1,517 research outputs found

    Caustic graphene plasmons with Kelvin angle

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    A century-long argument made by Lord Kelvin that all swimming objects have an effective Mach number of 3, corresponding to the Kelvin angle of 19.5 degree for ship waves, has been recently challenged with the conclusion that the Kelvin angle should gradually transit to the Mach angle as the ship velocity increases. Here we show that a similar phenomenon can happen for graphene plasmons. By analyzing the caustic wave pattern of graphene plasmons stimulated by a swift charged particle moving uniformly above graphene, we show that at low velocities of the charged particle, the caustics of graphene plasmons form the Kelvin angle. At large velocities of the particle, the caustics disappear and the effective semi-angle of the wave pattern approaches the Mach angle. Our study introduces caustic wave theory to the field of graphene plasmonics, and reveals a novel physical picture of graphene plasmon excitation during electron energy-loss spectroscopy measurement.Comment: 15 pages, 4 figure

    Computational Studies On Alpha-Synuclein In Explicit Solvent: Implications In Parkinson’S Disease

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    α-Synuclein (αS) is a cytosolic protein expressed at high levels in the human brain and concentrated in presynaptic nerve terminals. Although the precise nature of αS in vivo remains unclear, the aggregation of αS, from its soluble, functional forms into highly organized amyloid fibrils, has been substantially implicated in the pathology of a number of neurodegenerative diseases collectively known as synucleinopathies. The long-term goal of this project is to understand the molecular mechanisms that initiate αS oligomerization in aqueous solution. A novel computational methodology involving protein modeling and atomistic molecular dynamics (MD) simulations is used in this work. The objective included in this dissertation is to produce an ensemble of small soluble αS species, and then identify aggregation-prone species with a characterization of their dynamic structures in explicit water. In Chapter 2, based on the results from currently available experimental studies on tetrameric αS, we develop a systematic computational methodology to create tetramer models. With such models, we simulate their dynamic conformations and identified the hydrophobic core and important salt-bridges that stabilize the tetramers. In Chapter 3, we simulate the most hydrophobic region in αS sequence with strong tendency of self-assembly, also known as the non-amyloid β component (NAC) of amyloid plaques in Alzheimer’s disease at both room and near-boil temperatures. From the ensemble of monomer species, the one with high tendency of forming β-sheet is identified and then used to generate the dimeric species. The simulations with those dimer species suggest that the N- and C-terminal regions of NAC are likely to be the regions where initial β-sheet structure forms in small oligomers of αS. In Chapter 4, simulations with the monomeric wild-type αS and three missense mutations at various temperatures suggest that all three mutations induce the loss of helix of αS, which might promote formation of β-sheet structure. Additionally, the results support in vitro studies of αS’s thermal behavior that suggest wild-type αS is a heat-resistant protein, and further predict that some missense mutations might cause faster changes of secondary structure of αS upon heat treatment

    Improving data quality for 3D electron diffraction (3D ED) by Gatan Image Filter and a new crystal tracking method

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    3D ED is an effective technique to determine the structures of submicron- or nano-sized crystals. In this paper, we implemented energy-filtered 3D ED using a Gatan Energy Filter (GIF) in both selected area electron diffraction mode and micro/nanoprobe mode. We explained the setup in detail, which improves the accessibility of energy-filtered 3D ED experiments as more electron microscopes are equipped with a GIF than an in-column filter. We also proposed a crystal tracking method in STEM mode using live HAADF image stream. This method enables us to collect energy-filtered 3D ED datasets in STEM mode with a larger tilt range without foregoing any frames. In order to compare the differences between energy-filtered 3D ED and normal 3D ED data, three crystalline samples have been studied in detail. We observed that the final R1 will improve 20% to 30% for energy-filtered datasets compared with unfiltered datasets and the structure became more reasonable. We also discussed the possible reasons that lead to the improvement

    Population structure of Coilia nasus in the Yangtze River revealed by insertion of short interspersed elements

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    AbstractCoilia nasus is found in the Yangtze River and the coastal waters of China, Korea, and Japan. Two ecotypes (anadromous and freshwater-resident populations) are distributed throughout the Yangtze River basin based on their ecology and behavior, but relatively little is known about the population structure of this species. Analysis of short interspersed element (SINE) insertions, which vary among individuals, has been acknowledged to provide a unique way to study population divergence. SINEs isolated from C. nasus were characterized, and this enabled analysis of the SINE insertion pattern in six populations distributed throughout the Yangtze River basin. In all populations, four SINE loci displayed individual polymorphism, and two SINE loci showed a stochastic loss in all individuals of two resident populations. The correlation between genetic and geographic populations indicated a degree of genetic isolation in this species. In contrast with Coilia grayii and Coilia mystus, two SINE loci appeared only in C. nasus. Sequencing analysis indicated that the high insertion variability of SINEs was attributed mainly to the tails, which contained various repeat copies. The results in this study will be useful for sustainable management of fishery resources and conservation of this species

    Cerebral oxygen desaturation occurs frequently in patients with hypertension undergoing major abdominal surgery

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    Hypertensive patients are more likely to experience latent cerebral ischemia causing regional cerebral oxygen saturation (rSO2) decrease during general anesthesia. The aim of this prospective observational study was to assess the incidence of decreased rSO2 in hypertensive patients undergoing major abdominal surgery and the perioperative factors affecting this change in rSO2. A total of 41 hypertensive patients were enrolled and stratified according to their hypertension as controlled and uncontrolled. The intraoperative rSO2 and physiological data were routinely collected. The Mini-Mental State Exam (MMSE) was used to test cognitive function before surgery and after 4 days. Cerebral desaturation was defined as a decrease in rSO2 of more than 20% of the baseline value. There were 20 patients (49%) suffering intraoperative cerebral desaturation classified into cerebral desaturation group (group D) and those 21 without intraoperative desaturation classified into normal group (group N). The area under the curve below 90 and 80% of baseline (AUCrSO2 <90% of baseline and AUCrSO2 <80% of baseline) was lower in patients of group N (2752.4 ± 1453.3 min% and 0.0 min%) than in patients of group D (6264.9 ± 1832.3 min% and 4486.5 ± 1664.9 min%, P < 0.001). Comparing the two groups, the number of uncontrolled hypertensive individuals in group D (12/20) was significantly more than group N (4/21) (P = 0.007). A significant correlation was observed between relative decrease in MAP and relative decrease in rSO2 (r2 = 0.495, P < 0.001). Moreover, nine patients (45%) in group D occurred early postoperative cognitive function decline were more than three patients (14.3%) in group N (P = 0.031). This pilot study showed a large proportion of hypertensive patient experienced cerebral desaturation during major abdominal surgery and uncontrolled hypertension predisposed to this desaturation. NCT02147275 (registered at http://www.clinicaltrials.gov)
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