy of MCG localization must further improve to be clinically useful. More realistic models of the thorax are probably required to achieve this goal.

Adult↗

Digital x-ray imaging using amorphous selenium: reduction of aliasing.

Alias reduction is analyzed with the concept of an equivalent presampling filter, and a mathematical approach is established to find the equivalent presampling filter corresponding to specific digital image processing algorithms. The effects of different sampling period T and sampling aperture tau on aliasing artifacts and on the resultant detective quantum efficiency (DQE) for a self-scanned, flat-panel, amorphous selenium detector are obtained. Different effective apertures can be obtained from the same detector by averaging signals over adjacent pixels. It is shown that adding outputs from M adjacent pixels is equivalent to introducing an equivalent presampling filter with special properties. Appropriate selection of the averaging parameters (M and weights) is shown to reduce the aliasing artifact in the resultant image. The effect of incomplete charge collection due to geometrical effects (fill factor) is examined. It is shown that a large fill factor is desirable for aliasing reduction. The relationship between a digital filter applied to the sampled signal and its equivalent presampling analog filter is also established. Analytical formulas for the sampled spectrum of white signal and for the sampled power spectrum of white noise are obtained for aperture functions with a spatially uniform response. These formulas take into accounts aliasing artifacts, signal correlation and aperture function response, and demonstrate the dependence of sampled spectra on T and tau. With these formulas the detective quantum efficiency DQE is derived. It is shown that the resultant DQE depends only on the fill factor and the size of readout electrode tau 0, but is completely independent of the degree or type of pixel averaging. That is, even though the pixel averaging method reduces aliasing it leaves DQE (omega) unchanged. When significant amplifier noise is present the DQE obtained with the pixel averaging method can be better than those obtained with an analog presampling filter. Finally, it is pointed out that the requirement of reducing aliasing artifacts conflicts with other requirements for a detector such as maximizing modulation transfer function (MTF). A careful and practical compromise has to be made by a detector designer in choosing the extent to which the aliasing artifacts are eliminated.

Algorithms↗

Multichannel pseudogap Kondo model: large-N solution and quantum-critical dynamics.

We discuss a multichannel SU(N) Kondo model which displays nontrivial zero-temperature phase transitions due to a conduction electron density of states vanishing with a power law at the Fermi level. In a particular large- N limit, the system is described by coupled integral equations corresponding to a dynamic saddle point. We exactly determine the universal low-energy behavior of spectral densities at the scale-invariant fixed points, obtain anomalous exponents, and compute scaling functions describing the crossover near the quantum-critical points. We argue that our findings are relevant to recent experiments on impurity-doped d-wave superconductors.

Journal Article↗

Modeling biotransformation reactions by combined quantum mechanical/molecular mechanical approaches: from structure to activity.

An overview of the combined quantum mechanical/molecular mechanical (QM/MM) approach and its application to studies of biotransformation enzymes and drug metabolism is given. Theoretical methods to simulate enzymatic reactions have rapidly developed during the last decade. In particular, QM/MM methods provide detailed insights into enzyme catalyzed reactions, which can be extremely valuable in complementing experimental research. QM/MM methods allow the reacting groups in the active site of an enzyme to be studied at a quantum mechanical level, while the surrounding protein and solvent is included at a classical (and computationally less expensive) molecular mechanical level. Existing QM/MM implementations vary in the level of interaction between the QM and MM regions and in the way the partitioning into QM and MM regions is setup. Some general considerations concerning reaction modeling are discussed and a number of QM/MM studies related to drug metabolism are described. These studies illustrate that theoretical modeling of important metabolic reactions provides detailed insights into mechanisms of reaction and specific catalytic effects of enzyme residues as well as explaining variation in rates of conversion of different metabolites. Such information is essential in the development of methods to predict metabolism of drugs and to understand metabolic effects of genetic polymorphism in biotransformation enzymes.

Animals↗

Signal, noise power spectrum, and detective quantum efficiency of indirect-detection flat-panel imagers for diagnostic radiology.

The performance of an indirect-detection, active matrix flat-panel imager (FPI) at diagnostic energies is reported in terms of measured and theoretical signal size, noise power spectrum (NPS), and detective quantum efficiency (DQE). Based upon a 1536 x 1920 pixel, 127 microns pitch array of a-Si:H thin-film transistors and photodiodes, the FPI was developed as a prototype for examination of the potential of flat-panel technology in diagnostic x-ray imaging. The signal size per unit exposure (x-ray sensitivity) was measured for the FPI incorporating five commercially available Gd2O2S:Tb converting screens at energies 70-120 kVp. One-dimensional and two-dimensional NPS and DQE were measured for the FPI incorporating three such converters and as a function of the incident exposure. The measurements support the hypothesis that FPIs have significant potential for application in diagnostic radiology. A cascaded systems model that has shown good agreement with measured individual pixel signal and noise properties is employed to describe the performance of various FPI designs and configurations under a variety of diagnostic imaging conditions. Theoretical x-ray sensitivity, NPS, and DQE are compared to empirical results, and good agreement is observed in each case. The model is used to describe the potential performance of FPIs incorporating a recently developed, enhanced array that is commercially available and has been proposed for testing and application in diagnostic radiography and fluoroscopy. Under conditions corresponding to chest radiography, the analysis suggests that such systems can potentially meet or even exceed the DQE performance of existing technology, such as screen-film and storage phosphor systems; however, under conditions corresponding to general fluoroscopy, the typical exposure per frame is such that the DQE is limited by the total system gain and additive electronic noise. The cascaded systems analysis provides a valuable means of identifying the limiting stages of the imaging system, a tool for system optimization, and a guide for developing strategies of FPI design for various imaging applications.

Equipment Design↗