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At least 1,171 records · Page 65

Cross-Feeding of a Toxic Metabolite in a Synthetic Lignocellulose-Degrading Microbial Community

The recalcitrance of complex organic polymers such as lignocellulose is one of the major obstacles to sustainable energy production from plant biomass, and the generation of toxic intermediates can negatively impact the efficiency of microbial lignocellulose degradation. Here, we describe the development of a model microbial consortium for studying lignocellulose degradation, with the specific goal of mitigating the production of the toxin formaldehyde during the breakdown of methoxylated aromatic compounds. Included are Pseudomonas putida, a lignin degrader; Cellulomonas fimi, a cellulose degrader; and sometimes Yarrowia lipolytica, an oleaginous yeast. Unique to our system is the inclusion of Methylorubrum extorquens, a methylotroph capable of using formaldehyde for growth. We developed a defined minimal “Model Lignocellulose” growth medium for reproducible coculture experiments. We demonstrated that the formaldehyde produced by P. putida growing on vanillic acid can exceed the minimum inhibitory concentration for C. fimi, and, furthermore, that the presence of M. extorquens lowers those concentrations. We also uncovered unexpected ecological dynamics, including resource competition, and interspecies differences in growth requirements and toxin sensitivities. Finally, we introduced the possibility for a mutualistic interaction between C. fimi and M. extorquens through metabolite exchange. This study lays the foundation to enable future work incorporating metabolomic analysis and modeling, genetic engineering, and laboratory evolution, on a model system that is appropriate both for fundamental eco-evolutionary studies and for the optimization of efficiency and yield in microbially-mediated biomass transformation.

Methylorubrum extorquens↗

Exclusive dielectron production in ultraperipheral Pb+Pb collisions at $\sqrt{s_{\textrm{NN}}}$ = 5.02 TeV with ATLAS

Exclusive production of dielectron pairs, γγ → e + e – , is studied using $\mathcal{L}_{int}$ = 1.72 nb –1 of data from ultraperipheral collisions of lead nuclei at $\sqrt{s_{NN}}$ = 5.02 TeV recorded by the ATLAS detector at the LHC. The process of interest proceeds via photon–photon interactions in the strong electromagnetic fields of relativistic lead nuclei. Dielectron production is measured in the fiducial region defined by following requirements: electron transverse momentum $p^{e}_{T}$ > 2.5 GeV, absolute electron pseudorapidity |η e | < 2.5, dielectron invariant mass m ee > 5 GeV, and dielectron transverse momentum $p^{ee}_{T}$ < 2 GeV. Differential cross-sections are measured as a function of m ee , average $p^{e}_{T}$, absolute dielectron rapidity |y ee |, and scattering angle in the dielectron rest frame, |cos θ*|, in the inclusive sample, and also with a requirement of no activity in the forward direction. The total integrated fiducial cross-section is measured to be 215 ± 1 (stat) $^{+23}_{-20}$ (syst.) ± 4 (lumi.) μ b. Within experimental uncertainties the measured integrated cross-section is in good agreement with the QED predictions from the Monte Carlo programs STARLIGHT and SUPERCHIC, confirming the broad features of the initial photon fluxes. The differential cross-sections show systematic differences from these predictions which are more pronounced at high |y ee | and |cos θ*| values.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Spin densities from subsystem density-functional theory: Assessment and application to a photosynthetic reaction center complex model

Subsystem density-functional theory (DFT) is a powerful and efficient alternative to Kohn-Sham DFT for large systems composed of several weakly interacting subunits. Here, we provide a systematic investigation of the spin-density distributions obtained in subsystem DFT calculations for radicals in explicit environments. This includes a small radical in a solvent shell, a {pi}-stacked guanine-thymine radical cation, and a benchmark application to a model for the special pair radical cation, which is a dimer of bacteriochlorophyll pigments, from the photosynthetic reaction center of purple bacteria. We investigate the differences in the spin densities resulting from subsystem DFT and Kohn-Sham DFT calculations. In these comparisons, we focus on the problem of overdelocalization of spin densities due to the self-interaction error in DFT. It is demonstrated that subsystem DFT can reduce this problem, while it still allows to describe spin-polarization effects crossing the boundaries of the subsystems. In practical calculations of spin densities for radicals in a given environment, it may thus be a pragmatic alternative to Kohn-Sham DFT calculations. In our calculation on the special pair radical cation, we show that the coordinating histidine residues reduce the spin-density asymmetry between the two halves of this system, while inclusion of a larger binding pocket model increases this asymmetry. The unidirectional energy transfer in photosynthetic reaction centers is related to the asymmetry introduced by the protein environment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Electronic structure and lattice dynamics of 1⁢𝑇−VSe 2 : Origin of the three-dimensional charge density wave

To characterize in detail the charge density wave (CDW) transition of 1⁢𝑇−VSe 2 , its electronic structure and lattice dynamics are comprehensively studied by means of x-ray diffraction, muon spectroscopy, angle resolved photoemission (ARPES), diffuse and inelastic x-ray scattering, and state-of-the-art first-principles density functional theory calculations. Resonant elastic x-ray scattering does not show any resonant enhancement at either V or Se, indicating that the CDW peak at the 𝐾 edges describes a purely structural modulation of the electronic ordering. ARPES experiments identify (i) a pseudogap at 𝑇 > 𝑇⁢ CDW , which leads to a depletion of the density of states in the ML-M'L' plane at 𝑇 < 𝑇⁢ CDW , and (ii) anomalies in the electronic dispersion reflecting a sizable impact of phonons on it. A diffuse scattering precursor, characteristic of soft phonons, is observed at room temperature (RT) and leads to the full collapse of the low-energy phonon (𝜔 1 ) with propagation vector (0.25 0 −0.3) r.l.u. Here, we show that the frequency and linewidth of this mode are anisotropic in momentum space, reflecting the momentum dependence of the electron-phonon interaction (EPI), hence demonstrating that the origin of the CDW is, to a much larger extent, due to the momentum dependent EPI with a small contribution from nesting. The pressure dependence of the 𝜔 1 soft mode remains nearly constant up to 13 GPa at RT, with only a modest softening before the transition to the high-pressure monoclinic C2/m phase. The wide set of experimental data is well captured by our state-of-the art first-principles anharmonic calculations with the inclusion of van der Waals corrections in the exchange-correlation functional. The comprehensive description of the electronic and dynamical properties of VSe 2 reported here adds important pieces of information to the understanding of the electronic modulations in the family of transition-metal dichalcogenides.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Open charm production in double parton scattering processes in the forward kinematics

We calculate the rate of double open charm production in the forward kinematics studied recently in the LHCb experiment.We find that the mean field approximation for the double partonGPD (generalized parton distributions), which neglects parton–parton correlations, underestimates the rate by a factor of 2. The enhancement due to the perturbative QCD correlation 1Ⓧ2 mechanism which explains the rate of double parton interactions at the central rapidities is found to explain 60 ÷ 80% of the discrepancy. We argue that the nonperturbative fluctuations leading to nonfactorized (correlated) contributions to the initial conditions for the DGLAP collinear evolution of the double parton GPD play an important role in this kinematics. Combined, the two correlation mechanisms provide a good description of the rate of double charm production reported by the LHCb. We also give predictions for the variation of the σeff (i.e. the ratio of double and square of single inclusive rates) in the discussed kinematics as a function of pt . The account for two correlation mechanisms strongly reduces the sensitivity of the results to the starting point of the QCD evolution.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Graphene composite for improvement in the conversion efficiency of flexible poly 3-hexyl-thiophene:[6,6]-phenyl C{sub 71} butyric acid methyl ester polymer solar cells

The solution of thin graphene-sheets obtained from a simple ultrasonic exfoliation process was found to chemically interact with [6,6]-phenyl C{sub 71} butyric acid methyl ester (PCBM) molecules. The thinner graphene-sheets have significantly altered the positions of highest occupied molecular orbital and lowest unoccupied molecular orbital of PCBM, which is beneficial for the enhancement of the open circuit voltage of the solar cells. Flexible bulk heterojunction solar cells fabricated using poly 3-hexylthiophene (P3HT):PCBM-graphene exhibited a power conversion efficiency of 2.51%, which is a ∼2-fold increase as compared to those fabricated using P3HT:PCBM. Inclusion of graphene-sheets not only improved the open-circuit voltage but also enhanced the short-circuit current density owing to an improved electron transport.

36 MATERIALS SCIENCE↗

Hadronization of quarks and correlated di-hadron production in hard scattering

Understanding the dynamics of partons in general, and non perturbative sea, in particular, will be crucial for the understanding of strong interactions. Correlations of the spin of the target or/and the momentum and the spin of quarks, combined with final state interactions define the azimuthal distributions of produced particles. Production of correlated hadron pairs, in addition, will play an increasingly important role in the interpretation of pion electroproduction data in general, and hadronization process of quarks, in particular. More significant, than originaly anticipated, fraction of pions coming from correlated di-hadrons, indicated by recent CLAS12 measurements, and supported by various realistic models describing the hadronization process, may have a significant impact on various aspects of data analysis, including the modeling, composition, and interpretation of semi-inclusive DIS data, as well as calculations of radiative corrections. Studies of the nucleon structure beyond the traditional leading twist and current fragmentation of inclusive hadrons, provide qualitatively new tools to study the nucleon structure and extension of large x region well covered by JLab, to large Q2 at the EIC where it will be very important in interpretation of the data from JLab.

Avakian, Harut↗

Package for Interactive Analysis of Line Emission (Analysis of UV-X-Ray High-Resolution Emission Spectra)

PINTofALE is an IDL based package to analyze high-resolution grating spectra. The first version was made available to the public on 3 February 2001. Since then we have carried out numerous changes, and the current release is version 1.5, released on 9 October 2002. The changes include upgrades to handle higher versions of IDL, the new version of the CHIANTI database (v4), major enhancements in user-friendliness, improved handling of response matrices, the ability to handle 24-bit color, access to the Atomic Plasma Emission Database (APED), and beta releases of Markov Chain Monte Carlo (MCMC) based DEM fitting routines. Plans for the future include: inclusion of MCMC techniques in the fitting programs, enhanced graphics capabilities, an overhaul of the line and continuum database structure, and bug fixes. In September 2002, we hired a data analyst (LiWei Lin) to work on PINTofALE. Mr.Lin is concentrating on incorporating MCMC as well as simpler Monte-Carlo techniques, fast RMF convolution, etc., into the code base, as well as reviewing the existing documentation and searching for bugs. A detailed description of the package, together with fairly detailed documentation, example walks-throughs, and downloadable tar files, are available on-line from http://hea-www. harvard.edu/PINTofALE/

Kashyap, Vinay↗

Impact of boundary layer simulation on predicting radioactive pollutant dispersion: a case study for HANARO Research Reactor using the WRF-MMIF-CALPUFF modeling system

Wind plays an important role in cases of unexpected radioactive pollutant dispersion, deciding distribution and concentration of the leaked substance. The accurate prediction of wind has been challenging in numerical weather prediction models, especially near the surface because of the complex interaction between turbulent flow and topographic effect. As such, in this study, we investigated the characteristics of atmospheric dispersion of radioactive material (i.e. 137 Cs) according to the simulated boundary layer around the HANARO research nuclear reactor in Korea using the Weather Research and Forecasting (WRF)-Mesoscale Model Interface (MMIF)-California Puff (CALPUFF) model system. We examined the impacts of orographic drag on wind field, stability calculation methods, and planetary boundary layer parameterizations on the dispersion of radioactive material under a radioactive leaking scenario. We found that inclusion of the orographic drag effect in the WRF model improved the wind prediction most significantly over the complex terrain area, leading the model system to estimate the radioactive concentration near the reactor more conservatively. We also emphasized the importance of the stability calculation method and employing the skillful boundary layer parameterization to ensure more accurate low atmospheric conditions, in order to simulate more feasible spatial distribution of the radioactive dispersion in leaking scenarios.

54 ENVIRONMENTAL SCIENCES↗

Polarization Effects in Water-Mediated Selective Cation Transport across a Narrow Transmembrane Channel

We report despite the progress in modeling complex molecular systems of ever-increasing complexity, a quantitatively accurate computational treatment of ion permeation through narrow membrane channels remains challenging. An important factor to reach this goal is induced electronic polarization, which is likely to impact the permeation rate of small ions through narrow molecular pores. In this work, we extended the recently developed polarizable force field based on the classical Drude oscillators to assess the role of induced polarization effects on the energetics of sodium and potassium ion transport across the gramicidin A (gA) ion channel. The inclusion of induced polarization lowers barriers present in 1D potential of mean force (PMF) for cation permeation by ~50% compared to those obtained with the additive force field. Conductance properties calculated with 1D PMFs from Drude simulations are in better agreement with experimental results. Polarization of single-file water molecules and protein atoms forming the narrow pore has a direct impact on the free-energy barriers and cation-specific solid-state NMR chemical shifts. Sensitivity analysis indicates that small changes to water–channel interactions can alter the free energy barrier for ion permeation. These results, illustrating polarization effects present in the complex electrostatic environment of the gA channel, have broad implications for revising proposed mechanisms of ion permeation and selectivity in a variety of ion channels.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Aspects of renormalization in finite-density field theory

We study the renormalization of the Fermi surface coupled to a massless boson near three spatial dimensions. For this, we set up a Wilsonian RG with independent decimation procedures for bosons and fermions, where the four-fermion interaction “Landau parameters” run already at tree level. Our explicit one-loop analysis resolves previously found obstacles in the renormalization of finite-density field theory, including logarithmic divergences in nonlocal interactions and the appearance of multilogarithms. The key aspects of the RG are the above tree-level running, and a UV-IR mixing between virtual bosons and fermions at the quantum level, which is responsible for the renormalization of the Fermi velocity. We apply this approach to the renormalization of 2 k F singularities, and to Fermi surface instabilities in a companion paper, showing how multilogarithms are properly renormalized. We end with some comments on the renormalization of finite-density field theory with the inclusion of Landau damping of the boson.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

On the Role of Global Magnetic Field Configuration in Affecting Ring Current Dynamics

Plasma and field interaction is one important aspect of inner magnetospheric physics. The magnetic field controls particle motion through gradient, curvature drifts and E cross B drift. In this presentation, we show how the global magnetic field affects dynamics of the ring current through simulations of two moderate geomagnetic storms (20 November 2007 and 8-9 March 2008). Preliminary results of coupling the Comprehensive Ring Current Model (CRCM) with a three-dimensional plasma force balance code (to achieve self-consistency in both E and B fields) indicate that inclusion of self-consistency in B tends to mitigate the intensification of the ring current as other similar coupling efforts have shown. In our approach, self-consistency in the electric field is already an existing capability of the CRCM. The magnetic self-consistency is achieved by computing the three-dimensional magnetic field in force balance with anisotropic ring current ion distributions. We discuss the coupling methodology and its further improvement. In addition, comparative studies by using various magnetic field models will be shown. Simulation results will be put into a global context by analyzing the morphology of the ring current, its anisotropy and characteristics ofthe interconnected region 2 field-aligned currents.

Zheng, Y.↗

Can Aerosol Direct Radiative Effects Account for Analysis Increments of Temperature in the Tropical Atlantic?

In the late 1990's, prior to the launch of the Terra satellite, atmospheric general circulation models (GCMs) did not include aerosol processes because aerosols were not properly monitored on a global scale and their spatial distributions were not known well enough for their incorporation in operational GCMs. At the time of the first GEOS Reanalysis (Schubert et al. 1993), long time series of analysis increments (the corrections to the atmospheric state by all available meteorological observations) became readily available, enabling detailed analysis of the GEOS-1 errors on a global scale. Such analysis revealed that temperature biases were particularly pronounced in the Tropical Atlantic region, with patterns depicting a remarkable similarity to dust plumes emanating from the African continent as evidenced by TOMS aerosol index maps. Yoram Kaufman was instrumental encouraging us to pursue this issue further, resulting in the study reported in Alpert et al. (1998) where we attempted to assess aerosol forcing by studying the errors of a the GEOS-1 GCM without aerosol physics within a data assimilation system. Based on this analysis, Alpert et al. (1998) put forward that dust aerosols are an important source of inaccuracies in numerical weather-prediction models in the Tropical Atlantic region, although a direct verification of this hypothesis was not possible back then. Nearly 20 years later, numerical prediction models have increased in resolution and complexity of physical parameterizations, including the representation of aerosols and their interactions with the circulation. Moreover, with the advent of NASA's EOS program and subsequent satellites, atmospheric aerosols are now monitored globally on a routine basis, and their assimilation in global models are becoming well established. In this talk we will reexamine the Alpert et al. (1998) hypothesis using the most recent version of the GEOS-5 Data Assimilation System with assimilation of aerosols. We will explicitly calculate the impact of aerosols on the temperature analysis increments in the tropical Atlantic and assess the extent to which inclusion of atmospheric aerosols have reduced these increments.

General Circulation Models↗

Tracing Nebular Reservoirs and Processes Via In-situ Trace Element Analyses of Chondrule Rims in Allende

Introduction: Layered rims of dust-sized material surround some chondrules and other early formed nebular particles, such as calcium aluminum inclusions in chondritic meteorites. Most chondrules (~85%) in the Allende meteorite (CV3) are un-rimmed and in direct contact with the host material or matrix. For the 15% of rimmed particles, rim thickness is correlated to the underlying particle size, arguing for pre-parent body formation of rimmed particles as they traversed distinct (cooler and/or dustier) nebular environments. Nebular rim formation involves accretion of unequilibrated dust to chondrule surfaces, recording evidence for the formation of at least two separate particle populations (chondrules and dust) that interacted in the nebula, and therefore potentially record distinct nebular reservoirs.

J B Setera↗

Quantifying Turbine-Level Risk to Golden Eagles Using a High-Fidelity Updraft Model and a Stochastic Behavioral Model

To minimize the effects of wind farms on Golden Eagle (Aquila chrysaetos) populations while enabling sustainable development of renewable energy resources, it is important to understand how eagles interact with atmospheric flows, terrain features, and anthropogenic structures. Models that predict migratory flight paths provide one tool that helps us grasp how the location of wind farms may influence interactions and impacts on migrating Golden Eagles. The current state-of-the-art in predicting migratory flight paths uses a deterministic fluid-flow analogy to predict eagle trajectory using only an orographic updraft potential computed from topographical features. This model does not take into account variables, such as thermal updrafts and time varying atmospheric conditions that are known to influence migratory behavior. In this work, we improve on the model with the objective of developing tools that advance our understanding of how atmospheric flows and terrain features affect migratory eagle behavior and their interactions with wind farms. Specifically, we 1) incorporate both orographic and thermal updraft information in simulating eagle flight paths; 2) incorporate stochasticity into eagle travel patterns to better capture the influence of exogenous factors on, and the inherent stochasticity of eagle behavior; 3) consider spatio-temporal atmospheric data at wind-farm-scale when computing updraft potential; and 4) account for how atmospheric conditions and the direction of migration change seasonally and how these changes affect eagle migratory flight behavior. We tested the model using a 50km by 50km region with 50 m resolution in the western United States. We simulated 900 independent, probabilistic eagle tracks during southerly and northerly migration, assuming eagles solely rely on orographic updrafts. The preliminary results indicate that the inclusion of finer resolution atmospheric data allows for the inclusion of realistic conditions that an eagle experiences. The stochasticity in eagle tracks provides a platform to include uncertainty in eagle decision making and help produce robust eagle presence maps. We will deploy updraft and downdraft velocities computed using a high-fidelity, wind farm scale, computational fluid dynamics solver under development at National Renewable Energy Laboratory. This work is a first step in the development of a predictive and generalizable eagle behavior model at the wind farm scale that does not rely on empirical data collection. Although the current model is intended for migratory eagles, we will extend and refine this model to inform the development of additional behavioral modes, including resident eagle behavior. This modeling approach improves our ability to understand eagle use of the landscape at a fine scale, and it is our hope that this work will ultimately help advance strategies that minimize the impact of wind development on Golden Eagle populations.

49 EE - Wind and Water Power Program - Wind (EE-4W↗

Measurements of W + W - + ≥ 1 jet production cross-sections in pp collisions at $ \sqrt{s} $ = 13 TeV with the ATLAS detector

Fiducial and differential cross-section measurements of W + W - production in association with at least one hadronic jet are presented. These measurements are sensitive to the properties of electroweak-boson self-interactions and provide a test of perturbative quantum chromodynamics and the electroweak theory. The analysis is performed using proton-proton collision data collected at $ \sqrt{s} $ = 13 TeV with the ATLAS experiment, corresponding to an integrated luminosity of 139 fb -1 . Events are selected with exactly one oppositely charged electron-muon pair and at least one hadronic jet with a transverse momentum of p T > 30 GeV and a pseudorapidity of |η| < 4.5. After subtracting the background contributions and correcting for detector effects, the jet-inclusive W + W - + ≥ 1 jet fiducial cross-section and W + W - + jets differential cross-sections with respect to several kinematic variables are measured. These measurements include leptonic quantities, such as the lepton transverse momenta and the transverse mass of the W + W - system, as well as jet-related observables such as the leading jet transverse momentum and the jet multiplicity. Limits on anomalous triple-gauge-boson couplings are obtained in a phase space where interference between the Standard Model amplitude and the anomalous amplitude is enhanced.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Understanding the Origins of Time-Dependent Inhibition by Polypeptide Deformylase Inhibitors

The continual bacterial adaptation to antibiotics creates an ongoing medical need for the development of novel therapeutics. Polypeptide deformylase (PDF) is a highly conserved bacterial enzyme, which is essential for viability. It has previously been shown that PDF inhibitors represent a promising new area for the development of antimicrobial agents, and that many of the best PDF inhibitors demonstrate slow, time-dependent binding. To improve our understanding of the mechanistic origin of this time-dependent inhibition, we examined in detail the kinetics of PDF catalysis and inhibition by several different PDF inhibitors. Varying pH and solvent isotope led to clear changes in time-dependent inhibition parameters, as did inclusion of NaCl, which binds to the active site metal of PDF. Quantitative analysis of these results demonstrated that the observed time dependence arises from slow binding of the inhibitors to the active site metal. However, we also found several metal binding inhibitors that exhibited rapid, non-time-dependent onset of inhibition. By a combination of structural and chemical modification studies, we show that metal binding is only slow when the rest of the inhibitor makes optimal hydrogen bonds within the subsites of PDF. Both of these interactions between the inhibitor and enzyme were found to be necessary to observe time-dependent inhibition, as elimination of either leads to its loss.

08 HYDROGEN↗

Computer Simulation of Electron Thermalization in CsI and CsI(Tl)

A Monte Carlo (MC) model was developed and implemented to simulate the thermalization of electrons in inorganic scintillator materials. The model incorporates electron scattering with both longitudinal optical and acoustic phonons. In this paper, the MC model was applied to simulate electron thermalization in CsI, both pure and doped with a range of thallium concentrations. The inclusion of internal electric fields was shown to increase the fraction of recombined electron-hole pairs and to broaden the thermalization distance and thermalization time distributions. The MC simulations indicate that electron thermalization, following {gamma}-ray excitation, takes place within approximately 10 ps in CsI and that electrons can travel distances up to several hundreds of nanometers. Electron thermalization was studied for a range of incident {gamma}-ray energies using electron-hole pair spatial distributions generated by the MC code NWEGRIM (NorthWest Electron and Gamma Ray Interaction in Matter). These simulations revealed that the partition of thermalized electrons between different species (e.g., recombined with self-trapped holes or trapped at thallium sites) vary with the incident energy. Implications for the phenomenon of nonlinearity in scintillator light yield are discussed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗