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At least 1,783 records · Page 99Linked to original sources
PubMed2000

Optimization of x-ray imaging geometry (with specific application to flat-panel cone-beam computed tomography).

A theoretical method is presented that allows identification of optimal x-ray imaging geometry, considering the effects of x-ray source distribution, imaging task, x-ray scatter, and imager detective quantum efficiency (DQE). Each of these factors is incorporated into the ICRU-recommended figure of merit for image quality, the detectability index, which is maximized to determine the optimal system configuration. Cascaded systems analysis of flat-panel imagers (FPIs) is extended to incorporate the effects of x-ray scatter directly in the DQE, showing that x-ray scatter degrades DQE as an additive noise source. Optimal magnification is computed for FPI configurations appropriate to (but not limited to) cone-beam computed tomography (CBCT). The sensitivity of the results is examined as a function of focal spot size, imaging task (e.g., ideal observer detection or discrimination tasks), x-ray scatter fraction, detector resolution, and additive noise. Nominal conditions for FPI-CBCT result in optimal magnification of approximately 1.4-1.6, depending primarily on the magnitude of the x-ray scatter fraction. The methodology is sufficiently general that examination of optimal geometry for other FPI applications (e.g., chest radiography, fluoroscopy, and mammography) is possible. The degree to which increased exposure can be used to compensate for x-ray scatter degradation is quantified.

Algorithms↗
PubMed2002

[Digital mammography and computer assisted diagnosis].

Until recently, the film has remained the only medium of information in mammography. The film is used to record, to exploit, to store and to transmit the image. Computerization of images allows to dissociate and to optimize these different functions. Among classical factors of image quality (spatial resolution, contrast, noise), new factors should be added like the detective quantum efficiency and the conversion factor. Radioluminescent screens, then digital sensors for breast stereotactic imaging have been marketed. Manufacturers are now testing full field digital mammographs. Digital imaging allows many applications (computed-aided diagnostic, 3D imaging.) and permits the easy transfer of images for diagnosis and teaching. Three parts are presented in this chapter. The first one describes the different imaging modalities and gives a reminder of the different elements related to image quality. The second one is related to the practical aspects of full field mammography, the reading of mammograms on a review station, ergonomy in full field mammography and to possible changes for screening mammography. The third part is devoted to computed aided diagnosis and its possible application in screening.

Diagnosis, Computer-Assisted↗
PubMed2005

The excited-state chemistry of phycocyanobilin: a semiempirical study.

Based on previous time-resolved absorption studies, phycocyanobilin undergoes a photoreaction from an A- into a B- and C-form, with the latter two photoproducts showing absorption spectra red-shifted from A. To identify the molecular mechanism involved in the excited-state reactions, the structural origin of the red shift in the absorption spectra is investigated. Using semiempirical AM1 calculations that include configuration interaction by pair doubles excitation configuration interaction, the absorption spectra of different conformers as well as different protonation states were calculated. The results clearly indicate a pronounced red shift in the spectra of structures either protonated or deprotonated at the basic/acidic centres of the tetrapyrrole chromophore whereas, in contrast, conformational changes alone result in a blue shift. Furthermore, it is shown by quantum chemical calculations that the basicity of phycocyanobilin is much higher in the excited than in the ground state, with a decrease in the excited-state pK(B)* of approximately 9.5 units. The acidity is only slightly enhanced with a drop in pK(A)* of only approximately 1.6 units. From these findings, a reaction model for the excited-state processes in phycocyanobilin is proposed. According to this model, photoexcitation of phycocyanobilin triggers an excited-state proton transfer giving rise to the formation of a protonated species. In parallel, the local increase in the medium pH associated with protonation then forwards a deprotonation at an acidic NH-group so that in effect both protonated and deprotonated phycocyanobilin would arise from the initial photoreaction and account for the observed red shift in the spectra of the B- and C-forms.

Computer Simulation↗
PubMed2000

Nitric oxide binding to ferric cytochrome P450: a computational study.

The interaction between nitric oxide (NO) and the active site of ferric cytochrome P450 was studied by means of density functional theory (DFT), at the generalized gradient approximation level, and of the SAM1 semiempirical method. The electrostatic effects of the protein environment were included in our DFT scheme by using a hybrid quantum classical approach. The active-site model consisted of an iron(III) porphyrin, the adjacent cysteine residue, and one coordinated water molecule. For this system, spin populations and relative energies for selected spin states were computed. Interestingly, the unpaired electron density, the HOMO, and the LUMO were found to be highly localized on the iron and in an appreciable extent on the sulfur coordinated to the metal. This provides central information about the reactivity of nitric oxide with the active site. Since the substitution of a molecule of H2O by NO has been proposed as being responsible for the inhibition of the cytochrome in the presence of nitric oxide, we have analyzed the thermodynamic feasibility of the ligand exchange process. The structure of the nitrosylated active site was partially optimized using SAM1. A low-spin ground state was obtained for the nitrosyl complex, with a linear Fe-N-O angle. The trends found in Fe-N-O angles and Fe-N lengths of the higher energy spin states provided a notable insight into the electronic configuration of the complex within the framework of the Enemark and Feltham formalism. In relation to the protein environment, it was assessed that the electrostatic field has significant effects on several computed properties. However, in both vacuum and protein environments, the ligand exchange reaction turned out to be exergonic and the relative orders of spin states of the relevant species were the same.

Binding Sites↗
PubMed2003

Boundary of quantum evolution under decoherence.

Relaxation effects impose fundamental limitations on our ability to coherently control quantum mechanical phenomena. In this article, we use principles of optimal control theory to establish physical limits on how closely a quantum mechanical system can be steered to a desired target state in the presence of relaxation. In particular, we explicitly compute the maximum amplitude of coherence or polarization that can be transferred between coupled heteronuclear spins in large molecules at high magnetic fields in the presence of relaxation. Very general decoherence mechanisms that include cross-correlated relaxation have been included in our analysis. We give analytical characterization for the pulse sequences (control laws) that achieve these physical limits and provide supporting experimental evidence. Exploitation of cross-correlation effects has recently led to the development of powerful methods in NMR spectroscopy to study very large biomolecules in solution. For two heteronuclear spins, we demonstrate with experiments that cross-correlated relaxation optimized pulse (CROP) sequences provide significant gains over the state-of-the-art methods. It is shown that despite large relaxation rates, coherence can be transferred between coupled spins without any loss in special cases where cross-correlated relaxation rates can be tuned to autocorrelated relaxation rates.

Magnetic Resonance Spectroscopy↗
PubMed1998

Tautomeric equilibria in 8-oxopurines: implications for mutagenicity.

Free-radical-induced DNA damage by ionizing radiation leads to a number of oxidized purines, of which 7H-8-oxoguanine (8OG) and 7H-8-oxoadenine (8OA) are predominant and known to cause an appreciable amount of cellular damage. A detailed quantum mechanical study at various levels of theory in both the gas phase and in an aqueous solution has been carried out in order to assess the tautomeric preferences of the bases. The calculated energies of various plausible tautomers suggest that at higher levels of ab initio theory with inclusion of electron correlation, the 8-keto-6-enolic form of 8-oxoguanine (8OG2) would predominate over the 6,8-diketo form (8OG1) in the gas phase whereas the 6-amino-8-keto form (8OA1) predominates over the other possible tautomers of 8-oxoadenine. Aqueous solvation, however, changes the gas-phase order for 8-oxoguanine, 8OG1 turning out to be the major tautomeric species in an aqueous medium. The estimated free energies of hydration by polarized continuum models are indicative that the mutagenically significant amounts of minor tautomeric forms of 8-oxoguanine and 8-oxoadenine exist in the aqueous phase and might be held responsible for inducing transversional as well as transitional mutations.

Computer Simulation↗
PubMed2006

Theoretical analysis of high-resolution digital mammography.

The performance of a high-resolution charge coupled device-based full-field digital mammography imager was analysed using a mathematical framework based on an adaptation of cascaded linear systems theory described by other investigators. This work has been conducted in order to understand the impact of various design parameters on the physical performance characteristics of the imager. Specifically, the effect of pixel size, scintillator thickness and packing density, x-ray spectra, air kerma, dark current, charge integration time, and pixel fill-factor on the frequency dependent detective quantum efficiency was studied using a charge-coupled device as a reference platform. The imaging system was modelled as a series of physical processes with gain and spatial spreading. For each stage, the signal and noise power spectra were computed and propagated through the imaging chain as inputs to subsequent stages. Good agreement between experimental and theoretical predictions was obtained for various x-ray spectral conditions that were investigated. The modulation transfer function, MTF(f) and detective quantum efficiency DQE(f) characteristics obtained in this study are encouraging and comparable to other digital mammography systems. The results of this study strongly suggest the feasibility of large area scintillator-based digital mammography imagers with pixel sizes below 100 microm.

Algorithms↗
PubMed2003

Continuum and discrete calculation of fractional contributions to solvation free energy.

Approaches to compute fractional contributions to the solvation free energy are developed in the context of continuum self consistent reaction field calculations (both classical and quantum mechanical), as well as in the framework of discrete molecular dynamics simulations. It is found that for a series of typical pharmacological drugs there is a good agreement between the different fractional descriptions. Algorithms reported here can be easily applied as molecular descriptors in the context of quantitative structure-activity relationships.

Algorithms↗
PubMed2004

A canonical averaging in the second-order quantized Hamilton dynamics.

Quantized Hamilton dynamics (QHD) is a simple and elegant extension of classical Hamilton dynamics that accurately includes zero-point energy, tunneling, dephasing, and other quantum effects. Formulated as a hierarchy of approximations to exact quantum dynamics in the Heisenberg formulation, QHD has been used to study evolution of observables subject to a single initial condition. In present, we develop a practical solution for generating canonical ensembles in the second-order QHD for position and momentum operators, which can be mapped onto classical phase space in doubled dimensionality and which in certain limits is equivalent to thawed Gaussian. We define a thermal distribution in the space of the QHD-2 variables and show that the standard beta=1/kT relationship becomes beta'=2/kT in the high temperature limit due to an overcounting of states in the extended phase space, and a more complicated function at low temperatures. The QHD thermal distribution is used to compute total energy, kinetic energy, heat capacity, and other canonical averages for a series of quartic potentials, showing good agreement with the quantum results.

Journal Article↗
PubMed2005

IR spectra of N-methylacetamide in water predicted by combined quantum mechanical/molecular mechanical molecular dynamics simulations.

We applied the combined quantum mechanical (QM)/molecular mechanical (MM) molecular dynamics (MD) simulation method in assessing IR spectra of N-methylacetamide and its deuterated form in aqueous solutions. The model peptide is treated at the Austin Model 1 (AM1) level and the induced dipole effects by the solvent are incorporated in fluctuating solute dipole moments, which are calculated using partial charges from Mulliken population analyses without resorting to any available high-level ab initio dipole moment data. Fourier transform of the solute dipole autocorrelation function produces in silico IR spectra, in which the relative peak intensities and bandwidths of major amide bands are quantitatively compatible with experimental results only when both geometric and electronic polarizations of the peptide by the solvent are dealt with at the same quantum-mechanical level. We cast light on the importance of addressing dynamic charge fluctuations of the solute in calculating IR spectra by comparing classical and QM/MM MD simulation results. We propose the adjustable scaling factors for each amide mode to be directly compared with experimental data.

Acetamides↗
PubMedDate not supplied

In silico prediction of buffer solubility based on quantum-mechanical and HQSAR- and topology-based descriptors.

We present an artificial neural network (ANN) model for the prediction of solubility of organic compounds in buffer at pH 6.5, thus mimicking the medium in the human gastrointestinal tract. The model was derived from consistently performed solubility measurements of about 5000 compounds. Semiempirical VAMP/AM1 quantum-chemical wave function derived, HQSAR-derived logP, and topology-based descriptors were employed after preselection of significant contributors by statistical and data mining approaches. Ten ANNs were trained each with 90% as a training set and 10% as a test set, and deterministic analysis of prediction quality was used in an iterative manner to optimize ANN architecture and descriptor space, based on Corina 3D molecular structure and AM1/COSMO single point wave function. In production mode, a mean prediction value of the 10 ANNs is created, as is a standard deviation based quality parameter. The productive ANN based on Corina geometries and AM1/COSMO wave function gives an r2cv of 0.50 and a root-mean-square error of 0.71 log units, with 87 and 96% of the compounds having an error of less than 1 and 1.5 log units, respectively. The model is able to predict permanently charged species, e.g. zwitterions or quaternary amines, and problematic structures such as tautomers and unresolved diastereomers almost as well as neutral compounds.

Buffers↗
PubMed2006

Towards optimization in digital chest radiography using Monte Carlo modelling.

A Monte Carlo based computer model of the x-ray imaging system was used to investigate how various image quality parameters of interest in chest PA radiography and the effective dose E vary with tube voltage (90-150 kV), additional copper filtration (0-0.5 mm), anti-scatter method (grid ratios 8-16 and air gap lengths 20-40 cm) and patient thickness (20-28 cm) in a computed radiography (CR) system. Calculated quantities were normalized to a fixed value of air kerma (5.0 microGy) at the automatic exposure control chambers. Soft-tissue nodules were positioned at different locations in the anatomy and calcifications in the apical region. The signal-to-noise ratio, SNR, of the nodules and the nodule contrast relative to the contrast of bone (C/C(B)) as well as relative to the dynamic range in the image (C(rel)) were used as image quality measures. In all anatomical regions, except in the densest regions in the thickest patients, the air gap technique provides higher SNR and contrast ratios than the grid technique and at a lower effective dose E. Choice of tube voltage depends on whether quantum noise (SNR) or the contrast ratios are most relevant for the diagnostic task. SNR increases with decreasing tube voltage while C/C(B) increases with increasing tube voltage.

Humans↗
PubMed2003

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations.

Molecular mechanics models have been applied extensively to study the dynamics of proteins and nucleic acids. Here we report the development of a third-generation point-charge all-atom force field for proteins. Following the earlier approach of Cornell et al., the charge set was obtained by fitting to the electrostatic potentials of dipeptides calculated using B3LYP/cc-pVTZ//HF/6-31G** quantum mechanical methods. The main-chain torsion parameters were obtained by fitting to the energy profiles of Ace-Ala-Nme and Ace-Gly-Nme di-peptides calculated using MP2/cc-pVTZ//HF/6-31G** quantum mechanical methods. All other parameters were taken from the existing AMBER data base. The major departure from previous force fields is that all quantum mechanical calculations were done in the condensed phase with continuum solvent models and an effective dielectric constant of epsilon = 4. We anticipate that this force field parameter set will address certain critical short comings of previous force fields in condensed-phase simulations of proteins. Initial tests on peptides demonstrated a high-degree of similarity between the calculated and the statistically measured Ramanchandran maps for both Ace-Gly-Nme and Ace-Ala-Nme di-peptides. Some highlights of our results include (1) well-preserved balance between the extended and helical region distributions, and (2) favorable type-II poly-proline helical region in agreement with recent experiments. Backward compatibility between the new and Cornell et al. charge sets, as judged by overall agreement between dipole moments, allows a smooth transition to the new force field in the area of ligand-binding calculations. Test simulations on a large set of proteins are also discussed.

Algorithms↗
PubMed2004

Development of high quantum efficiency, flat panel, thick detectors for megavoltage x-ray imaging: a novel direct-conversion design and its feasibility.

Most electronic portal imaging devices (EPIDs) developed to date, including recently developed flat panel systems, have low x-ray absorption, i.e., low quantum efficiency (QE) of 2%-4% as compared to the theoretical limit of 100%. A significant increase of QE is desirable for applications such as a megavoltage cone-beam computed tomography (MVCT) and megavoltage fluoroscopy. However, the spatial resolution of an imaging system usually decreases significantly with an increase of QE. The key to the success in the design of a high QE detector is therefore to maintain the spatial resolution. Recently, we demonstrated theoretically that it is possible to design a portal imaging detector with both high QE and high resolution [see Pang and Rowlands, Med. Phys. 29, 2274 (2002)]. In this paper, we introduce such a novel design consisting of a large number of microstructured plates (made by, e.g., photolithographic patterning of evaporated or electroplated layers) packed together and aligned with the incident x rays. On each plate, microstrip charge collectors are focused toward the x-ray source to collect charges generated in the ionization medium (e.g., air or gas) surrounded by high-density materials that act as x-ray converters. The collected charges represent the x-ray image and can be read out by various means, including a two-dimensional (2-D) active readout matrix. The QE, spatial resolution, and sensitivity of the detector have been calculated. It has been shown that the new design will have a QE of more than an order of magnitude higher and a spatial resolution equivalent to that of flat panel systems currently used for portal imaging. The new design is also quantum noise limited down to very low doses (approximately 1-2 radiation pulses of the linear accelerator).

Equipment Design↗
PubMed2005

Scaled quantum chemical studies of the structure and vibrational spectra of 2-(methylthio) benzimidazole.

The solid phase FT-IR and FT-Raman spectra of 2-(methylthio) benzimidazole (2-MTBI) have been recorded in the regions 4000-50 cm(-1) and 3500-100 cm(-1), respectively. The spectra were interpreted with the aid of normal coordinate analysis following full structure optimization and force field calculations based on density functional theory (DFT) using standard B3LYP/6-31G* and B3LYP/6-311+G** methods and basis set combinations and was scaled using various scale factors yielding fairly good agreement between observed and calculated frequencies. Based on the present good quality scaled quantum mechanical (SQM) force field, a reliable description of the fundamentals was provided and the assignments have been proposed with the aid of normal coordinate analysis. The infrared and Raman spectra were also predicted from the calculated intensities. Comparison of the simulated spectra with the experimental spectra provides important information about the ability of the computational method to describe the vibrational modes.

Benzimidazoles↗
PubMed1996

Quantum molecular modeling of the interaction between guanine and alkylating agents--1--sulfur mustard.

Interaction between Guanine and the episulfonium form of Sulfur mustard (HD) was studied using the ab initio LCAO-MO method at the HF/6-31G level. The alkylation mechanism on guanine-N7 was analyzed by using a supermolecular modeling. Our stereostructural results associated with the molecular electrostatic potentials and HOMO-LUMO properties, show that in vacuum the alkylation of the N7 of guanine by HD in the aggressive episulfonium form is a direct process without transition state and of which the pathway is determined.

Alkylating Agents↗
PubMed2002

Electronic excitations of biomolecules studied by quantum chemistry.

Significant methodological advances have been made over the past ten years in developing reliable quantum chemical methods for the treatment of electronically excited states. These methods can nowadays be used routinely by the experienced researcher to accurately compute excitation spectra of medium-sized organic molecules; results have been reported for several popular photobiological systems, including green fluorescent protein. First steps are currently being taken to account for the solvochromic shifts of chromophore excitations caused by particular protein environments and to dynamically simulate photochemical reactions in the excited states.

Bacterial Proteins↗
PubMed2006

Protein-bound chromophores astaxanthin and phytochromobilin: excited state quantum chemical studies.

We present an overview of excited state quantum chemical calculations aimed at elucidating controversial issues regarding the photochemistry of the protein-bound chromophores astaxanthin and phytochromobilin. In particular, we show how the application of time-dependent density functional theory and other single-reference quantum chemical excited state methods have contributed to shed new light on the origin of the >0.5 eV bathochromic shift of the electronic absorption by the carotenoid astaxanthin in the protein macromolecular complex crustacyanin, and the mechanism for C15-Z,syn --> C15-E,anti isomerization of the tetrapyrrole phytochromobilin that underlies the photoactivation of the plant photoreceptor phytochrome. Within the approximation that exciton coupling is neglected, the calculations on astaxanthin provide support for the notion that the bathochromic shift, which is responsible for the slate-blue coloration of lobster shell, is due to polarization rather than a conformational change of the chromophore in the protein-bound state. Furthermore, the polarization is attributed to a hydrogen-bonded protonated histidine residue. The calculations on phytochromobilin, in turn, suggest that a stepwise C15-Z,syn --> C15-E,syn (photochemical), C15-E,syn --> C15-E,anti (thermal) mechanism is much more favorable than a concerted, fully photochemical mechanism, and that neutral forms of the chromophore are much less likely to photoisomerize than the parent, protonated form. Accordingly, the calculations indirectly support the view that the photoactivation of phytochrome does not involve a proton transfer from the chromophore to the surrounding protein.

Biliverdine↗