Inferring Histories of Adaptive Divergence with Gene Flow: Genetic, Demographic and Geographic Effects.

As genomic data is increasingly available even for non-model organisms, the traditional boundaries among fields such as phylogenetics, phylogeography and genetics of adaptation are disappearing. This thesis provides a synthetic framework for studying ecological genomics, which considers selective processes (such as adaptation to new niches) and neutral processes (such as population size changes due to environmental shifts) simultaneously. Conventionally, studies that look for targets of selection on a genome assume a simple demographic model without validations from the species' ecological or phylogeographic histories. The work demonstrates that one cannot reliably identify selection unless realistic demographic histories are inferred for the species or even a specific genomic region. In particular, I investigate the evolutionary history of large polymorphic inversions in Anopheles gambiae, which maintains adaptive divergence among ecologically divergent populations. By modeling the unique origin and introgression histories of each inversion, I am able to identify target regions of selection within inversions through training discriminant functions with pure drift versus selection simulations. The thesis also extends the existing theory of local adaptation model via chromosomal inversions to consider the source of inversion variation, as well as evaluates the likelihood of such adaptations under different parameter spaces. The findings are particularly important for understanding mosaic genomic evolution in the early stages of speciation, where accumulation of divergence is dampened by gene flow. Finally, I examine how historical events, such as habitat contractions or recolonization, influence current genetic pattern and the application of spatially-explicit demographic modeling under Approximate Bayesian Computation statistics to distinguish different phylogeographic scenarios. The work represents a flexible framework for researchers to translate dynamic phylogeographic hypotheses into testable coalescent models by integrating all the available information of the species, such as distribution records, habitat preference, paleo-climate models, and competition between species. In general, with the amount of information as well as inherent heterogeneity of genomic data, this thesis contributes to the ongoing paradigm shift from studying separate evolutionary processes towards a holistic analysis of the interactions of selective and neutral processes under a rigorous statistical framework.PHDEcology and Evolutionary BiologyUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/111443/1/heqixin_1.pd

Quantifying asymptomatic infection and transmission of COVID-19 in New York City using observed cases, serology, and testing capacity

The contributions of asymptomatic infections to herd immunity and community transmission are key to the resurgence and control of COVID-19, but are difficult to estimate using current models that ignore changes in testing capacity. Using a model that incorporates daily testing information fit to the case and serology data from New York City, we show that the proportion of symptomatic cases is low, ranging from 13 to 18%, and that the reproductive number may be larger than often assumed. Asymptomatic infections contribute substantially to herd immunity, and to community transmission together with presymptomatic ones. If asymptomatic infections transmit at similar rates as symptomatic ones, the overall reproductive number across all classes is larger than often assumed, with estimates ranging from 3.2 to 4.4. If they transmit poorly, then symptomatic cases have a larger reproductive number ranging from 3.9 to 8.1. Even in this regime, presymptomatic and asymptomatic cases together comprise at least 50% of the force of infection at the outbreak peak. We find no regimes in which all infection subpopulations have reproductive numbers lower than three. These findings elucidate the uncertainty that current case and serology data cannot resolve, despite consideration of different model structures. They also emphasize how temporal data on testing can reduce and better define this uncertainty, as we move forward through longer surveillance and second epidemic waves. Complementary information is required to determine the transmissibility of asymptomatic cases, which we discuss. Regardless, current assumptions about the basic reproductive number of severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) should be reconsidered

Spatiotemporal Arbitrage of Large-Scale Portable Energy Storage for Grid Congestion Relief

Energy storage has great potential in grid congestion relief. By making large-scale energy storage portable through trucking, its capability to address grid congestion can be greatly enhanced. This paper explores a business model of large-scale portable energy storage for spatiotemporal arbitrage over nodes with congestion. We propose a spatiotemporal arbitrage model to determine the optimal operation and transportation schedules of portable storage. To validate the business model, we simulate the schedules of a Tesla Semi full of Tesla Powerpack doing arbitrage over two nodes in California with local transmission congestion. The results indicate that the contributions of portable storage to congestion relief are much greater than that of stationary storage, and that trucking storage can bring net profit in energy arbitrage applications.Comment: Submitted to IEEE PES GM 2019; 5 pages,4 figure

Biosynthesis of thiocarboxylic acid-containing natural products.

Thiocarboxylic acid-containing natural products are rare and their biosynthesis and biological significance remain unknown. Thioplatensimycin (thioPTM) and thioplatencin (thioPTN), thiocarboxylic acid congeners of the antibacterial natural products platensimycin (PTM) and platencin (PTN), were recently discovered. Here we report the biosynthetic origin of the thiocarboxylic acid moiety in thioPTM and thioPTN. We identify a thioacid cassette encoding two proteins, PtmA3 and PtmU4, responsible for carboxylate activation by coenzyme A and sulfur transfer, respectively. ThioPTM and thioPTN bind tightly to β-ketoacyl-ACP synthase II (FabF) and retain strong antibacterial activities. Density functional theory calculations of binding and solvation free energies suggest thioPTM and thioPTN bind to FabF more favorably than PTM and PTN. Additionally, thioacid cassettes are prevalent in the genomes of bacteria, implicating that thiocarboxylic acid-containing natural products are underappreciated. These results suggest that thiocarboxylic acid, as an alternative pharmacophore, and thiocarboxylic acid-containing natural products may be considered for future drug discovery

Joint Oscillation Damping and Inertia Provision Service for Converter-Interfaced Generation

As renewable generation becomes more prevalent, traditional power systems dominated by synchronous generators are transitioning to systems dominated by converter-interfaced generation. These devices, with their weaker damping capabilities and lower inertia, compromise the system's ability to withstand disturbances, pose a threat to system stability, and lead to oscillations and poor frequency response performance. While some new converter-interfaced generations are capable of providing superior damping and fast frequency control, there is a lack of effective measures to incentivize manufacturers to adopt them. To address this gap, this paper defines the joint oscillation damping and inertia provision services at the system level, seeking to encourage converter-interfaced generation to provide enhanced damping and fast frequency response capabilities. Our approach is anchored in a novel convex parametric formulation that combines oscillation mode and frequency stability constraints. These constraints ensure a sufficient damping ratio for all oscillation modes and maintain transient frequency trajectories within acceptable limits. They are designed to integrate smoothly into various operational and planning optimization frameworks. Using this formulation, we introduce a joint service for oscillation damping and inertia provision based on a cost-minimization problem. This facilitates the optimal allocation of damping and virtual inertia to converters, achieving both small-signal stability and frequency stability. Furthermore, we investigate the economic effects of introducing this service into a new ancillary service market, assessing its impact on system operations and cost-efficiency. Numerical tests highlight the service's efficacy in ensuring both small-signal stability and frequency stability, and offer insights into potential economic benefits.Comment: Submitted for IEEE PES journal for possible publication

O2ATH: An OpenMP Offloading Toolkit for the Sunway Heterogeneous Manycore Platform

The next generation Sunway supercomputer employs the SW26010pro processor, which features a specialized on-chip heterogeneous architecture. Applications with significant hotspots can benefit from the great computation capacity improvement of Sunway many-core architectures by carefully making intensive manual many-core parallelization efforts. However, some legacy projects with large codebases, such as CESM, ROMS and WRF, contain numerous lines of code and do not have significant hotspots. The cost of manually porting such applications to the Sunway architecture is almost unaffordable. To overcome such a challenge, we have developed a toolkit named O2ATH. O2ATH forwards GNU OpenMP runtime library calls to Sunway's Athread library, which greatly simplifies the parallelization work on the Sunway architecture.O2ATH enables users to write both MPE and CPE code in a single file, and parallelization can be achieved by utilizing OpenMP directives and attributes. In practice, O2ATH has helped us to port two large projects, CESM and ROMS, to the CPEs of the next generation Sunway supercomputers via the OpenMP offload method. In the experiments, kernel speedups range from 3 to 15 times, resulting in 3 to 6 times whole application speedups.Furthermore, O2ATH requires significantly fewer code modifications compared to manually crafting CPE functions.This indicates that O2ATH can greatly enhance development efficiency when porting or optimizing large software projects on Sunway supercomputers.Comment: 15 pages, 6 figures, 5 tables