An expanded cellular automata model for enantiomer separations using a ß-cyclodextrin stationary phase.

Chromatographic scale enantiomer separation has not been modeled using cellular automata (CA). CA uses easy to adjust equations to different enantiomers under various chromatographic conditions. Previous work has demonstrated that CA modeling can accurately predict the strength of one-to-one binding interactions between enantiomers and ß-cyclodextrin (CD) [1]. In this work, the model is expanded to a chromatographic scale grid environment in order to transform model output into HPLC chromatograms. The model accurately predicted the lack of chromatographic selectivity of mandelic enantiomers (1.05 published, 1.01 modeled) and the separation of brompheniramine enantiomers (1.13 published, 1.12 modeled) previously modeled in one-to-one interactions. By examining cyclohexylphenylglycolic acid (CHPGA) enantiomers, the model accurately predicted both the selectivity and resolution of the enantiomer peaks at varying chromatographic temperatures. Modeled changes in mobile phase pH agree with laboratory outcomes when examining peak resolution and selectivity. Changes in injection volume resulted in an increase in retention time of the modeled enantiomers as was observed in the published laboratory results.

A cellular automata model of proton hopping down a channel.

Proton hopping is the process where a H-atom on a hydronium ion forms a H-bond with the O-atom of a neighboring H(2)O molecule. There is then an exchange of bonding forces when that covalent bond of the H-atom in the hydronium ion changes to a H-bond, and the previous H-bond changes to a covalent bond with the neighboring O-atom. The neighboring molecule now becomes a hydronium (H(3)O(+)) ion. This process repeats itself very rapidly among neighboring hydronium and H(2)O molecules. There is a flow of protonic character through bulk H(2)O, referred to as proton hopping. This process carries information through living systems where H(2)O is present. A cellular automata model of proton hopping down a channel has been created and studied. Variations in the rate of proton entry into the channel and the effects of the polar character of the channel walls was studied using the model. The behavior of the models corresponds to experimental results.

Effect of initial temperature on water aggregation at a cold surface.

Cellular automata models of water at two initial temperatures were created. Each model was exposed to a freezing surface. The formation of fully bonded water cells, f(4), was observed over time, beginning with a model of initially warm water and with initially cool water. The warm water formed more f(4) cells earlier than the initially cool water. A high percentage of f(4) cells is interpreted as the formation of ice. This is a model of the Mpemba effect. A description of the initial states for these two temperatures is offered in explanation of this effect.

A highly sensitive method for molecular diagnosis of fungal keratitis: a dot hybridization assay.

PURPOSE: Fungal keratitis (FK) is an important cause of ocular morbidity, especially for people living in the agricultural communities of the developing world. Current diagnostic methods may lack sensitivity (direct microscopy) or are time consuming (culture). The aim of this study was to develop a dot hybridization assay for sensitive and rapid diagnosis of FK. DESIGN: Evaluation of diagnostic test or technology. PARTICIPANTS AND CONTROLS: Fifty corneal scrapes (49 patients) from consecutive cases of clinically suspected microbial keratitis were analyzed prospectively. METHODS: Molecular detection of fungi in the scrapes was performed by amplification of the internal transcribed spacer region (ITS) that contained the target gene (5.8S rRNA gene) by polymerase chain reaction (PCR), followed by hybridization of the PCR product to a fungus-specific oligonucleotide probe immobilized on a nylon membrane. The results were compared with those obtained by gram-stain microscopy, culture, and gel electrophoresis of the PCR products. Discrepant results were resolved by cloning and resequencing of the amplified ITS fragments. MAIN OUTCOME MEASURES: Performance of the dot hybridization assay, including sensitivity, specificity, and positive and negative predictive values, was evaluated. RESULTS: Ten scrapes demonstrated positive results by both the dot hybridization assay and culture. However, 11 scrapes demonstrated positive results by the dot hybridization assay, but demonstrated negative results by culture, and 10 of the 11 samples were considered to be positive for FK by cloning and resequencing of the amplified ITS fragment and by a pathologic examination or clinical course review. The sensitivities for diagnosis of FK by the dot hybridization assay and culture were 100% and 50%, respectively, whereas the specificities were 96.7% and 100%, respectively. CONCLUSIONS: The dot hybridization assay is a highly sensitive and specific diagnostic tool for FK. The method provides a much higher sensitivity than that of culture (100% vs. 50%; P<0.001). The hybridization procedure can be finished within a working day. It is expected that the method can have an impact on the diagnosis and treatment of FK in the future. FINANCIAL DISCLOSURE(S): The author(s) have no proprietary or commercial interest in any materials discussed in this article.

A cellular automata model of enantiomer binding strengths to ß-cyclodextrin.

As yet, the analytical process of chromatographic enantiomer separation has not been modeled using cellular automata (CA). This approach uses mathematical systems that are easily adaptable to different enantiomer analytical binding interactions. A CA model of analyte to cyclodextrin (CD) interaction accurately (R(2)=0.9960) predicts one-to-one molecular binding strengths through correlation with experimental complex stability constants while exhibiting established chromatographic behavior (i.e. retention site dependency and band broadening). The model is expanded to enantiomer HPLC retention interactions with ß-CD that accurately predicts one-to-one binding strengths through the development of probabilistic rules and factors from chromatographic results. The proposed model predicts the strength of binding interactions and the degree of chromatographic separation (or lack thereof) of six enantiomer pairs that agree with published potential binding energies of enantiomer-(ß-CD) complexes and published experimental HPLC separations.

A cellular automata model of ligand passage over a protein hydrodynamic landscape.

The subject of ligand passage to an active site on a protein is addressed. Current views on the mechanism and the possible role of surface water are discussed. A theory is presented in which the pattern of hydropathic states of protein surface amino acid side chains is invoked as the influence on the relative hydrophobic effects of nearby water. The theory describes a ligand passage through the hydrodynamic near-surface water which exhibits temporary organized cavities resembling the chreodes introduced by Waddington. The passage of the ligand to the active site is facilitated by this dynamic mechanism. Cellular automata models of preferential directional diffusion through these chreodes support the theory. The theory may be invoked to explain a number of ligand-active site observations and serves as an idea for further studies.

A cellular automata model of water structuring by a chiral solute.

The organization of water around a solute molecule with surface features of varying hydropathic states is studied. A stationary solute molecule and mobile water solvent molecules are modeled using cellular automata dynamics. It is shown that varying hydropathic states of solute molecule surface features influence the relative affinities of water for these features. In the case of a simulated chiral solute, a chiral pattern of associated water molecules binding to the surface is produced. This finding is in agreement with published simulations and circular dichroism measurements. A pattern of water molecules at locations beyond the surface of the solute molecules is detected, evidence of an emergent property in this solvent-solute system.