Fast Compression of MCMC Output

We propose cube thinning, a novel method for compressing the output of an MCMC (Markov chain Monte Carlo) algorithm when control variates are available. It allows resampling of the initial MCMC sample (according to weights derived from control variates), while imposing equality constraints on the averages of these control variates, using the cube method (an approach that originates from survey sampling). The main advantage of cube thinning is that its complexity does not depend on the size of the compressed sample. This compares favourably to previous methods, such as Stein thinning, the complexity of which is quadratic in that quantity.     

Synthesis,Characterization and X-ray Crystal Structure of the Di-Mannich Base 2,2′-(3aR,7aR/3aS,7aS)-Hexahydro-1<Emphasis Type="Italic">H</Emphasis>-benzo[<Emphasis Type="Italic">d</Emphasis>]imidazole-1,3(2<Emphasis Type="Italic">H</Emphasis>)-diyl)bis(methylene)bis(4-methylphenol)

Abstract  

The crystal structure of new racemic di-Mannich base 2,2′-(3aR,7aR/3aS,7aS)-hexahydro-1H-benzo[d]imidazole-1,3(2H)-diyl)bis(methylene)bis(4-methylphenol) (4), is reported. The structure of the title compound, C₂₃H₃₀N₂O₂, shows two intramolecular O–H···N hydrogen bonding interactions. This compound crystallizes in triclinic symmetry, in space group P−1, with lattice constants: a = 6.2563(3) ?, b = 12.1743(7) ?, c = 14.7257(7) ?, α = 108.11(1)°, β = 99.77(1)°, γ = 98.78(1), V = 1024.97(9) ?³, Z = 2, F(000) = 396, R ₁  = 8.3%, wR ₂  = 14.7%.     

Single-photon atomic cooling

We report the cooling of an atomic ensemble with light, where each atom scatters only a single photon on average. This is a general method that does not require a cycling transition and can be applied to atoms or molecules that are magnetically trapped. We discuss the application of this new approach to the cooling of hydrogenic atoms for the purpose of precision spectroscopy and fundamental tests.     

Multiple avalanches across the metal-insulator transition of vanadium oxide nanoscaled junctions

The metal-insulator transition of nanoscaled VO2 devices is drastically different from the smooth transport curves generally reported. The temperature driven transition occurs through a series of resistance jumps ranging over 2 decades in magnitude, indicating that the transition is caused by avalanches. We find a power law distribution of the jump sizes, demonstrating an inherent property of the VO2 films. We report a surprising relation between jump magnitude and device size. A percolation model captures the general transport behavior, but cannot account for the statistical behavior.     

Investigating the formation of an adduct of formamide with dioxane by means of Raman spectroscopy

Raman experiments of formamide (FA) and p‐dioxane (DX) mixtures at different compositions were carried out. A red shift of the C O stretching band of DX was observed upon dilution, while blue shifts were observed for the C H stretching and C O C bending bands. In this latter region, the new band at ∼441 cm⁻¹, whose intensity shows large dependence on the FA concentration, has been assigned to an FA–DX adduct and it is reported for the first time in the literature. The spectral changes observed in the C O C bending region allowed to determine a proportion of 4:1 FA–DX and this experimental evidence is also presented for the first time by Raman spectroscopy. The present work shows an excellent agreement with our previous investigation, where the 2:1 FA—THF (tetrahydrofuran) adduct was characterized. Copyright © 2008 John Wiley & Sons, Ltd.     

Node similarity within subgraphs of protein interaction networks

We propose a biologically motivated quantity, twinness, to evaluate local similarity between nodes in a network. The twinness of a pair of nodes is the number of connected, labeled subgraphs of size n in which the two nodes possess identical neighbours. The graph animal algorithm is used to estimate twinness for each pair of nodes (for subgraph sizes n=4 to n=12) in four different protein interaction networks (PINs). These include an Escherichia coli PIN and three Saccharomyces cerevisiae PINs — each obtained using state-of-the-art high-throughput methods. In almost all cases, the average twinness of node pairs is vastly higher than that expected from a null model obtained by switching links. For all n, we observe a difference in the ratio of type twins (which are unlinked pairs) to type twins (which are linked pairs) distinguishing the prokaryote E. coli from the eukaryote S. cerevisiae. Interaction similarity is expected due to gene duplication, and whole genome duplication paralogues in S. cerevisiae have been reported to co-cluster into the same complexes. Indeed, we find that these paralogous proteins are over-represented as twins compared to pairs chosen at random. These results indicate that twinness can detect ancestral relationships from currently available PIN data.     

Wigner Surmise for Domain Systems

In random matrix theory the spacing distribution functions p ⁽ⁿ⁾(s) are well fitted by the Wigner surmise and its generalizations. In this approximation the spacing functions are completely described by the behavior of the exact functions in the limits s→0 and s→∞. Most non equilibrium systems do not have analytical solutions for the spacing distribution and correlation functions. Because of that, we explore the possibility to use the Wigner surmise approximation in these systems. We found that this approximation provides a first approach to the statistical behavior of complex systems, in particular we use it to find an analytical approximation to the nearest neighbor distribution of the annihilation random walk.     

Features,Questions and Future Challenges in Layered Silicates Clay Nanocomposites with Semicrystalline Polymer Matrices

The present features review article discusses the crystallisation of the polymer matrix when containing silicate layers. The accent is put on nylons (polyamides) and poly(ethylene oxide) as typical hydrophilic polymers and, poly(propylene) from the hydrophobic group. The effects of the clay, either intercalated or exfoliated, on the crystallisation behaviour of the matrix are highlighted. In addition, the crucial aspects of the semicrystalline morphology of the matrix in the presence of the clay platelets are also debated. The overall crystallisation rate is reported to slow down for most of the crystallisable polymer matrices on account of a retarding growth effect exerted by the clay platelets. As far as the location of the exfoliated clay platelets in the polymer matrix is concerned, they are assumed to be rejected from the crystalline phase in the interspherulitic space.

     

The effect of canopy roughness density on the constitutive components of the dispersive stresses

How to represent the effects of variable canopy morphology on turbulence remains a fundamental challenge yet to be confronted. Planar averaging over some minimal area can be applied to average-out this sort of spatial variability in the time-averaged mean momentum balance. Because of the multiply connected air-spaces, spatial averaging gives rise to covariance or dispersive stress terms that are produced by the spatial correlations of the time-averaged quantities. These terms are “unclosed” and require parameterization, which to date remains lacking due to the absence of data. Here, flume experiments were conducted to quantify the magnitude and sign of the dispersive stresses for a cylindric canopy where the rod density was varied but the individual rod dimensions (rod height h _c and rod diameter d _r) remained the same. Quadrant analysis was used to explore the genesis of their spatial coherency inside the canopy for a wide range of rod densities. When compared to the conventional turbulent stresses, these dispersive stresses can be significant in the lowest layers of sparse canopies. For dense canopies, the dispersive terms remain negligible when compared to the conventional momentum fluxes at all the canopy levels consistent with previous experiments in vegetated and urban canopies. It was also shown that the spatial locations contributing most to the dispersive terms were in the immediate vicinity downstream of the rods. In the deeper layers of sparse canopies, these positions contributed large and negative stresses, but in the upper levels of the canopy, they contributed large but positive stresses. Because the longitudinal velocity spatial perturbation behind the rods is negative, the switch in sign in these stresses was connected with the sign of the vertical velocity spatial perturbation Simplified scaling arguments, using a reduced mean continuity equation and the vertical mean momentum balance for the flow field near the rods, offer clues as to why in much of the lower canopy levels (about 0.75 h _c ) while in the upper canopy levels.     

Polycaprolactone-b-Poly(ethylene oxide) Biocompatible Micelles as Drug Delivery Nanocarriers: Dynamic Light Scattering and Fluorescence Experiments

Summary: Dynamic light scattering (DLS) and fluorescence experiments were carried out to study PCL₄₄-b-PEO₁₁₄ biocompatible micelles used as nanocarriers in drug delivery. Micelles prepared by a simple procedure (THF removal under nitrogen flow) exhibited a narrow size distribution with an average diameter of 100 nm. For micelles containing a hydrophobic model compound (pyrene) within the PCL core, a smaller average micellar size of 80 nm was observed, with a simultaneous broadening in the size distribution profile. In parallel to DLS results, fluorescence experiments showed evidence of pyrene encapsulation, and that the onset of the micellization process occurs at approximately 10/90 (v/v) THF/water mixtures in the case of PCL₄₄-b-PEO₁₁₄ polymer.