412 research outputs found
DL_MG: a parallel multigrid Poisson and Poisson−Boltzmann solver for electronic structure calculations in vacuum and solution
No full textThe solution of the Poisson equation is a crucial step in electronic structure calculations, yielding the electrostatic potential—a key component of the quantum mechanical Hamiltonian. In recent decades, theoretical advances and increases in computer performance have made it possible to simulate the electronic structure of extended systems in complex environments. This requires the solution of more complicated variants of the Poisson equation, featuring nonhomogeneous dielectric permittivities, ionic concentrations with nonlinear dependencies, and diverse boundary conditions. The analytic solutions generally used to solve the Poisson equation in vacuum (or with homogeneous permittivity) are not applicable in these circumstances, and numerical methods must be used. In this work, we present DL_MG, a flexible, scalable, and accurate solver library, developed specifically to tackle the challenges of solving the Poisson equation in modern large-scale electronic structure calculations on parallel computers. Our solver is based on the multigrid approach and uses an iterative high-order defect correction method to improve the accuracy of solutions. Using two chemically relevant model systems, we tested the accuracy and computational performance of DL_MG when solving the generalized Poisson and Poisson–Boltzmann equations, demonstrating excellent agreement with analytic solutions and efficient scaling to ∼109 unknowns and 100s of CPU cores. We also applied DL_MG in actual large-scale electronic structure calculations, using the ONETEP linear-scaling electronic structure package to study a 2615 atom protein–ligand complex with routinely available computational resources. In these calculations, the overall execution time with DL_MG was not significantly greater than the time required for calculations using a conventional FFT-based solver
The XMM-Newton long look of NGC 1365: uncovering of the obscured X-ray source
No full textWe present an analysis of the extreme obscuration variability observed during an XMM–Newton 5-d continuous monitoring of the active galactic nuclei (AGN) in NGC 1365. The source was in a reflection-dominated state in the first ∼1.5 d, then a strong increase in the 7–10 keV emission was observed in ∼10 h, followed by a symmetric decrease. The spectral analysis of the different states clearly shows that this variation is due to an uncovering of the X-ray source. From this observation, we estimate a size of the X-ray source DS < 1013 cm, a distance of the obscuring clouds R∼ 1016 cm and a density n∼ 1011 cm−3. These values suggest that the X-ray absorption/reflection originates from the broad-line region clouds. This is also supported by the resolved width of the iron narrow Kα emission line, consistent with the width of the broad Hβ line
Long-term wind-driven X-ray spectral variability of NGC 1365 with Swift
No full textWe present long-term (months–years) X-ray spectral variability of the Seyfert 1.8 galaxy NGC 1365 as observed by Swift, which provides well-sampled observations over a much longer time-scale (six years) and a much larger flux range than is afforded by other observatories. At very low luminosities, the spectrum is very soft, becoming rapidly harder as the luminosity increases and then, above a particular luminosity, softening again. At a given flux level, the scatter in hardness ratio is not very large, meaning that the spectral shape is largely determined by the luminosity. The spectra were therefore summed in luminosity bins and fitted with a variety of models. The best-fitting model consists of two power laws, one unabsorbed and another, more luminous, which is absorbed. In this model, we find a range of intrinsic 0.5–10.0 keV luminosities of approximately 1.1–3.5 erg s?1, and a very large range of absorbing columns, of approximately 1022–1024 cm?2. Interestingly, we find that the absorbing column decreases with increasing luminosity, but that this result is not due to changes in ionization. We suggest that these observations might be interpreted in terms of a wind model in which the launch radius varies as a function of ionizing flux and disc temperature and therefore moves out with increasing accretion rate, i.e. increasing X-ray luminosity. Thus, depending on the inclination angle of the disc relative to the observer, the absorbing column may decrease as the accretion rate goes up. The weaker, unabsorbed, component may be a scattered component from the wind
Theory of the electronic states of semiconductor heterostructures
No full textThis thesis is concerned with theoretical calculations of the properties of electronic bound states in semiconductor heterostructures. The complex band structure empirical pseudopotential method (EPM) is used as the foundation of the work. Spin orbit coupling and strain effects (due to lattice mismatch) are included in familiar ways, as is the transfer matrix method, allowing the study of arbitrarily configured heterostructures. These techniques are used to investigate the unusually deep InAs/AlSb conduction band well. The strong possibility of intraband transitions at electro magnetic wavelengths around 1.55µm is predicted, with corresponding enhanced momentum matrix elements and joint density of states over interband transitions. An InAs/GaSb/AlSb asymmetric well is investigated, paying particular attention to the bound states in the vicinity of the InAs/GaSb band overlap. The electron-like states are found to cross with heavy hole and anti-cross with light hole-like states, as a function of heterostructure dimension or applied electrostatic field. This is analogous to the hybridisation of states in the in-plane band structure, except that for zero in-plane wave vector there can be no appreciable hybridisation of electron and heavy hole states. A technique is described that has been developed to extract envelope functions from heterostructure wavefunctions calculated using the realistic complex band structure EPM approach. These envelope functions conform to Burt’s theory (M. G. Burt, J. Phys.: Condens. Matt. 4, 6651 (1992)) in that they are uniquely defined, continuous and smooth over all space. Comparisons with traditional effective mass envelope functions are made. The extracted envelope functions are used to demonstrate conclusively Burt's predictions (M. G. Burt, Superlatt. Mi- crostruct. 17, 335 (1995)) concerning the inadequacy of certain approximations for the calculation of interband dipole matrix elements and charge oscillation. Finally, the issue of k • p operator ordering is convincingly settled, in favour of 'ordered' over 'symmetrised' Hamiltonians, by comparison to EPM calculations, and using EPM derived k • p parameters
A positron annihilation study of crystalline, quasicrystalline and amorphous Al-Cu-T (T=Fe,V) alloys
No full textPT: J; CR: BANCEL PA, 1989, PHYS REV LETT, V63, P2741 BETTERTON JO, 1952, J I MET, V80, P459 BRANDT W, 1967, POSITRON ANNIHILATIO, P155 CALVAYRAC Y, 1990, J PHYS-PARIS, V51, P417 CHIDAMBARAM R, 1990, B AM PHYS SOC, V35, P331 CHIDAMBARAM R, 1990, J PHYS-CONDENS MAT, V2, P251 DUNLAP RA, 1986, J PHYS F MET PHYS, V16, P11 DUNLAP RA, 1986, J PHYS F MET PHYS, V16, P1247 DUNLAP RA, 1987, J PHYS F MET PHYS, V17, L39 DUNLAP RA, 1988, CAN J PHYS, V66, P476 GURYAN CA, 1989, PHYS REV LETT, V62, P2409 HEINEY PA, 1987, SCIENCE, V238, P660 HIRAGA K, 1988, JPN J APPL PHYS, V27, L951 HUMEROTHERY W, 1962, STRUCTURE METALS ALL JANOT C, 1988, J NONCRYSTALLINE SOL, V106, P193 JANOT C, 1989, J PHYS-CONDENS MAT, V1, P1029 JANSSEN T, 1986, ACTA CRYSTALLOGR A, V42, P261 KIZUKA T, 1989, PHYS REV B, V40, P796 LAWTHER DW, 1989, CAN J PHYS, V67, P463 PEARSON WB, 1972, CRYSTAL CHEM PHYSICS, CH4 SANYAL MK, 1989, J PHYS-CONDENS MATT, V1, P3733 SCHULTZ PJ, 1988, REV MOD PHYS, V60, P701 SHECHTMAN D, 1984, PHYS REV LETT, V53, P1951 SIEGEL RW, 1980, ANNU REV MATER SCI, V10, P393 TSAI AP, 1987, JPN J APPL PHYS, V26, P1505 VAKS VG, 1988, PHYS LETT A, V132, P131 WAGNER JL, 1988, PHYS REV B, V38, P7436 WAGNER JL, 1989, PHYS REV B, V39, P8091; NR: 28; TC: 10; J9: J PHYS-CONDENS MATTER; PG: 6; GA: DN624Source type: Electronic(1
Fast identification of biological pathways associated with a quantitative trait using group lasso with overlaps.
No full textWhere causal SNPs (single nucleotide polymorphisms) tend to accumulate within biological pathways, the incorporation of prior pathways information into a statistical model is expected to increase the power to detect true associations in a genetic association study. Most existing pathways-based methods rely on marginal SNP statistics and do not fully exploit the dependence patterns among SNPs within pathways.We use a sparse regression model, with SNPs grouped into pathways, to identify causal pathways associated with a quantitative trait. Notable features of our "pathways group lasso with adaptive weights" (P-GLAW) algorithm include the incorporation of all pathways in a single regression model, an adaptive pathway weighting procedure that accounts for factors biasing pathway selection, and the use of a bootstrap sampling procedure for the ranking of important pathways. P-GLAW takes account of the presence of overlapping pathways and uses a novel combination of techniques to optimise model estimation, making it fast to run, even on whole genome datasets.In a comparison study with an alternative pathways method based on univariate SNP statistics, our method demonstrates high sensitivity and specificity for the detection of important pathways, showing the greatest relative gains in performance where marginal SNP effect sizes are small
An examination of the thermophysical nature of solar-control films using an illuminated hot box and computer based simulation modelling techniques
No full textSolar-control films are increasingly being retrofitted to the windows of buildings as a
means of reducing solar gain. At present, there is a dearth of information concerning
how these films effect the thermal comfort of occupants within buildings where these
films have been applied. An illuminated hot box, utilising a xenon lamp to simulate
sunlight, has been designed as a testing facility. The illuminated hot box has been used
to obtain information on how much thermal radiation enters the internal space from a
window fitted with a solar-control film. The data from the experimental apparatus was
verified using a finite-difference model written on a personal computer, with the aim of
the computer program being used to compare different films, and thereby avoiding
expensive experiments. The experimental rig produced usable data for the tested films
only when the lamp was orthogonal to the plane of the glass, with errors occurring, and
increasing, as the angle of incidence between the lamp and the glass increased. This
conclusion was verified by the computer based model. It was seen that the illuminated
hot box was too small to give accurate measurements for angles of incidence other than
0°. It is suggested that a larger illuminated hot box which is able to eliminate the
problems encountered when measuring for angles of incidence above 10° would be
desirable. Furthermore, a more complex transient finite-difference computer based
simulation model is needed, taking into account the conclusions that were made during
this study
Pope Francis' 2013 Book of Spiritual Exercise, and Walter J. Ong's Thought
No full textSee the above abstract.In my 3,200-word review essay "Pope Francis' 2013 Book of Spiritual Exercises, and Walter J. Ong's Thought," I highlight the short 135-page July 2013 book In Him Alone Is Our Hope: Spiritual Exercises Given to His Brother Bishops [of Spain] in the Manner of Saint Ignatius of Loyola, edited by Romain Lize; translated by Vincent Capuano, S.J., and Andrew Matt (New York, Paris, Madrid, Oxford: Magnificat). On the book's title page, the author is identified as Jorge Mario Bergoglio/ Pope Francis, because then-Cardinal Bergoglio preached the retreat for the bishops of Spain before he was elected pope in March 2013. In addition, I highlight the thought of the American Jesuit Renaissance specialist and cultural historian Walter J. Ong (1912-2003; Ph.D. in English, Harvard University, 1955). I also briefly discuss the Victorian Jesuit classicist and poet Gerard Manley Hopkins (1844-1889).N/AFarrell, Thomas. (2021). Pope Francis' 2013 Book of Spiritual Exercise, and Walter J. Ong's Thought. Retrieved from the University Digital Conservancy, https://hdl.handle.net/11299/220065
Systematic Comparison of Genetic Algorithm and Basin Hopping Approaches to the Global Optimization of Si(111) Surface Reconstructions
No full textWe present a systematic study of two widely used material structure prediction methods, the Genetic Algorithm and Basin Hopping approaches to global optimization, in a search for the 3 × 3, 5 × 5, and 7 × 7 reconstructions of the Si(111) surface. The Si(111) 7 × 7 reconstruction is the largest and most complex surface reconstruction known, and finding it is a very exacting test for global optimization methods. In this paper, we introduce a modification to previous Genetic Algorithm work on structure search for periodic systems, to allow the efficient search for surface reconstructions, and present a rigorous study of the effect of the different parameters of the algorithm. We also perform a detailed comparison with the recently improved Basin Hopping algorithm using Delocalized Internal Coordinates. Both algorithms succeeded in either resolving the 3 × 3, 5 × 5, and 7 × 7 DAS surface reconstructions or getting “sufficiently close”, i.e., identifying structures that only differ for the positions of a few atoms as well as thermally accessible structures within kBT/unit area of the global minimum, with T = 300 K. Overall, the Genetic Algorithm is more robust with respect to parameter choice and in success rate, while the Basin Hopping method occasionally exhibits some advantages in speed of convergence. In line with previous studies, the results confirm that robustness, success, and speed of convergence of either approach are strongly influenced by how much the trial moves tend to preserve favorable bonding patterns once these appear
Epigenetic regulation of neuroinflammation in the aged mouse brain
No full textAs the average lifespan continues to rise, there is a significant increase in the number of people suffering from age-related chronic inflammatory diseases such as autoimmune disorders, cancer, and neurodegenerative diseases. Therefore, there is a greater need to understand the factors that contribute to quality of life in the elderly. Growing evidence indicates that the immune system plays a critical role in regulating the progression of brain aging. However, an important question remains of whether inflammatory pathways become hyperactivated with age, or whether deficient immune responses, which fail to cope with age-related deterioration, may contribute to disease.
Microglia, the resident immune cells of the brain, are key players in regulating neuroinflammation. They function as the primary immune surveillance, provide the first host defense by secreting factors such as cytokines and chemokines, and carry out specific central nervous system functions such as synaptic pruning and secretion of neurotrophic factors. Of note, microglia are also long-lived within the brain and have a limited turnover, suggesting that they are a likely target for epigenetic regulation.
In order to determine possible causes and targets for interventions to promote healthy aging, the current dissertation explored the role of epigenetic regulation in microglia as well as potential pharmacological and dietary interventions that could be beneficial for chronic age-related neuroinflammation. This dissertation was divided into three major sections. In Chapter 2, we determined that aged mice had decreased methylation of the Il1b gene promoter in primary microglia basally or following systemic lipopolysaccharide (LPS) that is associated with increased Il1b mRNA, intracellular IL-1β production, as well as prolonged sickness behavior. We also determined changes in epigenetic regulator gene expression with both age and LPS. Furthermore, we found that inhibiting DNA methylation increased Il1b gene expression and decreased DNA methylation of BV2 and primary microglial cells similar to microglia from aged mice. In Chapter 3, we investigated whether inhibiting DNA methylation in the brain of adult mice would alter sickness behavior, DNA methylation of the Il1b promoter and expression of inflammatory genes in microglia similar to aged mice. However, we found that inhibiting DNA methylation and injecting LPS in the brain of adult mice produced faster recovery of burrowing behavior compared to mice treated only with LPS. Genes of inflammatory markers, epigenetic regulators, and the microglial sensory apparatus (i.e. the sensome) were also differentially expressed by inhibiting DNA methylation alone or in combination with LPS. Lastly, DNA methylation of Il1b proximal promoter was changed by inhibiting DNA methylation alone or in combination with LPS, and these changes persisted 48 hours after LPS treatment. In Chapter 4, we investigated whether injections of butyrate or increases in butyrate through a highly fermentable diet could affect microglial activation, and specifically microglial activation in aging. We determined that gene expression of inflammatory markers, epigenetic regulators, and the microglial sensome were altered by both diet and age, in that aged animals had a more anti-inflammatory profile on the high fiber diet.
In summary, the studies outlined in this dissertation comprise evidence that epigenetic changes are present in aging microglia, and that pharmacological agents and nutrients that act as epigenetic modifiers can alter microglial phenotypes. This could lead to the development of therapeutic interventions aimed at specifically promoting beneficial microglia reactivity associated with infection, which may be important for fostering better recovery from sickness and reducing cognitive deficits and age-associated disease in the elderly.Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2020-05-01The student, Stephanie Matt, accepted the attached license on 2018-03-04 at 16:43.The student, Stephanie Matt, submitted this Dissertation for approval on 2018-03-13 at 14:45.This Dissertation was approved for publication on 2018-03-16 at 16:52.DSpace SAF Submission Ingestion Package generated from Vireo submission #12054 on 2018-08-31 at 17:17:13Made available in DSpace on 2018-09-04T20:33:49Z (GMT). No. of bitstreams: 3
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