Development of High Fidelity Soot Aerosol Dynamics Models using Method of Moments with Interpolative Closure

The method of moments with interpolative closure (MOMIC) for soot formation and growth provides a detailed modeling framework maintaining a good balance in generality, accuracy, robustness, and computational efficiency. This study presents several computational issues in the development and implementation of the MOMIC-based soot modeling for direct numerical simulations (DNS). The issues of concern include a wide dynamic range of numbers, choice of normalization, high effective Schmidt number of soot particles, and realizability of the soot particle size distribution function (PSDF). These problems are not unique to DNS, but they are often exacerbated by the high-order numerical schemes used in DNS. Four specific issues are discussed in this article: the treatment of soot diffusion, choice of interpolation scheme for MOMIC, an approach to deal with strongly oxidizing environments, and realizability of the PSDF. General, robust, and stable approaches are sought to address these issues, minimizing the use of ad hoc treatments such as clipping. The solutions proposed and demonstrated here are being applied to generate new physical insight into complex turbulence-chemistry-soot-radiation interactions in turbulent reacting flows using DNS

Direct Numerical Simulations of Non-premixed ethylene–Air Flames: Local Flame Extinction Criterion

Direct Numerical Simulations (DNS) of ethylene/air diffusion flame extinctions in decaying two-dimensional turbulence were performed. A Damköhler-number-based flame extinction criterion as provided by classical large activation energy asymptotic (AEA) theory is assessed for its validity in predicting flame extinction and compared to one based on Chemical Explosive Mode Analysis (CEMA) of the detailed chemistry. The DNS code solves compressible flow conservation equations using high order finite difference and explicit time integration schemes. The ethylene/air chemistry is simulated with a reduced mechanism that is generated based on the directed relation graph (DRG) based methods along with stiffness removal. The numerical configuration is an ethylene fuel strip embedded in ambient air and exposed to a prescribed decaying turbulent flow field. The emphasis of this study is on the several flame extinction events observed in contrived parametric simulations. A modified viscosity and changing pressure (MVCP) scheme was adopted in order to artificially manipulate the probability of flame extinction. Using MVCP, pressure was changed from the baseline case of 1 atm to 0.1 and 10 atm. In the high pressure MVCP case, the simulated flame is extinction-free, whereas in the low pressure MVCP case, the simulated flame features frequent extinction events and is close to global extinction. Results show that, despite its relative simplicity and provided that the global flame activation temperature is correctly calibrated, the AEA-based flame extinction criterion can accurately predict the simulated flame extinction events. It is also found that the AEA-based criterion provides predictions of flame extinction that are consistent with those provided by a CEMA-based criterion. This study supports the validity of a simple Damköhler-number-based criterion to predict flame extinction in engineering-level CFD models

Mechanism of efficient anti-Markovnikov olefin hydroarylation catalyzed by homogeneous Ir(III) complexes

The mechanism of the hydroarylation reaction between unactivated olefins (ethylene, propylene, and styrene) and benzene catalyzed by [(R)Ir(μ-acac-O,O,C^3)-(acac-O,O)_2]_2 and [R-Ir(acac-O,O)_2(L)] (R = acetylacetonato, CH_3, CH_2CH_3, Ph, or CH_2CH_2Ph, and L = H_2O or pyridine) Ir(III) complexes was studied by experimental methods. The system is selective for generating the anti-Markovnikov product of linear alkylarenes (61 : 39 for benzene + propylene and 98 : 2 for benzene + styrene). The reaction mechanism was found to follow a rate law with first-order dependence on benzene and catalyst, but a non-linear dependence on olefin. ^(13)C-labelling studies with CH_3^(13)CH_2-Ir-Py showed that reversible β-hydride elimination is facile, but unproductive, giving exclusively saturated alkylarene products. The migration of the ^(13)C-label from the α to β-positions was found to be slower than the C–H activation of benzene (and thus formation of ethane and Ph-d_5-Ir-Py). Kinetic analysis under steady state conditions gave a ratio of the rate constants for CH activation and β-hydride elimination (k_(CH): k_β) of 0.5. The comparable magnitude of these rates suggests a common rate determining transition state/intermediate, which has been shown previously with B3LYP density functional theory (DFT) calculations. Overall, the mechanism of hydroarylation proceeds through a series of pre-equilibrium dissociative steps involving rupture of the dinuclear species or the loss of L from Ph-Ir-L to the solvento, 16-electron species, Ph-Ir(acac-O,O)_2-Sol (where Sol refers to coordinated solvent). This species then undergoes trans to cis isomerization of the acetylacetonato ligand to yield the pseudo octahedral species cis-Ph-Ir-Sol, which is followed by olefin insertion (the regioselective and rate determining step), and then activation of the C–H bond of an incoming benzene to generate the product and regenerate the catalyst

Prevalence of obesity, type II diabetes mellitus, hyperlipidemia, and hypertension in the United States: findings from the GE Centricity Electronic Medical Record database.

This study analyzed GE Centricity Electronic Medical Record (EMR) data to examine the effects of body mass index (BMI) and obesity, key risk factor components of metabolic syndrome, on the prevalence of 3 chronic diseases: type II diabetes mellitus, hyperlipidemia, and hypertension. These chronic diseases occur with high prevalence and impose high disease burdens. The rationale for using Centricity EMR data is 2-fold. First, EMRs may be a good source of BMI/obesity data, which are often underreported in surveys and administrative databases. Second, EMRs provide an ideal means to track variables over time and, thus, allow longitudinal analyses of relationships between risk factors and disease prevalence and progression. Analysis of Centricity EMR data showed associations of age, sex, race/ethnicity, and BMI with diagnosed prevalence of the 3 conditions. Results include uniform direct correlations between age and BMI and prevalence of each disease; uniformly greater disease prevalence for males than females; varying differences by race/ethnicity (ie, African Americans have the highest prevalence of diagnosed type II diabetes and hypertension, while whites have the highest prevalence of diagnosed hypertension); and adverse effects of comorbidities. The direct associations between BMI and disease prevalence are consistent for males and females and across all racial/ethnic groups. The results reported herein contribute to the growing literature about the adverse effects of obesity on chronic disease prevalence and about the potential value of EMR data to elucidate trends in disease prevalence and facilitate longitudinal analyses

Universal fluctuating regime in triangular chromate antiferromagnets

We report x-ray diffraction, magnetic susceptibility, heat capacity, $^{1}$H nuclear magnetic resonance (NMR), and muon spin relaxation ($\mu$SR) measurements, as well as density-functional band-structure calculations for the frustrated $S=3/2$ triangular lattice Heisenberg antiferromagnet (TLHAF) $\alpha$-HCrO$_{2}$ (trigonal, space group: $R\bar{3}m$). This compound undergoes a clear magnetic transition at $T_{\rm N} \simeq 22.5$~K, as seen from the drop in the muon paramagnetic fraction and concurrent anomalies in the magnetic susceptibility and specific heat. Local probes (NMR and $\mu$SR) reveal a broad regime with slow fluctuations down to $0.7\,T_{\rm N}$, this temperature corresponding to the maximum in the $\mu$SR relaxation rate and in the NMR wipe-out. From the comparison with NaCrO$_{2}$ and $\alpha$-KCrO$_{2}$, the fluctuating regime and slow dynamics below $T_{\rm N}$ appear to be hallmarks of the TLHAF with $ABC$ stacking that leads to a frustration of interlayer couplings between the triangular planes. This interlayer frustration is a powerful lever to generate spin states with persistent dynamics and may bear implications to spin-liquid candidates with the triangular geometry.Comment: 14 pages, 11 figures, 2 table

Assaying Rho GTPase–dependent processes in Dictyostelium discoideum

The model organism D. discoideum is well-suited to investigate basic questions of molecular and cell biology, particularly those related to the structure, regulation and dynamics of the cytoskeleton, signal transduction, cell-cell adhesion and development. D. discoideum cells make use of Rho-regulated signaling pathways to reorganize the actin cytoskeleton during chemotaxis, endocytosis and cytokinesis. In this organism the Rho family encompasses 20 members, several belonging to the Rac subfamily, but there are no representatives of the Cdc42 and Rho subfamilies. Here we present protocols suitable for monitoring the actin polymerization response and the activation of Rac upon stimulation of aggregation competent cells with the chemoattractant cAMP, and for monitoring the localization and dynamics of Rac activity in live cells

Rpb1 Sumoylation in Response to UV Radiation or Transcriptional Impairment in Yeast

Covalent modifications of proteins by ubiquitin and the Small Ubiquitin-like MOdifier (SUMO) have been revealed to be involved in a plethora of cellular processes, including transcription, DNA repair and DNA damage responses. It has been well known that in response to DNA damage that blocks transcription elongation, Rpb1, the largest subunit of RNA polymerase II (Pol II), is ubiquitylated and subsequently degraded in mammalian and yeast cells. However, it is still an enigma regarding how Pol II responds to damaged DNA and conveys signal(s) for DNA damage-related cellular processes. We found that Rpb1 is also sumoylated in yeast cells upon UV radiation or impairment of transcription elongation, and this modification is independent of DNA damage checkpoint activation. Ubc9, an E2 SUMO conjugase, and Siz1, an E3 SUMO ligase, play important roles in Rpb1 sumoylation. K1487, which is located in the acidic linker region between the C-terminal domain and the globular domain of Rpb1, is the major sumoylation site. Rpb1 sumoylation is not affected by its ubiquitylation, and vice versa, indicating that the two processes do not crosstalk. Abolishment of Rpb1 sumoylation at K1487 does not affect transcription elongation or transcription coupled repair (TCR) of UV-induced DNA damage. However, deficiency in TCR enhances UV-induced Rpb1 sumoylation, presumably due to the persistence of transcription-blocking DNA lesions in the transcribed strand of a gene. Remarkably, abolishment of Rpb1 sumoylation at K1487 causes enhanced and prolonged UV-induced phosphorylation of Rad53, especially in TCR-deficient cells, suggesting that the sumoylation plays a role in restraining the DNA damage checkpoint response caused by transcription-blocking lesions. Our results demonstrate a novel covalent modification of Rpb1 in response to UV induced DNA damage or transcriptional impairment, and unravel an important link between the modification and the DNA damage checkpoint response

Ordered Patterns of Cell Shape and Orientational Correlation during Spontaneous Cell Migration

BACKGROUND: In the absence of stimuli, most motile eukaryotic cells move by spontaneously coordinating cell deformation with cell movement in the absence of stimuli. Yet little is known about how cells change their own shape and how cells coordinate the deformation and movement. Here, we investigated the mechanism of spontaneous cell migration by using computational analyses. METHODOLOGY: We observed spontaneously migrating Dictyostelium cells in both a vegetative state (round cell shape and slow motion) and starved one (elongated cell shape and fast motion). We then extracted regular patterns of morphological dynamics and the pattern-dependent systematic coordination with filamentous actin (F-actin) and cell movement by statistical dynamic analyses. CONCLUSIONS/SIGNIFICANCE: We found that Dictyostelium cells in both vegetative and starved states commonly organize their own shape into three ordered patterns, elongation, rotation, and oscillation, in the absence of external stimuli. Further, cells inactivated for PI3-kinase (PI3K) and/or PTEN did not show ordered patterns due to the lack of spatial control in pseudopodial formation in both the vegetative and starved states. We also found that spontaneous polarization was achieved in starved cells by asymmetric localization of PTEN and F-actin. This breaking of the symmetry of protein localization maintained the leading edge and considerably enhanced the persistence of directed migration, and overall random exploration was ensured by switching among the different ordered patterns. Our findings suggest that Dictyostelium cells spontaneously create the ordered patterns of cell shape mediated by PI3K/PTEN/F-actin and control the direction of cell movement by coordination with these patterns even in the absence of external stimuli

Caffeine Prevents Transcription Inhibition and P-TEFb/7SK Dissociation Following UV-Induced DNA Damage

Background: The mechanisms by which DNA damage triggers suppression of transcription of a large number of genes are poorly understood. DNA damage rapidly induces a release of the positive transcription elongation factor b (P-TEFb) from the large inactive multisubunit 7SK snRNP complex. P-TEFb is required for transcription of most class II genes through stimulation of RNA polymerase II elongation and cotranscriptional pre-mRNA processing. Methodology/Principal Findings: We show here that caffeine prevents UV-induced dissociation of P-TEFb as well as transcription inhibition. The caffeine-effect does not involve PI3-kinase-related protein kinases, because inhibition of phosphatidylinositol 3-kinase family members (ATM, ATR and DNA-PK) neither prevents P-TEFb dissociation nor transcription inhibition. Finally, caffeine prevention of transcription inhibition is independent from DNA damage. Conclusion/Significance: Pharmacological prevention of P-TEFb/7SK snRNP dissociation and transcription inhibitio