Melting of Branched RNA Molecules

Stability of the branching structure of an RNA molecule is an important condition for its function. In this letter we show that the melting thermodynamics of RNA molecules is very sensitive to their branching geometry for the case of a molecule whose groundstate has the branching geometry of a Cayley Tree and whose pairing interactions are described by the Go model. Whereas RNA molecules with a linear geometry melt via a conventional continuous phase transition with classical exponents, molecules with a Cayley Tree geometry are found to have a free energy that seems smooth, at least within our precision. Yet, we show analytically that this free energy in fact has a mathematical singularity at the stability limit of the ordered structure. The correlation length appears to diverge on the high-temperature side of this singularity.Comment: 4 pages, 3 figure

Molecular Electroporation and the Transduction of Oligoarginines

Certain short polycations, such as TAT and polyarginine, rapidly pass through the plasma membranes of mammalian cells by an unknown mechanism called transduction as well as by endocytosis and macropinocytosis. These cell-penetrating peptides (CPPs) promise to be medically useful when fused to biologically active peptides. I offer a simple model in which one or more CPPs and the phosphatidylserines of the inner leaflet form a kind of capacitor with a voltage in excess of 180 mV, high enough to create a molecular electropore. The model is consistent with an empirical upper limit on the cargo peptide of 40--60 amino acids and with experimental data on how the transduction of a polyarginine-fluorophore into mouse C2C12 myoblasts depends on the number of arginines in the CPP and on the CPP concentration. The model makes three testable predictions.Comment: 15 pages, 5 figure

Anomalously Slow Domain Growth in Fluid Membranes with Asymmetric Transbilayer Lipid Distribution

The effect of asymmetry in the transbilayer lipid distribution on the dynamics of phase separation in fluid vesicles is investigated numerically for the first time. This asymmetry is shown to set a spontaneous curvature for the domains that alter the morphology and dynamics considerably. For moderate tension, the domains are capped and the spontaneous curvature leads to anomalously slow dynamics, as compared to the case of symmetric bilayers. In contrast, in the limiting cases of high and low tensions, the dynamics proceeds towards full phase separation.Comment: 4 pages, 5 figure

Quiescence: a mechanism for escaping the effects of drug on cell populations

We point out that a simple and generic strategy to lower the risk for extinction consists in the developing a dormant stage in which the organism is unable to multiply but may die. The dormant organism is protected against the poisonous environment. The result is to increase the survival probability of the entire population by introducing a type of zero reproductive fitness. This is possible, because the reservoir of dormant individuals act as a buffer that can cushion fatal fluctuations in the number of births and deaths which without the dormant population would have driven the entire population to extinction.Comment: 18 pages and 9 figure

Phase Transitions in Multicomponent String Model

We propose a one-dimensional model of a string decorated with adhesion molecules (stickers) to mimic multicomponent membranes in restricted geometries. The string is bounded by two parallel walls and it interacts with one of them by short range attractive forces while the stickers are attracted by the other wall. The exact solution of the model in the case of infinite wall separation predicts both continuous and discontinuous transitions between phases characterised by low and high concentration of stickers on the string. Our model exhibits also coexistence of these two phases, similarly to models of multicomponent membranes.Comment: letter, 8 pages, 3 figure

Domain Growth, Budding, and Fission in Phase Separating Self-Assembled Fluid Bilayers

A systematic investigation of the phase separation dynamics in self-assembled multi-component bilayer fluid vesicles and open membranes is presented. We use large-scale dissipative particle dynamics to explicitly account for solvent, thereby allowing for numerical investigation of the effects of hydrodynamics and area-to-volume constraints. In the case of asymmetric lipid composition, we observed regimes corresponding to coalescence of flat patches, budding, vesiculation and coalescence of caps. The area-to-volume constraint and hydrodynamics have a strong influence on these regimes and the crossovers between them. In the case of symmetric mixtures, irrespective of the area-to-volume ratio, we observed a growth regime with an exponent of 1/2. The same exponent is also found in the case of open membranes with symmetric composition

A Classical Density-Functional Theory for Describing Water Interfaces

We develop a classical density functional for water which combines the White Bear fundamental-measure theory (FMT) functional for the hard sphere fluid with attractive interactions based on the Statistical Associating Fluid Theory (SAFT-VR). This functional reproduces the properties of water at both long and short length scales over a wide range of temperatures, and is computationally efficient, comparable to the cost of FMT itself. We demonstrate our functional by applying it to systems composed of two hard rods, four hard rods arranged in a square and hard spheres in water

Surface tension in bilayer membranes with fixed projected area

We study the elastic response of bilayer membranes with fixed projected area to both stretching and shape deformations. A surface tension is associated to each of these deformations. By using model amphiphilic membranes and computer simulations, we are able to observe both the types of deformation, and thus, both the surface tensions, related to each type of deformation, are measured for the same system. These surface tensions are found to assume different values in the same bilayer membrane: in particular they vanish for different values of the projected area. We introduce a simple theory which relates the two quantities and successfully apply it to the data obtained with computer simulations

Development of a novel LC-MS/MS method for the detection of adulteration of South African sauvignon blanc wines with 3-alkyl-2-methoxypyrazines

Thesis (MSc (Chemistry and Polymer Science))--University of Stellenbosch, 2008.A method for the detection of adulteration of South African Sauvignon blanc wines, by enrichment with foreign sources of 3-alkyl-2-methoxypyrazenes, is described. The levels of three 3-alkyl-2-methoxypyrazenes (3-isobutyl-, 3- isopropyl- and 3-sec-butyl-2-methoxypyrazine) in South African Sauvignon blanc wines were measured with liquid chromatography-mass spectrometry. Sample preparation involved clean-up and pre-concentration by distillation followed by solvent extraction of the distillate with dichloromethane. Extracts were acidified and concentrated by evaporation and finally reconstituted to a fixed volume to affect quantitative pre-concentration of the samples. Sample extracts were separated with reversed phase liquid chromatography utilizing a phenyl-hexyl separation column. Residues were measured with liquid chromatography-mass spectrometry utilizing a tandem quadrupole mass spectrometric detector operated in multiple reaction monitoring mode for optimal trace level quantitation. Atmospheric pressure chemical ionization was utilized as electrospray ionization was found to suffer from quenching effects attributed to the sample matrix. Qualitative information was obtained from the relevant molecular ions as well as two secondary ion transitions (and one ion ratio) in each case. Recoveries obtained by the extraction procedure were better than 90% with coefficient of variance of better than 10% at concentrations from 1 to 100 ng/L. The limit of detection of the method was 0.03 ng/L and the limit of quantification 0.10 ng/L for the three analytes measured. The described LC-MS method is more sensitive for the determination of 3-alkyl-2-methoxypyrazines in wine than GC methods reported for the same purpose. From the experimental data, a set of parameters were established to discriminate adulterated South African Sauvignon blanc wines. It was demonstrated that the 3-isobutyl-2-methoxypyrazine concentration, despite showing considerable variance, was confined to a relatively narrow range spanning approximately two orders of magnitude (0.20 to 22 ng/L). A clear indication of possible maximum values for this compound in South African Sauvignon blanc wines was obtained from the analysis of a large number of samples (577), spanning most relevant wine producing regions and representing vintages 2003 to 2006. It was also demonstrated that South African Sauvignon blanc wines contain the major 3- alkyl-2-methoxypyrazenes in reasonably distinct relative amounts and that the said ratios of abundance may be used to elucidate authenticity. The expected effect of adulteration with green pepper extracts or some synthetic preparations on the 3-isobutyl-2-methoxypyrazine concentration as well as the relative abundances were also determined by characterizing the corresponding profiles in green peppers and some synthetic flavor preparations. Two adulterated samples in the dataset were identified by both outlined criteria. A limited number of wines of other cultivars were also analyzed. The results represent the most complete and accurate data on the 3-alkyl-2-methoxypyrazine content of South African Sauvignon blanc wines to date. A publication covering the work presented in this thesis is currently in preparation

Fluctuation-Driven Molecular Transport in an Asymmetric Membrane Channel

Channel proteins, that selectively conduct molecules across cell membranes, often exhibit an asymmetric structure. By means of a stochastic model, we argue that channel asymmetry in the presence of non-equilibrium fluctuations, fueled by the cell's metabolism as observed recently, can dramatically influence the transport through such channels by a ratchet-like mechanism. For an aquaglyceroporin that conducts water and glycerol we show that a previously determined asymmetric glycerol potential leads to enhanced inward transport of glycerol, but for unfavorably high glycerol concentrations also to enhanced outward transport that protects a cell against poisoning.Comment: REVTeX4, 4 pages, 3 figures; Accepted for publication in Phys. Rev. Let