Engineering topics
Sun, Yan
Publications and source records attributed to Sun, Yan.
SARS-CoV-2 wastewater variant surveillance: pandemic response leveraging FDA’s GenomeTrakr network
ABSTRACT Wastewater surveillance has emerged as a crucial public health tool for population-level pathogen surveillance. Supported by funding from the American Rescue Plan Act of 2021, the FDA‘s genomic epidemiology program, GenomeTrakr, was leveraged to sequence SARS-CoV-2 from wastewater sites across the United States. This initiative required the evaluation, optimization, development, and publication of new methods and analytical tools spanning sample collection through variant analyses. Version-controlled protocols for each step of the process were developed and published on protocols.io. A custom data analysis tool and a publicly accessible dashboard were built to facilitate real-time visualization of the collected data, focusing on the relative abundance of SARS-CoV-2 variants and sub-lineages across different samples and sites throughout the project. From September 2021 through June 2023, a total of 3,389 wastewater samples were collected, with 2,517 undergoing sequencing and submission to NCBI under the umbrella BioProject,PRJNA757291. Sequence data were released with explicit quality control (QC) tags on all sequence records, communicating our confidence in the quality of data. Variant analysis revealed wide circulation of Delta in the fall of 2021 and captured the sweep of Omicron and subsequent diversification of this lineage through the end of the sampling period. This project successfully achieved two important goals for the FDA’s GenomeTrakr program: first, contributing timely genomic data for the SARS-CoV-2 pandemic response, and second, establishing both capacity and best practices for culture-independent, population-level environmental surveillance for other pathogens of interest to the FDA. IMPORTANCE This paper serves two primary objectives. First, it summarizes the genomic and contextual data collected during a Covid-19 pandemic response project, which utilized the FDA’s laboratory network, traditionally employed for sequencing foodborne pathogens, for sequencing SARS-CoV-2 from wastewater samples. Second, it outlines best practices for gathering and organizing population-level next generation sequencing (NGS) data collected for culture-free, surveillance of pathogens sourced from environmental samples.
Weyl nodal ring states and Landau quantization with very large magnetoresistance in square-net magnet EuGa 4
Magnetic topological semimetals allow for an effective control of the topological electronic states by tuning the spin configuration. Among them, Weyl nodal line semimetals are thought to have the greatest tunability, yet they are the least studied experimentally due to the scarcity of material candidates. Here, using a combination of angle-resolved photoemission spectroscopy and quantum oscillation measurements, together with density functional theory calculations, we identify the square-net compound EuGa 4 as a magnetic Weyl nodal ring semimetal, in which the line nodes form closed rings near the Fermi level. The Weyl nodal ring states show distinct Landau quantization with clear spin splitting upon application of a magnetic field. At 2 K in a field of 14 T, the transverse magnetoresistance of EuGa 4 exceeds 200,000%, which is more than two orders of magnitude larger than that of other known magnetic topological semimetals. Our theoretical model suggests that the non-saturating magnetoresistance up to 40 T arises as a consequence of the nodal ring state.
Unimolecular Reactions of E -Glycolaldehyde Oxide and Its Reactions with One and Two Water Molecules
The kinetics of Criegee intermediates are important for atmospheric modeling. However, the quantitative kinetics of Criegee intermediates are still very limited, especially for those with hydroxy groups. Here, we calculate rate constants for the unimolecular reaction of E-glycolaldehyde oxide [E-hydroxyethanal oxide, E-(CH 2 OH)CHOO], for its reactions with H 2 O and (H 2 O) 2 , and for the reaction of the E-(CH 2 OH)CHOO…H 2 O complex with H 2 O. For the highest level of electronic structure, we use W3X-L//CCSD(T)-F12a/cc-pVDZ-F12 for the unimolecular reaction and the reaction with water and W3X-L//DF-CCSD(T)-F12b/jun-cc-pVDZ for the reaction with 2 water molecules. For the dynamics, we use a dual-level strategy that combines conventional transition state theory with the highest level of electronic structure and multistructural canonical variational transition state theory with small-curvature tunneling with a validated density functional for the electronic structure. This dynamical treatment includes high-frequency anharmonicity, torsional anharmonicity, recrossing effects, and tunneling. We find that the unimolecular reaction of E-(CH 2 OH)CHOO depends on both temperature and pressure. The calculated results show that E-(CH 2 OH)CHOO…H 2 O + H 2 O is the dominant entrance channel, while previous investigations only considered Criegee intermediates + (H 2 O) 2 . In addition, we find that the atmospheric lifetime of E-(CH 2 OH)CHOO with respect to 2 water molecules is particularly short with a value of 1.71 × 10 –6 s at 0 km, which is about 2 orders of magnitude shorter than those usually assumed for Criegee intermediate reactions with water dimer. We also find that the OH group in E-(CH 2 OH)CHOO enhances its reactivity.
Reply to: Low-frequency quantum oscillations in LaRhIn 5 : Dirac point or nodal line?
We thank G.P. Mikitik and Yu.V. Sharlai for contributing this note and the cordial exchange about it. First and foremost, we note that the aim of our paper is to report a methodology to diagnose topological (semi)metals using magnetic quantum oscillations. Thus far, such diagnosis has been based on the phase offset of quantum oscillations, which is extracted from a “Landau fan plot”. A thorough analysis of the Onsager–Lifshitz–Roth quantization rules has shown that the famous π-phase shift can equally well arise from orbital or spin magnetic moments in topologically trivial systems with strong spin-orbit coupling or small effective masses. Therefore, the “Landau fan plot” does not by itself constitute a proof of a topologically nontrivial Fermi surface. In the paper at hand, we report an improved analysis method that exploits the strong energy dependence of the effective mass in linearly dispersing bands. This leads to a characteristic temperature dependence of the oscillation frequency which is a strong indicator of nontrivial topology, even for multi-band metals with complex Fermi surfaces. Three materials, Cd 3 As 2 , Bi 2 O 2 Se and LaRhIn5 served as test cases for this method. Linear band dispersions were detected for Cd 3 As 2 , as well as the F ≈ 7 T pocket in LaRhIn 5 .
Convergence in phosphorus constraints to photosynthesis in forests around the world
Tropical forests take up more carbon (C) from the atmosphere per annum by photosynthesis than any other type of vegetation. Phosphorus (P) limitations to C uptake are paramount for tropical and subtropical forests around the globe. Yet the generality of photosynthesis-P relationships underlying these limitations are in question, and hence are not represented well in terrestrial biosphere models. Here we demonstrate the dependence of photosynthesis and underlying processes on both leaf N and P concentrations. The regulation of photosynthetic capacity by P was similar across four continents. Implementing P constraints in the ORCHIDEE-CNP model, gross photosynthesis was reduced by 36% across the tropics and subtropics relative to traditional N constraints and unlimiting leaf P. Our results provide a quantitative relationship for the P dependence for photosynthesis for the front-end of global terrestrial C models that is consistent with canopy leaf measurements.
Identifying intragenic functional modules of genomic variations associated with cancer phenotypes by learning representation of association networks
Background Genome-wide Association Studies (GWAS) aims to uncover the link between genomic variation and phenotype. They have been actively applied in cancer biology to investigate associations between variations and cancer phenotypes, such as susceptibility to certain types of cancer and predisposed responsiveness to specific treatments. Since GWAS primarily focuses on finding associations between individual genomic variations and cancer phenotypes, there are limitations in understanding the mechanisms by which cancer phenotypes are cooperatively affected by more than one genomic variation. Results This paper proposes a network representation learning approach to learn associations among genomic variations using a prostate cancer cohort. The learned associations are encoded into representations that can be used to identify functional modules of genomic variations within genes associated with early- and late-onset prostate cancer. The proposed method was applied to a prostate cancer cohort provided by the Veterans Administration’s Million Veteran Program to identify candidates for functional modules associated with early-onset prostate cancer. The cohort included 33,159 prostate cancer patients, 3181 early-onset patients, and 29,978 late-onset patients. The reproducibility of the proposed approach clearly showed that the proposed approach can improve the model performance in terms of robustness. Conclusions To our knowledge, this is the first attempt to use a network representation learning approach to learn associations among genomic variations within genes. Associations learned in this way can lead to an understanding of the underlying mechanisms of how genomic variations cooperatively affect each cancer phenotype. This method can reveal unknown knowledge in the field of cancer biology and can be utilized to design more advanced cancer-targeted therapies.
Future reversal of warming-enhanced vegetation productivity in the Northern Hemisphere
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Giant anomalous Nernst signal in the antiferromagnet YbMnBi 2
A large anomalous Nernst effect (ANE) is crucial for thermoelectric energy conversion applications because the associated unique transverse geometry facilitates module fabrication. Topological ferromagnets with large Berry curvatures show large ANEs; however, they face drawbacks such as strong magnetic disturbances and low mobility due to high magnetization. Herein, we demonstrate that YbMnBi 2 , a canted antiferromagnet, has a large ANE conductivity of ~10 A m –1 K –1 that surpasses large values observed in other ferromagnets (3–5 A m –1 K –1 ). The canted spin structure of Mn guarantees a non-zero Berry curvature, but generates only a weak magnetization three orders of magnitude lower than that of general ferromagnets. The heavy Bi with a large spin–orbit coupling enables a large ANE and low thermal conductivity, whereas its highly dispersive p x/y orbitals ensure low resistivity. The high anomalous transverse thermoelectric performance and extremely small magnetization make YbMnBi 2 an excellent candidate for transverse thermoelectrics.
Temperature dependence of quantum oscillations from non-parabolic dispersions
The phase offset of quantum oscillations is commonly used to experimentally diagnose topologically nontrivial Fermi surfaces. This methodology, however, is inconclusive for spin-orbit-coupled metals where π -phase-shifts can also arise from non-topological origins. Here, we show that the linear dispersion in topological metals leads to a T 2 -temperature correction to the oscillation frequency that is absent for parabolic dispersions. We confirm this effect experimentally in the Dirac semi-metal Cd 3 As 2 and the multiband Dirac metal LaRhIn 5 . Both materials match a tuning-parameter-free theoretical prediction, emphasizing their unified origin. For topologically trivial Bi 2 O 2 Se, no frequency shift associated to linear bands is observed as expected. However, the π -phase shift in Bi 2 O 2 Se would lead to a false positive in a Landau-fan plot analysis. Our frequency-focused methodology does not require any input from ab-initio calculations, and hence is promising for identifying correlated topological materials.
Sondheimer oscillations as a probe of non-ohmic flow in WP 2 crystals
As conductors in electronic applications shrink, microscopic conduction processes lead to strong deviations from Ohm’s law. Depending on the length scales of momentum conserving (l MC ) and relaxing (l MR ) electron scattering, and the device size (d), current flows may shift from ohmic to ballistic to hydrodynamic regimes. So far, an in situ methodology to obtain these parameters within a micro/nanodevice is critically lacking. In this context, we exploit Sondheimer oscillations, semi-classical magnetoresistance oscillations due to helical electronic motion, as a method to obtain l MR even when l MR $\gg$ d. We extract l MR from the Sondheimer amplitude in WP 2 , at temperatures up to T ~ 40 K, a range most relevant for hydrodynamic transport phenomena. Our data on μm-sized devices are in excellent agreement with experimental reports of the bulk l MR and confirm that WP 2 can be microfabricated without degradation. These results conclusively establish Sondheimer oscillations as a quantitative probe of l MR in micro-devices.
Dynamical basis sets for algebraic variational calculations in quantum-mechanical scattering theory
New basis sets are proposed for linear algebraic variational calculations of transition amplitudes in quantum-mechanical scattering problems. These basis sets are hybrids of those that yield the Kohn variational principle (KVP) and those that yield the generalized Newton variational principle (GNVP) when substituted in Schlessinger's stationary expression for the T operator. Trial calculations show that efficiencies almost as great as that of the GNVP and much greater than the KVP can be obtained, even for basis sets with the majority of the members independent of energy.
Direct calculation of the reactive transition matrix by L-squared quantum mechanical variational methods with complex boundary conditions
A new formalism of the generalized Newton variational principle for the calculation of quantum mechanical state-to-state reaction probabilities is presented. The reformulation involves solving directly for the transition matrix rather than the reactance mtrix so that calculations may be carried out for individual columns of the transition matrix without obtaining solutions for all possible initial channels. The convergence of calculations with real and complex boundary conditions are compared for H + H2 - H2 + H, O + H2 - OH + H, and O + HD - OH + D and OD + H.
Converged quantum dynamics calculations for the F + H2 reaction on the well-studied M5 potential-energy surface
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Computational strategies and improvements in the linear algebraic variational approach to rearrangement scattering
The computational steps in calculating quantum mechanical reactive scattering amplitudes by the L2 generalized Newton variational principle are discussed with emphasis on computational strategies and recent improvements that make the calculations more efficient. Special emphasis is placed on quadrature techniques, storage management strategies, use of symmetry, and boundary conditions. It is concluded that an efficient implementation of these procedures provides a powerful algorithm for the accurate solution of the Schroedinger equation for rearrangements.