Splitting probabilities as a test of reaction coordinate choice in single-molecule experiments

To explain the observed dynamics in equilibrium single-molecule measurements of biomolecules, the experimental observable is often chosen as a putative reaction coordinate along which kinetic behavior is presumed to be governed by diffusive dynamics. Here, we invoke the splitting probability as a test of the suitability of such a proposed reaction coordinate. Comparison of the observed splitting probability with that computed from the kinetic model provides a simple test to reject poor reaction coordinates. We demonstrate this test for a force spectroscopy measurement of a DNA hairpin

Freezing Transition of Random Heteropolymers Consisting of an Arbitrary Set of Monomers

Mean field replica theory is employed to analyze the freezing transition of random heteropolymers comprised of an arbitrary number ($q$) of types of monomers. Our formalism assumes that interactions are short range and heterogeneity comes only from pairwise interactions, which are defined by an arbitrary $q \times q$ matrix. We show that, in general, there exists a freezing transition from a random globule, in which the thermodynamic equilibrium is comprised of an essentially infinite number polymer conformations, to a frozen globule, in which equilibrium ensemble is dominated by one or very few conformations. We also examine some special cases of interaction matrices to analyze the relationship between the freezing transition and the nature of interactions involved.Comment: 30 pages, 1 postscript figur

The color of polarization in cuprate superconductors

A technique for the identification of individual anisotropic grains in a heterogeneous and opaque material involves the observation of grain color in reflected light through crossed polarizers (color of polarization). Such colors are generally characteristic of particular phases. When grains of many members of the class of hole carrier cuprate superconductors are so viewed, using a xenon light source (600 K color temperature), a characteristic color of polarization is observed. This color was studied in many of these cuprate superconductors and a strong correlation was found between color and the existence of superconductivity. One of the members of the electron carrier cuprate superconductors (Nd(1.85)Ce(.15)CuO(4-x) was examined and found that it possesses the same color of polarization as all the electron hole carrier cuprate superconductors so far examined. The commonality of the characteristic color in the cuprate superconductors indicated that the presence of this color is independent of the nature of charge carriers. The correlation of this color with existence of superconductivity suggests that the origin of the color relates to the origin of superconductivity in the cuprate superconductors. Photometric techniques are also discussed

Small-intestinal bacterial overgrowth in cirrhosis is related to the severity of liver disease

Background: Small-intestinal bacterial overgrowth (SIBO) is known to be present in patients with cirrhosis, predisposing to various complications. Aim To determine the frequency of SIBO in cirrhotics and correlate with severity of cirrhosis. Methods: Small-intestinal bacterial overgrowth was determined by glucose-hydrogen breath test (GHBT). A basal breath-hydrogen >20 ppm or a rise by ≥12 ppm above baseline following glucose administration was taken as positive test. Prevalence of SIBO in cirrhotics was compared with healthy controls and correlated with severity of cirrhosis. Results: Of the 53 cirrhotics, 26 (49%) had SIBO, compared to one (8%) control (P = 0.010). The prevalence of SIBO increased with severity of cirrhosis (Child-Pugh A 20%, B 52% and C 73%; P = 0.013). On multivariate analysis, SIBO was independently associated with serum bilirubin and ascites. The best cut-off of serum bilirubin was ≥2 mg/dL [AUROC 0.77 (95% CI 0.64-0.90)] predicting SIBO with sensitivity 65%, specificity 81%, positive predictive value 77%, negative predictive value 71% and accuracy 74%. Patients having combination of ascites and serum bilirubin ≥2 mg/dL had 82% chance, while patients having neither had only 10% chance of having SIBO. Conclusions: Small-intestinal bacterial overgrowth was prevalent in about half of cirrhotics. Its frequency increased with increase in severity of cirrhosis. Ascites and raised serum bilirubin reliably predicted presence of SIBO

Free Energy Self-Averaging in Protein-Sized Random Heteropolymers

Current theories of heteropolymers are inherently macrpscopic, but are applied to folding proteins which are only mesoscopic. In these theories, one computes the averaged free energy over sequences, always assuming that it is self-averaging -- a property well-established only if a system with quenched disorder is macroscopic. By enumerating the states and energies of compact 18, 27, and 36mers on a simplified lattice model with an ensemble of random sequences, we test the validity of the self-averaging approximation. We find that fluctuations in the free energy between sequences are weak, and that self-averaging is a valid approximation at the length scale of real proteins. These results validate certain sequence design methods which can exponentially speed up computational design and greatly simplify experimental realizations.Comment: 4 pages, 3 figure

A New Method for Determination of Percentage Grafting in Starch-Polyacrylonitrile Graft Copolymer

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Random walks in the space of conformations of toy proteins

Monte Carlo dynamics of the lattice 48 monomers toy protein is interpreted as a random walk in an abstract (discrete) space of conformations. To test the geometry of this space, we examine the return probability $P(T)$, which is the probability to find the polymer in the native state after $T$ Monte Carlo steps, provided that it starts from the native state at the initial moment. Comparing computational data with the theoretical expressions for $P(T)$ for random walks in a variety of different spaces, we show that conformational spaces of polymer loops may have non-trivial dimensions and exhibit negative curvature characteristic of Lobachevskii (hyperbolic) geometry.Comment: 4 pages, 3 figure