Theory of Direct Scattering, Trapping and Desorption in Atom-Surface Collisions

When gas atoms or molecules collide with clean and ordered surfaces, under many circumstances the energy-resolved scattering spectra exhibit two clearly distinct features due to direct scattering and to trapping in the physisorption well with subsequent desorption. James Clerk Maxwell is credited with being the first to describe this situation by invoking the simple assumption that when an impinging gas beam is scattered from a surface it can be divided into a part that exchanges no energy and specularly reflects and another part that equilibrates or accommodates completely and then desorbs with an equilibrium distribution. In this paper a scattering theory is developed, using an iterative algorithm and classical mechanics for the collision process, that describes both direct scattering and trapping-desorption of the incident beam. The initially trapped fraction of particles can be followed as they continue to make further interactions with the surface until they are all eventually promoted back into the positive energy continuum and leave the surface region. Consequently, this theory allows a rigorous test of the Maxwell assumption and determines the conditions under which it is valid. The theory also gives quantitative explanations of recent experimental measurements which exhibit both a direct scattering contribution and a trapping-desorption fraction in the energy-resolved spectra.Comment: 46 pages including 14 figure

Inelastic neutron scattering in random binary alloys : an augmented space approach

Combining the augmented space representation for phonons with a generalized version of Yonezawa-Matsubara diagrammatic technique, we have set up a formalism to seperate the coherent and incoherent part of the total intensity of thermal neutron scattering from disordered alloys. This is done exacly without taking any recourse to mean-field like approximation (as done previously). The formalism includes disorder in masses, force constants and scattering lengths. Implementation of the formalism to realistic situations is performed by an augmented space Block recursion which calculates entire Green matrix and self energy matrix which in turn is needed to evaluate the coherent and incoherent intensities. we apply the formalism to NiPd and NiPt alloys. Numerical results on coherent and incoherent scattering cross sections are presented along the highest symmetry directions. Finally the incoherent intensities are compared with the CPA and also with experiments.Comment: 18 pages, 13 figure

Automated Protein Subfamily Identification and Classification

Function prediction by homology is widely used to provide preliminary functional annotations for genes for which experimental evidence of function is unavailable or limited. This approach has been shown to be prone to systematic error, including percolation of annotation errors through sequence databases. Phylogenomic analysis avoids these errors in function prediction but has been difficult to automate for high-throughput application. To address this limitation, we present a computationally efficient pipeline for phylogenomic classification of proteins. This pipeline uses the SCI-PHY (Subfamily Classification in Phylogenomics) algorithm for automatic subfamily identification, followed by subfamily hidden Markov model (HMM) construction. A simple and computationally efficient scoring scheme using family and subfamily HMMs enables classification of novel sequences to protein families and subfamilies. Sequences representing entirely novel subfamilies are differentiated from those that can be classified to subfamilies in the input training set using logistic regression. Subfamily HMM parameters are estimated using an information-sharing protocol, enabling subfamilies containing even a single sequence to benefit from conservation patterns defining the family as a whole or in related subfamilies. SCI-PHY subfamilies correspond closely to functional subtypes defined by experts and to conserved clades found by phylogenetic analysis. Extensive comparisons of subfamily and family HMM performances show that subfamily HMMs dramatically improve the separation between homologous and non-homologous proteins in sequence database searches. Subfamily HMMs also provide extremely high specificity of classification and can be used to predict entirely novel subtypes. The SCI-PHY Web server at http://phylogenomics.berkeley.edu/SCI-PHY/ allows users to upload a multiple sequence alignment for subfamily identification and subfamily HMM construction. Biologists wishing to provide their own subfamily definitions can do so. Source code is available on the Web page. The Berkeley Phylogenomics Group PhyloFacts resource contains pre-calculated subfamily predictions and subfamily HMMs for more than 40,000 protein families and domains at http://phylogenomics.berkeley.edu/phylofacts/

Bayesian testing for process capability indices

Process capability indices have been widely used in the manufacturing industry. They measure the ability of a manufacturing process to produce items that meet certain specifications. A capability index relates the voice of the customer (specification limits) to the voice of the process. There is a need to understand and interpret process capability indices. Most of the existing work in this area has been devoted to classical frequentist large sample theory. An alternative approach to the problem of making inference about capability indices is the Bayesian approach. In this paper a Bayesian version of Tukey’s method is used for constructing simultaneous credibility intervals for all pairwise differences. A Bayesian procedure for testing all possible contrasts is also given. The problem of selecting the best supplier(s) has received considerable attention in the literature, but mainly from a classical frequentist point of view. A Bayesian simulation procedure is also illustrated to find the best supplier or group of suppliers.This method seems much easier to perform than the Monte Carlo integration method given in Wu, Shiau, Pearn and Hung (2016). In section 10, a sensitivity analysis regarding the prior choice is considered and in the last section, t-distributed data are analysed

Anomalous thermal expansion in 1D transition-metal cyanides: what makes the novel trimetallic cyanide Cu1/3Ag1/3Au1/3CN behave differently?

The structural dynamics of a quasi-one-dimensional (1D) mixed-metal cyanide, Cu1/3Ag1/3Au1/3CN, with intriguing thermal properties is explored. All the current known related compounds with straight-chain structures, such as group 11 cyanides CuCN, AgCN, AuCN and bimetallic cyanides MxM’1-xCN (M, M’ = Cu, Ag, Au), exhibit 1D negative thermal expansion (NTE) along the chains and positive thermal expansion (PTE) perpendicular to them. Cu1/3Ag1/3Au1/3CN exhibits similar PTE perpendicular to the chains, however PTE, rather than NTE, is also observed along the chains. In order to understand the origin of this unexpected behavior, inelastic neutron scattering (INS) measurements were carried out, underpinned by lattice-dynamical density-functional-theory (DFT) calculations. Synchrotron-based pair-distribution-function (PDF) analysis and 13C solid-state nuclear-magnetic-resonance (SSNMR) measurements were also performed to build an input structural model for the lattice dynamical study. The results indicate that transverse motions of the metal ions are responsible for the PTE perpendicular to the chains, as is the case for the related group 11 cyanides. However NTE along the chain due to the tension effect of these transverse motions is not observed. As there are different metal-to-cyanide bond lengths in Cu1/3Ag1/3Au1/3CN, the metals in neighboring chains cannot all be truly co-planar in a straight-chain model. For this system, DFT-based phonon calculations predict small PTE along the chain due to low-energy chain-slipping modes induced by a bond-rotation effect on the weak metallophilic bonds. However the observed PTE is greater than that predicted with the straight-chain model. Small bends in the chain to accommodate truly co-planar metals provide an alternative explanation for thermal behavior. These would mitigate the tension effect induced by the transverse motions of the metals and, as temperature increases and the chains move further apart, a straightening could occur resulting in the observed PTE. This hypothesis is further supported by unusual evolution in the phonon spectra, which suggest small changes in local symmetry with temperature

What is known about the health and living conditions of the indigenous people of northern Scandinavia, the Sami?

The Sami are the indigenous ethnic population of northern Scandinavia. Their health condition is poorly known, although the knowledge has improved over the last decade.The aim was to review the current information on mortality, diseases, and risk factor exposure in the Swedish Sami population.Health-related research on Sami cohorts published in scientific journals and anthologies was used to compare the health condition among the Sami and the majority non-Sami population. When relevant, data from the Sami populations in Swedish were compared with corresponding data from Norwegian and Finnish Sami populations.Life expectancy and mortality patterns of the Sami are similar to those of the majority population. Small differences in incidences of cancer and cardiovascular diseases have been reported. The traditional Sami lifestyle seems to contain elements that reduce the risk to develop cancer and cardiovascular diseases, e.g. physical activity, diet rich in antioxidants and unsaturated fatty acids, and a strong cultural identity. Reindeer herding is an important cultural activity among the Sami and is associated with high risks for accidents. Pain in the lower back, neck, shoulders, elbows, and hands are frequent among both men and women in reindeer-herding families. For men, these symptoms are related to high exposure to terrain vehicles, particularly snowmobile, whereas for women psychosocial risk factors seem to more important, e.g. poor social support, high effort, low reward, and high economical responsibilities.Although the health condition of the Sami population appears to be rather similar to that of the general Swedish population, a number of specific health problems have been identified, especially among the reindeer-herding Sami. Most of these problems have their origin in marginalization and poor knowledge of the reindeer husbandry and the Sami culture in the majority population. It is suggested that the most sustainable measure to improve the health among the reindeer-herding Sami would be to improve the conditions of the reindeer husbandry and the Sami culture

Parental cancer diagnosis and child mortality : a population-based cohort study in Sweden

OBJECTIVE: Cancer diagnosis is known to induce severe psychological stress for the diagnosed patients; however, how it affects the next-of-kin is less well documented. This study aimed to assess the impact of parental cancer on the risk of childhood death. METHODS: A population-based cohort study was conducted using the Swedish national registries, including 2,871,242 children followed during the period of 1991-2009. Parental cancer diagnosis was defined as a time-varying exposure. We used Cox proportional hazards regression to calculate the hazard ratio (HR) and its corresponding 95% confidence interval (CI) as an estimate of the association between parental cancer and childhood mortality. We adjusted for attained age, sex, gestational age, mode of delivery and birth weight of the child, maternal age at child's birth, as well as educational level and socio-economic classification of the parents in the analyses. RESULTS: Among 113,555 children with parental cancer, 127 deaths occurred during 561,198 person-years of follow-up. A parental cancer diagnosis was associated with an increased rate of death among children at the age of 1-18 (HR for all-cause death: 1.39; 95% CI: 1.16-1.66). For young children (aged 1-12), an increased rate was only noted for death due to cancer (HR: 2.06; 95% CI: 1.13-3.75) after parental cancer diagnosis. Among adolescents (aged 13-18), an increased rate was noted for all-cause death (HR: 1.52; 95% CI: 1.25-1.86), and for both non-cancer-related (HR: 1.43; 95% CI: 1.14-1.79) and cancer-related (HR: 2.07; 95% CI: 1.33-3.24) death in the exposed children. CONCLUSION: Children have an increased rate of death if they have a parent diagnosed with cancer as compared to children without such experience; this association appears to be slightly stronger among adolescents.Swedish Research CouncilSwedish Research Council for Health Working Life & Welfare (Forte), 2012-0498Swedish Research Council SIMSAM, 80748301, 340-2013-5867China Scholarship Council, 201206100002Swedish Society for Medical Research (SSMF)Karolinska InstitutetPublishe

Quasiparticle Effective Mass for the Two- and Three-Dimensional Electron Gas

We calculate the quasiparticle effective mass for the electron gas in two and three dimensions in the metallic region. We employ the single particle scattering potential coming from the Sj\"{o}lander-Stott theory and enforce the Friedel sum rule by adjusting the effective electron mass in a scattering calculation. In 3D our effective mass is a monotonically decreasing function of $r_s$ throughout the whole metallic domain, as implied by the most recent numerical results. In 2D we obtain reasonable agreement with the experimental data, as well as with other calculations based on the Fermi liquid theory. We also present results of a variety of different treatments for the effective mass in 2D and 3D.Comment: 12 pages, 2 figure

Familial liability for eating disorders and suicide attempts : evidence from a population registry in Sweden

Importance: Suicide attempts are common in individuals with eating disorders. More precise understanding of the mechanisms underlying their co-occurrence is needed. Objective: To examine the association between eating disorders and suicide attempts and whether familial risk factors contribute to the association. Design: A cohort design following a Swedish birth cohort 1979-2001 from age 6 until 31/12/2009. Setting: Information was acquired from Swedish national registers. Participants: Individuals born 1979-2001 and living in Sweden before age 6 (N= 2,268,786) were eligible for the study. Each individual was linked to his/her biological full-siblings, maternal half-siblings, paternal half-siblings, full-cousins, and half-cousins. Eating disorders were captured by three variables: any eating disorder, anorexia nervosa (AN), and bulimia nervosa (BN), identified by any lifetime diagnoses recorded in the registers. Suicide attempts were defined as any suicide attempts, including death by suicide, recorded in the registers. We examined the association between eating disorders and death by suicide separately, but were underpowered to explore familial liability for this association. Results: Individuals with any eating disorder had increased risk of suicide attempts (OR=5.28, 95%CI [5.04, 5.54]) and death by suicide (OR=5.39, 95%CI [4.00, 7.25]). The risks attenuated but remained significant after adjusting for comorbid major depressive disorder, anxiety disorders, and substance use disorder. Similar results were found for AN and BN, except that adjusted OR of death by suicide in BN became insignificant, possibly due to insufficient power. Individuals (index) who had a full-sibling with any eating disorder had increased risk of suicide attempts (OR=1.41, 95%CI [1.29, 1.53]). The risk attenuated for any eating disorder in more distant relatives (maternal half-siblings, OR=1.10, 95%CI [0.90, 1.34]; paternal half-siblings, OR=1.21, 95%CI [0.98, 1.49]; full-cousins, OR=1.11, 95%CI [1.06, 1.18]; half-cousins, OR=0.90, 95%CI [0.78, 1.03]). This familial pattern remained stable after adjusting for the index individuals’ eating disorders. Similar patterns were found for AN and BN. Conclusions and Relevance: Our results suggest increased risk of suicide attempts in individuals with lifetime eating disorders and their relatives. The pattern of familial co-aggregation suggests familial liability for the association between eating disorders and suicide. Psychiatric comorbidities partially explain this association, suggesting particularly high-risk presentations.China Scholarship CouncilAmerican Foundation for Suicide PreventionSwedish Initiative for Research on Microdata in the Social and Medical Sciences framework, 340-2013-5867Swedish Research Council, 538-2013Global Foundation for Eating DisordersSwedish Research Council, 538-2013-8864Manuscrip

Interaction of photons with plasmas and liquid metals: photoabsorption and scattering

Formulas to describe the photoabsorption and the photon scattering by a plasma or a liquid metal are derived in a unified manner with each other. It is shown how the nuclear motion, the free-electron motion and the core-electron behaviour in each ion in the system determine the structure of photoabsorption and scattering in an electron-ion mixture. The absorption cross section in the dipole approximation consists of three terms which represent the absorption caused by the nuclear motion, the absorption owing to the free-electron motion producing optical conductivity or inverse Bremsstrahlung, and the absorption ascribed to the core-electron behaviour in each ion with the Doppler correction. Also, the photon scattering formula provides an analysis method for experiments observing the ion-ion dynamical structure factor (DSF), the electron-electron DSF giving plasma oscillations, and the core-electron DSF yielding the X-ray Raman (Compton) scattering with a clear definition of the background scattering for each experiment, in a unified manner. A formula for anomalous X-ray scattering is also derived for a liquid metal. At the same time, Thomson scattering in plasma physics is discussed from this general point of view.Comment: LaTeX file: 18 pages without figur