S-Nitrosylation inhibits the kinase activity of tomato phosphoinositide-dependent kinase 1 (PDK1)
Not Available
59 BASIC BIOLOGICAL SCIENCES↗
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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Context Dependence of Biological Circuits
It has been an ongoing scientific debate whether biological parameters are conserved across experimental setups with different media, pH values, and other experimental conditions. Our work explores this question using Bayesian probability as a rigorous framework to assess the biological context of parameters in a model of the cell growth controller in You et al. When this growth controller is uninduced, the E. coli cell population grows to carrying capacity; however, when the circuit is induced, the cell population growth is regulated to remain well below carrying capacity. This growth control controller regulates the E. coli cell population by cell to cell communication using the signaling molecule AHL and by cell death using the bacterial toxin CcdB. To evaluate the context dependence of parameters such as the cell growth rate, the carrying capacity, the AHL degradation rate, the leakiness of AHL, the leakiness of toxin CcdB, and the IPTG induction factor, we collect experimental data from the growth control circuit in two different media, at two different pH values, and with several induction levels. We define a set of possible context dependencies that describe how these parameters may differ with the experimental conditions and we develop mathematical models of the growth controller across the different experimental contexts. We then determine whether these parameters are shared across experimental contexts or whether they are context dependent. For each of these possible context dependencies, we use Bayesian inference to assess its plausibility and to estimate the parameters of the growth controller. Ultimately, we find that there is significant experimental context dependence in this circuit. Furthermore, we also find that the estimated parameter values are sensitive to our assumption of a context relationship.
59 BASIC BIOLOGICAL SCIENCES↗
Detailed study of the nuclear dependence of the EMC effect and short-range correlations
Not Available
Arrington, J.↗
Motional displacements in proteins: The origin of wave-vector-dependent values
In the case of average mean-square displacement, r 2 , of H atoms in a protein, it is frequently determined using incoherent neutron-scattering experiments. r 2 is obtained from the observed elastic incoherent dynamic structure factor, S i (Q,ω =0), assuming the form S i (Q, ω =0) =exp( -Q 2 r 2 /3). Moreover, this is often referred to as the Gaussian approximation (GA) to S i (Q, ω =0). r 2 obtained in this way depends on the value of the wave vector, Q considered. Equivalently, the observed S i (Q, ω =0) deviates from the GA. We investigate the origin of the Q dependence of r 2 by evaluating the scattering functions in different approximations using molecular dynamics (MD) simulation of the protein lysozyme. We find that keeping only the Gaussian term in a cumulant expansion of S(Q, ω ) is an accurate approximation and is not the origin of the Q dependence of r 2 . We demonstrated by showing that the term beyond the Gaussian is negligible and that the GA is valid for an individual atom in the protein. Rather, the Q dependence (deviation from the GA) arises from the dynamical heterogeneity of the H in the protein. Specifically it arises from representing, in the analysis of data, this diverse dynamics by a single average scattering center that has a single, average r 2 . The observed Q dependence of r 2 can be used to provide information on the dynamical heterogeneity in proteins.
59 BASIC BIOLOGICAL SCIENCES↗
Thickness;#8208;dependent domain wall reorientation in 70/30 lead magnesium niobate;#8208; lead titanate thin films
Abstract not provided
Keech, Ryan↗
The simulated features of heliospheric cosmic-ray modulation with a time-dependent drift model. II - On the energy dependence of the onset of new modulation in 1987
Time-dependent heliospheric cosmic-ray modulation for the period 1985-1989 is simulated by means of a time-dependent axially symmetric drift model with an emulated wavy heliospheric neutral sheet (HNS). The model is used to extend previous calculations to other energies in order to study a possible energy-dependence of the onset of new modulation at various radial distances in 1987. The model, with the outward propagating changes of the HNS as the only time-dependent parameters, is found to predict essentially no energy-dependence in the time when new modulation started in the simulated 1987. When a more practical approach in defining 'constant' modulation in 1987 is followed, the present calculations can be interpreted to indicate that the end of the recovery period in 1987 happened progressively earlier and the onset of new modulation progressively later the higher the rigidity of the cosmic rays. This period of relatively unchanged modulation is predicted to last longer with increasing radial distance.
Le Roux, J. A.↗
Time-dependent non-equilibrium dielectric response in QM/continuum approaches
The Polarizable Continuum Models (PCMs) are some of the most inexpensive yet successful methods for including the effects of solvation in quantum-mechanical calculations of molecular systems. However, when applied to the electronic excitation process, these methods are restricted to dichotomously assuming either that the solvent has completely equilibrated with the excited solute charge density (infinite-time limit), or that it retains the configuration that was in equilibrium with the solute prior to excitation (zero-time limit). This renders the traditional PCMs inappropriate for resolving time-dependent solvent effects on non-equilibrium solute electron dynamics like those implicated in the instants following photoexcitation of a solvated molecular species. To extend the existing methods to this non-equilibrium regime, we herein derive and apply a new formalism for a general time-dependent continuum embedding method designed to be propagated alongside the solute’s electronic degrees of freedom in the time domain. Given the frequency-dependent dielectric constant of the solvent, an equation of motion for the dielectric polarization is derived within the PCM framework and numerically integrated simultaneously with the time-dependent Hartree fock/density functional theory equations. Results for small molecular systems show the anticipated dipole quenching and electronic state dephasing/relaxation resulting from out-of-phase charge fluctuations in the dielectric and embedded quantum system.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Lie algebraic approach to the time-dependent quantum general harmonic oscillator and the bi-dimensional charged particle in time-dependent electromagnetic fields
We discuss the one-dimensional, time-dependent general quadratic Hamiltonian and the bi-dimensional charged particle in time-dependent electromagnetic fields through the Lie algebraic approach. Such method consists in finding a set of generators that form a closed Lie algebra in terms of which it is possible to express a quantum Hamiltonian and therefore the evolution operator. The evolution operator is then the starting point to obtain the propagator as well as the explicit form of the Heisenberg picture position and momentum operators. First, the set of generators forming a closed Lie algebra is identified for the general quadratic Hamiltonian. This algebra is later extended to study the Hamiltonian of a charged particle in electromagnetic fields exploiting the similarities between the terms of these two Hamiltonians. These results are applied to the solution of five different examples: the linear potential which is used to introduce the Lie algebraic method, a radio frequency ion trap, a Kanai–Caldirola-like forced harmonic oscillator, a charged particle in a time dependent magnetic field, and a charged particle in constant magnetic field and oscillating electric field. In particular we present exact analytical expressions that are fitting for the study of a rotating quadrupole field ion trap and magneto-transport in two-dimensional semiconductor heterostructures illuminated by microwave radiation. In these examples we show that this powerful method is suitable to treat quadratic Hamiltonians with time dependent coefficients quite efficiently yielding closed analytical expressions for the propagator and the Heisenberg picture position and momentum operators. -- Highlights: •We deal with the general quadratic Hamiltonian and a particle in electromagnetic fields. •The evolution operator is worked out through the Lie algebraic approach. •We also obtain the propagator and Heisenberg picture position and momentum operators. •Analytical expressions for a rotating quadrupole field ion trap are presented. •Exact solutions for magneto-transport in variable electromagnetic fields are shown.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Two-stream instability with time-dependent drift velocity
The classical two-stream instability driven by a constant relative drift velocity between two plasma components is extended to the case with time-dependent drift velocity. A solution method is developed to rigorously define and calculate the instability growth rate for linear perturbations relative to the time-dependent unperturbed two-stream motions. The stability diagrams for the oscillating two-stream instability are presented over a large region of parameter space. It is shown that the growth rate for the classical two-stream instability can be significantly reduced by adding an oscillatory component to the relative drift velocity.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Multi-fluid transport code modeling of time-dependent recycling in ELMy H-mode
Simulations of a high-confinement-mode (H-mode) tokamak discharge with infrequent giant type-I ELMs are performed by the multi-fluid, multi-species, two-dimensional transport code UEDGE-MB, which incorporates the Macro-Blob approach for intermittent non-diffusive transport due to filamentary coherent structures observed during the Edge Localized Modes (ELMs) and simple time-dependent multi-parametric models for cross-field plasma transport coefficients and working gas inventory in material surfaces. Temporal evolutions of pedestal plasma profiles, divertor recycling, and wall inventory in a sequence of ELMs are studied and compared to the experimental time-dependent data. Short- and long-time-scale variations of the pedestal and divertor plasmas where the ELM is described as a sequence of macro-blobs are discussed. It is shown that the ELM recovery includes the phase of relatively dense and cold post-ELM divertor plasma evolving on a several ms scale, which is set by the transport properties of H-mode barrier. The global gas balance in the discharge is also analyzed. The calculated rates of working gas deposition during each ELM and wall outgassing between ELMs are compared to the ELM particle losses from the pedestal and neutral-beam-injection fueling rate, correspondingly. A sensitivity study of the pedestal and divertor plasmas to model assumptions for gas deposition and release on material surfaces is presented. The performed simulations show that the dynamics of pedestal particle inventory is dominated by the transient intense gas deposition into the wall during each ELM followed by continuous gas release between ELMs at roughly a constant rate.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Sublinear scaling for time-dependent stochastic density functional theory
A stochastic approach to time-dependent density functional theory is developed for computing the absorption cross section and the random phase approximation (RPA) correlation energy. The core idea of the approach involves time-propagation of a small set of stochastic orbitals which are first projected on the occupied space and then propagated in time according to the time-dependent Kohn-Sham equations. The evolving electron density is exactly represented when the number of random orbitals is infinite, but even a small number (≈16) of such orbitals is enough to obtain meaningful results for absorption spectrum and the RPA correlation energy per electron. We implement the approach for silicon nanocrystals using real-space grids and find that the overall scaling of the algorithm is sublinear with computational time and memory.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Frequency-dependent polarization-angle-phase-shift in the microwave-induced magnetoresistance oscillations
Linear polarization angle, θ, dependent measurements of the microwave radiation-induced oscillatory magnetoresistance, R{sub xx}, in high mobility GaAs/AlGaAs 2D electron devices have shown a θ dependence in the oscillatory amplitude along with magnetic field, frequency, and extrema-dependent phase shifts, θ{sub 0}. Here, we suggest a microwave frequency dependence of θ{sub 0}(f) using an analysis that averages over other smaller contributions, when those contributions are smaller than estimates of the experimental uncertainty.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Growth temperature dependence of Si doping efficiency and compensating deep level defect incorporation in Al{sub 0.7}Ga{sub 0.3}N
The growth temperature dependence of Si doping efficiency and deep level defect formation was investigated for n-type Al{sub 0.7}Ga{sub 0.3}N. It was observed that dopant compensation was greatly reduced with reduced growth temperature. Deep level optical spectroscopy and lighted capacitance-voltage were used to understand the role of acceptor-like deep level defects on doping efficiency. Deep level defects were observed at 2.34 eV, 3.56 eV, and 4.74 eV below the conduction band minimum. The latter two deep levels were identified as the major compensators because the reduction in their concentrations at reduced growth temperature correlated closely with the concomitant increase in free electron concentration. Possible mechanisms for the strong growth temperature dependence of deep level formation are considered, including thermodynamically driven compensating defect formation that can arise for a semiconductor with very large band gap energy, such as Al{sub 0.7}Ga{sub 0.3}N.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Temperature-dependent optical measurements of the dominant recombination mechanisms in InAs/InAsSb type-2 superlattices
Temperature-dependent measurements of carrier recombination rates using a time-resolved optical pump-probe technique are reported for mid-wave infrared InAs/InAs{sub 1−x}Sb{sub x} type-2 superlattices (T2SLs). By engineering the layer widths and alloy compositions, a 16 K band-gap of ∼235 ± 10 meV was achieved for five unintentionally and four intentionally doped T2SLs. Carrier lifetimes were determined by fitting lifetime models based on Shockley-Read-Hall (SRH), radiative, and Auger recombination processes to the temperature and excess carrier density dependent data. The minority carrier (MC), radiative, and Auger lifetimes were observed to generally increase with increasing antimony content and decreasing layer thickness for the unintentionally doped T2SLs. The MC lifetime is limited by SRH processes at temperatures below 200 K in the unintentionally doped T2SLs. The extracted SRH defect energy levels were found to be near mid-bandgap. Also, it is observed that the MC lifetime is limited by Auger recombination in the intentionally doped T2SLs with doping levels greater than n ∼ 10{sup 16} cm{sup −3}.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Size-dependent error of the density functional theory ionization potential in vacuum and solution
Density functional theory is often the method of choice for modeling the energetics of large molecules and including explicit solvation effects. It is preferable to use a method that treats systems of different sizes and with different amounts of explicit solvent on equal footing. However, recent work suggests that approximate density functional theory has a size-dependent error in the computation of the ionization potential. We here investigate the lack of size-intensivity of the ionization potential computed with approximate density functionals in vacuum and solution. We show that local and semi-local approximations to exchange do not yield a constant ionization potential for an increasing number of identical isolated molecules in vacuum. Instead, as the number of molecules increases, the total energy required to ionize the system decreases. Rather surprisingly, we find that this is still the case in solution, whether using a polarizable continuum model or with explicit solvent that breaks the degeneracy of each solute, and we find that explicit solvent in the calculation can exacerbate the size-dependent delocalization error. We demonstrate that increasing the amount of exact exchange changes the character of the polarization of the solvent molecules; for small amounts of exact exchange the solvent molecules contribute a fraction of their electron density to the ionized electron, but for larger amounts of exact exchange they properly polarize in response to the cationic solute. In vacuum and explicit solvent, the ionization potential can be made size-intensive by optimally tuning a long-range corrected hybrid functional.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
A temperature-dependent coarse-grained model for the thermoresponsive polymer poly(N-isopropylacrylamide)
A coarse-grained (CG) model is developed for the thermoresponsive polymer poly(N-isopropylacrylamide) (PNIPAM), using a hybrid top-down and bottom-up approach. Nonbonded parameters are fit to experimental thermodynamic data following the procedures of the SDK (Shinoda, DeVane, and Klein) CG force field, with minor adjustments to provide better agreement with radial distribution functions from atomistic simulations. Bonded parameters are fit to probability distributions from atomistic simulations using multi-centered Gaussian-based potentials. The temperature-dependent potentials derived for the PNIPAM CG model in this work properly capture the coil–globule transition of PNIPAM single chains and yield a chain-length dependence consistent with atomistic simulations.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Time-dependent analysis of visible helium line-ratios for electron temperature and density diagnostic using synthetic simulations on NSTX-U
Helium line-ratios for electron temperature (T{sub e}) and density (n{sub e}) plasma diagnostic in the Scrape-Off-Layer (SOL) and edge regions of tokamaks are widely used. Due to their intensities and proximity of wavelengths, the singlet, 667.8 and 728.1 nm, and triplet, 706.5 nm, visible lines have been typically preferred. Time-dependency of the triplet line (706.5 nm) has been previously analyzed in detail by including transient effects on line-ratios during gas-puff diagnostic applications. In this work, several line-ratio combinations within each of the two spin systems are analyzed with the purpose of eliminating transient effects to extend the application of this powerful diagnostic to high temporal resolution characterization of plasmas. The analysis is done using synthetic emission modeling and diagnostic for low electron density NSTX SOL plasma conditions by several visible lines. Quasi-static equilibrium and time-dependent models are employed to evaluate transient effects of the atomic population levels that may affect the derived electron temperatures and densities as the helium gas-puff penetrates the plasma. The analysis of a wider range of spectral lines will help to extend this powerful diagnostic to experiments where the wavelength range of the measured spectra may be constrained either by limitations of the spectrometer or by other conflicting lines from different ions.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Main-sequence Scatter is Real: The Joint Dependence of Galaxy Clustering on Star Formation and Stellar Mass
We present new measurements of the clustering of stellar-mass-complete samples of ∼40,000 SDSS galaxies at z ∼ 0.03 as a joint function of stellar mass and specific star formation rate (sSFR). Our results confirm what Coil et al. find at z ∼ 0.7: galaxy clustering is a stronger function of sSFR at fixed stellar mass than of stellar mass at fixed sSFR. We also find that galaxies above the star-forming main sequence (SFMS) with higher sSFR are less clustered than galaxies below the SFMS with lower sSFR, at a given stellar mass. A similar trend is present for quiescent galaxies. This confirms that main-sequence scatter, and scatter within the quiescent sequence, is physically connected to the large-scale cosmic density field. We compare the resulting galaxy bias versus sSFR, and relative bias versus sSFR ratio, for different galaxy samples across 0 < z < 1.2 to mock galaxy catalogs based on the empirical galaxy evolution model of Behroozi et al. This model fits PRIMUS and DEEP2 clustering data well at intermediate redshift, but agreement with SDSS is not as strong. We show that increasing the correlation between galaxy SFR and halo accretion rate at z ∼ 0 in the model substantially improves agreement with SDSS data. Mock catalogs suggest that central galaxies contribute substantially to the dependence of clustering on sSFR at a given stellar mass and that the signal is not simply an effect of satellite galaxy fraction differences with sSFR. Our results are highly constraining for galaxy evolution models and show that the stellar-to-halo mass relation depends on sSFR.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗