Massively parallel split-step Fourier techniques for simulating quantum systems on graphics processing units

The split-step Fourier method is a powerful technique for solving partial differential equations and simulating ultracold atomic systems of various forms. In this body of work, we focus on several variations of this method to allow for simulations of one, two, and three-dimensional quantum systems, along with several notable methods for controlling these systems. In particular, we use quantum optimal control and shortcuts to adiabaticity to study the non-adiabatic generation of superposition states in strongly correlated one-dimensional systems, analyze chaotic vortex trajectories in two dimensions by using rotation and phase imprinting methods, and create stable, threedimensional vortex structures in Bose–Einstein condensates through artificial magnetic fields generated by the evanescent field of an optical nanofiber. We also discuss algorithmic optimizations for implementing the split-step Fourier method on graphics processing units. All computational methods present in this work are demonstrated on physical systems and have been incorporated into a state-of-the-art and open-source software suite known as GPUE, which is currently the fastest quantum simulator of its kind.Okinawa Institute of Science and Technology Graduate Universit

Master of Science

thesisRed Butte Canyon is a federally protected research area located outside Salt Lake City, Utah east of the University of Utah. The Wasatch Fault Zone, an active fault capable of producing magnitude 7.0 earthquakes, is also located less than one mile west of Red Butte Canyon. A series of geomorphic features exist in Red Butte Canyon including landslides, rock falls, creep, and steep slopes within both the primary Red Butte Creek channel and the secondary Parleys Fork channel. Possible paleochannels exist adjacent to a mapped landslide at Red Butte Creek and Parleys Fork. A detailed geologic and engineering investigation was executed to address these unusual geomorphic features. Research objectives included detailed geologic mapping in the study area to better evaluate geologic characteristics and determine the characteristics of subsurface sediments. Additional objectives included performing a groundwater and slope stability evaluation within selected areas of the study area. Methods included drilling and sampling, seismic refraction, groundwater measurements, geotechnical engineering testing, slope stability modeling, and radiocarbon dating to evaluate the geological and geotechnical characteristics of geomorphic features. A combination of sediment type, grain size distributions of soils and radiocarbon dating suggest that subsurface sediments closest to the landslide area formed in an alluvial / lacustrine depositional environment suggesting a lake existed in Red Butte Canyon behind a landslide dam at some point in the past. Charcoal samples discovered in the subsurface yielded radiocarbon ages of 4,370 ± 30 years, in close agreement with independent paleoseismology studies for on the Wasatch Fault dated 4,000 ± 500 years ago, suggesting the lacustrine sediments formed in response to the earthquake and landslide. Slope stability analysis investigated undrained and drained conditions and utilized the Pseudostatic Method. The results show that selected slopes within the field site were stable under drained conditions except when a high groundwater table exists. Slopes were also less stable under drained conditions, particularly when a peak horizontal ground acceleration exceeded 0.1 g - 0.15 g. The reduced stability of slopes under seismic loading conditions also suggests that the landslide was triggered by an earthquake in the aforementioned time frame

Controlled creation of three-dimensional vortex structures in Bose--Einstein condensates using artificial magnetic fields

The physics of quantized vortex excitations in atomic Bose-Einstein condensates has been extensively studied in recent years.Although simple vortex lines are relatively easy to create, control, and measure in experiments, it is a lot more difficult to do the same for vortex ring structures.Here we suggest and explore a method for generating and controlling superfluid vortex rings, vortex ring lattices, and other three dimensional vortex structures in toroidally-trapped superfluid Bose--Einstein condensates by using the artificial magnetic field produced by an optical nanofiber.The presence of the fiber also necessitates a multiply-connected geometry and we show that in this situation the presence of these vortex structures can be deduced from exciting the scissors mode of the condensate.Comment: 8 pages, 6 figure

Spin-orbit coupling in symmetric and mixed spin-symmetry

Synthetically spin-orbit coupling in cold atoms couples the pseudo-spin and spatial degrees of freedom, and therefore the inherent spin symmetry of the system plays an important role. In systems of two pseudo-spin degrees, two particles configure symmetric states and anti-symmetric states, but the spin symmetry can be mixed for more particles. We study the role of mixed spin symmetry in the presence of spin-orbit coupling and consider the system of three bosons with two hyper-fine states trapped in a harmonic potential. We investigate the ground state and the energy spectrum by implementing exact diagonalization. It is found that the interplay between spin-orbit coupling and repulsive interactions between anti-aligned pseudo-spins increases the population of the unaligned spin components in the ground state. The emergence of the mixed spin symmetric states compensates for the rise of the interaction energy. With the aligned interaction on, the avoided crossing between the ground state and the first excited state is observed only for small interaction, and this causes shape changes in the spin populations. Furthermore, we find that the pair correlation of the ground state shows similarly to that of Tonks-Girardeau gas even for relatively small contact interactions and such strong interaction feature is enhanced by the spin-orbit coupling.Comment: 10 pages, 9 figure

Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples

Numerous studies are currently underway to characterize the microbial communities inhabiting our world. These studies aim to dramatically expand our understanding of the microbial biosphere and, more importantly, hope to reveal the secrets of the complex symbiotic relationship between us and our commensal bacterial microflora. An important prerequisite for such discoveries are computational tools that are able to rapidly and accurately compare large datasets generated from complex bacterial communities to identify features that distinguish them

Quantum Electronics

Contains report on ten research projects split into three sections.Joint Services Electronics Program (Contract DAAG29-78-C-0020)National Science Foundation (Grant PHY77-07156)U. S. Air Force-Office of Scientific Research (Grant AFOSR-3042)National Science Foundation (Grant ENG77-24981

Decade-long bacterial community dynamics in cystic fibrosis airways

The structure and dynamics of bacterial communities in the airways of persons with cystic fibrosis (CF) remain largely unknown. We characterized the bacterial communities in 126 sputum samples representing serial collections spanning 8–9 y from six age-matched male CF patients. Sputum DNA was analyzed by bar-coded pyrosequencing of the V3–V5 hypervariable region of the 16S rRNA gene, defining 662 operational taxonomic units (OTUs) from > 633,000 sequences. Bacterial community diversity decreased significantly over time in patients with typically progressive lung disease but remained relatively stable in patients with a mild lung disease phenotype. Antibiotic use, rather than patient age or lung function,was the primary driver of decreasing diversity. Interpatient variability in community structure exceeded intrapatient variability in serial samples. Antibiotic treatment was associated with pronounced shifts in community structure, but communities showed both short- and longterm resilience after antibiotic perturbation. There was a positive correlation between OTU occurrence and relative abundance, with a small number of persistent OTUs accounting for the greatest abundance. Significant changes in community structure, diversity, or total bacterial density at the time of pulmonary exacerbation were not observed. Despite decreasing community diversity in patients with progressive disease, total bacterial density remained relatively stable over time. These findings show the critical relationship between airway bacterial community structure, disease stage, and clinical state at the time of sample collection. These features are the key parameters with which to assess the complex ecology of the CF airway.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/91945/1/2012 PNAS Decade-long bacterial community dynamics in cystic fibrosis airways.pd

Quantum Electronics

Contains reports on eight research projects divided into three sections.National Science Foundation (Grant PHY79-09739)Joint Services Electronics Program (Contract DAAG29-78-C-0020)U.S. Air Force Geophysics Laboratory (AFSC) (Contract F19628-79-C-0082)National Science Foundation (Grant ENG79-09980

Soil foraging animals alter the composition and co-occurrence of microbial communities in a desert shrubland

Animals that modify their physical environment by foraging in the soil can have dramatic effects on ecosystem functions and processes. We compared bacterial and fungal communities in the foraging pits created by bilbies and burrowing bettongs with undisturbed surface soils dominated by biocrusts. Bacterial communities were characterized by Actinobacteria and Alphaproteobacteria, and fungal communities by Lecanoromycetes and Archaeosporomycetes. The composition of bacterial or fungal communities was not observed to vary between loamy or sandy soils. There were no differences in richness of either bacterial or fungal operational taxonomic units (OTUs) in the soil of young or old foraging pits, or undisturbed soils. Although the bacterial assemblage did not vary among the three microsites, the composition of fungi in undisturbed soils was significantly different from that in old or young foraging pits. Network analysis indicated that a greater number of correlations between bacterial OTUs occurred in undisturbed soils and old pits, whereas a greater number of correlations between fungal OTUs occurred in undisturbed soils. Our study suggests that digging by soil-disturbing animals is likely to create successional shifts in soil microbial and fungal communities, leading to functional shifts associated with the decomposition of organic matter and the fixation of nitrogen. Given the primacy of organic matter decomposition in arid and semi-arid environments, the loss of native soil-foraging animals is likely to impair the ability of these systems to maintain key ecosystem processes such as the mineralization of nitrogen and the breakdown of organic matter, and to recover from disturbance

Quantum Electronics

Contains thirteen research projects split into three sections.U.S. Air Force - Rome Air Development Center (Contract F19628-80-C-0077)National Science Foundation (Grant PHY79-09739)Joint Services Electronics Program (Contract DAAG29-78-C-0020)Joint Services Electronics Program (Contract DAAG29-80-C-0104)U.S. Air Force Geophysics Laboratory (AFSC) (Contract F19628-79-C-0082)National Science Foundation (Grant ECS79-19475)National Science Foundation (Grant DAR80-08752)National Science Foundation (Grant ENG79-09980