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At least 433 records · Page 24Linked to original sources
PubMed1999

Noise power spectra of images from digital mammography detectors.

Noise characterization through estimation of the noise power spectrum (NPS) is a central component of the evaluation of digital x-ray systems. We begin with a brief review of the fundamentals of NPS theory and measurement, derive explicit expressions for calculation of the one- and two-dimensional (1D and 2D) NPS, and discuss some of the considerations and tradeoffs when these concepts are applied to digital systems. Measurements of the NPS of two detectors for digital mammography are presented to illustrate some of the implications of the choices available. For both systems, two-dimensional noise power spectra obtained over a range of input fluence exhibit pronounced asymmetry between the orthogonal frequency dimensions. The 2D spectra of both systems also demonstrate dominant structures both on and off the primary frequency axes indicative of periodic noise components. Although the two systems share many common noise characteristics, there are significant differences, including markedly different dark-noise magnitudes, differences in NPS shape as a function of both spatial frequency and exposure, and differences in the natures of the residual fixed pattern noise following flat fielding corrections. For low x-ray exposures, quantum noise-limited operation may be possible only at low spatial frequency. Depending on the method of obtaining the 1D NPS (i.e., synthetic slit scanning or slice extraction from the 2D NPS), on-axis periodic structures can be misleadingly smoothed or missed entirely. Our measurements indicate that for these systems, 1D spectra useful for the purpose of detective quantum efficiency calculation may be obtained from thin cuts through the central portion of the calculated 2D NPS. On the other hand, low-frequency spectral values do not converge to an asymptotic value with increasing slit length when 1D spectra are generated using the scanned synthetic slit method. Aliasing can contribute significantly to the digital NPS, especially near the Nyquist frequency. Calculation of the theoretical presampling NPS and explicit inclusion of aliased noise power shows good agreement with measured values.

Biophysics↗
PubMed2002

Computational approaches to the prediction of the blood-brain distribution.

This review attempts to summarise present knowledge related to the theoretical modelling of drug transport across the blood-brain barrier. Several computational protocols are described ranging from quantum mechanics-based approaches through molecular mechanics-related techniques to simple and fast procedures based on only the 2-D graph of the investigated structures. Amazingly, few descriptors have been shown to influence the derived relationships in a significant manner and a cornerstone in most of the described models are terms describing hydrogen bonding. A very quick quantitative assessment of the brain partitioning of a compound has also been devised using the following two rules: If N+O (the number of nitrogen and oxygen atoms) in a molecule is less than or equal to five, it has a high chance of entering the brain. The second rule predicts that if log P-(N+O) is positive then log BB is positive.

Algorithms↗
PubMed1991

Molecular structure and dynamics of cis(Z)-and trans(E)-flupenthixol and clopenthixol.

The three-dimensional structures and molecular electrostatic potentials of the cis(Z) and trans(E)-isomers of flupenthixol and clopenthixol were examined by computer graphics and molecular mechanical and quantum mechanical calculations, and their internal molecular motions were studied by molecular dynamics simulations in vacuo and in aqueous solution. The simulations demonstrated that both the side chains and the tricyclic ring systems of clopenthixol and flupenthixol are highly flexible. The angle between the two phenyl ring planes varied between 105 and 171 degrees during the simulations in solution. The electrostatic potentials around the 2-substituent were significantly more negative in the trans(E)-isomers than in the cis(Z)-isomers. The stronger negative potentials may weaken electrostatic receptor interactions and, thereby, cause the trans(E)-isomers to be less active than cis(Z)-isomers. Differences both in three-dimensional structure and in electronic structure may cause the difference in pharmacological activity between cis(Z)- and trans(E)-thioxanthenes.

Clopenthixol↗
PubMed1991

Three-dimensional structure and molecular dynamics of cis(Z)- and trans(E)-chlorprothixene.

cis(Z)-Chlorprothixene has antidopaminergic potency, while trans(E)-chlorprothixene is virtually inactive. In order to reveal the structural features causing the difference in activity, the three-dimensional molecular and electronic structures of cis(Z)- and trans(E)-chlorprothixene were examined by computer graphics and molecular mechanical and quantum mechanical calculations. The internal molecular motions of the isomers were studied by molecular dynamics simulations in vacuo and in aqueous solution. The cis(Z)-isomer had lower potential molecular energy than the trans(E)-isomer, mainly due to electrostatic interactions within the side-chain and between the dimethylamino group and the chlorine atom. During molecular dynamics simulations in aqueous solution, the side-chain of the trans(E)-isomer stayed closer to the central S-C axis of the ring system than did the side-chain of the cis(Z)-isomer. The molecular electrostatic potentials were significantly lower in the vicinity of the chlorine atom in the trans(E)- than in the cis(Z)-isomer. Differences in molecular electrostatic potentials and in three-dimensional structure are suggested to be the main reasons for the difference in pharmacological activities of cis(Z)- and trans(E)-chlorprothixene.

Chlorprothixene↗
PubMed1987

Nuclear magnetic resonance spectroscopic and computer-stimulated structural analyses of a heptapeptide sequence found around the N-glycosylation site of a proline-rich glycoprotein from human parotid saliva.

The proline-rich glycoprotein from human parotid saliva has a common heptapeptide sequence around four of six N-glycosylation sites (Maeda, N., H. S. Kim, E. A. Azen, and O. J. Smithies, 1985, J. Biol. Chem., 20:11123-11130). A synthetic model of the heptamer protein sequence, NH2-Q(1)-G(2)-G(3)-N(4)-Q(5)-S(6)-Q(7)-CONH2, was examined by nuclear magnetic resonance (NMR) spectroscopy and the ECEPP/2-VAO4A (Empirical Conformation Energy Program for Peptides) energy minimization computer algorithm (Scheraga, H. A., 1982, Quantum Chemistry Program Exchange, 454; Powell, M. J. D., 1964, Quantum Chemistry Program Exchange, 60). The NMR spectrum was almost completely assigned in dimethylsulfoxide-d6 (DMSO), and the amide chemical shift temperature dependence, phi dihedral angles, and chi 1 rotamer populations elucidated. These data indicated that a significant population of the heptamer could exist as a type I beta-turn [4----1 between Q(5) and G(2)] and/or a type II' beta-turn [4----1 between (Q)5 and G(2) and/or a gamma-turn [3----1 between Q(5) and G(3)] with the amino acid chi 1 torsion angles weighted toward the gauche- conformation. Starting from these three possible conformations, the ECEPP/2-VAO4A rigid geometry energy minimization program was used to find the localized predominant in vacuo structures of this heptapeptide sequence. The type II' beta-turn conformation best fits the data based on internuclear hydrogen-bonding distances, minimum potential energy considerations, and the NMR parameters.

Computer Simulation↗
PubMed1987

Osteoporosis: the state of the art in 1987: a review.

Osteoporosis affects approximately 15 to 20 million people in the United States and is the underlying cause of 1.3 million new fractures per year in people over age 45. The more common risk factors recognized in this disorder are older age, female sex, white race, physical inactivity, and early menopause. We now have available equipment which can measure bone density at various sites. These include single- and dual-photon densitometry, and single and dual quantitative computed tomography. These procedures are a quantum improvement over plain x-ray in the assessment of the severity of osteoporosis, but measurement at one site may not reflect the density at other sites. The value of these techniques in screening the general population for osteoporosis remains to be demonstrated. They are valuable when used to monitor patients longitudinally to assess the progression of disease and the effects of specific therapeutic regimens. There is no established effective therapy for osteoporosis so prevention is the goal. The effectiveness of different programs of physical activity in preventing bone loss and fractures is unknown but isotonic exercises three times a week for thirty minutes is recommended. There is general agreement that adequate calcium intake is important for maintenance of skeletal integrity, but there is no proof that a high dietary calcium alone will prevent osteoporosis. Estrogen therapy clearly prevents the accelerated bone loss which occurs in all white women at the time of menopause, but the question still remains who should be started on estrogens, and within what period of time after menopause are estrogens still useful in preventing postmenopausal bone loss, and for how long do we continue hormone therapy. Many questions are left to be answered but at least now osteoporosis is recognized as a major medical problem and much research is being done to answer the above questions.

Aged↗
PubMed2000

Stereoselectivity and chiral recognition in copper(I) olefin complexes with a chiral diamine

Trigonal copper(I) complexes of the chiral bidentate ligand (1S,2S)-N,N'-Bis-(mesitylmethyl)-1,2-diphenyl-1,2-ethanediamine ((S,S)-1) have been prepared with hydrocarbon olefins, as well as with allylic alcohols and ethers. The stereochemistry of the complexes has been investigated by 1H NMR spectroscopy and by combined quantum mechanics and molecular mechanics (QM/MM) computational methods. The coordinated chiral nitrogen atoms can display equal (R, R) or opposite (R, S) configuration, the latter being disfavored if steric hindrance is present above and below the coordination plane. Although the complexes exist as rapidly equilibrated mixtures of stereoisomers, one of these is often dominant, and prochiral olefins are coordinated with high enantioface selection. In addition, the [(S,S)-1]-Cu+ fragment selectively recognizes the R enantiomer of secondary allylic alcohols and ethers, as confirmed by the X-ray crystal structure analysis of the adduct with (R)-1-buten-3-ol. The reasons for the observed selectivities have been elucidated, and lead to some implications which are consistent with the enantioselection observed in catalytic cyclopropanation reactions promoted by copper complexes of the same ligand.

Journal Article↗
PubMed1992

On the suitability of semiempirical calculations as sources of force field parameters.

The suitability of Dewar's Hamiltonians as a source of bonded force field parameters is explored from the comparison analysis between up to 270 semiempirically derived force field parameters and experimentally derived values reported in some of the most popular force fields. From the statistical analysis of the results, some general conclusions about the semiempirical parametrization are formulated.

Mathematical Computing↗
PubMed1993

Fluorescence decay of DPH in lipid membranes: influence of the external refractive index.

The radiative decay rate of a fluorescent probe in an optically thin layer is known to depend on the orientation of the probe and on the refractive indices inside and outside the layer (W. Lukosz, Phys. Rev. B 22 (1980) 3030). Fluorescent probes in phospholipid bilayer membranes approximate such a system. The natural lifetime is expected to vary with the refractive index of the medium surrounding the bilayer. The lifetime variation with the refractive index depends on the orientation of the fluorescent probe. This can be used to retrieve the second-rank orientational order parameter, . The fluorescence decay of all-trans 1,6-diphenyl-1,3,5-hexatriene in L-alpha-dipalmitoyl-phosphatidylcholine large unilamellar vesicles (LUVs) was measured at a temperature well below that of the phase transition. The refractive index of the medium was varied by addition of glycerol or sucrose. The observed change of decay time with the refractive index followed the theoretical prediction. The value of the order parameter, , recovered is significantly lower than that obtained from fluorescence polarization data. Possible reasons for this disagreement are discussed.

1,2-Dipalmitoylphosphatidylcholine↗
PubMedDate not supplied

Scanning tunneling microscopy and spectroscopy investigations of QCA molecules.

Quantum-dot cellular automata (QCA), a computation paradigm based on the Coulomb interactions between neighboring cells. The key idea is to represent binary information, not by the state of a current switch (transistor), but rather by the configuration of charge in a bistable cell. In its molecular realization, the QCA cell can be a single molecule. QCA is ideally suited for molecular implementation since it exploits the molecule's ability to contain charge, and does not rely on any current flow between the molecules. We have examined using an UHV-STM some of the QCA molecules like silicon phthalocyanines and Fe-Ru complexes on Au (111) and Si (111) surfaces, which are suitable candidates for the molecular QCA approach.

Journal Article↗
PubMed2003

Optical spectroscopic investigations of model beta-sheet hairpins in aqueous solution.

In this contribution we report optical spectroscopic data on a series of designed beta hairpins previously shown by NMR to contain a substantial population of beta-sheet structure. These models contain a designed hydrophobic cluster and a (D)Pro-Gly sequence to promote formation of a turn geometry. FTIR, electronic and vibrational CD (ECD and VCD) spectra for these small peptides are comparable to expected bandshapes for peptides of high beta-sheet content. The (D)Pro-Gly sequence provides a better turn motif than Asn-Gly as measured by its beta-sheet spectral characteristics. IR and VCD spectra are in qualitative agreement with theoretical simulations based on transfer of parameters from ab initio quantum mechanical force field and intensity computations for the turn and strands. These calculations provide assignments for some distinguishing modes in both IR and VCD spectra. Increased sheet structure can be induced in these hairpins by use of mixed solvent conditions. Thermal denaturation studies reveal that these hairpins undergo very broad unfolding transitions. Guanidine hydrochloride unfolding transitions for the selected hairpin models are similarly broad. However, the "end-states" of temperature and chaotropic denaturation are spectroscopically differentiable.

Circular Dichroism↗
PubMed2002

Descriptors, physical properties, and drug-likeness.

We have investigated techniques for distinguishing between drugs and nondrugs using a set of molecular descriptors derived from semiempirical molecular orbital (AM1) calculations. The "drug" data set of 2105 compounds was derived from the World Drug Index (WDI) using a procedure designed to select real drugs. The "nondrug" data set was the Maybridge database. We have first investigated the dimensionality of physical properties space based on a set of 26 descriptors that we have used successfully to build absorption, distribution, metabolism, and excretion-related quantitative structure-property relationship models. We discuss the general nature of the descriptors for physical property space and the ability of these descriptors to distinguish between drugs and nondrugs. The third most significant principal component of this set of descriptors serves as a useful numerical index of drug-likeness, but no others are able to distinguish between drugs and nondrugs. We have therefore extended our set of descriptors to a total of 66 and have used recursive partitioning to identify the descriptors that can distinguish between drugs and nondrugs. This procedure pointed to two of the descriptors that play an important role in the principal component found above and one more from the set of 40 extra descriptors. These three descriptors were then used to train a Kohonen artificial neural net for the entire Maybridge data set. Projecting the drug database onto the map obtained resulted in a clear distinction not only between drugs and nondrugs but also, for instance, between hormones and other drugs. Projection of 42 131 compounds from the WDI onto the Kohonen map also revealed pronounced clustering in the regions of the map assigned as druglike.

Chemical Phenomena↗
PubMed1995

Synthesis and characterization of adducts of alachlor and 2-chloro-N-(2,6-diethylphenyl)acetamide with 2'-deoxyguanosine, thymidine, and their 3'-monophosphates.

Adducts of the preemergence herbicide 2-chloro-N-(methoxymethyl)-N-(2,6-diethylphenyl)-acetamide (alachlor) and 2-chloro-N-(2,6-diethylphenyl)acetamide (CDEPA) with 2'-deoxyguanosine, thymidine, 2'-deoxyguanosine 3'-monophosphate, and thymidine 3'-monophosphate have been synthesized and characterized. Under mildly basic conditions alachlor and CDEPA form N-1 adducts with 2'-deoxyguanosine and N-3 adducts with thymidine as a result of chlorine displacement. In addition, alachlor formed an N-7 adduct with 2'-deoxyguanosine, 7-[[(N-(methoxymethyl)-N-(2,6-diethylphenyl)carbamoyl]methyl]guani ne. N-1 adducts of alachlor and CDEPA with 2'-deoxyguanosine 3'-monophosphate and N-3 adducts with thymidine 3'-monophosphate are also described. In addition to spectroscopic data, structural proof included the dephosphorylation of each nucleotide adduct to its corresponding nucleoside adduct by nuclease P1. Alachlor and alachlor adducts but not CDEPA and CDEPA adducts exhibited rotational isomerism as evidenced by proton and 13C NMR studies. These rotamers were attributed to hindered rotation about the shortened N-carbonyl bond. Computational methods employing molecular mechanics and quantum mechanics were used to characterize the structures and energies of these rotamers to account for the patterns of duplicate NMR resonances observed.

Acetamides↗
PubMed2003

Electrochemical potentials and pressures of biofluids from common experimental data.

Many biosystems are complex mixtures of disparate biofluids. To study contact and transport phenomena in these mixtures, one has to apply much information on the biofluids which are components of the mixtures. A lot of the corresponding data can be extracted by means of experiments. However, it is not always easy to obtain experimental results on rather deep physical characteristics of biofluids, especially if the bioparticles are complicated systems and the fluid coexists in the mixture with a large number of other fluids. In these cases, the necessary data can, in principle, be extracted from those results which are easier to obtain experimentally. The present work proposes a method to evaluate the biofluid equilibrium pressure and electrochemical potential from common experimental values of the fluid concentration and absolute temperature as well as the fluid-particle mass, volume and spin. In so doing, the nonzero values of the particle volume are accounted for. The procedure is illustrated with a numerical example on the fluid of red blood cells (or erythrocytes) in human blood. The pressure values obtained are 49.1 and 38.8 micropascals for men and women respectively whereas the electrochemical-potential values are -2.124 and -2.130 electronvolts for men and women respectively.

Body Fluids↗
PubMed2000

Entropy computing via integration over fractal measures.

We discuss the properties of invariant measures corresponding to iterated function systems (IFSs) with place-dependent probabilities and compute their Renyi entropies, generalized dimensions, and multifractal spectra. It is shown that with certain dynamical systems, one can associate the corresponding IFSs in such a way that their generalized entropies are equal. This provides a new method of computing entropy for some classical and quantum dynamical systems. Numerical techniques are based on integration over the fractal measures. (c) 2000 American Institute of Physics.

Journal Article↗
PubMed2000

Energetics of the interaction between water and the helical peptide group and its role in determining helix propensities.

The alanine helix provides a model system for studying the energetics of interaction between water and the helical peptide group, a possible major factor in the energetics of protein folding. Helix formation is enthalpy-driven (-1.0 kcal/mol per residue). Experimental transfer data (vapor phase to aqueous) for amides give the enthalpy of interaction with water of the amide group as approximately -11.5 kcal/mol. The enthalpy of the helical peptide hydrogen bond, computed for the gas phase by quantum mechanics, is -4.9 kcal/mol. These numbers give an enthalpy deficit for helix formation of -7.6 kcal/mol. To study this problem, we calculate the electrostatic solvation free energy (ESF) of the peptide groups in the helical and beta-strand conformations, by using the delphi program and parse parameter set. Experimental data show that the ESF values of amides are almost entirely enthalpic. Two key results are: in the beta-strand conformation, the ESF value of an interior alanine peptide group is -7.9 kcal/mol, substantially less than that of N-methylacetamide (-12.2 kcal/mol), and the helical peptide group is solvated with an ESF of -2.5 kcal/mol. These results reduce the enthalpy deficit to -1.5 kcal/mol, and desolvation of peptide groups through partial burial in the random coil may account for the remainder. Mutant peptides in the helical conformation show ESF differences among nonpolar amino acids that are comparable to observed helix propensity differences, but the ESF differences in the random coil conformation still must be subtracted.

Alanine↗
PubMed2003

Tuning heme redox potentials in the cytochrome C subunit of photosynthetic reaction centers.

The photosynthetic reaction center (RC) from Rhodopseudomonas viridis contains four cytochrome c hemes. They establish the initial part of the electron transfer (ET) chain through the RC. Despite their chemical identity, their midpoint potentials cover an interval of 440 mV. The individual heme midpoint potentials determine the ET kinetics and are therefore tuned by specific interactions with the protein environment. Here, we use an electrostatic approach based on the solution of the linearized Poisson-Boltzmann equation to evaluate the determinants of individual heme redox potentials. Our calculated redox potentials agree within 25 meV with the experimentally measured values. The heme redox potentials are mainly governed by solvent accessibility of the hemes and propionic acids, by neutralization of the negative charges at the propionates through either protonation or formation of salt bridges, by interactions with other hemes, and to a lesser extent, with other titratable protein side chains. In contrast to earlier computations on this system, we used quantum chemically derived atomic charges, considered an equilibrium-distributed protonation pattern, and accounted for interdependencies of site-site interactions. We provide values for the working potentials of all hemes as a function of the solution redox potential, which are crucial for calculations of ET rates. We identify residues whose site-directed mutation might significantly influence ET processes in the cytochrome c part of the RC. Redox potentials measured on a previously generated mutant could be reproduced by calculations based on a model structure of the mutant generated from the wild type RC.

Binding Sites↗
PubMed2000

Decay and slowing down of the multiquanta Davydov-like solitons in molecular chains.

Dynamics and the stability of the multivibron solitons in molecular chains have been examined by means of the perturbation method based upon the inverse scattering transform. We demonstrate that due to the coupling with phonons the soliton radiates energy which causes its slowing down and gradual decay of its amplitude. It was shown that the soliton lifetime depends strongly on temperature and the values of the basic physical parameters of the system. On the basis of these results the possible role of the multivibron solitons in the intramolecular vibrational energy transfer has been critically assessed.

Energy Transfer↗