Calculation of Critical Nucleation Rates by the Persistent Embryo Method: Application to Quasi Hard Sphere Models

We study crystal nucleation of the Weeks-Chandler-Andersen (WCA) model, using the recently introduced Persistent Embryo Method (PEM). The method provides detailed characterization of pre-critical, critical and post-critical nuclei, as well as nucleation rates that compare favorably with those obtained using other methods (umbrella sampling, forward flux sampling or seeding). We further map our results to a hard sphere model allowing to compare with other existing predictions. Implications for experiments are also discussed.Comment: 27 pages, 11 figure

Active Galactic Nuclei Feedback in an Elliptical Galaxy with the Most Updated AGN Physics (I): Low-angular Momentum Case

We investigate the effects of AGN feedback on the cosmological evolution of an isolated elliptical galaxy by performing two-dimensional high-resolution hydrodynamical numerical simulations. The inner boundary of the simulation is chosen so that the Bondi radius is resolved. Compared to previous works, the two accretion modes, namely hot and cold, which correspond to different accretion rates and have different radiation and wind outputs, are carefully discriminated and the feedback effects by radiation and wind in each mode are taken into account. The most updated AGN physics, including the descriptions of radiation and wind from the hot accretion flows and wind from cold accretion disks, are adopted. Physical processes like star formation, Type Ia and Type II supernovae are taken into account. We study the AGN light curve, typical AGN lifetime, growth of the black hole mass, AGN duty-cycle, star formation, and the X-ray surface brightness of the galaxy. We compare our simulation results with observations and find general consistency. Comparisons with previous simulation works find significant differences, indicating the importance of AGN physics. The respective roles of radiation and wind feedbacks are examined and it is found that they are different for different problems of interest such as AGN luminosity and star formation. We find that it is hard to neglect any of them, so we suggest to use the names of "cold feedback mode" and "hot feedback mode" to replace the currently used ones.Comment: 25 pages, 14 figures, accepted for publication to ApJ (Revised to match version published in ApJ

Structural and Chemical Orders in Ni64.5Zr35.5 Metallic Glass by Molecular Dynamics Simulation

The atomic structure of Ni64.5Zr35.5 metallic glass has been investigated by molecular dynamics (MD) simulations. The calculated structure factors from the MD glassy sample at room temperature agree well with the X-ray diffraction (XRD) and neutron diffraction (ND) experimental data. Using the pairwise cluster alignment and clique analysis methods, we show that there are three types dominant short-range order (SRO) motifs around Ni atoms in the glass sample of Ni64.5Zr35.5, i.e., Mixed-Icosahedron(ICO)-Cube, Twined-Cube and icosahedron-like clusters. Furthermore, chemical order and medium-range order (MRO) analysis show that the Mixed-ICO-Cube and Twined-Cube clusters exhibit the characteristics of the crystalline B2 phase. Our simulation results suggest that the weak glass-forming ability (GFA) of Ni64.5Zr35.5 can be attributed to the competition between the glass forming ICO SRO and the crystalline Mixed-ICO-Cube and Twined-Cube motifs

Effect of Samarium doping on the nucleation of fcc-Aluminum in undercooled liquids

The effect of Sm doping on the fcc-Al nucleation was investigated in Al-Sm liquids with low Sm concentrations (xSm) with molecular dynamics simulations. The nucleation in the moderately undercooled liquid is achieved by the recently developed persistent-embryo method. Systematically computing the nucleation rate with different xSm (xSm=0%, 1%, 2%, 3%, 5%) at 700 K, we found Sm dopant reduces the nucleation rate by up to 25 orders of magnitudes with only 5% doping concentration. This effect is mostly associated with the increase in the free energy barrier with a minor contribution from suppression of the attachment to the nucleus caused by Sm doping.Comment: 4 figure

Assembling a cellulase cocktail and a cellodextrin transporter into a yeast host for CBP ethanol production

Background: Many microorganisms possess enzymes that can efficiently degrade lignocellulosic materials, but donot have the capability to produce a large amount of ethanol. Thus, attempts have been made to transform suchenzymes into fermentative microbes to serve as hosts for ethanol production. However, an efficient host for aconsolidated bioprocess (CBP) remains to be found. For this purpose, a synthetic biology technique that cantransform multiple genes into a genome is instrumental. Moreover, a strategy to select cellulases that interactsynergistically is needed.Results: To engineer a yeast for CBP bio-ethanol production, a synthetic biology technique, called “promoter-basedgene assembly and simultaneous overexpression” (PGASO), that can simultaneously transform and express multiplegenes in a kefir yeast, Kluyveromyces marxianus KY3, was recently developed. To formulate an efficient cellulasecocktail, a filter-paper-activity assay for selecting heterologous cellulolytic enzymes was established in this study andused to select five cellulase genes, including two cellobiohydrolases, two endo-β-1,4-glucanases and onebeta-glucosidase genes from different fungi. In addition, a fungal cellodextrin transporter gene was chosen totransport cellodextrin into the cytoplasm. These six genes plus a selection marker gene were one-step assembledinto the KY3 genome using PGASO. Our experimental data showed that the recombinant strain KR7 could expressthe five heterologous cellulase genes and that KR7 could convert crystalline cellulose into ethanol.Conclusion: Seven heterologous genes, including five cellulases, a cellodextrin transporter and a selection marker,were simultaneously transformed into the KY3 genome to derive a new strain, KR7, which could directly convertcellulose to ethanol. The present study demonstrates the potential of our strategy of combining a cocktailformulation protocol and a synthetic biology technique to develop a designer yeast host

The use of corticosteroids in patients with COPD or asthma does not decrease lung squamous cell carcinoma

BACKGROUND: Asthma and COPD (chronic obstructive pulmonary disease) lead to persistent airway inflammation and are associated with lung cancer. The objective of the study was to assess the relationship between inhaled (ICS) and oral corticosteroid (OCS) use, and risk of lung squamous cell carcinoma (SqCC). METHODS: This study was a nested case–control study. Patients with newly diagnosed asthma or COPD between 2003 and 2010 were identified from the National Health Insurance Database. Cases were defined as patients diagnosed with SqCC after enrollment. For each case, four control individuals who were randomly matched for sex and age and date diagnosis of asthma or COPD were selected. RESULTS: From the 1,672,455 eligible participants, 793 patients with SqCC were matched with 3,172 controls. The odds ratios (ORs) of SqCC in men who received high and low-dose ICS were 2.18 (95 %CI, 1.56–3.04) and 1.77 (1.22–2.57), respectively. Similarly, the ORs were 1.46 (95 %CI, 1.16–1.84) and 1.55 (95 %CI, 1.22–1.98) for men who were placed on low and high dose OCS. However, there was no significant association between cumulative ICS and/or OCS and risk of SqCC in women. Recent dose increase in corticosteriod was significantly associated with risk of SqCC. Specifically, among men, the ORs for SqCC were 8.08 (95 %CI, 3.22–20.30) for high-dose ICS + OCS, 4.49 (95 % CI, 2.05–9.85) for high-dose ICS, and 3.54 (95 % CI, 2.50–5.01) for high-dose OCS treatments, respectively. The OR for SqCC in women who received high-dose OCS was 6.72 (95 %CI, 2.69–16.81). CONCLUSION: Corticosteroid use did not decrease SqCC in patients with asthma or COPD. Recent dose increase in corticosteroids was associated with SqCC

Model-Driven Cosmology With Bayesian Machine Learning and Population Inference

This thesis presents new directions for cosmological data analysis using Bayesian techniques and machine learning. First, I introduce a novel machine learning spectroscopic analysis technique to detect absorption systems in the Lyman-α forest. Using Gaussian processes, I build data-driven models for the quasar emission and apply Bayesian model selection to classify the damped Lyman alpha absorbers (DLAs), which are high column density absorption systems found in quasar spectra. The Gaussian process DLA finder (GP-DLA) is applied to the Sloan Digital Sky Survey (SDSS) quasar spectra and and now adopted by the Dark Energy Spectroscopic Instrument (DESI) collaboration. This GP-DLA technique allows us to construct probabilistic catalogs of damped Lyman-α absorbers, offering a new approach to studying the intergalactic medium and cosmology at z = 2 - 5.Next, I present a new method to infer cosmological parameters using Bayesian surrogate modeling with multi-fidelity emulators. Multi-fidelity emulators are a type of surrogate model that use information from multiple levels of fidelity to improve the accuracy of the surrogate model. This approach accelerates both the analysis of cosmological simulations and the inference of cosmological parameters, providing a probabilistic method to quantify and correct the resolution in cosmological simulations. Multi-fidelity emulators make it possible to perform fast and accurate parameter inference on large-scale structure data, such as the matter power spectrum, using computationally expensive simulations in high-dimensional parameter spaces.Finally, I discuss population inference of gravitational wave (GW) data using a mixture model approach. The population statistics of GW events can provide insights into the formation and evolution of binary black holes (BBHs). I present a data-driven method to infer the mixing fraction between BH populations, along with a Bayesian hierarchical approach to correct for selection effects. The results of the mixing fraction analysis suggest that the population of 35 M⊙ BHs is likely separate from the rest of the population, indicating that current formation channels for this mass bump need to be revised to include explanations for the separation of these massive 35 M⊙ binaries