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

Transforming Post-Secondary Education in Mathematics

In this manuscript, I introduce and describe the work of mathematicians and mathematics educators in the group Transforming Post-Secondary Education in Mathematics (TPSE Math or TPSE, pronounced "tipsy", for short). TPSE aims to coordinate and drive constructive change in education in the mathematical sciences at two-year colleges, four-year colleges, and universities across the nation. It seeks to build on the successes of the entire mathematical sciences community. This manuscript reviews the events that led to the founding of TPSE Math and articulates its vision and mission. In its first phase with national events, TPSE found broad consensus with the mathematical sciences community on the challenges facing the community. Learning from educational transformations experiences in other scientific fields, and with the support of the Mathematical Advisory Group of 34 mathematical sciences department chairs and leaders, TPSE moves into a second phase focused on action. This is a snapshot in time, and TPSE's ongoing activities will continue to be documented and disseminated. The piece concludes with a reflection of the impact that my involvement in this work has had on my career.Comment: 17 page

Magnetic ground state and magnon-phonon interaction in multiferroic h-YMnO3_3

Inelastic neutron scattering has been used to study the magneto-elastic excitations in the multiferroic manganite hexagonal YMnO$_3$. An avoided crossing is found between magnon and phonon modes close to the Brillouin zone boundary in the $(a,b)$-plane. Neutron polarization analysis reveals that this mode has mixed magnon-phonon character. An external magnetic field along the $c$-axis is observed to cause a linear field-induced splitting of one of the spin wave branches. A theoretical description is performed, using a Heisenberg model of localized spins, acoustic phonon modes and a magneto-elastic coupling via the single-ion magnetostriction. The model quantitatively reproduces the dispersion and intensities of all modes in the full Brillouin zone, describes the observed magnon-phonon hybridized modes, and quantifies the magneto-elastic coupling. The combined information, including the field-induced magnon splitting, allows us to exclude several of the earlier proposed models and point to the correct magnetic ground state symmetry, and provides an effective dynamic model relevant for the multiferroic hexagonal manganites.Comment: 12 pages, 10 figure

Universality of the Ising Model on Sphere-like Lattices

We study the 2D Ising model on three different types of lattices that are topologically equivalent to spheres. The geometrical shapes are reminiscent of the surface of a pillow, a 3D cube and a sphere, respectively. Systems of volumes ranging up to O($10^5$) sites are simulated and finite size scaling is analyzed. The partition function zeros and the values of various cumulants at their respective peak positions are determined and they agree with the scaling behavior expected from universality with the Onsager solution on the torus ($\nu=1$). For the pseudocritical values of the coupling we find significant anomalies indicating a shift exponent $\neq 1$ for sphere-like lattice topology.Comment: 24 pages, LaTeX, 8 figure

Biofilter aquaponic system for nutrients removal from fresh market wastewater

Aquaponics is a significant wastewater treatment system which refers to the combination of conventional aquaculture (raising aquatic organism) with hydroponics (cultivating plants in water) in a symbiotic environment. This system has a high ability in removing nutrients compared to conventional methods because it is a natural and environmentally friendly system (aquaponics). The current chapter aimed to review the possible application of aquaponics system to treat fresh market wastewater with the intention to highlight the mechanism of phytoremediation occurs in aquaponic system. The literature revealed that aquaponic system was able to remove nutrients in terms of nitrogen and phosphorus

Theoretical study of the insulating oxides and nitrides: SiO2, GeO2, Al2O3, Si3N4, and Ge3N4

An extensive theoretical study is performed for wide bandgap crystalline oxides and nitrides, namely, SiO_{2}, GeO_{2}, Al_{2}O_{3}, Si_{3}N_{4}, and Ge_{3}N_{4}. Their important polymorphs are considered which are for SiO_{2}: $\alpha$-quartz, $\alpha$- and $\beta$-cristobalite and stishovite, for GeO_{2}: $\alpha$-quartz, and rutile, for Al_{2}O_{3}: $\alpha$-phase, for Si_{3}N_{4} and Ge_{3}N_{4}: $\alpha$- and $\beta$-phases. This work constitutes a comprehensive account of both electronic structure and the elastic properties of these important insulating oxides and nitrides obtained with high accuracy based on density functional theory within the local density approximation. Two different norm-conserving \textit{ab initio} pseudopotentials have been tested which agree in all respects with the only exception arising for the elastic properties of rutile GeO_{2}. The agreement with experimental values, when available, are seen to be highly satisfactory. The uniformity and the well convergence of this approach enables an unbiased assessment of important physical parameters within each material and among different insulating oxide and nitrides. The computed static electric susceptibilities are observed to display a strong correlation with their mass densities. There is a marked discrepancy between the considered oxides and nitrides with the latter having sudden increase of density of states away from the respective band edges. This is expected to give rise to excessive carrier scattering which can practically preclude bulk impact ionization process in Si_{3}N_{4} and Ge_{3}N_{4}.Comment: Published version, 10 pages, 8 figure

Field-induced electronic phase separation in a cuprate high temperature superconductor

We present a combined neutron diffraction (ND) and high-field muon spin rotation ($\mu$SR) study of the magnetic and superconducting phases of the high-temperature superconductor La$_{1.94}$Sr$_{0.06}$CuO$_{4+y}$ ($T_{c} = 38$~K). We observe a linear dependence of the ND signal from the modulated antiferromagnetic order (m-AFM) on the applied field. The magnetic volume fraction measured with $\mu$SR increases linearly from 0\% to $\sim$40\% with applied magnetic field up to 8~T. This allows us to conclude, in contrast to earlier field-dependent neutron diffraction studies, that the long-range m-AFM regions are induced by an applied field, and that their ordered magnetic moment remains constant

Pleosporales

One hundred and five generic types of Pleosporales are described and illustrated. A brief introduction and detailed history with short notes on morphology, molecular phylogeny as well as a general conclusion of each genus are provided. For those genera where the type or a representative specimen is unavailable, a brief note is given. Altogether 174 genera of Pleosporales are treated. Phaeotrichaceae as well as Kriegeriella, Zeuctomorpha and Muroia are excluded from Pleosporales. Based on the multigene phylogenetic analysis, the suborder Massarineae is emended to accommodate five families, viz. Lentitheciaceae, Massarinaceae, Montagnulaceae, Morosphaeriaceae and Trematosphaeriaceae

TS-AMIR: a topology string alignment method for intensive rapid protein structure comparison

<p>Abstract</p> <p>Background</p> <p>In structural biology, similarity analysis of protein structure is a crucial step in studying the relationship between proteins. Despite the considerable number of techniques that have been explored within the past two decades, the development of new alternative methods is still an active research area due to the need for high performance tools.</p> <p>Results</p> <p>In this paper, we present TS-AMIR, a Topology String Alignment Method for Intensive Rapid comparison of protein structures. The proposed method works in two stages: In the first stage, the method generates a topology string based on the geometric details of secondary structure elements, and then, utilizes an n-gram modelling technique over entropy concept to capture similarities in these strings. This initial correspondence map between secondary structure elements is submitted to the second stage in order to obtain the alignment at the residue level. Applying the Kabsch method, a heuristic step-by-step algorithm is adopted in the second stage to align the residues, resulting in an optimal rotation matrix and minimized RMSD. The performance of the method was assessed in different information retrieval tests and the results were compared with those of CE and TM-align, representing two geometrical tools, and YAKUSA, 3D-BLAST and SARST as three representatives of linear encoding schemes. It is shown that the method obtains a high running speed similar to that of the linear encoding schemes. In addition, the method runs about 800 and 7200 times faster than TM-align and CE respectively, while maintaining a competitive accuracy with TM-align and CE.</p> <p>Conclusions</p> <p>The experimental results demonstrate that linear encoding techniques are capable of reaching the same high degree of accuracy as that achieved by geometrical methods, while generally running hundreds of times faster than conventional programs.</p

Need for enforcement of ethicolegal education – an analysis of the survey of postgraduate clinical trainees

BACKGROUND: The number of medical lawsuits in Japan was between 14 and 21 each year before 1998, but increased to 24 to 35 per year after 1999. There were 210 lawsuits during this 10-year period. There is a need for skills and knowledge related to ethics, which is as fundamental to the practice of medicine as basic sciences or clinical skills. in Japan education in ethics is relatively rare and its importance is not yet recognized. Establishing ethics education using legal precedents, which has already been achieved in Western countries, will be a very important issue in Japan. In the present study, a questionnaire survey was conducted among graduate intern doctors, in order to investigate whether ethics education using precedents might have a positive effect in Japan. METHODS: In 2002, a questionnaire survey entitled Physicians' Clinical Ethics was carried out in a compulsory orientation lecture given to trainees before they started clinical practice in our hospital. The attendees at this lecture were trainees who came from colleges in various districts of Japan. During the lecture, 102 questionnaires were distributed, completed by attendees and collected. The recovery rate was 100%. The questionnaire consisted of 22 questions (in three categories), of which 20 were answered by multiple choices, and the other two were answered by description. The time required to complete the questionnaire was about 10 minutes. RESULTS: The recovered questionnaires were analyzed using statistical analysis software (SPSS for Windows, Release 10.07J-1/June/2000), in addition to simple statistical analysis. answers using multiple choices for the 20 questions in the questionnaire were input into SPSS. The principal component analysis was performed for each question. As a result, the item that came to the fore was "legal precedent". Since many intern doctors were interested in understanding laws and precedents, learning about ethical considerations through education using precedents might better meet with their needs and interests. CONCLUSION: We applied a new method in which the results of principal component analysis and frequencies of answers to other questions were combined. From this we deduced that the precedent education used in Western countries was useful to help doctors acquire ethical sensitivity and was not against their will. A relationship was found between reading precedents and the influence of lawsuits, and it was thought that student participation-type precedent education would be useful for doctors in order to acquire ethical sensitivity