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PubMed2000

Magnetic breakdown at high fields: semiclassical and quantum treatments

The effects of finite temperature and noninteracting spins on magnetic breakdown (MB) in a quasi-two-dimensional organic conductor have been determined by computing the field-dependent free energy using a realistic crystal structure with no adjustable parameters. The de Haas-van Alphen oscillation spectra, including the MB phenomena, are thereby obtained microscopically. Within the range of computed magnetic field, from 170 to 1400 T, we find remarkable agreement between the predictions of the semiclassical and quantum treatment. We also find that the Zeeman effect leads to splitting of a frequency corresponding to the fundamental orbit.

Journal Article↗
PubMed1995

QMView: a computational chemistry three-dimensional visualization tool at the interface between molecules and mankind.

QMView is designed to facilitate the visualization and interpretation of quantum mechanical data. Capabilities include display of chemical structure, animation of quantum mechanically determined vibrational modes, and depiction of electronic properties and three-dimensional molecular orbitals. QMView has a user-friendly interface that allows users to interactively manipulate many features of the molecular structure and/or property, including positioning and structure representation, via mouse-activated dialog boxes. Although the interface allows input from results of any of the popularly used quantum mechanical software, we have focused on GAMESS, a widely distributed quantum chemistry code. QMView has been designed with the special feature of working in distributed mode with GAMESS, the latter running on a supercomputer, the former running on a Silicon Graphics platform. Ancillary programs provide a method of obtaining output of graphic images in various media, including hardcopy, PostScript files, slide, and/or video. These and other original features discussed in this article provide a graphic interface that is unique compared to others that are currently available. Examples of images produced by QMView are presented.

Computer Graphics↗
PubMed2000

Electronic portal imaging with an avalanche-multiplication-based video camera.

The aim of this study is to investigate the degree to which the imaging quality of an existing (video-based) electronic portal imaging device (EPID) system may be improved by using an avalanche-multiplication-based video camera (called the avalanche-gain method). Due to avalanche multiplication in the target of the video camera tube, the new camera can be made up to several hundred times more sensitive than a camera using a conventional video (e.g., Saticon) tube. As a result, the camera noise which limits the performance of current video-based EPIDs should be overwhelmed and made negligible. The detective quantum efficiency (DQE) of an EPID using the avalanche-gain method has been measured with 6 MV and 18 MV beams obtained using a linear accelerator. It is shown that the camera noise is indeed much smaller than quantum noise and that the DQE of the system is significantly increased compared to conventional video-based EPIDs. Variation of DQE of the avalanche-gain video portal system with a change of demagnification was also investigated. It has been shown that the improvement of optical coupling has less effect in this system than that in a conventional video-based EPID system.

Humans↗
PubMed1988

Quantum simulation of ferrocytochrome c.

The dramatic progress in the understanding of the dynamics of biomolecules has been largely fuelled by computer simulations based on the law of classical mechanics. However in some respects biomolecules are at the borders of the domain of applicability of classical mechanics. The role of quantum mechanical effects in biomolecular structure and function is therefore worth investigating. Here we present preliminary results from a quantum simulation of a protein and contrast them with results from full classical simulations. The most significant differences are found in motions of high frequency, such as bond stretching or the torsional oscillation of groups that bear hydrogen atoms. The amplitudes of such motions are significantly increased by the penetration of atoms into classically forbidden regions. These differences will directly influence the rates of such processes as proton and electron transfer.

Cytochrome c Group↗
PubMed1993

Azapsoralens-DNA interactions: crystal structure characterization of furan-side monoadduct and computer-aided studies.

In this paper a theoretical study, concerning molecular mechanics optimised structures, obtained by quantum mechanics as well as molecular mechanics calculations was carried out with the aim of correlating the theoretical model of the interactions between azapsoralens and DNA with the data experimentally obtained. The theoretical model suggests that both furan-side and pyrone-side double bonds may be involved in the cycloaddition with pyrimidines (although the cycloaddition at the level of furan is preferred), and is in line with the capacity of these compounds to form inter-strand cross-links. Moreover, concerning the theoretical intercalation model calculations on 3,4,4',5'-tetramethylazapsoralen intercalated inside a polynucleotide, they suggest a cis-syn arrangement between furan-side of the intercalated ligand and the above situated thymine, with which, under light activation, a cycloadduct may take place, having a cis-syn steric arrangement. Also this datum is in agreement with the cis-syn regio and stereochemistry of the isolated 4,4',5'-trimethylazapsoralen-thymine cycloadduct. Finally, from theoretical data, the role of nitrogen seems not important: in fact only small differences were found with the corresponding methylpsoralens so that the small differences observed may be mainly attributed to steric rather than to electronic effects. In general a good correlation between the theoretical model and the experimental data was observed.

Chromatography, High Pressure Liquid↗
PubMed1978

Three-dimensional molecular illustrations I: Isoelectron density contours and isoelectrostatic energy contours.

A method of depicting dimensional illustrations of molecules in vacuo that are sensitive to small electronic perturbations was attempted. This method would be useful in determining the effects of either perturbing groups from other molecules or changes produced by the addition or modification of an existing atom or chemical group on the same molecule. Isoelectron density contours for small molecules such as benzene, ammonia, and formaldehyde were first considered using the CNDO/2 molecular approximation method and then extended to the use of deorthogonalized CNDO/2 eigenvectors. These methods were similar in molecular projections but insensitive to electronic alterations. Therefore, the electrostatic potential energy was considered in developing contour surfaces of several of the molecules studied. In this case, acute and visually discernible changes were evidenced by electron exchange in the three-dimensional illustration of formaldehyde. The effect on the two-dimensional contour map of ammonia was strikingly altered by the addition of a proton, further substantiating the sensitivity of electrostatic contours to perturbing influences. These methods are considered and amplified in this report.

Ammonia↗
PubMed1999

Multiple echoes, multiple quantum coherence, and the dipolar field: demonstrating the significance of higher order terms in the equilibrium density matrix.

It is well known that dipolar field effects lead to multiple spin echoes in a simple two-RF pulse experiment (the MSE experiment). We show here that coherence transfer echoes (which identify the existence of multiple quantum coherences in liquid NMR) and multiple spin echoes have a common origin. Using density matrix theory we have calculated the phase and timing of multiple spin echoes from all quadrature phase combinations of RF pulses. We show for the MSE experiment that there is a one-to-one correspondence between the time domain echo order and the multiple quantum coherence order. The experimental confirmation of these phase predictions shows that multiple spin echoes provide independent evidence for the breakdown of the high temperature approximation as proposed by Warren et al. (Science 262, 2005 (1993)).

Artifacts↗
PubMed1994

Electrode potentials for bioreductive agents from neural networks.

The one-electron electrode potentials at pH 7 have been predicted to an average accuracy of about 70 mV for a number of nitrobenzenes, nitrofurans and nitroimidazoles using a neural network. The inputs were the heat of formation and the free energy of hydration of both the nitroarene and its radical anion. The heats of formation were calculated using semiempirical molecular orbital methods; the free energies of hydration were calculated using a modified Born equation with additional semiempirical terms. Since these inputs can be calculated quickly, the neural network promises to be very useful in the design of molecules such as bioreductive agents where the electrode potential is of crucial importance. The success of the neural network in this problem implies that the errors, primarily in the semiempirical heat of formation, are systematic, and offers the hope that these may be corrected in future generations of the semiempirical methods.

Antineoplastic Agents↗
PubMed1991

Prediction of the reactivities of cyclopenta-polynuclear aromatic hydrocarbons by quantum mechanical methods.

1. The direction of epoxide ring opening may be predicted using the techniques of theoretical chemistry by comparing the computed total energy of the two possible carbocations formed. 2. To predict the direction of epoxide ring opening and the potential binding of aceanthrylene 1,2-epoxide to biopolymers, quantum mechanical calculations were performed on the two potential hydroxy carbocations. 3. The 2-hydroxy carbocation (II) was favoured over the 1-hydroxy carbocation by 11.8 kcal/mol. Molecule II had more positive charge at the meso carbon group than at the nominally charged 1 position. Both the lowest unoccupied molecular orbital and the molecular electrostatic potential confirm this result, and indicate the possibility of unusual adducts to biopolymers. 4. Similar calculations on the equivalent epoxides of acenaphthylene and acephenanthrylene do not show the same results. 5. Modelling the addition products of II with small nucleophiles indicates that these unusual addition products do not form, and that the interaction is controlled by electronic effects and not electrostatic effects. 6. The calculations on acephenanthrylene demonstrate the importance of including the hydroxyl group when making predictions relative to epoxide ring opening. 7. Molecular descriptors are surrogates for the interaction of that molecule with an often unknown biological target. In cases where molecular descriptors are used without information about the target, small quantitative differences may not be appropriate discriminators.

Chemical Phenomena↗
PubMed1997

A quantum accounting and detective quantum efficiency analysis for video-based portal imaging.

The quality of images generated with radiographic imaging systems can be degraded if an inadequate number of secondary quanta are used at any stage before production of the final image. A theoretical technique known as a "quantum accounting diagram" (QAD) analysis has been developed recently to predict the detective quantum efficiency (DQE) of an imaging system as a function of spatial frequency based on an analysis of the propagation of quanta. It is used to determine the "quantum sink" stage(s) (stages which degrade the DQE of an imaging system due to quantum noise caused by a finite number of quanta), and to suggest design improvements to maximize image quality. We have used this QAD analysis to evaluate a video-based portal imaging system to determine where changes in design will have the most benefit. The system consists of a thick phosphor layer bonded to a 1 mm thick copper plate which is viewed by a T.V. camera. The imaging system has been modeled as ten cascaded stages, including: (i) conversion of x-ray quanta to light quanta; (ii) collection of light by a lens; (iii) detection of light quanta by a T.V. camera; (iv) the various blurring processes involved with each component of the imaging system; and, (v) addition of noise from the T.V. camera. The theoretical DQE obtained with the QAD analysis is in excellent agreement with the experimental DQE determined from previously published data. It is shown that the DQE is degraded at low spatial frequencies (< 0.25 cycles/mm) by quantum sinks both in the number of detected x rays and the number of detected optical quanta. At higher spatial frequencies, the optical quantum sink becomes the limiting factor in image quality. The secondary quantum sinks can be prevented, up to a spatial frequency of 0.5 cycles/mm, by increasing the overall system gain by a factor of 9 or more, or by improving the modulation transfer function (MTF) of components in the optical chain.

Biophysical Phenomena↗
PubMed1999

Simple linear QSAR models based on quantum similarity measures.

A novel QSAR approach based on quantum similarity measures was developed and tested in this paper. This approach consists of replacing the usual physicochemical parameters employed in QSAR analysis, such as octanol-water partition coefficient or Hammett sigma constant, by appropriate quantum chemical descriptors. The methodological basis for this substitution is found in recent theoretical studies [J. Comput. Chem. 1998, 19, 1575-1583, J. Comput. -Aided Mol. Des. 1999, 13, 259-270], in which it was demonstrated that both molecular hydrophobic character and electronic substituent effect can be modeled by appropriately chosen quantum self-similarity measures (QS-SM). The most important aim of this study was to prove that selected QS-SM descriptors can be advantageously used in empirical QSAR analysis instead of classical descriptors. For this purpose several QSAR correlations are proposed, in which empirical descriptors such as Hammett sigma constants or log P values are replaced by the appropriate QS-SM. These examples involve: (i) a set of benzenesulfonamides which bind to human carbonic anhydrase, (ii) a set of benzylamines as competitive inhibitors of the enzyme trypsin, and (iii) a set of indole derivatives which are benzodiazepine receptor inverse agonist site ligands. Simple linear QSAR models were developed in order to obtain mathematical relationships between the biological activity and the pertinent quantum chemical descriptors. The validity of the obtained QSAR models is supported by comparison of the observed and predicted values of the biological activity and by a statistical analysis based on a randomization test.

Benzylamines↗
PubMed1998

Anesthesia, consciousness and hydrophobic pockets--a unitary quantum hypothesis of anesthetic action.

1. A consensus view holds that anesthetics act by van der Waals forces in hydrophobic pockets of select brain proteins to ablate consciousness. 2. What is consciousness? Enigmatic features of consciousness (e.g. 'qualia', binding, non-computability, pre-conscious-->conscious transition, nondeterministic free will) may be explained by the occurrence of quantum coherent states in the brain. 3. Van der Waals electron pair couplings (London forces) in hydrophobic pockets in non-anesthetic (conscious) conditions are a particular type of quantum capable of supporting macroscopic quantum coherence. 4. The mechanism of anesthetics may be to inhibit electron mobility and London forces necessary for quantum states and consciousness in hydrophobic pockets of select brain proteins.

Anesthesia↗
PubMed1998

Design principles and applications of a cooled CCD camera for electron microscopy.

Cooled CCD cameras offer a number of advantages in recording electron microscope images with CCDs rather than film which include: immediate availability of the image in a digital format suitable for further computer processing, high dynamic range, excellent linearity and a high detective quantum efficiency for recording electrons. In one important respect however, film has superior properties: the spatial resolution of CCD detectors tested so far (in terms of point spread function or modulation transfer function) are inferior to film and a great deal of our effort has been spent in designing detectors with improved spatial resolution. Various instrumental contributions to spatial resolution have been analysed and in this paper we discuss the contribution of the phosphor-fibre optics system in this measurement. We have evaluated the performance of a number of detector components and parameters, e.g. different phosphors (and a scintillator), optical coupling with lens or fibre optics with various demagnification factors, to improve the detector performance. The camera described in this paper, which is based on this analysis, uses a tapered fibre optics coupling between the phosphor and the CCD and is installed on a Philips CM12 electron microscope equipped to perform cryo-microscopy. The main use of the camera so far has been in recording electron diffraction patterns from two dimensional crystals of bacteriorhodopsin--from wild type and from different trapped states during the photocycle. As one example of the type of data obtained with the CCD camera a two dimensional Fourier projection map from the trapped O-state is also included. With faster computers, it will soon be possible to undertake this type of work on an on-line basis. Also, with improvements in detector size and resolution, CCD detectors, already ideal for diffraction, will be able to compete with film in the recording of high resolution images.

Fiber Optic Technology↗
PubMed1996

Neural networks as a tool for compact representation of ab initio molecular potential energy surfaces.

Ab initio quantum chemical calculations of molecular properties such as, e.g., torsional potential energies, require massive computational effort even for moderately sized molecules, if basis sets with a reasonable quality are employed. Using ab initio data on conformational properties of the cofactor (6R,1'R,2'S)-5,6,7,8-tetrahydrobiopterin, we demonstrate that error backpropagation networks can be established that efficiently approximate complicated functional relationships such as torsional potential energy surfaces of a flexible molecule. Our pilot simulations suggest that properly trained neural networks might provide an extremely compact storage medium for quantum chemically obtained information. Moreover, they are outstandingly comfortable tools when it comes to making use of the stored information. One possible application is demonstrated, namely, computation of relaxed torsional energy surfaces.

Biopterins↗
PubMed1991

Medical informatics--an Australian perspective.

Computers, like the X-ray and stethoscope can be seen as clinical tools, that provide physicians with improved expertise in solving patient management problems. As tools they enable us to extend our clinical information base, and they also provide facilities that improve the delivery of the health care we provide. Automation (computerisation) in the health domain will cause the computer to become a more integral part of health care management and delivery before the start of the next century. To understand how the computer assists those who deliver and manage health care, it is important to be aware of its functional capabilities and how we can use them in medical practice. The rapid technological advances in computers over the last two decades has had both beneficial and counterproductive effects on the implementation of effective computer applications in the delivery of health care. For example, in the 1990s the computer hobbyist is able to make an investment of less than $10,000 on computer hardware that will match or exceed the technological capacities of machines of the 1960s. These rapid technological advances, which have produced a quantum leap in our ability to store and process information, have tended to make us overlook the need for effective computer programmes which will meet the needs of patient care. As the 1990s begin, those delivering health care (eg, physicians, nurses, pharmacists, administrators ...) need to become more involved in directing the effective implementation of computer applications that will provide the tools for improved information management, knowledge processing, and ultimately better patient care.

Australia↗