Introduction to Configuration Path Integral Monte Carlo

In low-temperature high-density plasmas quantum effects of the electrons are becoming increasingly important. This requires the development of new theoretical and computational tools. Quantum Monte Carlo methods are among the most successful approaches to first-principle simulations of many-body quantum systems. In this chapter we present a recently developed method---the configuration path integral Monte Carlo (CPIMC) method for moderately coupled, highly degenerate fermions at finite temperatures. It is based on the second quantization representation of the $N$-particle density operator in a basis of (anti-)symmetrized $N$-particle states (configurations of occupation numbers) and allows to tread arbitrary pair interactions in a continuous space. We give a detailed description of the method and discuss the application to electrons or, more generally, Coulomb-interacting fermions. As a test case we consider a few quantum particles in a one-dimensional harmonic trap. Depending on the coupling parameter (ratio of the interaction energy to kinetic energy), the method strongly reduces the sign problem as compared to direct path integral Monte Carlo (DPIMC) simulations in the regime of strong degeneracy which is of particular importance for dense matter in laser plasmas or compact stars. In order to provide a self-contained introduction, the chapter includes a short introduction to Metropolis Monte Carlo methods and the second quantization of quantum mechanics.Comment: chapter in book "Introduction to Complex Plasmas: Scientific Challenges and Technological Opportunities", Michael Bonitz, K. Becker, J. Lopez and H. Thomsen (Eds.) Springer Series "Atomic, Optical and Plasma Physics", vol. 82, Springer 2014, pp. 153-194 ISBN: 978-3-319-05436-0 (Print) 978-3-319-05437-7 (Online

Observational and Physical Classification of Supernovae

This chapter describes the current classification scheme of supernovae (SNe). This scheme has evolved over many decades and now includes numerous SN Types and sub-types. Many of these are universally recognized, while there are controversies regarding the definitions, membership and even the names of some sub-classes; we will try to review here the commonly-used nomenclature, noting the main variants when possible. SN Types are defined according to observational properties; mostly visible-light spectra near maximum light, as well as according to their photometric properties. However, a long-term goal of SN classification is to associate observationally-defined classes with specific physical explosive phenomena. We show here that this aspiration is now finally coming to fruition, and we establish the SN classification scheme upon direct observational evidence connecting SN groups with specific progenitor stars. Observationally, the broad class of Type II SNe contains objects showing strong spectroscopic signatures of hydrogen, while objects lacking such signatures are of Type I, which is further divided to numerous subclasses. Recently a class of super-luminous SNe (SLSNe, typically 10 times more luminous than standard events) has been identified, and it is discussed. We end this chapter by briefly describing a proposed alternative classification scheme that is inspired by the stellar classification system. This system presents our emerging physical understanding of SN explosions, while clearly separating robust observational properties from physical inferences that can be debated. This new system is quantitative, and naturally deals with events distributed along a continuum, rather than being strictly divided into discrete classes. Thus, it may be more suitable to the coming era where SN numbers will quickly expand from a few thousands to millions of events.Comment: Extended final draft of a chapter in the "SN Handbook". Comments most welcom

MSH3 polymorphisms and protein levels affect CAG repeat instability in huntington's disease mice

Expansions of trinucleotide CAG/CTG repeats in somatic tissues are thought to contribute to ongoing disease progression through an affected individual's life with Huntington's disease or myotonic dystrophy. Broad ranges of repeat instability arise between individuals with expanded repeats, suggesting the existence of modifiers of repeat instability. Mice with expanded CAG/CTG repeats show variable levels of instability depending upon mouse strain. However, to date the genetic modifiers underlying these differences have not been identified. We show that in liver and striatum the R6/1 Huntington's disease (HD) (CAG)~100 transgene, when present in a congenic C57BL/6J (B6) background, incurred expansion-biased repeat mutations, whereas the repeat was stable in a congenic BALB/cByJ (CBy) background. Reciprocal congenic mice revealed the Msh3 gene as the determinant for the differences in repeat instability. Expansion bias was observed in congenic mice homozygous for the B6 Msh3 gene on a CBy background, while the CAG tract was stabilized in congenics homozygous for the CBy Msh3 gene on a B6 background. The CAG stabilization was as dramatic as genetic deficiency of Msh2. The B6 and CBy Msh3 genes had identical promoters but differed in coding regions and showed strikingly different protein levels. B6 MSH3 variant protein is highly expressed and associated with CAG expansions, while the CBy MSH3 variant protein is expressed at barely detectable levels, associating with CAG stability. The DHFR protein, which is divergently transcribed from a promoter shared by the Msh3 gene, did not show varied levels between mouse strains. Thus, naturally occurring MSH3 protein polymorphisms are modifiers of CAG repeat instability, likely through variable MSH3 protein stability. Since evidence supports that somatic CAG instability is a modifier and predictor of disease, our data are consistent with the hypothesis that variable levels of CAG instability associated with polymorphisms of DNA repair genes may have prognostic implications for various repeat-associated diseases

Dusty Planetary Systems

Extensive photometric stellar surveys show that many main sequence stars show emission at infrared and longer wavelengths that is in excess of the stellar photosphere; this emission is thought to arise from circumstellar dust. The presence of dust disks is confirmed by spatially resolved imaging at infrared to millimeter wavelengths (tracing the dust thermal emission), and at optical to near infrared wavelengths (tracing the dust scattered light). Because the expected lifetime of these dust particles is much shorter than the age of the stars (>10 Myr), it is inferred that this solid material not primordial, i.e. the remaining from the placental cloud of gas and dust where the star was born, but instead is replenished by dust-producing planetesimals. These planetesimals are analogous to the asteroids, comets and Kuiper Belt objects (KBOs) in our Solar system that produce the interplanetary dust that gives rise to the zodiacal light (tracing the inner component of the Solar system debris disk). The presence of these "debris disks" around stars with a wide range of masses, luminosities, and metallicities, with and without binary companions, is evidence that planetesimal formation is a robust process that can take place under a wide range of conditions. This chapter is divided in two parts. Part I discusses how the study of the Solar system debris disk and the study of debris disks around other stars can help us learn about the formation, evolution and diversity of planetary systems by shedding light on the frequency and timing of planetesimal formation, the location and physical properties of the planetesimals, the presence of long-period planets, and the dynamical and collisional evolution of the system. Part II reviews the physical processes that affect dust particles in the gas-free environment of a debris disk and their effect on the dust particle size and spatial distribution.Comment: 68 pages, 25 figures. To be published in "Solar and Planetary Systems" (P. Kalas and L. French, Eds.), Volume 3 of the series "Planets, Stars and Stellar Systems" (T.D. Oswalt, Editor-in-chief), Springer 201

Impacts of organic and conventional crop management on diversity and activity of free-living nitrogen fixing bacteria and total bacteria are subsidiary to temporal effects

A three year field study (2007-2009) of the diversity and numbers of the total and metabolically active free-living diazotophic bacteria and total bacterial communities in organic and conventionally managed agricultural soil was conducted at the Nafferton Factorial Systems Comparison (NFSC) study, in northeast England. The result demonstrated that there was no consistent effect of either organic or conventional soil management across the three years on the diversity or quantity of either diazotrophic or total bacterial communities. However, ordination analyses carried out on data from each individual year showed that factors associated with the different fertility management measures including availability of nitrogen species, organic carbon and pH, did exert significant effects on the structure of both diazotrophic and total bacterial communities. It appeared that the dominant drivers of qualitative and quantitative changes in both communities were annual and seasonal effects. Moreover, regression analyses showed activity of both communities was significantly affected by soil temperature and climatic conditions. The diazotrophic community showed no significant change in diversity across the three years, however, the total bacterial community significantly increased in diversity year on year. Diversity was always greatest during March for both diazotrophic and total bacterial communities. Quantitative analyses using qPCR of each community indicated that metabolically active diazotrophs were highest in year 1 but the population significantly declined in year 2 before recovering somewhat in the final year. The total bacterial population in contrast increased significantly each year. Seasonal effects were less consistent in this quantitative study

EhMAPK, the Mitogen-Activated Protein Kinase from Entamoeba histolytica Is Associated with Cell Survival

Mitogen Activated Protein Kinases (MAPKs) are a class of serine/threonine kinases that regulate a number of different cellular activities including cell proliferation, differentiation, survival and even death. The pathogen Entamoeba histolytica possess a single homologue of a typical MAPK gene (EhMAPK) whose identification was previously reported by us but its functional implications remained unexplored. EhMAPK, the only mitogen-activated protein kinase from the parasitic protist Entamoeba histolytica with Threonine-X-Tyrosine (TXY) phosphorylation motif was cloned, expressed in E. coli and functionally characterized under different stress conditions. The expression profile of EhMAPK at the protein and mRNA level remained similar among untreated, heat shocked and hydrogen peroxide-treated samples in all cases of dose and time. But a significant difference was obtained in the phosphorylation status of the protein in response to different stresses. Heat shock at 43°C or 0.5 mM H2O2 treatment enhanced the phosphorylation status of EhMAPK and augmented the kinase activity of the protein whereas 2.0 mM H2O2 treatment induced dephosphorylation of EhMAPK and loss of kinase activity. 2.0 mM H2O2 treatment reduced parasite viability significantly but heat shock and 0.5 mM H2O2 treatment failed to adversely affect E. histolytica viability. Therefore, a distinct possibility that activation of EhMAPK is associated with stress survival in E. histolytica is seen. Our study also gives a glimpse of the regulatory mechanism of the protein under in vivo conditions. Since the parasite genome lacks any typical homologue of mammalian MEK, the dual specificity kinases which are the upstream activators of MAPK, indications of the existence of some alternate regulatory mechanisms of the EhMAPK activity is perceived. These may include the autophosphorylation activity of the protein itself in combination with some upstream phosphatases which are not yet identified

Reproductive Capacities and Development of a Seed Bruchid Beetle, Acanthoscelides macrophthalmus, a Potential Host for the Mass Rearing of the Parasitoid, Dinarmus basalis

The reproductive capacities and development of the seed beetle Acanthoscelides macrophthalmus (Schaeffer) (Coleoptera: Bruchidae), found in Togo, were determined under natural conditions in a Guinean zone for its use as a substitute host for the mass rearing of the parasitoid Dinarmus basalts Rond (Hymenoptera: Pteromalidae), a biological agent for the control of beetles that are pests of cowpea, Vigna unguiculata (L.) Walpers (Fabales: Fabaceae). Population dynamics at the field level; and survival, fecundity and offspring production by A. macrophthalmus under laboratory conditions were measured when fed on its natural plant-host Leucaena leucocephala (Lamark) deWit (Fabales: Mimosaceae). The data resulting from the laboratory study were used to calculate the demographic parameters of A. macrophthalmus by establishing its fertility and life tables. Contrary to cultivated leguminous food plants, L. leucocephala is a perennial sub-spontaneous leguminous plant whose pods are available year round. Although A. macrophthalmus was present in nature throughout the year, its infestation rate of the pods fluctuated according to the phenology of the plant. The maximum infestation of L. leucocephala pods was observed between August and December. Four larval stages and one pupal stage of A. macrophthalmus were identified in the laboratory. The total mean development time varied on average 33.75 ± 2.87 days on the mature pods and 33.39 ± 2.02 days on seeds. The adult female lived from one to two weeks. During its life time, the female laid an average of 62.3 ± 19 and 43.1 ± 13 eggs on the mature pods and seeds respectively and produced an average of 36.7 ± 11.3 offspring on the mature pods and 21.8 ± 8.4 offspring on seeds. On seeds, the net reproduction rate was 5.88 females per female and the intrinsic rate of population increase 0.051 per day. The generation time was 34.59 days and the doubling time 13.59 days. The demographic parameters of A. macrophthalmus in this study are close to those of Callobruchus maculatus F. (Bruchidae), the natural host of D. basalts in a previous study. A. macrophthalmus could therefore be used as substitute host for the mass rearing of D. basalts and subsequently its release in farmers' storage containers. The data presented in this study provide some baseline information regarding the reproductive capacities of A. macrophthalmus that may be useful for its promotion as a substitute host for mass rearing of D. basalts

Suppression of charged particle production at large transverse momentum in central Pb-Pb collisions at sNN=2.76\sqrt{s_{\rm NN}} = 2.76 TeV

Inclusive transverse momentum spectra of primary charged particles in Pb-Pb collisions at $\sqrt{s_{_{\rm NN}}}$ = 2.76 TeV have been measured by the ALICE Collaboration at the LHC. The data are presented for central and peripheral collisions, corresponding to 0-5% and 70-80% of the hadronic Pb-Pb cross section. The measured charged particle spectra in $|\eta|<0.8$ and $0.3 < p_T < 20$ GeV/$c$ are compared to the expectation in pp collisions at the same $\sqrt{s_{\rm NN}}$, scaled by the number of underlying nucleon-nucleon collisions. The comparison is expressed in terms of the nuclear modification factor $R_{\rm AA}$. The result indicates only weak medium effects ($R_{\rm AA} \approx$ 0.7) in peripheral collisions. In central collisions, $R_{\rm AA}$ reaches a minimum of about 0.14 at $p_{\rm T}=6$-7GeV/$c$ and increases significantly at larger $p_{\rm T}$. The measured suppression of high-$p_{\rm T}$ particles is stronger than that observed at lower collision energies, indicating that a very dense medium is formed in central Pb-Pb collisions at the LHC.Comment: 15 pages, 5 captioned figures, 3 tables, authors from page 10, published version, figures at http://aliceinfo.cern.ch/ArtSubmission/node/98

Two-pion Bose-Einstein correlations in central Pb-Pb collisions at sNN\sqrt{s_{\rm NN}} = 2.76 TeV

The first measurement of two-pion Bose-Einstein correlations in central Pb-Pb collisions at $\sqrt{s_{\rm NN}} = 2.76$ TeV at the Large Hadron Collider is presented. We observe a growing trend with energy now not only for the longitudinal and the outward but also for the sideward pion source radius. The pion homogeneity volume and the decoupling time are significantly larger than those measured at RHIC.Comment: 17 pages, 5 captioned figures, 1 table, authors from page 12, published version, figures at http://aliceinfo.cern.ch/ArtSubmission/node/388

Supercurrent reversal in quantum dots

When two superconductors become electrically connected by a weak link a zero-resistance supercurrent can flow. This supercurrent is carried by Cooper pairs of electrons with a combined charge of twice the elementary charge, e. The 2e charge quantum is clearly visible in the height of Shapiro steps in Josephson junctions under microwave irradiation and in the magnetic flux periodicity of h/2e in superconducting quantum interference devices. Several different materials have been used to weakly couple superconductors, such as tunnel barriers, normal metals, or semiconductors. Here, we study supercurrents through a quantum dot created in a semiconductor nanowire by local electrostatic gating. Due to strong Coulomb interaction, electrons only tunnel one-by-one through the discrete energy levels of the quantum dot. This nevertheless can yield a supercurrent when subsequent tunnel events are coherent. These quantum coherent tunnelling processes can result in either a positive or a negative supercurrent, i.e. in a normal or a pi-junction, respectively. We demonstrate that the supercurrent reverses sign by adding a single electron spin to the quantum dot. When excited states of the quantum dot are involved in transport, the supercurrent sign also depends on the character of the orbital wavefunctions