Holographic effective actions from black holes

Using the Wald?s relation between the Noether charge of diffeomorphisms and the entropy for a generic spacetime possessing a bifurcation surface, we introduce a method to obtain a family of higher order derivatives effective actions from the entropy of black holes. We consider the entropy as the starting point and we analyze the procedure of derivation of the action functional. We specialize to a particular class of theories which simplifies the calculations, f(R) theories. We apply the procedure to loop quantum gravity and to a general class of log-corrected entropy formulas.     

The native ensemble and folding of a protein molten-globule: functional consequence of downhill folding

The continually emerging functional significance of intrinsic disorder and conformational flexibility in proteins has challenged the long-standing dogma of a well-defined structure contributing to a specific function. Molten-globular states, a class of proteins with significant secondary-structure but a fluid hydrophobic core, is one such example. They have however been difficult to characterize due to the complexity of experimental data and lack of computational avenues. Here, we dissect the folding mechanism of the α-helical molten-globular protein NCBD from three fundamentally different approaches: statistical-mechanical variable barrier model, C(α)-based Gō-model and explicit water all-atom molecular dynamics (MD) simulations. We find that NCBD displays the characteristics of a one-state globally downhill folder but is significantly destabilized. Using simulation techniques, we generate a highly constrained but a heterogeneous native ensemble of the molten-globule for the first time that is consistent with experimental data including small angle X-ray scattering (SAXS), circular dichroism (CD), and nuclear magnetic resonance (NMR). The resulting native ensemble populates conformations reported in other bound-forms providing direct evidence to the mechanism of conformational selection for binding multiple partners in this domain. Importantly, our simulations reveal a connection between downhill folding and large conformational flexibility in this domain that has been evolutionarily selected and functionally exploited resulting in large binding promiscuity. Finally, the multimodel approach we employ here serves as a powerful methodology to study mechanisms and suggests that the thermodynamic features of molten-globules fall within the array of folding mechanisms available to small single-domain proteins.     

Hydrolytic degradation of poly(ε‐caprolactone) with different end groups and poly(ε‐caprolactone‐co‐γ‐butyrolactone): characterization and kinetics of hydrocortisone delivery

Asymmetric telechelic α‐hydroxyl‐ω‐(carboxylic acid)‐poly(ε‐caprolactone) (HA‐PCL), α‐hydroxyl‐ω‐(benzylic ester)‐poly(ε‐caprolactone) (HBz‐PCL), and an asymmetric telechelic copolymer α‐hydroxyl‐ω‐(carboxylic acid)‐poly(ε‐caprolactone‐co‐γ‐butyrolactone) (HA‐PCB) were synthesized by ring‐opening polymerization of ε‐caprolactone (CL). CL and CL/γ‐butyrolactone mixture were used to obtain homopolymers and copolymer respectively at 150°C and 2 hr using ammonium decamolybdate (NH₄) [Mo₁₀O₃₄] (Dec) as a catalyst. Water (HA‐PCL and HA‐PCB) or benzyl alcohol (HBz‐PCL) were used as initiators. The three polylactones reached initial molecular weights between 2000 and 3000 Da measured by proton nuclear magnetic resonance (¹H‐NMR). Compression‐molded polylactone caplets were allowed to degrade in 0.5 M aqueous p‐toluenesulfonic acid at 37°C and monitored up to 60 days for weight loss behavior. Data showed that the copolymer degraded faster than the PCL homopolymers, and that there was no difference in the weight loss behavior between HA‐PCL and HBz‐PCL. Caplets of the three polylactones containing 1% (w/w) hydrocortisone were placed in two different buffer systems, pH 5.0 with citrate buffer and pH 7.4 with phosphate buffer at 37°C, and monitored up to 50 days for their release behavior. The release profiles of hydrocortisone presented two stages. The introduction of a second monomer in the polymer chain significantly increased the release rate, the degradation rate for HA‐PCB being faster than those for HBz‐PCL and HA‐PCL. At the pH studied, only slight differences on the liberation profiles were observed. SEM micrographs indicate that hydrolytic degradation occurred mainly by a surface erosion mechanism. Copyright © 2009 John Wiley & Sons, Ltd.     

Structure of triplex DNA in the gas phase

Extensive (more than 90 microseconds) molecular dynamics simulations complemented with ion-mobility mass spectrometry experiments have been used to characterize the conformational ensemble of DNA triplexes in the gas phase. Our results suggest that the ensemble of DNA triplex structures in the gas phase is well-defined over the experimental time scale, with the three strands tightly bound, and for the most abundant charge states it samples conformations only slightly more compact than the solution structure. The degree of structural alteration is however very significant, mimicking that found in duplex and much larger than that suggested for G-quadruplexes. Our data strongly supports that the gas phase triplex maintains an excellent memory of the solution structure, well-preserved helicity, and a significant number of native contacts. Once again, a linear, flexible, and charged polymer as DNA surprises us for its ability to retain three-dimensional structure in the absence of solvent. Results argue against the generally assumed roles of the different physical interactions (solvent screening of phosphate repulsion, hydrophobic effect, and solvation of accessible polar groups) in modulating the stability of DNA structures.     

Lifetime measurement of the 9s level of atomic francium

We use two-photon resonant excitation and time-correlated single-photon counting techniques on a sample of 210Fr atoms confined and cooled in a magneto-optical trap to measure the lifetime of the 9s excited level. Direct measurement of the decay through the 7P(3/2) level at 851 nm yields a lifetime of 107.53 +/- 0.80 ns.     

On the suitability of semiempirical calculations as sources of force field parameters

Summary The suitability of Dewar's Hamiltonians as a source of bonded force field parameters is explored from the comparison analysis between up to 270 semiempirically derived force field parameters and experimentally derived values reported in some of the most popular force fields. From the statistical analysis of the results, some general conclusions about the semiempirical parametrization are formulated.     

Are the Hydrogen Bonds of RNA (A⋅U) Stronger Than those of DNA (A⋅T)? A Quantum Mechanics Study

The intrinsic stability of Watson-Crick d(AT) and r(AU) hydrogen bonds was analyzed by employing a variety of quantum-mechanical techniques, such as energy calculations, determination of reactivity indexes, and analysis of electron density topology. The analyses were performed not only for equilibrium gas-phase geometries, but also on hundreds of conformations derived from molecular dynamics (MD) and database analysis. None of our results support the idea that r(AU) hydrogen bonds are intrinsically more stable than those of d(AT). Instead, our data are in accordance with the traditional view that the greater stability of RNA relative to DNA is attributable to a variety of effects (e.g., stacking, sugar puckering, solvation) rather than to a significant difference in the hydrogen bonding of DNA and RNA base pairs.     

High-throughput screening of magnetic properties of quenched metallic-alloy thin-film composition spreads

A novel method for capturing and characterizing high-temperature phases of metallic-alloys in thin-film composition spreads has been developed. A high-vacuum (10⁻⁸ Torr) high-temperature annealing and quenching furnace system has been developed that allows formation of high-temperature phases in thin-film composition-spread samples deposited on 3 in. silicon wafers. Scanning SQUID microscopy and magneto-optical Kerr effect measurements were used to map the remnant magnetization and the hysteresis loops of the spreads of magnetic materials quenched at high temperatures. The combination of these techniques can be used to obtain comprehensive information on the magnetic properties of various metallic-alloy systems.     

E5M7+ (E=C–Pb,M=Li–Cs): A Source of Viable Star‐Shaped Clusters

Herein we report the systematic exploration of the potential energy surfaces of a series of clusters with formula E₅M₇⁺ (E=C‐Pb and M=Li‐Cs). Fifteen of these combinations adopt a D_5h three‐dimensional seven‐pointed star‐like structure in a singlet state, where M atoms interact electrostatically with the E₅ ring. The determining factors in the relative preference of having the D_5h structure over the most competitive isomer or vice‐versa are analyzed. These star‐shaped systems satisfy the 4n+2 Hückel's rule and exhibit a strong diatropic (σ and π) response to an external magnetic field.