Dissecting entropic coiling and poor solvent effects in protein collapse

The early events in protein collapse and folding are guided by the protein's elasticity. The contributions of entropic coiling and poor solvent effects like hydrophobic forces to the elastic response of proteins are currently unknown. Using molecular simulations of stretched ubiquitin in comparison with models of proteins as entropic chains, we find a surprisingly high stiffness of the protein backbone, reflected by a persistence length of 1.2 nm, which is significantly reduced by hydrophobic forces acting between protein side chains to an apparent persistence length of 0.3-0.6 nm frequently observed in single-molecule stretching experiments. Thus, the poor solvent conditions of a protein in water lead to a protein compaction much beyond the coiling of an entropic chain and thereby allow a protein to appear softer than when using good solvents.     

How does a dipolar Bose-Einstein condensate collapse?

We emphasize that the macroscopic collapse of a dipolar Bose-Einstein condensate in a pancake-shaped trap occurs through local density fluctuations, rather than through a global collapse to the trap center. This hypothesis is supported by a recent experiment in a chromium condensate.     

Increasing the output length of zero‐error dispersers

Let $\cal{C}$ be a class of probability distributions over a finite set Ω. A function $D : \Omega \mapsto\{0,1\}^{m}$ is a disperser for $\cal{C}$ with entropy threshold $k$ and error $\epsilon$ if for any distribution X in $\cal{C}$ such that X gives positive probability to at least $2^{k}$ elements we have that the distribution $D(X)$ gives positive probability to at least $(1-\epsilon)2^{m}$ elements. A long line of research is devoted to giving explicit (that is polynomial time computable) dispersers (and related objects called “extractors”) for various classes of distributions while trying to maximize m as a function of k. For several interesting classes of distributions there are explicit constructions in the literature of zero‐error dispersers with “small” output length m. In this paper we develop a general technique to improve the output length of zero‐error dispersers. This strategy works for several classes of sources and is inspired by a transformation that improves the output length of extractors (which was given by Shaltiel (CCC'06; Proceedings of the 21st Annual IEEE Conference on Computational Complexity, (2006) 46–60.) building on earlier work by Gabizon, Raz and Shaltiel (SIAM J Comput 36 (2006) 1072–1094). Our techniques are different than those of Shaltiel (CCC'06; Proceedings of the 21st Annual IEEE Conference on Computational Complexity (2006) 46–60) and in particular give non‐trivial results in the errorless case. Using our approach we construct improved zero‐error 2‐source dispersers. More precisely, we show that for any constant $\delta >0$ there is a constant $\eta >0$ such that for sufficiently large n there is a poly‐time computable function $D :\{0,1\}^{n}\times\{0,1\}^{n}\mapsto\{0,1\}^{\eta n}$ such that for every two independent distributions $X_1,X_2$ over $\{0,1\}^{n}$ each with support size at least $2^{\delta n}$ , the output distribution $D(X_1,X_2)$ has full support. This improves the output length of previous constructions by Barak, Kindler, Shaltiel, Sudakov and Wigderson (Proceedings of the 37th Annual ACM Symposium on Theory of Computing (2005) 1–10) and has applications in Ramsey theory and in improved constructions of certain data structures from the work of Fiat and Naor [SIAM J Comput 22 (1993)]. We also use our techniques to give explicit constructions of zero‐error dispersers for bit‐fixing sources and affine sources over polynomially large fields. These constructions improve the best known explicit constructions due to Rao (unpublished data) and Gabizon and Raz [Combinatorica 28 (2008)] and achieve $m=\Omega(k)$ for bit‐fixing sources and $m=k-o(k)$ for affine sources over polynomial size fields. © 2011 Wiley Periodicals, Inc. Random Struct. Alg., 2011     

Special Moufang sets, their root groups and their {micro}-maps

We prove Timmesfeld's conjecture that special abstract rankone groups are quasisimple. We give two characterizations ofthe root groups in special Moufang sets: a normal subgroup ofthe point stabilizer is a root group if it is either regular,or nilpotent and transitive. We prove that if a root group ofa special Moufang set contains an involution, then it is ofexponent 2. We also show that the root groups are abelian ifand only if the so-called µ-maps are involutions.     

Effect of interface traps on Debye thickness semiconductor films

The presence of the boundary interface trapping states and their role in determining the properties of Debye thickness thin semiconductor films, are demonstrated experimentally, using PbTe films deposited on mica. These charged states could not be observed earlier and be studied directly, because of the screening by the relatively high carrier density of the ordinary PbTe. Thin, Debye length thickness, PbTe films with a high concentration of interface trapping centers, possess an extraordinary high resistance. In this case the thermostimulated capacitor discharge method can be successfully applied to determine the energy of these levels, their carrier capture cross-sections and their donor- or acceptor-like character. The experimental results and theoretical calculations are discussed.     

Electroaddressable Selective Functionalization of Electrode Arrays: Catalytic NADH Detection Using Aryl Diazonium Modified Gold Electrodes

We report the application of 4‐nitrophenyl diazonium modified electrodes towards the electrochemical detection of NADH. Selective activation of individual electrodes on a 5 element array by electro‐addressable conversion of nitro groups to amines and subsequent EDC/NHS crosslinking to the NADH oxidant, pyrroloquinoline quinone (PQQ), is demonstrated. Inactivated electrodes retained nitro functionality and were protected against non‐specific adsorption and mild chemical reactions. Electrodeposition conditions were used to control nitrophenyl film thickness and showed that while increased film thickness leads to greater functionalization density of PQQ, it also results in decreased electron transfer kinetics. The electrodeposition protocol can therefore serve as a method to control electrode functionalization density and film electron transfer kinetics. We believe this simple technique for selective electrode functionalization may facilitate the development of next generation multianalyte electrochemical sensors.     

Electrodeposition of Dye-Doped Titania Thin Films

We extend our novel low-voltage electrochemical method for oxide thin film formation from sol-gel monomers to include entrapment of organic molecules within the films. We also describe an extension of the method to titania thin films, which are obtained from titanium tetra-n-propoxide in alcoholic solutions by applying potentials in the range of +2.0 to ?1.4 V to indium tin oxide electrodes. The film thickness (ranging between 20–1000 nm) is controllable by changing either the potential or the duration of its application. We demonstrate that this electrochemical method provides a convenient way for entrapment of organic dopants within the film. Four dyes were used for that purpose: Basic Blue 41, methylene-blue, tris(2,2′-bipyridine)iron(II) and tris(2,2′-bipyridine)ruthenium(II).     

Electrochemically induced sol-gel deposition of zirconia thin films

A novel electrochemical method for deposition of ZrO(2) thin films is described. The films, 50-600 nm thick, were obtained by applying moderate positive or negative potentials (+2.5 V to -1.5 V versus SHE) on conducting surfaces immersed in a 2-propanol solution of zirconium tetra-n-propoxide [Zr(OPr)(4)] in the presence of minute quantities of water (water/monomer molar ratios in the range of 10(-5) to 10(-1)), which was the limiting reagent. Oxidative electrochemical formation of solvated H(+) and reductive formation of OH(-) catalyze the hydrolysis and condensation of the metal alkoxide precursor. The magnitude of the applied potential and its duration provide a convenient way of controlling the film thickness. The films consist of an amorphous phase, as revealed by XRD measurements. The effects of different parameters, such as the applied potential and its duration, the amount of added water and the current-time characteristics, were studied. A mechanism for the electrodeposition of the zirconia films which is in accordance with our findings is proposed.