On a class of three-phase checkerboards with unusual effective properties

We examine the band spectrum, and associated Floquet-Bloch eigensolutions, arising in a class of three-phase periodic checkerboards. On a periodic cell $[-1,1[^2$, the refractive index is defined by $n^2= 1+ g_1(x_1)+g_2(x_2)$ with $g_i(x_i)= r^2\quad {\rm for} \quad 0\leq x_i-1$ the lowest frequency branch goes through origin with linear behaviour, which leads to effective properties encountered in most periodic structures. However, the case whereby $r^2=-1$ is very unusual, as the frequency $\lambda$ behaves like $\sqrt{k}$ near the origin, where $k$ is the wavenumber. Finally, when $r^2<-1$, the lowest branch does not pass through the origin and a zero-frequency band gap opens up. In the last two cases, effective medium theory breaks down even in the quasi-static limit, while the high-frequency homogenization [Craster et al., Proc. Roy. Soc. Lond. A 466, 2341-2362, 2010] neatly captures the detailed features of band diagrams

A Solvent Model for Simulations of Peptides in Bilayers. I. Membrane-Promoting α-Helix Formation

AbstractWe describe an efficient solvation model for proteins. In this model atomic solvation parameters imitating the hydrocarbon core of a membrane, water, and weak polar solvent (octanol) were developed. An optimal number of solvation parameters was chosen based on analysis of atomic hydrophobicities and fitting experimental free energies of gas-cyclohexane, gas-water, and octanol-water transfer for amino acids. The solvation energy term incorporated into the ECEPP/2 potential energy function was tested in Monte Carlo simulations of a number of small peptides with known energies of bilayer-water and octanol-water transfer. The calculated properties were shown to agree reasonably well with the experimental data. Furthermore, the solvation model was used to assess membrane-promoting α-helix formation. To accomplish this, all-atom models of 20-residue homopolypeptides—poly-Leu, poly-Val, poly-Ile, and poly-Gly in initial random coil conformation—were subjected to nonrestrained Monte Carlo conformational search in vacuo and with the solvation terms mimicking the water and hydrophobic parts of the bilayer. All the peptides demonstrated their largest helix-forming tendencies in a nonpolar environment, where the lowest-energy conformers of poly-Leu, Val, Ile revealed 100, 95, and 80% of α-helical content, respectively. Energetic and conformational properties of Gly in all environments were shown to be different from those observed for residues with hydrophobic side chains. Applications of the solvation model to simulations of peptides and proteins in the presence of membrane, along with limitations of the approach, are discussed

K\"ahler-driven Tribrid Inflation

We discuss a new class of tribrid inflation models in supergravity, where the shape of the inflaton potential is dominated by effects from the K\"ahler potential. Tribrid inflation is a variant of hybrid inflation which is particularly suited for connecting inflation with particle physics, since the inflaton can be a D-flat combination of charged fields from the matter sector. In models of tribrid inflation studied so far, the inflaton potential was dominated by either loop corrections or by mixing effects with the waterfall field (as in "pseudosmooth" tribrid inflation). Here we investigate the third possibility, namely that tribrid inflation is dominantly driven by effects from higher-dimensional operators of the K\"ahler potential. We specify for which superpotential parameters the new regime is realized and show how it can be experimentally distinguished from the other two (loop-driven and "pseudosmooth") regimes.Comment: 28 pages, v2: added some references, this version matches the publication in JCA

A Solvent Model for Simulations of Peptides in Bilayers. II. Membrane-Spanning α-Helices

AbstractWe describe application of the implicit solvation model (see the first paper of this series), to Monte Carlo simulations of several peptides in bilayer- and water-mimetic environments, and in vacuum. The membrane-bound peptides chosen were transmembrane segments A and B of bacteriorhodopsin, the hydrophobic segment of surfactant lipoprotein, and magainin2. Their conformations in membrane-like media are known from the experiments. Also, molecular dynamics study of surfactant lipoprotein with different explicit solvents has been reported (Kovacs, H., A. E. Mark, J. Johansson, and W. F. van Gunsteren. 1995. J. Mol. Biol. 247:808–822). The principal goal of this work is to compare the results obtained in the framework of our solvation model with available experimental and computational data. The findings could be summarized as follows: 1) structural and energetic properties of studied molecules strongly depend on the solvent; membrane-mimetic media significantly promote formation of α-helices capable of traversing the bilayer, whereas a polar environment destabilizes α-helical conformation via reduction of solvent-exposed surface area and packing; 2) the structures calculated in a membrane-like environment agree with the experimental ones; 3) noticeable differences in conformation of surfactant lipoprotein assessed via Monte Carlo simulation with implicit solvent (this work) and molecular dynamics in explicit solvent were observed; 4) in vacuo simulations do not correctly reproduce protein-membrane interactions, and hence should be avoided in modeling membrane proteins

Pseudosmooth Tribrid Inflation

We explore a new class of supersymmetric models of inflation where the inflaton is realised as a combination of a Higgs field and (gauge non-singlet) matter fields, using a "tribrid" structure of the superpotential. Inflation is associated with a phase transition around GUT scale energies. The inflationary trajectory already preselects the later vacuum after inflation, which has the advantage of automatically avoiding the production of dangerous topological defects at the end of inflation. While at first sight the models look similar to smooth inflation, they feature a waterfall and are therefore only pseudosmooth. The new class of models offers novel possibilities for realising inflation in close contact with particle physics, for instance with supersymmetric GUTs or with supersymmetric flavour models based on family symmetries.Comment: 16 pages, 5 figures. v2 matches publication in JCA

Impact of system factors on the water saving efficiency of household grey water recycling

Copyright © 2010 Taylor & Francis. This is an Author's Accepted Manuscript of an article published in Desalination and Water Treatment Volume 24, Issue 1-3 (2010), available online at: http://www.tandfonline.com/10.5004/dwt.2010.1542A general concern when considering the implementation of domestic grey water recycling is to understand the impacts of system factors on water saving efficiency. Key factors include household occupancy, storage volumes, treatment capacity and operating mode. Earlier investigations of the impacts of these key factors were based on a one-tank system only. This paper presents the results of an investigation into the effect of these factors on the performance of a more realistic ‘two tank’ system with treatment using an object based household water cycle model. A Monte-Carlo simulation technique was adopted to generate domestic water appliance usage data which allows long-term prediction of the system's performance to be made. Model results reveal the constraints of treatment capacity, storage tank sizes and operating mode on percentage of potable water saved. A treatment capacity threshold has been discovered at which water saving efficiency is maximised for a given pair of grey and treated grey water tank. Results from the analysis suggest that the previous one-tank model significantly underestimates the tank volumes required for a given target water saving efficiency

A Novel Putative miRNA Target Enhancer Signal

It is known that miRNA target sites are very short and the effect of miRNA-target site interaction alone appears as being unspecific. Recent experiments suggest further context signals involved in miRNA target site recognition and regulation. Here, we present a novel GC-rich RNA motif downstream of experimentally supported miRNA target sites in human mRNAs with no similarity to previously reported functional motifs. We demonstrate that the novel motif can be found in at least one third of all transcripts regulated by miRNAs. Furthermore, we show that motif occurrence and the frequency of miRNA target sites as well as the stability of their duplex structures correlate. The finding, that the novel motif is significantly associated with miRNA target sites, suggests a functional role of the motif in miRNA target site biology. Beyond, the novel motif has the impact to improve prediction of miRNA target sites significantly

The mir-51 Family of microRNAs Functions in Diverse Regulatory Pathways in Caenorhabditis elegans

The mir-51 family of microRNAs (miRNAs) in C. elegans are part of the deeply conserved miR-99/100 family. While loss of all six family members (mir-51-56) in C. elegans results in embryonic lethality, loss of individual mir-51 family members results in a suppression of retarded developmental timing defects associated with the loss of alg-1. The mechanism of this suppression of developmental timing defects is unknown. To address this, we characterized the function of the mir-51 family in the developmental timing pathway. We performed genetic analysis and determined that mir-51 family members regulate the developmental timing pathway in the L2 stage upstream of hbl-1. Loss of the mir-51 family member, mir-52, suppressed retarded developmental timing defects associated with the loss of let-7 family members and lin-46. Enhancement of precocious defects was observed for mutations in lin-14, hbl-1, and mir-48(ve33), but not later acting developmental timing genes. Interestingly, mir-51 family members showed genetic interactions with additional miRNA-regulated pathways, which are regulated by the let-7 and mir-35 family miRNAs, lsy-6, miR-240/786, and miR-1. Loss of mir-52 likely does not suppress miRNA-regulated pathways through an increase in miRNA biogenesis or miRNA activity. We found no increase in the levels of four mature miRNAs, let-7, miR-58, miR-62 or miR-244, in mir-52 or mir-52/53/54/55/56 mutant worms. In addition, we observed no increase in the activity of ectopic lsy-6 in the repression of a downstream target in uterine cells in worms that lack mir-52. We propose that the mir-51 family functions broadly through the regulation of multiple targets, which have not yet been identified, in diverse regulatory pathways in C. elegans

Diffusion in Model Networks as Studied by NMR and Fluorescence Correlation Spectroscopy

We have studied the diffusion of small solvent molecules (octane) and larger hydrophobic dye probes in octane-swollen poly(dimethyl siloxane) linear-chain solutions and end-linked model networks, using pulsed-gradient nuclear magnetic resonance (NMR) and fluorescence correlation spectroscopy (FCS), respectively, focusing on diffusion in the bulk polymer up to the equilibrium degree of swelling of the networks, that is, 4.8 at most. The combination of these results allows for new conclusions on the feasibility of different theories describing probe diffusion in concentrated polymer systems. While octane diffusion shows no cross-link dependence, the larger dyes are increasingly restricted by fixed chemical meshes. The simple Fujita free-volume theory proved most feasible to describe probe diffusion in linear long-chain solutions with realistic parameters, while better fits were obtained assuming a stretched exponential dependence on concentration. Importantly, we have analyzed the cross-link specific effect on probe diffusion independently of any specific model by comparing the best-fit interpolation of the solution data with the diffusion in the networks. The most reasonable description is obtained by assuming that the cross-link effect is additive in the effective friction coefficient of the probes. The concentration dependences as well as the data compared at the equilibrium degrees of swelling indicate that swelling heterogeneities and diffusant shape have a substantial influence on small-molecule diffusion in networks.