Toward determining amyloid fibril structures using experimental constraints from Raman spectroscopy.

We present structural models for three different amyloid fibril polymorphs prepared from amylin20-29 (sequence SNNFGAILSS) and amyloid-ß25-35 (Aß25-35) (sequence GSNKGAIIGLM) peptides. These models are based on the amide C=O bond and Ramachandran ψ-dihedral angle data from Raman spectroscopy, which were used as structural constraints to guide molecular dynamics (MD) simulations. The resulting structural models indicate that the basic structural motif of amylin20-29 and Aß25-35 fibrils is extended ß-strands. Our data indicate that amylin20-29 forms both antiparallel and parallel ß-sheet fibril polymorphs, while Aß25-35 forms a parallel ß-sheet fibril structure. Overall, our work lays the foundation for using Raman spectroscopy in conjunction with MD simulations to determine detailed molecular-level structural models of amyloid fibrils in a manner that complements gold-standard techniques, such as solid-state nuclear magnetic resonance and cryogenic electron microscopy.

A comprehensive approach combining positive matrix factorization modeling, meteorology, and machine learning for source apportionment of surface ozone precursors: Underlying factors contributing to ozone formation in Houston, Texas.

Ozone concentrations in Houston, Texas, are among the highest in the United States, posing significant risks to human health. This study aimed to evaluate the impact of various emissions sources and meteorological factors on ozone formation in Houston from 2017 to 2021 using a comprehensive PMF-SHAP approach. First, we distinguished the unique sources of VOCs in each area and identified differences in the local chemistry that affect ozone production. At the urban station, the primary sources were n_decane, biogenic/industrial/fuel evaporation, oil and gas flaring/production, industrial emissions/evaporation, and ethylene/propylene/aromatics. At the industrial site, the main sources were industrial emissions/evaporation, fuel evaporation, vehicle-related sources, oil and gas flaring/production, biogenic, aromatic, and ethylene and propylene. And then, we performed SHAP analysis to determine the importance and impact of each emissions factor and meteorological variables. Shortwave radiation (SHAP values are ∼5.74 and ∼6.3 for Milby Park and Lynchburg, respectively) and humidity (∼4.87 and ∼4.71, respectively) were the most important variables for both sites. For the urban station, the most important emissions sources were n_decane (∼2.96), industrial emissions/evaporation (∼1.89), and ethylene/propylene/aromatics (∼1.57), while for the industrial site, they were oil and gas flaring/production (∼1.38), ethylene/propylene (∼1.26), and industrial emissions/evaporation (∼0.95). NOx had a negative impact on ozone production at the urban station due to the NOx-rich chemical regime, whereas NOx had positive impacts at the industrial site. The study's findings suggest that the PMF-SHAP approach is efficient, inexpensive, and can be applied to other similar applications to identify factors contributing to ozone-exceedance events. The study's results can be used to develop more effective air quality management strategies for Houston and other cities with high levels of ozone.

Large eddy simulation of sneeze plumes and particles in a poorly ventilated outdoor air condition: A case study of the University of Houston main campus.

Since the outbreak of the COVID-19 pandemic, many previous studies using computational fluid dynamics (CFD) have focused on the dynamics of air masses, which are believed to be the carriers of respiratory diseases, in enclosed indoor environments. Although outdoor air may seem to provide smaller exposure risks, it may not necessarily offer adequate ventilation that varies with different micro-climate settings. To comprehensively assess the fluid dynamics in outdoor environments and the efficiency of outdoor ventilation, we simulated the outdoor transmission of a sneeze plume in "hot spots" or areas in which the air is not quickly ventilated. We began by simulating the airflow over buildings at the University of Houston using an OpenFOAM computational fluid dynamics solver that utilized the 2019 seasonal atmospheric velocity profile from an on-site station. Next, we calculated the length of time an existing fluid is replaced by new fresh air in the domain by defining a new variable and selecting the hot spots. Finally, we conducted a large-eddy simulation of a sneeze in outdoor conditions and then simulated a sneeze plume and particles in a hot spot. The results show that fresh incoming air takes as long as 1000 s to ventilate the hot spot area in some specific regions on campus. We also found that even the slightest upward wind causes a sneeze plume to dissipate almost instantaneously at lower elevations. However, downward wind provides a stable condition for the plume, and forward wind can carry a plume even beyond six feet, the recommended social distance for preventing infection. Additionally, the simulation of sneeze droplets shows that the majority of the particles adhered to the ground or body immediately, and airborne particles can be transported more than six feet, even in a minimal amount of ambient air.

Role of sea fog over the Yellow Sea on air quality with the direct effect of aerosols.

In this study, we investigate the impact of sea fog over the Yellow Sea on air quality with the direct effect of aerosols for the entire year of 2016. Using the WRF-CMAQ two-way coupled model, we perform four model simulations with the up-to-date emission inventory over East Asia and dynamic chemical boundary conditions provided by hemispheric model simulations. During the spring of 2016, prevailing westerly winds and anticyclones caused the formation of a temperature inversion over the Yellow Sea, providing favorable conditions for the formation of fog. The inclusion of the direct effect of aerosols enhanced its strength. On foggy days, we find dominant changes of aerosols at an altitude of 150-200 m over the Yellow Sea resulted by the production through aqueous chemistry (~12.36% and ~3.08% increases in sulfate and ammonium) and loss via the wet deposition process (~-2.94% decrease in nitrate); we also find stronger wet deposition of all species occurring in PBL. Stagnant conditions associated with reduced air temperature caused by the direct effect of aerosols enhanced aerosol chemistry, especially in coastal regions, and it exceeded the loss of nitrate. The transport of air pollutants affected by sea fog extended to a much broader region. Our findings show that the Yellow Sea acts as not only a path of long-range transport but also as a sink and source of air pollutants. Further study should investigate changes in the impact of sea fog on air quality in conjunction with changes in the concentrations of aerosols and the climate.