The optimal P3M algorithm for computing electrostatic energies in periodic systems

We optimize Hockney and Eastwood's Particle-Particle Particle-Mesh (P3M) algorithm to achieve maximal accuracy in the electrostatic energies (instead of forces) in 3D periodic charged systems. To this end we construct an optimal influence function that minimizes the RMS errors in the energies. As a by-product we derive a new real-space cut-off correction term, give a transparent derivation of the systematic errors in terms of Madelung energies, and provide an accurate analytical estimate for the RMS error of the energies. This error estimate is a useful indicator of the accuracy of the computed energies, and allows an easy and precise determination of the optimal values of the various parameters in the algorithm (Ewald splitting parameter, mesh size and charge assignment order).Comment: 31 pages, 3 figure

Genes involved in carotene synthesis and mating in Blakeslea trispora

Mating of Blakeslea trispora and other molds of the order Mucorales requires the interaction of mycelia of opposite sex, (+) and (-), leading to the development of specialized structures and to an enhanced accumulation of beta-carotene. Industry obtains beta-carotene by co-cultivating appropriate strains of Blakeslea (mated cultures). Gene transcription in single and mated cultures was assayed by cDNA-AFLP, a technique to observe the differential expression of subsets of mRNA fragments. Overexpression in mated cultures is about ten times more frequent than underexpression. We obtained and sequenced fragments of 97 candidate genes that appeared to be overexpressed during mating and confirmed four of them by reverse transcription and real-time PCR. Comparisons with gene sequences from other organisms suggest functions in carotene biosynthesis (4 genes), energy metabolism (8), cell wall synthesis (1), transfer of acetyl groups (1), and regulatory processes (10). Sodium acetate inhibited sexual overexpression in about two-thirds of the candidate genes and acted as a signal with broad effects on the metabolism and the morphology of mated cultures. Our work offers new materials for the study of carotene biosynthesis and its regulation and for the improvement of carotene production with Mucorales

Measuring Dislocation Density in Aluminum with Resonant Ultrasound Spectroscopy

Dislocations in a material will, when present in enough numbers, change the speed of propagation of elastic waves. Consequently, two material samples, differing only in dislocation density, will have different elastic constants, a quantity that can be measured using Resonant Ultrasound Spectroscopy. Measurements of this effect on aluminum samples are reported. They compare well with the predictions of the theory.Comment: 4 pages, 2 figure

Characterization of Polyphosphoesters by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

FT-ICR mass spectrometry, together with collision-induced dissociation and electron capture dissociation, has been used to characterize the polyphosphoester poly[1,4-bis(hydroxyethyl)terephthalate-alt-ethyloxyphosphate] and its degradation products. Three degradation pathways were elucidated: hydrolysis of the phosphate–[1,4-bis(hydroxyethyl)terephthalate]bonds; hydrolysis of the phosphate–ethoxy bonds; and hydrolysis of the ethyl–terephthalate bonds. The dominant degradation reactions were those that involved the phosphate groups. This work constitutes the first application of mass spectrometry to the characterization of polyphosphoesters and demonstrates the suitability of high mass accuracy FT-ICR mass spectrometry, with CID and ECD, for the structural analysis of polyphosphoesters and their degradation products

Shaping soliton properties in optical Mathieu lattices

We address basic properties and stability of two-dimensional solitons in photonic lattices induced by the nondiffracting Mathieu beams. Such lattices allow for smooth topological transformation of radially symmetric Bessel lattices into quasi-one-dimensional periodic ones. The transformation of lattice topology drastically affects properties of ground-state and dipole-mode solitons, including their shape, stability and transverse mobility.Comment: 14 pages, 4 figures, to appear in Optics Letter

Molecular characterization and expression pattern of zona pellucida proteins in gilthead seabream (Sparus aurata)

The developing oocyte is surrounded by an acellular envelope that is composed of 2–4 isoforms of zona pellucida (ZP) proteins. The ZP proteins comprise the ZP1, ZP2, ZP3, and ZPX isoforms. While ZP1 (ZPB) and ZP3 (ZPC) are present in all species, ZP2 (ZPA) is not found in teleost fish and ZPX is not found in mammals. In the present study, we identify and characterize the ZP1, ZP3 and ZPX isoforms of gilthead seabream. Furthermore, by analyzing the conserved domains, which include the external hydrophobic patch and the internal hydrophobic patch, we show that ZP2 and ZPX are closely related isoforms. ZP proteins are synthesized in either the liver or ovary of most teleosts. Only in rainbow trout has it been shown that zp3 has dual transcription sites. In gilthead seabream, all four mRNA isoforms are transcribed in both the liver and ovary, with zp1a, zp1b, and zp3 being highly expressed in the liver, and zpx being primarily expressed in the ovary. However, determination of the ZP proteins in plasma showed high levels of ZP1b, ZP3, and ZPX, with low or non-detectable levels of ZP1a. In similarity to other teleost ZPs, the hepatic transcription of all four ZP isoforms is under estrogenic control. Previously, we have shown that cortisol can potentiate estrogen-induced ZP synthesis in salmonids, and now we show that this is not the case in the gilthead seabream. The present study shows for the first time the endocrine regulation of a teleost ZPX isoform, and demonstrates the dual-organ transcriptional activities of all the ZP proteins in one species

Nondiffracting vortex-beams in a birefringent chiral crystal

A vector wave analysis of nondiffracting beams propagating along a birefringent chiral crystal for the case of tensor character both of the optical activity and linear birefringence is presented, fields of eigen modes satisfying vector wave equation. We have written characteristic equations and found propagation constants and amplitude parameters of eigen modes. We have shown that the field of eigen modes is non-uniformly polarized in the beam cross-section. We have revealed that even a purely chiral crystal without a linear birefringent can generate optical vortices in an initially vortex-free Bessel beam.Comment: 9 pages, 5 figure

Extra-embryonic tissue spreading directs early embryo morphogenesis in killifish

The spreading of mesenchymal-like cell layers is critical for embryo morphogenesis and tissue repair, yet we know little of this process in vivo. Here we take advantage of unique developmental features of the non-conventional annual killifish embryo to study the principles underlying tissue spreading in a simple cellular environment, devoid of patterning signals and major morphogenetic cell movements. Using in vivo experimentation and physical modelling we reveal that the extra-embryonic epithelial enveloping cell layer, thought mainly to provide protection to the embryo, directs cell migration and the spreading of embryonic tissue during early development. This function relies on the ability of embryonic cells to couple their autonomous random motility to non-autonomous signals arising from the expansion of the extra-embryonic epithelium, mediated by cell membrane adhesion and tension. Thus, we present a mechanism of extra-embryonic control of embryo morphogenesis that couples the mechanical properties of adjacent tissues in the early killifish embryo