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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↗
PubMed1992

The structure and properties of liquid water: recent theoretical advances.

Computer simulations of water, and of water in the neighborhood of biological materials, are now commonplace. However, from the molecular physicist's viewpoint existing models of water/water, water/solute, and water/substrate interactions are incorrect and potentially misleading. Almost all existing simulations of biological interest assume that the molecules are rigid, or at least that the bonds do not vibrate. In this paper we review recent advances in the theory of water interactions, emphasizing the need to construct potential energy surfaces that include vibrational degrees of freedom.

Computer Simulation↗
PubMed1986

Ab-initio quantum mechanical calculations of NMR chemical shifts in nucleic acids constituents. III. Chemical shift variations due to base stacking.

Ab inito computations of the different contributions to chemical shift variations due to intra and interstrand stacking are reported for the GC, CG, AT and TA sequences of a B DNA helix. The results obtained for the non hydrogen atoms of the GC stacks show that the chemical shift variations are mainly due to the polarization contribution, the term which decreases slowly with the intermolecular distance. Because of the weaker polarity of adenine and thymine the geometric and polarization contributions are of closer absolute magnitude for the non hydrogen atoms of the intrastrand stacks but the polarization term is the determining contribution in the corresponding interstrand stacks. For the protons which undergo smaller shifts due to the polarization (or electric field effects) the role of the geometric contribution is more important and is even the leading one for the hydrogens of cytosine and thymine in the case of intrastrand stacking. The charge transfer plus exchange term has a non negligeable value for a limited number of cases corresponding to the shortest intermolecular interatomic distances. These results are discussed in relation with the qualitative differences observed between the proton and carbon spectra of dinucleotides and B-DNA duplexes.

Base Composition↗
PubMed1975

Effect of aromatic molecules on the aggregation of C-phycocyanin. Quantum chemical calculations on phycocyanobilin and phycoerythrobilin.

The energies of the highest occupied and lowest empty molecular orbitals were calculated for the chromophore groups of the proteins phycocyanin and phycoerythrin. These tetrapyrrole groups on the algal proteins are shown to provide them with the potential of ating as efficient electron donors and acceptors. In addition, the pi electron charges and bond orders were also computed.

Chemical Phenomena↗
PubMed1985

Electron density calculations as an extension of protein structure refinement. Streptomyces griseus protease A at 1.5 A resolution.

Ab initio quantum mechanical calculations have been used to obtain details of the electron density distribution in a high-resolution refined protein structure. It is shown that with accurate atomic co-ordinates, electron density may be calculated with a quality similar to that which can be obtained directly from crystallographic studies of small organic molecules, and that this density contains information relevant to the understanding of catalysis. Atomic co-ordinates from the 1.8 A and 1.5 A resolution refinements of the crystal structure of protease A from Streptomyces griseus have been used to examine the influence of the environment on the electron density in the side-chain of the active site histidine (His57). The neighbouring aspartic acid 102 is the dominant factor in the environment, and quantum mechanical calculations have been performed on these two residues. Most interesting from the point of view of understanding the catalytic process is the effect that Asp102 has on the electron density in the region of the imidazole nitrogen (N epsilon 2) adjacent to the active site serine 195. In the positively charged imidazolium species, there is a polarization of the N epsilon 2-H bond, reducing the bonding density in a manner that may lower the height of the energy barrier for proton transfer. In the uncharged imidazole species, the proximity of Asp102 causes a movement of density from the lone pair region of the N epsilon 2 into the pi bonding region above and below the plane of the ring. Although it is shown that the primary effect of the aspartic acid is electrostatic, this movement is perpendicular to the direction of the electric field inducing it.

Amino Acid Sequence↗
PubMed1989

A new algorithm for deriving pulsatile blood flow waveforms tested using stimulated dynamic angiographic data.

In vascular pathology the assessment of disease severity and monitoring of treatment requires quantitative and reproducible measurements of arterial blood flow. We have developed a new technique for processing sequences of dynamic digital X-ray angiographic images. We have tested it using computer simulated angiographic data which includes the effect of pulsatile blood flow and X-ray quantum noise. A parametric image was formed in which the image grey-level represents dye concentration as a function of time and distance along a vessel segment. Adjacent concentration--distance profiles in the parametric image were re-registered along the vessel axis until a match occurred. A match was defined as the point where the sum of squares of the differences in the two profiles was a minimum. The distance translated per frame interval is equal to the bolus velocity. We have tested several contrast medium injection methods including constant flow and a range of discrete pulses per second. The technique proved to be robust and independent of injection technique. Average blood flow was measured for simulated pulsatile waveforms with mean flows of up to 650 ml/min (peak velocities up to 186 cm/s) in a range of diameters from 2 mm to 6 mm. The standard deviation of the error in the mean flow estimates over the whole range of velocities and vessel sizes was +/- 1.4 cm/s.

Algorithms↗
PubMed1976

Molecular orbital calculations for parabens: a possible mechanism of action.

Molecular orbital calculations were carried out on the series benzoic acid, p-hydroxybenzoic acid, methylparaben, and ethylparaben. The characteristic trends of this entire series of preservatives are demonstrated by these members. The computer program used was Iterated Extended Hückel Theory. These systems were characterized in terms of atomic charge distributions, effect of hydroxyl and ester groups (both sterically and electronically), preferred molecular conformations, and distinguishing features of molecular orbitals. Through this approach, it was hoped that a common mode of action for all members of this series could be detected and that the trend(s) in this feature would correlate with known trends in activity of members of this series.

Chemical Phenomena↗
PubMed1979

Classification of drugs by discriminant analysis using fragment molecular connectivity values.

An investigation was made into the use of linear and quadratic discriminant analysis, along with K nearest-neighbor analysis, in the classification of a set of 51 compounds which were divided into five therapeutic categories. By superimposing each compound on a pattern structure, as first proposed by Cammarata, eight positions were assigned on the molecule. Each position was coded with the numerical value of a descriptor index. Relative molar refraction, which was the index used by Cammarata, was compared with a number of molecular connective indices. For each of the indices studied, it was found that only four of the eight positions contributed significantly to between-class differences. It was also found that first-order molecular connectivity, calculated as the sum of the contributions of each of the bonds joining a given position, resulted in consistently fewer misclassifications as compared with the other indices. Using first-order molecular connectivity, validation procedures were performed on the original set of compounds, on random samples drawn from this set, and on a set of ten compounds not included in the analysis. The results obtained were highly data dependent, but they, nevertheless, suggest that molecular connectivity indices should prove useful in structural classification procedures.

Analysis of Variance↗
PubMed1990

[A comparison of statistical methods for quantal analysis in computer and physiological experiments].

Amplitude distributions of postsynaptic potentials were simulated in computer experiments on the basis of binomial statistics. Influences of the sample size (N) and noise standard deviation (Sn) on the determination of the quantal content (m) and quantal size (v) were studied. Four methods of the quantal parameter estimation were modified and used: histogram, variance, failure and combined method. Three last methods gave satisfactory estimations (within +/- 10%) at N = 500-1000 and Sn less than 2v. The histogram method was adequate at Sn less than or equal to v. Similar results were obtained at N = 50-200, when the experiment was repeated about ten times. Applicability of similar methods was confirmed by the analysis of an intracellular record of inhibitory postsynaptic potentials (N = 1333) from the sensorimotor cortex of rabbit.

Action Potentials↗
PubMed1986

Estimating the time course of evoked quantal release at the frog neuromuscular junction using end-plate current latencies.

The use of end-plate current (e.p.c.) latency measurements to estimate the time course of the stochastic probabilistic process governing evoked release was investigated in the sciatic nerve-sartorius muscle preparation of the frog, Rana pipiens. We also examined the possibility that the release of a quantum depresses or enhances the subsequent release of additional quanta. Muscle end-plates were voltage clamped at 3-4 degrees C. Quantal release was restricted to a short, or localized, region of the nerve terminal using Ca2+-free, EGTA Ringer solution and a Ca2+-filled micropipette. The number of e.p.c.s containing 0, 1, 2, etc. quanta were totalled and compared to numbers predicted using Poisson's theorem. The differences between the actual and predicted numbers of events were not significant at the nineteen junctions studied (P less than 0.05). The latency of the first quantum observed in several hundred e.p.c.s was measured and used to calculate an estimate, alpha 1(t), of the time-dependent, probabilistic process, alpha (t), governing all evoked quantal release (Barrett & Stevens, 1972b). In three experiments, all quantal latencies were measured to obtain the actual alpha (t). The alpha 1(t) function gave an excellent approximation of alpha (t) (P greater than 0.2), in real and simulated latency data. The latency of the second quantum in the e.p.c.s was measured and used to provide another estimate, alpha 2(t), of alpha (t). The alpha 2(t) function was lower (depressed) during the first few milliseconds of the evoked release period, relative to alpha 1(t). The difference was significant (P greater than 0.01) in all experiments. Our measurement procedures were tested using computer-generated 'e.p.c.s' containing randomly occurring 'quanta'. These tests showed that the early depression was due to inadequate detection of the second quantum in the e.p.c.s. The effect of Sr2+ on evoked release was examined using double-barrelled pipettes containing 1 M-SrCl2 and CaCl2 solutions. The major result was that the durations of alpha 1(t) and alpha 2(t) were equally lengthened in Sr2+, relative to Ca2+.

Animals↗
PubMed1991

Fractal and chaotic dynamics in nervous systems.

The chaotic aspects of brain structure and dynamics have been discussed. The relation of chaos to fractal processes in the brain from the neurosystems level down to the molecule has been explored. It is found that chaos appears to play an integral, though not necessarily exclusive role in function at all levels of organization from the neurosystems to the molecular and quantum levels. An interesting consequence involving the possible interface between chaotic dynamics and quantum physics has been discussed because of its potential significance is resolving several of the most intractable conceptual problems to do with computability, the brain and the mind (Blakemore and Greenfield, 1987; Hooper and Teresi, 1987; Rose, 1973; Searle, 1979; Penrose, 1986, 1989).

Action Potentials↗
PubMed1985

Profiles of evoked release along the length of frog motor nerve terminals.

In order to determine the relative probability of evoked transmitter release from different parts of frog motor nerve terminals, a technique has been developed in which single quantum end-plate potentials (e.p.p.s) are recorded by two intracellular electrodes, located at opposite ends of identified junctions. The log of the ratio of the amplitudes recorded simultaneously at the two electrodes is a linear function of the distance of the site of origin of the event from each of the two electrodes. Using online computer data acquisition and analysis, and current pulses at known locations for spatial calibration, it is possible to localize the site of single quantum e.p.p.s to within +/- 10-20 micron. Using the frog cutaneous pectoris neuromuscular preparation and a low calcium, high magnesium Ringer solution to ensure mostly single quantum events and failures, several thousand responses were recorded from each junction, allowing construction of a profile of the numbers of single quantum events arising from each portion of the junction. By comparison of junctional morphology and release profiles, it is possible to construct a probability of release per unit length profile for the entire junction. This technique has several advantages over localization of release events by measurements of extracellular synaptic currents. It was found that, for most junctions, the central 60-90% of the terminal exhibited relatively uniform probability of release, with highest levels typically near the point where the axon first contacted the muscle fibre, or in regions with many short terminal branches. However, no instances have been found in which a small region of terminal (10% or less) showed extraordinarily high release levels (30-50% of the total release from the junction). Characteristically, but not invariably, there is reduced release near the ends of terminal branches, especially the longer branches, where release per unit length could be as little as 5-10% of that in proximal portions. Some junctions had large regions of terminal that released very little transmitter. These also showed multiple myelineated axonal inputs, and may have been polyneuronally innervated junctions in which one of the inputs was much weaker than the other.

Animals↗