A simple method for the simulation of multiple elastic scattering of electrons

A screened Rutherford cross section is modified by means of a correction factor to obtain the proper transport cross section computed by partial¿wave analysis. The correction factor is tabulated for electron energies in the range 0¿100 keV and for elements in the range from Z=4 to 82. The modified screened Rutherford cross section is shown to be useful as an approximation for the simulation of plural and multiple scattering. Its performance and limitations are exemplified for electrons scattered in Al and Au.

Monte Carlo simulation of kilovolt electron transport in solids

A Monte Carlo procedure to simulate the penetration and energy loss of low¿energy electron beams through solids is presented. Elastic collisions are described by using the method of partial waves for the screened Coulomb field of the nucleus. The atomic charge density is approximated by an analytical expression with parameters determined from the Dirac¿Hartree¿Fock¿Slater self¿consistent density obtained under Wigner¿Seitz boundary conditions in order to account for solid¿state effects; exchange effects are also accounted for by an energy¿dependent local correction. Elastic differential cross sections are then easily computed by combining the WKB and Born approximations to evaluate the phase shifts. Inelastic collisions are treated on the basis of a generalized oscillator strength model which gives inelastic mean free paths and stopping powers in good agreement with experimental data. This scattering model is accurate in the energy range from a few hundred eV up to about 50 keV. The reliability of the simulation method is analyzed by comparing simulation results and experimental data from backscattering and transmission measurements.

Simple method for the simulation of multiple elastic scattering of electrons

A screened Rutherford cross section is modified by means of a correction factor to obtain the proper transport cross section computed by partial¿wave analysis. The correction factor is tabulated for electron energies in the range 0¿100 keV and for elements in the range from Z=4 to 82. The modified screened Rutherford cross section is shown to be useful as an approximation for the simulation of plural and multiple scattering. Its performance and limitations are exemplified for electrons scattered in Al and Au.

Langevin approach to generate synthetic turbulent flows

We present an analytical scheme, easily implemented numerically, to generate synthetic Gaussian turbulent flows by using a linear Langevin equation, where the noise term acts as a stochastic stirring force. The characteristic parameters of the velocity field are well introduced, in particular the kinematic viscosity and the spectrum of energy. As an application, the diffusion of a passive scalar is studied for two different energy spectra. Numerical results are compared favorably with analytical calculations.

Front dynamics in turbulent media

A study of a stable front propagating in a turbulent medium is presented. The front is generated through a reaction-diffusion equation, and the turbulent medium is statistically modeled using a Langevin equation. Numerical simulations indicate the presence of two different dynamical regimes. These regimes appear when the turbulent flow either wrinkles a still rather sharp propagating interfase or broadens it. Specific dependences of the propagating velocities on stirring intensities appropriate to each case are found and fitted when possible according to theoretically predicted laws. Different turbulent spectra are considered.

Diffusion of passive scalars under stochastic convection

The diffusion of passive scalars convected by turbulent flows is addressed here. A practical procedure to obtain stochastic velocity fields with well¿defined energy spectrum functions is also presented. Analytical results are derived, based on the use of stochastic differential equations, where the basic hypothesis involved refers to a rapidly decaying turbulence. These predictions are favorable compared with direct computer simulations of stochastic differential equations containing multiplicative space¿time correlated noise.

Elastic scattering of fast electrons and positrons by atoms

Elastic scattering of relativistic electrons and positrons by atoms is considered in the framework of the static field approximation. The scattering field is expressed as a sum of Yukawa terms to allow the use of various approximations. Accurate phase shifts have been computed by combining Bühring¿s power-series method with the WKB and Born approximations. This combined procedure allows the evaluation of differential cross sections for kinetic energies up to several tens of MeV. Numerical results are used to analyze the validity of several approximate methods, namely the first- and second-order Born approximations and the screened Mott formula, which are frequently adopted as the basis of multiple scattering theories and Monte Carlo simulations of electron and positron transport.

Fingerlike aggregates in thin-layer electrodeposition

Electrodeposition experiments conducted in a thin-layer horizontal cell containing a nonbinary aqueous electrolyte prepared with cupric sulfate and sodium sulfate gave rise to fingerlike deposits, a novel and unexpected growth mode in this context. Both the leading instability from which fingers emerge and some distinctive features of their steady evolution are interpreted in terms of a simple model based on the existing theory of fingering in fluids.

Magnetic structure of Li2CuO2: From ab initio calculations to macroscopic simulations

The magnetic structure of the edge-sharing cuprate compound Li2CuO2 has been investigated with highly correlated ab initio electronic structure calculations. The first- and second-neighbor in-chain magnetic interactions are calculated to be 142 and -22 K, respectively. The ratio between the two parameters is smaller than suggested previously in the literature. The interchain interactions are antiferromagnetic in nature and of the order of a few K only. Monte Carlo simulations using the ab initio parameters to define the spin model Hamiltonian result in a Nel temperature in good agreement with experiment. Spin population analysis situates the magnetic moment on the copper and oxygen ions between the completely localized picture derived from experiment and the more delocalized picture based on local-density calculations.

Towards and ab initio description of magnetism in ionic solids

The physical contributions to the KNiF3 magnetic exchange coupling integral have been obtained from specially designed ab initio cluster model calculations. Three important mechanisms have been identified. These are the delocalization of the magnetic orbitals into the anion p band, the variational contribution of the second-order interactions, and the many-body terms hidden in the two-body operator and the Heisenberg Hamiltonian.

Self-similar community structure in a network of human interactions

We propose a procedure for analyzing and characterizing complex networks. We apply this to the social network as constructed from email communications within a medium sized university with about 1700 employees. Email networks provide an accurate and nonintrusive description of the flow of information within human organizations. Our results reveal the self-organization of the network into a state where the distribution of community sizes is self-similar. This suggests that a universal mechanism, responsible for emergence of scaling in other self-organized complex systems, as, for instance, river networks, could also be the underlying driving force in the formation and evolution of social networks.

RPS4Y gene family evolution in primates

Background: The RPS4 gene codifies for ribosomal protein S4, a very well-conserved protein present in all kingdoms. In primates, RPS4 is codified by two functional genes located on both sex chromosomes: the RPS4X and RPS4Y genes. In humans, RPS4Y is duplicated and the Y chromosome therefore carries a third functional paralog: RPS4Y2, which presents a testis-specific expression pattern. Results: DNA sequence analysis of the intronic and cDNA regions of RPS4Y genes from species covering the entire primate phylogeny showed that the duplication event leading to the second Y-linked copy occurred after the divergence of New World monkeys, about 35 million years ago. Maximum likelihood analyses of the synonymous and non-synonymous substitutions revealed that positive selection was acting on RPS4Y2 gene in the human lineage, which represents the first evidence of positive selection on a ribosomal protein gene. Putative positive amino acid replacements affected the three domains of the protein: one of these changes is located in the KOW protein domain and affects the unique invariable position of this motif, and might thus have a dramatic effect on the protein function.Conclusion: Here, we shed new light on the evolutionary history of RPS4Y gene family, especially on that of RPS4Y2. The results point that the RPS4Y1 gene might be maintained to compensate gene dosage between sexes, while RPS4Y2 might have acquired a new function, at least in the lineage leading to humans.

A proteomics approach to decipher the molecular nature of planarian stem cells.

Background In recent years, planaria have emerged as an important model system for research into stem cells and regeneration. Attention is focused on their unique stem cells, the neoblasts, which can differentiate into any cell type present in the adult organism. Sequencing of the Schmidtea mediterranea genome and some expressed sequence tag projects have generated extensive data on the genetic profile of these cells. However, little information is available on their protein dynamics. Results We developed a proteomic strategy to identify neoblast-specific proteins. Here we describe the method and discuss the results in comparison to the genomic high-throughput analyses carried out in planaria and to proteomic studies using other stem cell systems. We also show functional data for some of the candidate genes selected in our proteomic approach. Conclusions We have developed an accurate and reliable mass-spectra-based proteomics approach to complement previous genomic studies and to further achieve a more accurate understanding and description of the molecular and cellular processes related to the neoblasts.

Smed454 dataset: unravelling the transcriptome of Schmidtea mediterranea

Background: Freshwater planarians are an attractive model for regeneration and stem cell research and have become a promising tool in the field of regenerative medicine. With the availability of a sequenced planarian genome, the recent application of modern genetic and high-throughput tools has resulted in revitalized interest in these animals, long known for their amazing regenerative capabilities, which enable them to regrow even a new head after decapitation. However, a detailed description of the planarian transcriptome is essential for future investigation into regenerative processes using planarians as a model system. Results: In order to complement and improve existing gene annotations, we used a 454 pyrosequencing approach to analyze the transcriptome of the planarian species Schmidtea mediterranea Altogether, 598,435 454-sequencing reads, with an average length of 327 bp, were assembled together with the ~10,000 sequences of the S. mediterranea UniGene set using different similarity cutoffs. The assembly was then mapped onto the current genome data. Remarkably, our Smed454 dataset contains more than 3 million novel transcribed nucleotides sequenced for the first time. A descriptive analysis of planarian splice sites was conducted on those Smed454 contigs that mapped univocally to the current genome assembly. Sequence analysis allowed us to identify genes encoding putative proteins with defined structural properties, such as transmembrane domains. Moreover, we annotated the Smed454 dataset using Gene Ontology, and identified putative homologues of several gene families that may play a key role during regeneration, such as neurotransmitter and hormone receptors, homeobox-containing genes, and genes related to eye function. Conclusions: We report the first planarian transcript dataset, Smed454, as an open resource tool that can be accessed via a web interface. Smed454 contains significant novel sequence information about most expressed genes of S. mediterranea. Analysis of the annotated data promises to contribute to identification of gene families poorly characterized at a functional level. The Smed454 transcriptome data will assist in the molecular characterization of S. mediterranea as a model organism, which will be useful to a broad scientific community.