Linear and nonlinear spectroscopy from quantum master equations

We investigate the accuracy of the second-order time-convolutionless (TCL2) quantum master equation for the calculation of linear and nonlinear spectroscopies of multichromophore systems. We show that, even for systems with non-adiabatic coupling, the TCL2 master equation predicts linear absorption spectra that are accurate over an extremely broad range of parameters and well beyond what would be expected based on the perturbative nature of the approach; non-equilibrium population dynamics calculated with TCL2 for identical parameters are significantly less accurate. For third-order (two-dimensional) spectroscopy, the importance of population dynamics and the violation of the so-called quantum regression theorem degrade the accuracy of TCL2 dynamics. To correct these failures, we combine the TCL2 approach with a classical ensemble sampling of slow microscopic bath degrees of freedom, leading to an efficient hybrid quantum-classical scheme that displays excellent accuracy over a wide range of parameters. In the spectroscopic setting, the success of such a hybrid scheme can be understood through its separate treatment of homogeneous and inhomogeneous broadening. Importantly, the presented approach has the computational scaling of TCL2, with the modest addition of an embarrassingly parallel prefactor associated with ensemble sampling. The presented approach can be understood as a generalized inhomogeneous cumulant expansion technique, capable of treating multilevel systems with non-adiabatic dynamics.Comment: 9 pages, 4 figure

Kepler Studies of Low-Mass Eclipsing Binaries I. Parameters of the Long-Period Binary KIC 6131659

KIC 6131659 is a long-period (17.5 days) eclipsing binary discovered by the Kepler mission. We analyzed six quarters of Kepler data along with supporting ground-based photometric and spectroscopic data to obtain accurate values for the mass and radius of both stars, namely M_1=0.922 +/- 0.007 M_sun, R_1=0.8800 +/- 0.0028 R_sun, and M_2=0.685 +/- 0.005 M_sun, R_2=0.6395 +/- 0.0061 R_sun. There is a well-known issue with low mass (M <<0.8 M_sun) stars (in cases where the mass and radius measurement uncertainties are smaller than two or three percent) where the measured radii are almost always 5 to 15 percent larger than expected from evolutionary models, i.e. the measured radii are all above the model isochrones in a mass-radius plane. In contrast, the two stars in KIC 6131659 were found to sit on the same theoretical isochrone in the mass-radius plane. Until recently, all of the well-studied eclipsing binaries with low-mass stars had periods less than about three days. The stars in such systems may have been inflated by high levels of stellar activity induced by tidal effects in these close binaries. KIC 6131659 shows essentially no evidence of enhanced stellar activity, and our measurements support the hypothesis that the unusual mass-radius relationship observed in most low-mass stars is influenced by strong magnetic activity created by the rapid rotation of the stars in tidally-locked, short-period systems. Finally, using short cadence data, we show that KIC 6131657 has one of the smallest measured non-zero eccentricities of a binary with two main sequence stars, where e cos omega=(4.57 +/-0.02)*10^-5

Doctor of Philosophy

dissertationCopper zinc superoxide dismutase (Sod1) is a critical enzyme in limiting reactive oxygen species in both the cytosol and the mitochondrial inner membrane space. Sod1 dismutes superoxide anions to hydrogen peroxide and oxygen. The catalytic reaction is dependent on an active site copper ion and a disulfide-bonded conformation. The copper chaperone for superoxide dismutase (Ccs1) mediates the activation of Sod1 either through facilitated copper ion loading, disulfide bond formation or both. In the past several decades, Sod1 has been studied extensively due to frequent mutations found in the familial form of amyotrophic lateral sclerosis (ALS). To date, over 150 mutations have been characterized in Sod1; however, the basic maturation process of the enzyme is poorly understood. In this study, we explore the basic mechanism by which Sod1 matures. To define the activation process, we have performed extensive mutagenesis on the Cys residues in Ccs1. These mutations show a strict dependence on the CXC motif in domain 3, and the spacing of the two Cys residues. Mutations that alter the spacing or remove one of the cysteinyl residues from the CXC motif result in defects in copper metallation and disulfide oxidation. Mutations of the second Cys in the Ccs1 domain 3 or Cys146 of Sod1, which participates in the intramolecular disulfide, results in enhanced stalling of the heterdimeric complex between Ccs1 and Sod1 when affinity purification of Sod1 was performed. The two Sod1 cysteinyl residues exhibit differential phenotypes in copper loading. A C57S Sod1 mutant is catalytically dead and devoid of bound copper when purified from yeast. In contrast, a C146S mutant is partially copper loaded and exhibits weak Sod1 activity. C57S is proposed to serve as an entry site ligand during Cu(I) loading. In an attempt to observe an entry site Cu(I) site, X-ray absorption spectroscopy was performed on Sod1 and Ccs1 mutants that stall the heterodimer. The Cu(I) coordination site with thiolate ligands was observed. We believe that this entry site is functional, and that a single redox turnover of Cu(I) to Cu(II) is necessary to generate hydrogen peroxide. We characterize that through a reaction of hydrogen peroxide with a free thiol, cysteine146 of Sod1, a sulfenic acid intermediate is fomed. We propose that the sulfenic acid intermediate is able to undergo a nucleophilic attack, potential from a thiolate from the CXC motif in Ccs1, to promote a disulfide exchange reaction

Kepler Eclipsing Binary Stars. II. 2165 Eclipsing Binaries in the Second Data Release

The Kepler Mission provides nearly continuous monitoring of ~156 000 objects with unprecedented photometric precision. Coincident with the first data release, we presented a catalog of 1879 eclipsing binary systems identified within the 115 square degree Kepler FOV. Here, we provide an updated catalog augmented with the second Kepler data release which increases the baseline nearly 4-fold to 125 days. 386 new systems have been added, ephemerides and principle parameters have been recomputed. We have removed 42 previously cataloged systems that are now clearly recognized as short-period pulsating variables and another 58 blended systems where we have determined that the Kepler target object is not itself the eclipsing binary. A number of interesting objects are identified. We present several exemplary cases: 4 EBs that exhibit extra (tertiary) eclipse events; and 8 systems that show clear eclipse timing variations indicative of the presence of additional bodies bound in the system. We have updated the period and galactic latitude distribution diagrams. With these changes, the total number of identified eclipsing binary systems in the Kepler field-of-view has increased to 2165, 1.4% of the Kepler target stars.Comment: 29 pages, 12 figures. Submitted to the AJ. An online version of the catalog is maintained at http://keplerEBs.villanova.edu

The MOSDEF Survey: Kinematic and Structural Evolution of Star-Forming Galaxies at 1.4≤z≤3.81.4\leq z\leq 3.8

We present ionized gas kinematics for 681 galaxies at $z\sim 1.4-3.8$ from the MOSFIRE Deep Evolution Field survey, measured using models which account for random galaxy-slit misalignments together with structural parameters derived from CANDELS Hubble Space Telescope (HST) imaging. Kinematics and sizes are used to derive dynamical masses. Baryonic masses are estimated from stellar masses and inferred gas masses from dust-corrected star formation rates (SFRs) and the Kennicutt-Schmidt relation. We measure resolved rotation for 105 galaxies. For the remaining 576 galaxies we use models based on HST imaging structural parameters together with integrated velocity dispersions and baryonic masses to statistically constrain the median ratio of intrinsic ordered to disordered motion, $V/\sigma_{V,0}$. We find that $V/\sigma_{V,0}$ increases with increasing stellar mass and decreasing specific SFR (sSFR). These trends may reflect marginal disk stability, where systems with higher gas fractions have thicker disks. For galaxies with detected rotation we assess trends between their kinematics and mass, sSFR, and baryon surface density ($\Sigma_{\mathrm{bar},e}$). Intrinsic dispersion correlates most with $\Sigma_{\mathrm{bar},e}$ and velocity correlates most with mass. By comparing dynamical and baryonic masses, we find that galaxies at $z\sim 1.4-3.8$ are baryon dominated within their effective radii ($R_E$), with Mdyn/Mbaryon increasing over time. The inferred baryon fractions within $R_E$, $f_{\mathrm{bar}}$, decrease over time, even at fixed mass, size, or surface density. At fixed redshift, $f_{\mathrm{bar}}$ does not appear to vary with stellar mass but increases with decreasing $R_E$ and increasing $\Sigma_{\mathrm{bar},e}$. For galaxies at $z\geq2$, the median inferred baryon fractions generally exceed 100%. We discuss possible explanations and future avenues to resolve this tension.Comment: Accepted to ApJ. Added Figure 9, corrected sample size (main results unchanged). 28 pages, 13 figure

The MOSDEF Survey: The Metallicity Dependence of X-Ray Binary Populations at z ∼ 2

Population synthesis models predict that high-mass X-ray binary (HMXB) populations produced in low-metallicity environments should be more X-ray luminous, a trend supported by studies of nearby galaxies. This trend may be responsible for the observed increase of the X-ray luminosity (L X) per star formation rate (SFR) with redshift due to the decrease of metallicity (Z) at fixed stellar mass as a function of redshift. To test this hypothesis, we use a sample of 79 z ∼ 2 star-forming galaxies with oxygen abundance measurements from the MOSDEF survey, which obtained rest-frame optical spectra for ∼1500 galaxies in the CANDELS fields at 1.37 &lt; z &lt; 3.80. Using Chandra data from the Chandra AEGIS-X Deep, Chandra Deep Field North, and Chandra Deep Field South surveys, we stack the X-ray data at the galaxy locations in bins of redshift and Z because the galaxies are too faint to be individually detected. In agreement with previous studies, the average L X/SFR of our z ∼ 2 galaxy sample is enhanced by ≈0.4-0.8 dex relative to local HMXB L X-SFR scaling relations. Splitting our sample by Z, we find that L X/SFR and Z are anticorrelated with 97% confidence. This observed Z dependence for HMXB-dominated galaxies is consistent with both the local L X-SFR-Z relation and a subset of population synthesis models. Although the statistical significance of the observed trends is weak owing to the low X-ray statistics, these results constitute the first direct evidence connecting the redshift evolution of L X/SFR and the Z dependence of HMXBs

A unification of the Holstein polaron and dynamic disorder pictures of charge transport in organic semiconductors

We present a unified and nonperturbative method for calculating spectral and transport properties of Hamiltonians with simultaneous Holstein (diagonal) and Peierls (off-diagonal) electron-phonon coupling. Our approach is motivated by the separation of energy scales in semiconducting organic molecular cystals, in which electrons couple to high-frequency intramolecular Holstein modes and to low-frequency intermolecular Peierls modes. We treat Peierls modes as quasi-classical dynamic disorder, while Holstein modes are included with a Lang-Firsov polaron transformation and no narrow-band approximation. Our method reduces to the popular polaron picture due to Holstein coupling and the dynamic disorder picture due to Peierls coupling. We derive an expression for efficient numerical evaluation of the frequency-resolved optical conductivity based on the Kubo formula and obtain the DC mobility from its zero-frequency component. We also use our method to calculate the electron-addition Green's function corresponding to the inverse photoemission spectrum. For realistic parameters, temperature-dependent DC mobility is largely determined by the Peierls-induced dynamic disorder with minor quantitative corrections due to polaronic band-narrowing, and an activated regime is not observed at relevant temperatures. In contrast, for frequency-resolved observables, a quantum mechanical treatment of the Holstein coupling is qualitatively important for capturing the phonon replica satellite structure.Comment: 12 pages, 7 figure

Panel: Restoring Grocery Access: The Vinton, Ohio

The village of McArthur sits in rural Vinton County in Southeast Ohio, with approximately 1,300 residents. In 2013, McArthur’s grocery store, the only grocery store in the county, was sold to Dollar General, which does not sell fresh food. As a result, residents had to travel more than 30 minutes from McArthur to another county to get fresh produce and groceries. McArthur also has a large population of seniors and others for whom access to transportation and to grocery stores is particularly limited. Launched in March of 2016, the Healthy Food for Ohio (HFFO) program, a Healthy Food Financing Initiative (HFFI), was able to attract and support a local grocer, Campbell’s Market, restoring the county with fresh food. The Campbell’s family has been in the grocery industry for more than 85 years and opened a 12,000 square foot store, adjacent to the local high school, in the winter of 2017. Campbell’s has hired over 30 employees from the local community and accepts SNAP and WIC food assistance benefits