Learning dynamics on invariant measures using PDE-constrained optimization

We extend the methodology in [Yang et al., 2023] to learn autonomous continuous-time dynamical systems from invariant measures. The highlight of our approach is to reformulate the inverse problem of learning ODEs or SDEs from data as a PDE-constrained optimization problem. This shift in perspective allows us to learn from slowly sampled inference trajectories and perform uncertainty quantification for the forecasted dynamics. Our approach also yields a forward model with better stability than direct trajectory simulation in certain situations. We present numerical results for the Van der Pol oscillator and the Lorenz-63 system, together with real-world applications to Hall-effect thruster dynamics and temperature prediction, to demonstrate the effectiveness of the proposed approach.Comment: This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in Chaos: An Interdisciplinary Journal of Nonlinear Science, Volume 33, Issue 6, June 2023, and may be found at https://doi.org/10.1063/5.014967

C6 Wheels

This document details the C6 Wheels project being undertaken for senior design. The objective is to design and manufacture carbon fiber reinforced polymer wheels for the Cal Poly Formula Society of Automotive Engineers (FSAE) team. The wheel shells will be used on FSAE’s competition vehicles. FSAE requested the wheels to improve the handling characteristics of their vehicles by reducing the unsprung and rotational mass. They have attempted carbon fiber wheels previously but have not yet run any on their vehicles. FSAE specifically proposed the design of carbon fiber shells with an aluminum center as opposed to full carbon fiber wheels on the recommendation of the 2018 attempt. C6 Wheels is responsible for designing the wheel shells—including interfacing with the aluminum centers, designing and manufacturing the mold tooling, and molding of the carbon fiber wheel shells—including any post machining. The aluminum centers are being designed and manufactured by the FSAE team

High-Throughput Fabrication of Resonant Metamaterials with Ultrasmall Coaxial Apertures via Atomic Layer Lithography

We combine atomic layer lithography and glancing-angle ion polishing to create wafer-scale metamaterials composed of dense arrays of ultrasmall coaxial nanocavities in gold films. This new fabrication scheme makes it possible to shrink the diameter and increase the packing density of 2 nm-gap coaxial resonators, an extreme subwavelength structure first manufactured via atomic layer lithography, both by a factor of 100 with respect to previous studies. We demonstrate that the nonpropagating zeroth-order Fabry-Pérot mode, which possesses slow light-like properties at the cutoff resonance, traps infrared light inside 2 nm gaps (gap volume ∼ λ[superscript]3/10[superscript 6]). Notably, the annular gaps cover only 3% or less of the metal surface, while open-area normalized transmission is as high as 1700% at the epsilon-near-zero (ENZ) condition. The resulting energy accumulation alongside extraordinary optical transmission can benefit applications in nonlinear optics, optical trapping, and surface-enhanced spectroscopies. Furthermore, because the resonance wavelength is independent of the cavity length and dramatically red shifts as the gap size is reduced, large-area arrays can be constructed with λresonance ≫ period, making this fabrication method ideal for manufacturing resonant metamaterials.United States. Air Force Office of Scientific Research (Grants FA9550-12-1-0357 and FA9550-11-1-0141

Isolation and Characterization of a Novel Bacteriophage WO from Allonemobius Socius Crickets in Missouri

Wolbachia are endosymbionts of numerous arthropod and some nematode species, are important for their development and if present can cause distinct phenotypes of their hosts. Prophage DNA has been frequently detected in Wolbachia, but particles of Wolbachia bacteriophages (phage WO) have been only occasionally isolated. Here, we report the characterization and isolation of a phage WO of the southern ground cricket, Allonemobius socius, and provided the first whole-genome sequence of phage WO from this arthropod family outside of Asia. We screened A. socius abdomen DNA extracts from a cricket population in eastern Missouri by quantitative PCR for Wolbachia surface protein and phage WO capsid protein and found a prevalence of 55% and 50%, respectively, with many crickets positive for both. Immunohistochemistry using antibodies against Wolbachia surface protein showed many Wolbachia clusters in the reproductive system of female crickets. Whole-genome sequencing using Oxford Nanopore MinION and Illumina technology allowed for the assembly of a high-quality, 55 kb phage genome containing 63 open reading frames (ORF) encoding for phage WO structural proteins and host lysis and transcriptional manipulation. Taxonomically important regions of the assembled phage genome were validated by Sanger sequencing of PCR amplicons. Analysis of the nucleotides sequences of the ORFs encoding the large terminase subunit (ORF2) and minor capsid (ORF7) frequently used for phage WO phylogenetics showed highest homology to phage WOAu of Drosophila simulans (94.46% identity) and WOCin2USA1 of the cherry fruit fly, Rhagoletis cingulata (99.33% identity), respectively. Transmission electron microscopy examination of cricket ovaries showed a high density of phage particles within Wolbachia cells. Isolation of phage WO revealed particles characterized by 40-62 nm diameter heads and up to 190 nm long tails. This study provides the first detailed description and genomic characterization of phage WO from North America that is easily accessible in a widely distributed cricket species

Trans-activation, post-transcriptional maturation, and induction of antibodies to HERV-K (HML-2) envelope transmembrane protein in HIV-1 infection

Background Human Endogenous Retroviruses (HERVs) comprise about 8% of the human genome and have lost their ability to replicate or to produce infectious particles after having accumulated mutations over time. We assessed the kinetics of expression of HERV-K (HML-2) Envelope mRNA transcript and surface unit (SU) and transmembrane (TM) subunit proteins during HIV-1 infection. We also mapped the specificity of the humoral response to HERV-K (HML-2) Envelope protein in HIV-1 infected subjects at different stages of disease, and correlated the response with plasma viral load. Results We found that HIV-1 modified HERV-K (HML-2) Env mRNA expression, resulting in the expression of a fully N-glycosylated HERV-K (HML-2) envelope protein on the cell surface. Serological mapping of HERV-K (HML-2) envelope protein linear epitopes revealed two major immunogenic domains, one on SU and another on the ectodomain of TM. The titers of HERV-K (HML-2) TM antibodies were dramatically increased in HIV-1 infected subjects (p \u3c 0.0001). HIV-1 infected adults who control HIV-1 in the absence of therapy (“elite” controllers) had a higher titer response against TM compared to antiretroviral-treated adults (p \u3c 0.0001) and uninfected adults (p \u3c 0.0001). Conclusions These data collectively suggest that HIV-1 infection induces fully glycosylated HERV-K (HML-2) envelope TM protein to which antibodies are induced. These anti-HERV-K (HML-2) TM antibodies are a potential marker of HIV-1 infection, and are at higher titer in elite controllers. HERV-K (HML-2) envelope TM protein may be a new therapeutic target in HIV-1 infection

Cleveland Street Connection: A Transit Oriented Development Plan

The City of Richmond requested a plan that will inform the creation of a vibrant walkable community within a quarter mile of the Cleveland Street Pulse Station. The plan will focus on creating a cohesive, yet unique, station design that will draw together two neighborhoods: the Museum District and Scotts Addition, with Broad Street acting as the binding element. The Cleveland Street Connection will provide a vision for future development and infill in the area. The goals of the plan are to develop a walkable environment, create a distinctive Broad Street corridor, and provide a clear set of standards to drive and direct development in a way the complements the nature of the surrounding neighborhoods. Additionally, the plan seeks to preserve the historically industrial character of the Scotts Addition community while encouraging the organic growth currently occurring there, as well as enhance and preserve the Museum District through selective infill opportunities

Climate sensitivity increases under higher CO₂ levels due to feedback temperature dependence

Equilibrium climate sensitivity‐the equilibrium warming per CO2 doubling‐increases with CO2 concentration for 13 of 14 coupled general circulation models for 0.5–8 times the preindustrial concentration. In particular, the abrupt 4 × CO2 equilibrium warming is more than twice the 2 × CO2 warming. We identify three potential causes: nonlogarithmic forcing, feedback CO2 dependence, and feedback temperature dependence. Feedback temperature dependence explains at least half of the sensitivity increase, while feedback CO2 dependence explains a smaller share, and nonlogarithmic forcing decreases sensitivity in as many models as it increases it. Feedback temperature dependence is positive for 10 out of 14 models, primarily due to the longwave clear‐sky feedback, while cloud feedbacks drive particularly large sensitivity increases. Feedback temperature dependence increases the risk of extreme or runaway warming, and is estimated to cause six models to warm at least an additional 3K under 8 × CO2