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At least 1,765 records · Page 98Linked to original sources
PubMed2005

Popescu-Rohrlich correlations as a unit of nonlocality.

A set of nonlocal correlations that have come to be known as a Popescu-Rohrlich (PR) box suggest themselves as a natural unit of nonlocality, much as a singlet is a natural unit of entanglement. We present two results relevant to this idea. One is that a wide class of multipartite correlations can be simulated using local operations on PR boxes only. We show this with an explicit scheme, which has the interesting feature that the number of PR boxes required is related to the computational resources necessary to represent a function defining the multipartite box. The second result is that there are quantum multipartite correlations, arising from measurements on a cluster state, that cannot be simulated with n PR boxes, for any n.

Journal Article↗
PubMed2006

Screen optics effects on detective quantum efficiency in digital radiography: zero-frequency effects.

Indirect flat panel imagers have been developed for digital radiography, fluoroscopy and mammography, and are now in clinical use. Screens made from columnar structured cesium iodide (CsI) scintillators doped with thallium have been used extensively in these detectors. The purpose of this article is to investigate the effect of screen optics, e.g., light escape efficiency versus depth, on gain fluctuation noise, expressed as the Swank factor. Our goal is to obtain results useful in optimizing screens for digital radiography systems. Experimental measurements from structured CsI samples were used to derive their screen optics properties, and the same methods can also be applied to powder screens. CsI screens, all of the same thickness but with different optical designs and manufacturing techniques, were obtained from Hamamatsu Photonics Corporation. The pulse height spectra (PHS) of the screens were measured at different x-ray energies. A theoretical model was developed for the light escape efficiency and a method for deriving light escape efficiency versus depth from experimental PHS measurements was implemented and applied to the CsI screens. The results showed that the light escape efficiency varies essentially linearly as a function of depth in the CsI samples, and that the magnitude of variation is relatively small, leading to a high Swank factor.

Algorithms↗
PubMed1999

Asynchrony of quantal events in evoked multiquantal responses indicates presynaptic quantal interaction.

Asynchrony of quantal events in evoked multiquantal responses indicates presynaptic quantal interaction. We have analyzed the possibility of quantal interactions by inspecting action potential-evoked postsynaptic multiquantal responses recorded extracellularly from the lobster neuromuscular junction. These recorded responses were compared with simulated multiquantal responses constructed from statistically independent quantal events. The simulated multiquantal responses were generated by random superposition of single quantal responses aligned according to the timing of the action potential. The methods of analysis consisted of 1) the comparison of quantal contents obtained from direct counting or by measuring of the size of the responses and 2) the analysis of distributions of quantal latencies. This analysis revealed a large error in the detection of quantal events for responses simulated with no quantal interaction. In contrast, very few errors in quantal detection were made in the analysis of experimental recordings. Latency histograms of recorded responses demonstrate that the proportion of late quantal events (those with latencies of >/=5 ms) increased as a function of quantal content. This shift in latency histograms was not observed for simulated responses. Our interpretation is that quanta interact presynaptically to cause asynchrony of quantal events in evoked responses.

Action Potentials↗
PubMed2006

Emerging imaging techniques.

This article reviews recent developments in selected imaging technologies focused on the cardiovascular system. The techniques covered are: ultrasound biomicroscopy (UBM), microSPECT, microPET, near infrared imaging, and quantum dots. For each technique, the basic physical principles are explained and recent example applications demonstrated.

Animals↗
PubMed2006

Ground and excited states of retinal schiff base chromophores by multiconfigurational perturbation theory.

We have studied the wavelength dependence of retinal Schiff base absorbencies on the protonation state of the chromophore at the multiconfigurational level of theory using second order perturbation theory (CASPT2) within an atomic natural orbital basis set on MP2 optimized geometries. Quantitative agreement between calculated and experimental absorption maxima was obtained for protonated and deprotonated Schiff bases of all-trans- and 11-cis-retinal and intermediate states covering a wavelength range from 610 to 353 nm. These data will be useful as reference points for the calibration of more approximate schemes.

Computer Simulation↗
PubMed2006

Multicolor quantum dots for molecular diagnostics of cancer.

In the pursuit of sensitive and quantitative methods to detect and diagnose cancer, nanotechnology has been identified as a field of great promise. Semiconductor quantum dots are nanoparticles with intense, stable fluorescence, and could enable the detection of tens to hundreds of cancer biomarkers in blood assays, on cancer tissue biopsies, or as contrast agents for medical imaging. With the emergence of gene and protein profiling and microarray technology, high-throughput screening of biomarkers has generated databases of genomic and expression data for certain cancer types, and has identified new cancer-specific markers. Quantum dots have the potential to expand this in vitro analysis, and extend it to cellular, tissue and whole-body multiplexed cancer biomarker imaging.

Animals↗
PubMedDate not supplied

[Quant efficiency of the detection as a quality parameter of the visualization equipment].

The critical parameter of notion "quant efficiency of detection" is defined in the paper. Different methods of specifying the detection quant efficiency (DQE) are under discussion. Thus, techniques of DQE determination for a whole unit and means of DQE finding at terminal space frequency are addressed. The notion of DQE at zero frequency is in the focus of attention. Finally, difficulties occurring in determining the above parameter as well as its disadvantages (as a parameter characterizing the quality of X-ray irradiation visualizing systems) are also discussed.

Models, Theoretical↗
PubMed2005

Resonance Character of Hydrogen-bonding Interactions in Water and Other H-bonded Species.

Hydrogen bonding underlies the structure of water and all biochemical processes in aqueous medium. Analysis of modern ab initio wave functions in terms of natural bond orbitals (NBOs) strongly suggests the resonance-type "charge transfer" (CT) character of H-bonding, contrary to the widely held classical-electrostatic viewpoint that underlies current molecular dynamics (MD) modeling technology. Quantum cluster equilibrium (QCE) theory provides an alternative ab initio-based picture of liquid water that predicts proton-ordered two-coordinate H-bonding patterns, dramatically different from the ice-like picture of electrostatics-based MD simulations. Recent X-ray absorption and Raman scattering experiments of Nilsson and co-workers confirm the microstructural two-coordinate picture of liquid water. We show how such cooperative "unsaturated" ring/chain topologies arise naturally from the fundamental resonance-CT nature of B:cdots, three dots, centeredHA hydrogen bonding, which is expressed in NBO language as n(B)-->sigma(AH)(*) intermolecular delocalization from a filled lone pair n(B) of the Lewis base (B:) into the proximal antibond sigma(AH)(*) of the Lewis acid (HA). Stabilizing n(O)-->sigma(OH)(*) orbital delocalization, equivalent to partial mixing of resonance structures H(2)O:cdots, three dots, centeredHOH H(3)O(+) cdots, three dots, centered(-):OH, is thereby seen to be the electronic origin of general enthalpic and entropic propensities that favor relatively small cyclic clusters such as water pentamers W(5c) in the QCE liquid phase. We also discuss the thermodynamically competitive three-coordinate clusters (e.g., icosahedral water buckyballs, W(24)), which appear to play a role in hydrophobic solvation phenomena. We conclude with suggestions for incorporating resonance-CT aspects of H-bonding into empirical MD simulation potentials in a computationally tractable manner.

Hydrogen Bonding↗
PubMed2000

Molecular electronic density fitting using elementary Jacobi rotations under atomic shell approximation

Fitted electron density functions constitute an important step in quantum similarity studies. This fact not only is presented in the published papers concerning quantum similarity measures (QSM), but also can be associated with the success of the developed fitting algorithms. As has been demonstrated in previous work, electronic density can be accurately fitted using the atomic shell approximation (ASA). This methodology expresses electron density functions as a linear combination of spherical functions, with the constraint that expansion coefficients must be positive definite, to preserve the statistical meaning of the density function as a probability distribution. Recently, an algorithm based on the elementary Jacobi rotations (EJR) technique was proven as an efficient electron density fitting procedure. In the preceding studies, the EJR algorithm was employed to fit atomic density functions, and subsequently molecular electron density was built in a promolecular way as a simple sum of atomic densities. Following previously established computational developments, in this paper the fitting methodology is applied to molecular systems. Although the promolecular approach is sufficiently accurate for quantum QSPR studies, some molecular properties, such as electrostatic potentials, cannot be described using such a level of approximation. The purpose of the present contribution is to demonstrate that using the promolecular ASA density function as the starting point, it is possible to fit ASA-type functions easily to the ab initio molecular electron density. A comparative study of promolecular and molecular ASA density functions for a large set of molecules using a fitted 6-311G atomic basis set is presented, and some application examples are also discussed.

Journal Article↗
PubMed2006

A polarizable continuum approach for the study of heterogeneous dielectric environments.

We present a computational method, exploiting some features of the polarizable continuum model (PCM) to describe heterogeneous media; it belongs to the family of electrostatic embedding mixed methods, such as the more common quantum-mechanical (QM)/molecular mechanics approaches, with the electrostatic long range effects accounted for by a polarized continuum instead of atomic point charges. Provided effective dielectric constants are determined for the various parts of the system, the method is much faster than its atomistic counterpart, and allows for high-level QM calculations on the fragment of interest, using all the highly efficient computational tools developed for homogeneous PCM. Two case studies (the calculation of the pKa of solvent exposed acidic residues in a model protein, and the calculation of the electron spin resonance spectrum of a typical spin probe partially embedded in a membrane) are analyzed in some detail, to illustrate the application of the method to complex systems.

Algorithms↗
PubMedDate not supplied

Information and artifact in computed tomography image statistics.

In conventional computed tomography images only the average CT number, which is a first-order statistical parameter, is used to characterize the tissues by giving an estimate of tissue density. Second order statistical parameters such as the signal variance and cross-correlation function have also been used to obtain additional information to discriminate between certain tissues and lesions. However, the contribution of quantum noise to the signal variance and cross-correlation function creates, for the conventional CT patient dose, a background signal often larger than the signal containing the information about tissue structure. The misleading information, called "artifacts", in second-order image statistics caused by quantum noise, is studied.

Information Theory↗
PubMed2006

Cumulative reaction probabilities: A comparison between quasiclassical and quantum mechanical results.

This article presents a quasiclassical trajectory (QCT) method for determining the cumulative reaction probability (CRP) as a function of the total energy. The method proposed is based on a discrete sampling using integer values of the total and orbital angular momentum quantum numbers for each trajectory and on the development of equations that have a clear counterpart in the quantum mechanical (QM) case. The calculations comprise cumulative reaction probabilities at a given total angular momentum J, as well as those summed over J. The latter are used to compute QCT rate constants. The method is illustrated by comparing QCT and exact QM results for the H+H2, H+D2, D+H2, and H+HD reactions. The agreement between QCT and QM results is very good, with small discrepancies between the two data sets indicating some genuine quantum effects. The most important of these involves the value of the CRP at low energies which, due to the absence of tunneling, is lower in the QCT calculations, causing the corresponding rate constants to be smaller. The second is the steplike structure that is clearly displayed in the QM CRP for J = 0, which is much smoother in the corresponding QCT results. However, when the QCT density of reactive states, i.e., the derivatives of the QCT CRP with respect to the energy, is calculated, a succession of maxima and minima is obtained which roughly resembles those found in the QM calculations, although the latter are considerably sharper. The analysis of the broad peaks in the QCT density of reactive states indicates that the distributions of collision times associated with the maxima are somewhat broader, with a tail extending to larger collision times, than those associated with the minima. In addition, the QM and QCT dynamics of the isotopic variants mentioned above are compared in the light of their CRPs. Issues such as the compliance of the QCT CRP with the law of microscopic reversibility, as well as the similarity between the CRPs for ortho and para species in the QM and QCT cases, are also addressed.

Journal Article↗
PubMed2000

Use of electron-electron repulsion energy as a molecular descriptor in QSAR and QSPR studies.

Electron-electron repulsion energy ( ) is presented as a new molecular descriptor to be employed in QSAR and QSPR studies. Here it is shown that this electronic energy parameter is connected to molecular quantum similarity measures (MQSM), and as a consequence can be considered as a complement to steric and electronic parameters in description of molecular properties and biological responses of organic compounds. The present strategy considers the molecule as a whole, thus there is no need to employ contributions of isolated fragments as in many calculations of molecular descriptors, like log P or the Free-Wilson analysis. The procedure has been tested in a widespread set of molecules: alcohols, alkanamides, indole derivatives and 1-alkylimidazoles. Molecular properties, as well as toxicity, are correlated using as a parameter, and extensions to the method are given for handling difficult systems. In almost all studied cases, satisfactory linear relationships were finally obtained.

Computer-Aided Design↗
PubMed2005

New hints on the Ph-driven tautomeric equilibria of the topotecan anticancer drug in aqueous solutions from an integrated spectroscopic and quantum-mechanical approach.

The equilibria between the different forms of the topotecan anticancer drug have been studied at moderately acidic and physiological pH by an integrated computational tool rooted in the density functional theory and its time-dependent extension together with the polarizable continuum model. The results allow an unbiased selection between the different possible tautomeric forms and provide invaluable complements to experimental data. The ultraviolet-visible topotecan spectrum, recorded at moderately acidic pH, is accurately reproduced only by TD-DFT computations including solvent effects. Comparison of the experimental and calculated bands of the UV-vis spectrum at physiological pH indicates the presence of an equilibrium among different forms that is tuned by the microenvironment embedding the drug. The quantitative agreement between TD-DFT/PCM computations and experiments allows the identification of unequivocal spectroscopic signatures for different forms of topotecan.

Antineoplastic Agents↗
PubMed1999

Molecular recognition of modified adenine nucleotides by the P2Y(1)-receptor. 2. A computational approach.

The molecular recognition of C2- or C8-substituted ATP derivatives by the P2Y(1)-receptor (P2Y(1)-R) is analyzed using ab initio quantum mechanical calculations. Parameters that may determine ligand specificity toward P2Y(1)-R were examined on reduced models and correlated with the biochemical data for the parent compounds. These include tautomerism and protonation energy in the gas and aqueous phases, as well as molecular electrostatic potential (MEP) and dipole moment vector. The calculated electronic parameters cannot explain the inactivity of the C8-substituted ATP derivatives, nor the difference in activity among the C2-substituted ATP analogues. These results indicate that neither tautomerism nor changes in the electronic distribution of the adenine ring play a major role in determining binding specificity of adenine nucleotides to the receptor. It is suggested that the higher potency of the C2-substituted ATP derivatives, compared to ATP, might be due to interaction between the C2 side chain heteroatom and the receptor. Furthermore, the interaction of the C2 alkyl side chain with a hydrophobic pocket at the receptor binding site is suggested. In addition, NMR data in the companion paper indicate that the inactivity of the C8-substituted ATP analogues may be due to steric and conformational, rather than electronic, effects.

Adenine Nucleotides↗
PubMed2004

Quantum dynamics calculations using symmetrized, orthogonal Weyl-Heisenberg wavelets with a phase space truncation scheme. III. Representations and calculations.

In a previous paper [J. Theo. Comput. Chem. 2, 65 (2003)], one of the authors (B.P.) presented a method for solving the multidimensional Schrodinger equation, using modified Wilson-Daubechies wavelets, and a simple phase space truncation scheme. Unprecedented numerical efficiency was achieved, enabling a ten-dimensional calculation of nearly 600 eigenvalues to be performed using direct matrix diagonalization techniques. In a second paper [J. Chem. Phys. 121, 1690 (2004)], and in this paper, we extend and elaborate upon the previous work in several important ways. The second paper focuses on construction and optimization of the wavelength functions, from theoretical and numerical viewpoints, and also examines their localization. This paper deals with their use in representations and eigenproblem calculations, which are extended to 15-dimensional systems. Even higher dimensionalities are possible using more sophisticated linear algebra techniques. This approach is ideally suited to rovibrational spectroscopy applications, but can be used in any context where differential equations are involved.

Journal Article↗
PubMed2001

Molecular dynamics simulations of the mononuclear zinc-beta-lactamase from Bacillus cereus complexed with benzylpenicillin and a quantum chemical study of the reaction mechanism.

Herein, we present results from MD simulations of the Michaelis complex formed between the B. cereus zinc-beta-lactamase enzyme and benzylpenicillin. The structural and dynamical effects induced by substrate-binding, the specific role of the conserved residues, and the near attack conformers of the Michaelis complex are discussed. Quantum chemical methods (HF/6-31G* and B3LYP/6-31G*) are also applied to study the hydrolysis reaction of N-methylazetidinone catalyzed by a monozinc system consisting of the side chains of the histidine residues (His86, His88, and His149) complexed with Zn-OH and the side chains of Asp90 and His210. From this model system, we built molecular-mechanics representations of the prereactive complex and transition state configurations docked into the active site. Linear-scaling semiempirical calculations coupled with a continuum solvent model were then performed on these static models. We propose that the experimental rate data for the B. cereus enzyme is compatible with a one-step mechanism for the hydrolysis of beta-lactam substrates in which His210 acts as a proton donor.

Bacillus cereus↗
PubMed2006

Quantum catalysis in enzymes: beyond the transition state theory paradigm. A Discussion Meeting held at the Royal Society on 14 and 15 November 2005.

How do enzymes work? What is the physical basis of the phenomenal rate enhancements achieved by enzymes? Do we have a theoretical framework that accounts for observed catalytic rates? These are the foremost questions-with particular emphasis on tunnelling phenomena-debated at this Discussion Meeting by the leading practitioners in the field.

Biocatalysis↗