Stabilizing effect of electrostatic vs. aromatic interactions in diproline nucleated peptide beta-hairpins

The contribution of Tyr-His vs. Cys-His interacting pairs to the scaffold stability of (D)Pro-(L)Pro nucleated peptide beta-hairpins has been examined. We present direct evidence for the superiority of the Cys-His pairs, mediated by sulphur-imidazole interactions, as added stabilizing agents of the beta-hairpin scaffold.

Diversity order vs rate in an AWGN channel

We study the diversity order vs rate of an additive white Gaussian noise (AWGN) channel in the whole capacity region. We show that for discrete input as well as for continuous input, Gallager's upper bounds on error probability have exponential diversity in low and high rate region but only subexponential in the mid-rate region. For the best available lower bounds and for the practical codes one observes exponential diversity throughout the capacity region. However we also show that performance of practical codes is close to Gallager's upper bounds and the mid-rate subexponential diversity has a bearing on the performance of the practical codes. Finally we show that the upper bounds with Gaussian input provide good approximation throughout the capacity region even for finite constellation.

DEFINING alpha-HELIX GEOMETRY BY C-alpha ATOM TRACE vs (phi-psi) TORSION ANGLES: A COMPARATIVE ANALYSIS

A regular secondary structure is described by a well defined set of values for the backbone dihedral angles (phi,psi and omega) in a polypeptide chain. However in real protein structures small local variations give rise to distortions from the ideal structures, which can lead to considerable variation in higher order organization. Protein structure analysis and accurate assignment of various structural elements, especially their terminii, are important first step in protein structure prediction and design. Various algorithms are available for assigning secondary structure elements in proteins but some lacunae still exist. In this study, results of a recently developed in-house program ASSP have been compared with those from STRIDE, in identification of alpha-helical regions in both globular and membrane proteins. It is found that, while a combination of hydrogen bond patterns and backbone torsional angles (phi-psi) are generally used to define secondary structure elements, the geometry of the C-alpha atom trace by itself is sufficient to define the parameters of helical structures in proteins. It is also possible to differentiate the various helical structures by their C-alpha trace and identify the deviations occurring both at mid-positions as well as at the terminii of alpha-helices, which often lead to occurrence of 3(10) and pi-helical fragments in both globular and membrane proteins.

Strings vs. spins on the null orbifold

We study the null orbifold singularity in 2+1 d flat space higher spin theory as well as string theory. Using the Chern-Simons formulation of 2+1 d Einstein gravity, we first observe that despite the singular nature of this geometry, the eigenvalues of its Chern-Simons holonomy are trivial. Next, we construct a resolution of the singularity in higher spin theory: a Kundt spacetime with vanishing scalar curvature invariants. We also point out that the UV divergences previously observed in the 2-to-2 tachyon tree level string amplitude on the null orbifold do not arise in the at alpha' -> infinity limit. We find all the divergences of the amplitude and demonstrate that the ones remaining in the tensionless limit are physical IR-type divergences. We conclude with a discussion on the meaning and limitations of higher spin (cosmological) singularity resolution and its potential connection to string theory.

Coherent (photon) vs incoherent (current) detection of multidimensional optical signals from single molecules in open junctions

The nonlinear optical response of a current-carrying single molecule coupled to two metal leads and driven by a sequence of impulsive optical pulses with controllable phases and time delays is calculated. Coherent (stimulated, heterodyne) detection of photons and incoherent detection of the optically induced current are compared. Using a diagrammatic Liouville space superoperator formalism, the signals are recast in terms of molecular correlation functions which are then expanded in the many-body molecular states. Two dimensional signals in benzene-1,4-dithiol molecule show cross peaks involving charged states. The correlation between optical and charge current signal is also observed. (C) 2015 AIP Publishing LLC.

Improved capacity and stability of integrated Li and Mn rich layered-spinel Li1.17Ni0.25Mn1.08O3 cathodes for Li-ion batteries

A Li-rich layered-spinel material with a target composition Li1.17Ni0.25Mn1.08O3 (xLiLi1/3Mn2/3]O-2.(1 - x) LiNi0.5Mn1.5O4, (x = 0.5)) was synthesized by a self-combustion reaction (SCR), characterized by XRD, SEM, TEM, Raman spectroscopy and was studied as a cathode material for Li-ion batteries. The Rietveld refinement results indicated the presence of monoclinic (LiLi1/3Mn2/3]O-2) (52%), spinel (LiNi0.5Mn1.5O4) (39%) and rhombohedral LiNiO2 (9%). The electrochemical performance of this Li-rich integrated cathode material was tested at 30 degrees C and compared to that of high voltage LiNi0.5Mn1.5O4 spinel cathodes. Interestingly, the layered-spinel integrated cathode material exhibits a high specific capacity of about 200 mA h g(-1) at C/10 rate as compared to 180 mA h g(-1) for LiNi0.5Mn1.5O4 in the potential range of 2.4-4.9 V vs. Li anodes in half cells. The layered-spinel integrated cathodes exhibited 92% capacity retention as compared to 82% for LiNi0.5Mn1.5O4 spinel after 80 cycles at 30 degrees C. Also, the integrated cathode material can exhibit 105 mA h g(-1) at 2 C rate as compared to 78 mA h g(-1) for LiNi0.5Mn1.5O4. Thus, the presence of the monoclinic phase in the composite structure helps to stabilize the spinel structure when high specific capacity is required and the electrodes have to work within a wide potential window. Consequently, the Li1.17Ni0.25Mn1.08O3 composite material described herein can be considered as a promising cathode material for Li ion batteries.

Morphological and functional characterisation of the burrow systems of six earthworm species (Lumbricidae)

Earthworm burrow systems are generally described based on postulated behaviours associated with the three ecological types. In this study, we used X-ray tomography to obtain 3D information on the burrowing behaviour of six very common anecic (Aporrectodea nocturna and Lumbricus terrestris) and endogeic (Aporrectodea rosea, Allolobophora chlorotica, Aporrectodea caliginosa, Aporrectodea icterica) earthworm species, introduced into repacked soil cores for 6 weeks. A simple water infiltration test, the Beerkan method, was also used to assess some functional properties of these burrow systems. Endogeic worms make larger burrow systems, which are more highly branched, less continuous and of smaller diameter, than those of anecic worms. Among the anecic species, L. terrestris burrow systems are shorter (9.2 vs 21.2 m) with a higher number (14.5 vs 23.5) of less branched burrows (12.2 vs 20.2 branches m(-1)), which are also wider (7.78 vs 5.16 mm) than those of A. nocturna. In comparison, the burrow systems made by endogeic species appeared similar to each other. However, A. rosea burrows were short and narrow, whereas A. icterica had a longer burrow system (15.7 m), more intense bioturbation intensity (refilled macropores or soil lateral compaction around them) and thus a greater number of burrows. Regarding water infiltration, anecic burrow systems were far more efficient due to open burrows linking the top and bottom of the cores. For endogeic species, we observed a linear relationship between burrow length and the water infiltration rate (R (2) = 0.49, p < 0.01). Overall, the three main characteristics significantly influencing water infiltration were burrow length, burrow number and bioturbation volume. This last characteristic highlighted the effect of burrow refilling by casts.

Macropores generated during shrinkage in two paddy soils using X-ray micro-computed tomography

Soil shrinkage curve represents a decrease of total porosity or an increase of bulk density with water loss. However, our knowledge of the dynamics of pores and their geometry during soil shrinkage is scarce, partially due to lack of reliable methods for determining soil pores in relation to change in soil water. This study aimed to investigate the dynamics of macropores (>30 mu m) of paddy soils during shrinkage. Two, paddy soils, which were sampled from one paddy field cultivated for 20 years (YPF) and the other one for over 100 years (OPF), represented difference in crack geometry in the field. Macropore parameters (volume, connectivity, and orientation of pores) and soil shrinkage parameters were determined on the same undisturbed soil cores by X-ray microtomography and shrinkage curve, respectively. Macroporosity was on average four times larger in the YPF than in the OPF whereas the shrinkage capacity was lower in the YPF as compared to the OPF (0.09 vs. 0.15 COLE). Soil shrinkage increased the volume of pores by 3.7% in the YPF and by 1.6% in the OPF as well as their connectivity. The formation of macropores occurred mostly in the proportional shrinkage phase. As a result, the slope of the proportional shrinkage phase was smaller in the YPF (0.65) than in the OPF (0.89). New macropores were cracks and extended pre-existing pores in the range of 225-1215 pm size without any preferential orientation. This work provides image evidences that in paddy soils with high shrinkage capacity more macropores are generated in the soil presenting a smaller proportional shrinkage slope. (C) 2015 Elsevier B.V. All rights reserved.

In-plane modulated smectic (A)over-tilde vs smectic `A' lamellar structures in poly(ethyl or propyl ether imine) dendrimers

A pair of first and second generation poly(alkyl ether imine) dendrimers is prepared, having covalently attached cholesteryl moieties at their peripheries. The pairs in each generation differ in the alkyl-linker which constitute the dendritic core moieties, even when the number of cholesteryl moieties remains uniform in each pair. The dendrimer pairs are two first and second generation poly(ethyl ether imine) and poly(propyl ether imine) dendrimers, modified with 4 and 8 cholesteryl esters at the peripheries in each pair, respectively. The dendrimer pairs exhibit differing thermotropic mesophase properties. Microscopic, thermal and X-ray diffraction studies reveal a lamellar mesophase for the first generation ethyl-, first and second generation propyl-linker dendrimers. Whereas, the second generation ethyl-linker dendrimer exhibits a layered structure with a superimposed in-plane modulation, the length of which corresponds to a rectangular column width. The role of the dendrimer core moieties with differing linkers in modifying the mesophase properties is studied. (C) 2016 Elsevier Ltd. All rights reserved.