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PubMed1986

Hydrophobic and ionic hydration phenomena.

Computer simulation offers an increasing opportunity to examine the details of solvation structure for well-defined solution models. One can characterize idealized models that exemplify specific aspects of solution behavior or those that realistically model systems experimentally difficult to access. As an example from the first category, results are presented for the aqueous solvation structure and solvent hydrogen bonding in the presence of a small apolar solute, and these are contrasted with the quite different behavior observed for a large apolar surface. As an example from the second category, structural results are presented for hydration of an excess electron in bulk water. These latter results, obtained via recent path integral simulation methods, manifest significant solvent structural disruption compared to the case of a simple ion, due to the irregular and fluctuating shape of the quantum solute.

Chemical Phenomena↗
PubMed1980

[Determination of effective atomic number and electronic density by computed tomography with dual energies. Application to the thalamus (author's transl)].

The authors have studied seven thalamic hyperdense lesions of five patients in managing, at the same level, successively two scans with a computer tomograph at two different energies. After they recall their methodology of testing their C.T. and computations, they have found the effective atomic number and the electron density of these lesions. All (one Fahr disease and six old hemorrhages) have both high effective atomic number and electron density. They discuss the limits of this technic but they emphasize the great interest to see the chemical aspects of the structures observed in C.T.

Brain Diseases↗
PubMed1991

Interaction energy studies on antibiotics nucleoside analogs 2-azaadenine.

The 2-azaadenine antibiotic is known to be a potent cytotoxic nucleoside analog. Evaluation of the interaction energy of this molecule with nucleic acid bases and base pairs has been performed using a quantum-mechanical perturbation technique. Both in-plane and stacking energies have been computed. These energy values along with their sites of association have been compared with the standard energy values and spatial positions for the nucleic acid bases during transcription. The results have been examined in the light of their biological significance.

Adenine↗
PubMed1995

The application of stereolithography to the fabrication of accurate molecular models.

The process of stereolithography, which automatically fabricates plastic models from designs created in certain computer-aided design programs, has been applied to the production of accurate plastic molecular models. Atomic coordinates obtained from quantum mechanical calculations and from neutron diffraction data were used to locate spheres in the I-DEAS CAD program with radii proportional to the appropriate van der Waals radii. The sterolithography apparatus was used to build the models using a photosensitive liquid resin, resulting in hard plastic models that accurately represent the computed or experimental input structures. Three examples are given to illustrate how the models can be used to interpret experimental structure-activity data for systems of biological importance or host-guest chemistry: (1) Interpretation of kinetic data for the formation of a stable blocking complex between amiloride analogs and the epithelial sodium channel, (2) interpretation of binding and neural activity data for the interaction of certain amino acids and their analogs at the L-alanine taste receptor of the channel catfish, and (3) interpretation of shape selectivity and rate acceleration in cyclodextrin catalysis using models of the neutron diffraction structure of beta-cyclodextrin and of the transition state for the cleavage of phenyl acetate by the secondary hydroxyl oxygen of beta-cyclodextrin.

Acrylates↗
PubMed1995

Breakthrough of single-quantum coherence and its elimination in double-quantum filtering.

Breakthrough of single-quantum coherence is shown to occur after application of a double-quantum filter with the conventional four-step phase-cycling scheme. This single-quantum breakthrough is due to the intersequence stimulated echo which has been generated by the radiofrequency pulses in the preceding pulse sequence and appears at the same time as the double-quantum coherence signal in the current pulse sequence. Moreover, the phase of the intersequence stimulated echo is the same as the phase of the double-quantum coherence signal; i.e., the phase of the intersequence stimulated echo is twice the phase change of the radiofrequency pulses in the creation period when their phase is rotated in accordance with the conventional four-step phase-cycling scheme. Consequently, the intersequence stimulated echo passes through the double-quantum filtration in the conventional four-step phase-cycling scheme and gradient pulses. A new phase-cycling scheme which can filter out the single-quantum breakthrough signal is proposed here and its effectiveness is verified experimentally and by computer simulations.

Computer Simulation↗
PubMed1989

Computer modelling: future directions.

Recent developments in computing and in the theory of simulation have extended greatly the successes of the modelling of ionic crystals pioneered by Mott and Littleton. This has changed the way in which computer experiments are brought to bear on an increasing range of solid-state phenomena. Yet applied science creates new demands, both in the form of new types of system and in terms of the complexity and subtlety of what is studied. The author's brief survey looks at some of the successes and gaps from interfaces and catalysts to neurotransmitters and from superconductors to slags.

Computer Simulation↗
PubMed1992

Base compositional structure of genomes.

We model the base compositional structure of the human and Escherichia coli genomes. Three particular properties are first quantified: (1) There is a significant tendency for any region of either genome to have a strand-symmetric base composition. (2) The variation in base composition from region to region, within each genome, is very much larger than expected from common homogeneous stochastic models. (3) A given local base composition tends to persist over a scale of at least kilobases (E. coli) or tens of kilobases (human). Multidomain stochastic models from the literature are reviewed and sharpened. In particular, quantitative measurements of the third property lead us to suggest a significant shift in the style of domain models, in which the variation of A+T content with position is modeled by a random walk with frequent small steps rather than with large quantum jumps. As an application, we suggest a way to reduce the amount of computation in the assembly of large sequences from sequences of randomly chosen fragments.

Escherichia coli↗
PubMed1981

Time-resolved protein fluorescence studies of intermediates in the photochemical cycle of bacteriorhodopsin.

The photolysis-induced changes in the protein fluorescence intensity (at 320 nm) during the proton-pumping cycle of bacteriorhodopsin were examined by a delayed two-pulse technique in the time range 1 microsecond-20 msec at room temperature. No detectable change in the protein fluorescence intensity was observed on the earliest time scale within the lifetime of the intermediate K590, when retinal apparently undergoes the largest structural changes. The time dependence of the relative changes in fluorescence intensity did, however, display a close correlation with the population of the L550 and M412 intermediates. From a computer numerical fit of the data, with available published kinetic parameters, the protein fluorescence quantum yields of the K590, L550, and M412 intermediates are found to be 1.0, 0.92, and 0.80 of that for native bR570, respectively. The probable mechanisms of the observed fluorescence quenching during the photochemical cycle are qualitatively discussed.

Bacteriorhodopsins↗