Optimization and Parallelization of a force field for silicon using OpenMP

The force field by Lenosky and coworkers is the latest force field for silicon which is one of the most studied materials. It has turned out to be highly accurate in a large range of test cases. The optimization and parallelization of this force field using OpenMp and Fortan90 is described here. The optimized program allows us to handle a very large number of silicon atoms in large scale simulations. Since all the parallelization is hidden in a single subroutine that returns the total energies and forces, this subroutine can be called from within a serial program in an user friendly way.Comment: The program can be obtained upon request from the author ([email protected]

Electromagnetic analysis of arbitrarily shaped pinched carpets

We derive the expressions for the anisotropic heterogeneous tensors of permittivity and perme- ability associated with two-dimensional and three-dimensional carpets of an arbitrary shape. In the former case, we map a segment onto smooth curves whereas in the latter case we map a non convex region of the plane onto smooth surfaces. Importantly, these carpets display no singularity of the permeability and permeability tensor components, and this may lead to some broadband cloaking.Comment: 6 pages, 6 figures, Current Status of Manuscript: 19Apr10 26May10-Sent on appeal;report rcvd 29Dec09 13Apr10-Ed. decision and/or ref. comments to author;response rcvd 04Dec09 21Dec09-Ed. decision and/or ref. comments to author;response rcvd 01Dec09-Transferred from PRL to PRA 18Aug09 30Nov09-Ed.decision and/or ref. comments to author;response rcvd 14Aug09 - Correspondence sent to autho

Maximum Likelihood Estimation for Nets of Conics

We study the problem of maximum likelihood estimation for $3$-dimensional linear spaces of $3\times 3$ symmetric matrices from the point of view of algebraic statistics where we view these nets of conics as linear concentration or linear covariance models of Gaussian distributions on $\mathbb{R}^3$. In particular, we study the reciprocal surfaces of nets of conics which are rational surfaces in $\mathbb{P}^5$. We show that the reciprocal surfaces are projections from the Veronese surface and determine their intersection with the polar nets. This geometry explains the maximum likelihood degrees of these linear models. We compute the reciprocal maximum likelihood degrees. This work is based on Wall's classification of nets of conics from 1977

Maximum likelihood estimation for nets of conics

We study the problem of maximum likelihood estimation for 3-dimensional linear spaces of 3 x 3 symmetric matrices from the point of view of algebraic statistics where we view these nets of conics as linear concentration or linear covariance models of Gaussian distributions on R3. In particular, we study the reciprocal surfaces of nets of conics which are rational surfaces in P5. We show that the reciprocal surfaces are projections from the Veronese surface and determine their intersection with the polar nets. This geometry explains the maximum likelihood degrees of these linear models. We compute the reciprocal maximum likelihood degrees. This work is based on Wall's classification of nets of conics from 1977

In and Out of the Bursa-The Role of CXCR4 in Chicken B Cell Development

In contrast to mammals, early B cell differentiation and diversification of the antibody repertoire in chickens do not take place in the bone marrow but in a specialized gut associated lymphoid tissue (GALT), the bursa of Fabricius. During embryonic development, B cell precursors migrate to the bursa anlage, where they proliferate and diversify their B cell receptor repertoire. Around hatch these diversified B cells start to emigrate from the bursa of Fabricius and populate peripheral lymphoid organs, but very little is known how the migratory processes are regulated. As CXCL12 (syn. SDF-1) and CXCR4 were shown to be essential for the control of B cell migration during the development of lymphoid tissues in mammals, we analyzed expression and function of this chemokine/chemokine-receptor pair in the chicken bursa. We found a strong variation of mRNA abundance of CXCL12 and CXCR4 in different stages of bursa development, with high abundance of CXCL12 mRNA in the bursa anlage at embryonic day 10 (ED10).In situhybridization demonstrated disseminated CXCL12 expression in the early bursa anlage, which condensed in the developing follicles and was mainly restricted to the follicle cortex post-hatch. Flow cytometric analysis detected CXCR4 protein already on early B cell stages, increasing during bursal development. Post-hatch, a subpopulation with the hallmarks of emigrating B cells became detectable, which had lower CXCR4 expression, suggesting that downregulation of CXCR4 is necessary to leave the CXCL12-high bursal environment.In vivoblockade of CXCR4 using AMD3100 at the time of B cell precursor immigration strongly inhibited follicle development, demonstrating that CXCL12 attracts pre-bursal B cells into the bursal anlage. Altogether, we show that CXCL12 and its receptor CXCR4 are important for both populating the bursa with B cells and emigration of mature B cells into the periphery post hatch, and that CXCR4 function in primary B cell organs is conserved between mammals and birds

A specious unlinking strategy

We show that the following unlinking strategy does not always yield an optimal sequence of crossing changes: first split the link with the minimal number of crossing changes, and then unknot the resulting components

Serological differentiation of antibodies against Rickettsia helvetica, R. raoultii, R. slovaca, R. monacensis and R. felis in dogs from Germany by a micro-immunofluorescent antibody test

Background Spotted Fever Group (SFG) Rickettsiae can cause febrile diseases with or without rash in humans worldwide. In Germany only limited data are available about their medical significance. Serological screening tests for antibodies against rickettsiae usually only distinguish between SFG and Typhus Group (TG) Rickettsiae due to the strong cross reactivities within the groups. Seroprevalence rates in dogs, as possible sentinels for tick-borne diseases, could serve as an indicator for the distribution of different Rickettsia species. Methods In this study, a micro-immunofluorescence assay (micro-IFA) was established for detection and differentiation of antibodies against five Rickettsia species in dogs (R. helvetica, R. raoultii, R. slovaca, R. monacensis and R. felis). Dogs that never left Germany (n = 605) previously investigated with an SFG-ELISA were included in this study and screened at a 1:128 dilution. Endpoint titres of fifty randomly selected seropositive samples of each of the five investigated regions in Germany were determined in order to allow a differentiation of the causative Rickettsia species. Sensitivity and specificity of the micro-IFA were compared with ELISA results of the previous study. Results A total of 93.9% of the dogs were positive for antibodies of the SFG Rickettsiae at the screening titer of 1:128. Differentiation of SFG Rickettsiae with the micro-IFA was possible in 70.4%, but in 29.6% of the cases the detected antibodies were not differentiable. Considering a clear differentiation by a twofold titre difference between observed reactions, the seroprevalence rates were 66.0% for R. helvetica, 2.8% for R. raoultii, 1.6% for R. slovaca, but no serological reaction could be clearly attributed to R. monacensis or R. felis. No statistically significant regional differences were found for R. helvetica, R. slovaca and R. raoultii comparing the five regions of Germany. Comparison of micro-IFA with ELISA revealed a sensitivity of 82.0% and a specificity of 83.8% for the Rickettsia SFG ELISA. Conclusions The micro-IFA is a useful serological tool to differentiate antibodies against different Rickettsia species in dogs. Seroprevalence rates in dogs correspond to the prevalence rates and distribution of Rickettsia-carrying tick species

Revolution analysis of three-dimensional arbitrary cloaks

We extend the design of radially symmetric three-dimensional invisibility cloaks through transformation optics to cloaks with a surface of revolution. We derive the expression of the transformation matrix and show that one of its eigenvalues vanishes on the inner boundary of the cloaks, while the other two remain strictly positive and bounded. The validity of our approach is confirmed by finite edge-elements computations for a non-convex cloak of varying thickness.Comment: 6 pages, 4 figure