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DOE OSTI2025

Specificity and tunability of efflux pumps: A new role for the proton gradient?

Efflux pumps that transport antibacterial drugs out of bacterial cells have broad specificity, commonly leading to broad spectrum resistance and limiting treatment strategies for infections. It remains unclear how efflux pumps can maintain this broad spectrum specificity to diverse drug molecules while limiting the efflux of other cytoplasmic content. We have investigated the origins of this broad specificity using theoretical models informed by the experimentally determined structural and kinetic properties of efflux pumps. We developed a set of mathematical models describing operation of efflux pumps as a discrete cyclic stochastic process across a network of states characterizing pump conformations and the presence/absence of bound ligands and protons. These include a minimal three-state model that lends itself to clear analytic calculations as well as a five-state model that relaxes some of the simpler model’s most strict assumptions. We found that the pump specificity is determined not solely by the drug affinity to the pump–as is commonly assumed–but it is also directly affected by the periplasmic pH and the transmembrane potential. Therefore, changes to the proton concentration gradient and voltage drop across the membrane can influence how effective the pump is at extruding a particular drug molecule. Furthermore, we found that while both the proton concentration gradient across the membrane and the transmembrane potential contribute to the thermodynamic force driving the pump, their effects on the efflux enter not strictly in a combined proton motive force. Rather, they have two distinguishable effects on the overall throughput. These results highlight the unexpected effects of thermodynamic driving forces out of equilibrium and illustrate how efflux pump structure and function are conducive to the emergence of multidrug resistance.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1974

Calculation of turbulent shear stress in supersonic boundary layer flows

An analysis of turbulent boundary layer flow characteristics and the computational procedure used are discussed. The integrated mass and momentum flux profiles and differentials of the integral quantities are used in the computations so that local evaluation of the streamwise velocity gradient is not necessary. The computed results are compared with measured shear stress data obtained by using hot wire anemometer and laser velocimeter techniques. The flow measurements were made upstream and downstream of an adiabatic unseparated interaction of an oblique shock wave with the turbulent boundary layer on the flat wall of a two dimensional wind tunnel. A comparison of the numerical analysis and actual measurements is made and the effects of small differences in mean flow profiles on the computed shear stress distributions are discussed.

Sun, C. C.↗

DOE OSTI2022

Accurate parameterization of the kinetic energy functional for calculations using exact-exchange

In this report, electronic structure calculations based on Kohn-Sham density functional theory (KSDFT) that incorporate exact exchange or hybrid functionals are associated with large computational expense, a consequence of the inherent cubic scaling bottleneck and large associated prefactor, which limits the length and time scales that can be accessed. Though orbital-free density functional theory (OFDFT) calculations scale linearly with system size and are associated with significantly smaller prefactor, they are limited by the absence of accurate density-dependent kinetic energy functionals. Therefore, the development of accurate density-dependent kinetic energy functionals is important for OFDFT calculations of large realistic systems. To this end, we propose a method to train kinetic energy functional models at the exact-exchange level of theory by using a dictionary of physically relevant terms that have been proposed in the literature in conjunction with linear or nonlinear regression methods to obtain the fitting coefficients. For our dictionary, we use gradient expansion of the kinetic energy, nonlocal models proposed in the literature and their nonlinear combinations, such as a model that incorporates spatial correlations between higher order derivatives of electron density at two points. The predictive capabilities of these models are assessed by using a variety of model one-dimensional systems that exhibit diverse bonding characteristics, such as a chain of eight hydrogens, LiF, LiH, C 4 H 2 , C 4 N 2 and C 3 O 2 . We show that by using data from model one-dimensional KSDFT calculations performed using the exact-exchange functional for only a few neutral structures, it is possible to generate models with high accuracy for charged systems as well as electron and kinetic energy densities during self-consistent field iterations. In addition, we show that it possible to learn both the orbital dependent terms, i.e., the kinetic energy and the exact-exchange energy, and models that incorporate additional nonlinearities in spatial correlations, such as a quadratic model, are needed to capture subtle features of the kinetic energy density that are present in exact-exchange-based KSDFT calculations.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2018

Prediction of Half-Metallic Properties in Non-transition Metal-based Binary Compounds X Bi (X = Ba, Sr and Ca) with Zinc-Blende and Wurtzite Structures

In this study, structural, electronic and magnetic properties of non-transition metal-based binary compounds X Bi (X = Ba, Sr and Ca) in five different phases: rock salt, NiAs, wurtzite, zinc blende and CsCl, are investigated in order to find new sp magnetic materials used for real spintronic and other related applications. The calculations are performed by a developed full-potential augmented plane wave plus local orbitals (FP-L/APW + lo) method within the spin density functional theory. As exchange-correlation potential, we used the generalized gradient approximation of Perdew, Burke, and Ernzerhof (GGA-PBE) and the modified Becke-Johnson potential mBJ-GGA-PBE form. It is found that the magnetic moment in these compounds is mainly contributed by the spin-polarized p orbitals of Bi atoms. The WZ XBi are true half-metallic ferromagnet with opposite spin direction at Fermi energy having a magnetic moment of 2.00 μ B per formula unit.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2016

Analysis of the presence of perfluoroalkyl substances in water, sediment and biota of the Jucar River (E Spain). Sources, partitioning and relationships with water physical characteristics

The presence, sources and partitioning of 21 perfluoroalkyl substances (PFASs: C4–C14, C16, C18 carboxylate, C4, C6–C10 sulfonates and C8 sulfonamide) were assessed in water, sediment, and biota of the Jucar River basin (E Spain). Considering the three matrices, perfluoropentanoate (PFPeA) and perfluorooctane sulfonate (PFOS) were the most frequent compounds, being remarkable the high occurrence of short-chain PFASs (C≤8), which are intended to replace the long-chain ones in several industrial and commercial applications. In general, all samples were contaminated with at least one PFAS, with the exception of three fish samples. Mean concentrations detected in sediments (0.22–11.5 ng g{sup −1}) and biota (0.63–274 µg kg{sup −1}) samples were higher than those measured in water (0.04–83.1 ng L{sup −1}), which might suggest (bio) accumulation. The occurrence of PFAS is related to urban and industrial discharges (Cuenca city in the upper part of basin, and car's factory, and effluents of the sewage treatment plant (STP) of Alzira, in the lower part). Increasing pollution gradients were found. On the other hand, higher contamination levels were observed after regulation dams of the catchment pointing out their importance in the re-distribution of these contaminants. None of the hazard quotients (HQ) calculated indicate potential risk for the different tropic levels considered (algae, Daphnia sp. and fish). PFAS concentrations found in this study can be considered in acceptable levels if compared to existing Regulatory Legislation and, consequently, they do not pose an immediate human health risk. - Highlights: • Distribution of 21 PFASs in water, sediment, biota of Jucar River is established. • PFPeA and PFOS are the predominant but high PFDA levels are related to industry. • PFASs in water and sediment related to the increase in NaCl, conductivity and TDS. • PFAS concentration in sediment/biota suggests (bio)accumulation. • None of the calculated HQs indicate potential risk for the different tropic levels.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2014

Analytic derivative couplings for spin-flip configuration interaction singles and spin-flip time-dependent density functional theory

We revisit the calculation of analytic derivative couplings for configuration interaction singles (CIS), and derive and implement these couplings for its spin-flip variant for the first time. Our algorithm is closely related to the CIS analytic energy gradient algorithm and should be straightforward to implement in any quantum chemistry code that has CIS analytic energy gradients. The additional cost of evaluating the derivative couplings is small in comparison to the cost of evaluating the gradients for the two electronic states in question. Incorporation of an exchange-correlation term provides an ad hoc extension of this formalism to time-dependent density functional theory within the Tamm-Dancoff approximation, without the need to invoke quadratic response theory or evaluate third derivatives of the exchange-correlation functional. Application to several different conical intersections in ethylene demonstrates that minimum-energy crossing points along conical seams can be located at substantially reduced cost when analytic derivative couplings are employed, as compared to use of a branching-plane updating algorithm that does not require these couplings. Application to H{sub 3} near its D{sub 3h} geometry demonstrates that correct topology is obtained in the vicinity of a conical intersection involving a degenerate ground state.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2016

Investigation of structural, electronic, elastic and optical properties of Cd{sub 1-x-y}Zn{sub x}Hg{sub y}Te alloys

Structural, optical and electronic properties and elastic constants of Cd1{sub -x-y}Zn{sub x} Hg{sub y}Te alloys have been studied by employing the commercial code Castep based on density functional theory. The generalized gradient approximation and local density approximation were utilized as exchange correlation. Using elastic constants for compounds, bulk modulus, band gap, Fermi energy and Kramers–Kronig relations, dielectric constants and the refractive index have been found through calculations. Apart from these, X-ray measurements revealed elastic constants and Vegard’s law. It is seen that results obtained from theory and experiments are all in agreement.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2026

Validation of the GFS model for gyrokinetic stability of NSTX pedestal data

This study presents a large database validation of the gyro fluid system (GFS) model for linear gyrokinetic stability for high-mode (H-mode) edge transport barrier conditions in the national spherical torus experiment (NSTX) tokamak. The database of linear stability calculations with the CGYRO gyrokinetic code was produced using plasma profile measurements from NSTX discharges to identify kinetic ballooning modes (KBM), trapped electron modes (TEM), and micro-tearing modes (MTM) that limit the pressure profile gradient in the H-mode barrier. A novel Bayesian optimization approach determines optimal resolution parameters for GFS specifically for spherical tokamak pedestal conditions. Our results demonstrate that GFS, with optimized resolution, can achieve accurate linear stability analysis in NSTX pedestal conditions for reduced resolution compared to CGYRO. GFS can accurately find the KBM, TEM, and MTM instability branches. Parametric analysis reveals that GFS accuracy in this extreme pedestal parameter range is degraded for low magnetic shear and near the separatrix conditions. These findings establish GFS as a fast linear eigenmode solver for spherical tokamak pedestal gyrokinetic stability and demonstrate a systematic methodology for determining the optimum resolution settings.

Yang, Minglei [Oak Ridge National Laboratory (ORNL↗

DOE OSTI2013

LINE PROFILES OF CORES WITHIN CLUSTERS. II. SIGNATURES OF DYNAMICAL COLLAPSE DURING HIGH-MASS STAR FORMATION

Observations of atomic or molecular lines can provide important information about the physical state of star-forming regions. In order to investigate the line profiles from dynamical collapsing massive star-forming regions (MSFRs), we model the emission from hydrodynamic simulations of a collapsing cloud in the absence of outflows. By performing radiative transfer calculations, we compute the optically thick HCO{sup +} and optically thin N{sub 2}H{sup +} line profiles from two collapsing regions at different epochs. Due to large-scale collapse, the MSFRs have large velocity gradients, reaching up to 20 km s{sup -1} pc{sup -1} across the central core. The optically thin lines typically contain multiple velocity components resulting from the superposition of numerous density peaks along the line of sight. The optically thick lines are only marginally shifted to the blue side of the optically thin line profiles, and frequently do not have a central depression in their profiles due to self-absorption. As the regions evolve, the lines become brighter and the optically thick lines become broader. The lower-order HCO{sup +} (1-0) transitions are better indicators of collapse than the higher-order (4-3) transitions. We also investigate how the beam sizes affect profile shapes. Smaller beams lead to brighter and narrower lines that are more skewed to the blue in HCO{sup +} relative to the true core velocity, but show multiple components in N{sub 2}H{sup +}. High-resolution observations (e.g., with Atacama Large Millimeter Array) can test these predictions and provide insights into the nature of MSFRs.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2014

The compactness of presupernova stellar cores

The success or failure of the neutrino-transport mechanism for producing a supernova in an evolved massive star is known to be sensitive not only to the mass of the iron core that collapses, but also to the density gradient in the silicon and oxygen shells surrounding that core. Here we study the systematics of a presupernova core's 'compactness' as a function of the mass of the star and the physics used in its calculation. Fine-meshed surveys of presupernova evolution are calculated for stars from 15 to 65 M {sub ☉}. The metallicity and the efficiency of semiconvection and overshoot mixing are both varied and bare carbon-oxygen cores are explored as well as full hydrogenic stars. Two different codes, KEPLER and MESA, are used for the study. A complex interplay of carbon and oxygen burning, especially in shells, can cause rapid variations in the compactness for stars of very nearly the same mass. On larger scales, the distribution of compactness with main sequence mass is found to be robustly non-monotonic, implying islands of 'explodabilty,' particularly around 8-20 M {sub ☉} and 25-30 M {sub ☉}. The carbon-oxygen (CO) core mass of a presupernova star is a better, (though still ambiguous) discriminant of its core structure than the main sequence mass.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

Many-Body Effects in FeN4 Center Embedded in Graphene

We introduce a computational approach to study porphyrin-like transition metal complexes, bridging density functional theory and exact many-body techniques, such as the density matrix renormalization group (DMRG). We first derive a multi-orbital Anderson impurity Hamiltonian starting from first principles considerations that qualitatively reproduce generalized gradient approximation (GGA)+U results when ignoring inter-orbital Coulomb repulsion U ′ and Hund exchange J. An exact canonical transformation is used to reduce the dimensionality of the problem and make it amenable to DMRG calculations, including all many-body terms (both intra- and inter-orbital), which are treated in a numerically exact way. We apply this technique to FeN 4 centers in graphene and show that the inclusion of these terms has dramatic effects: as the iron orbitals become single occupied due to the Coulomb repulsion, the inter-orbital interaction further reduces the occupation, yielding a non-monotonic behavior of the magnetic moment as a function of the interactions, with maximum polarization only in a small window at intermediate values of the parameters. Furthermore, U ′ changes the relative position of the peaks in the density of states, particularly on the iron d z 2 orbital, which is expected to affect the binding of ligands greatly.

36 MATERIALS SCIENCE↗

NASA NTRS1975

Instability of a gravity gradient satellite due to thermal distortion

A nonlinear analytical model and a corresponding computer program were developed to study the influence of solar heating on the anomalous low frequency, orbital instability of the Naval Research Laboratory's gravity gradient satellite 164. The model's formulation was based on a quasi-static approach in which deflections of the satellite's booms were determined in terms of thermally induced bending without consideration of boom vibration. Calculations, which were made for variations in absorptivity, sun angle, thermal lag, and hinge stiffness, demonstrated that, within the confines of a relatively narrow stability criteria, the quasi-static model of NRL 164 not only becomes unstable, but, in a number of cases, responses were computed that closely resembled flight data.

Goldman, R. L.↗

NASA NTRS1976

An analysis of auroral E region neutral winds based on incoherent scatter radar observations at Chatanika

The physical origin of auroral E-region neutral winds during geomagnetic disturbances is investigated by comparing incoherent-backscatter radar observations made at Chatanika, Alaska, during such disturbances with detailed theoretical calculations of neutral velocities for these conditions. In the analysis, an ion-drag collisional-coupling model is adopted as the primary driving force for the neutral winds. Electric fields and electron number densities observed by the radar facility are used in the calculations, and the coupled ion and neutral momentum equations are solved numerically as functions of altitude and time in the ion-drag approximation. The altitude structure of the velocity field is examined, and the detailed response of the neutral gas to the ion-drag mechanism is delineated. Weighted altitude averages of the calculated velocities are obtained, the accuracy of the procedure for deriving neutral winds from incoherent-scatter radar observations is evaluated, and the comparison is carried out. It is concluded that both ion drag and pressure gradients appear to be required to explain the neutral winds observed in the auroral E-region during geomagnetic disturbances.

Comfort, R. H.↗

NASA NTRS1980

Thermal stress analysis of symmetric shells subjected to asymmetric thermal loads

The performance of the NASTRAN level 16.0 axisymmetric solid elements when subjected to both symmetric and asymmetric thermal loading was investigated. A ceramic radome was modeled using both the CTRAPRG and the CTRAPAX elements. The thermal loading applied contained severe gradients through the thickness of the shell. Both elements were found to be more sensitive to the effect of the thermal gradient than to the aspect ratio of the elements. Analysis using the CTRAPAX element predicted much higher thermal stresses than the analysis using the CTRAPRG element, prompting studies of models for which theoretical solutions could be calculated. It was found that the CTRAPRG element solutions were satisfactory, but that the CTRAPAX element was very geometry dependent. This element produced erroneous results if the geometry was allowed to vary from a rectangular cross-section. The most satisfactory solution found for this type of problem was to model a small segment of a symmetric structure with isoparametric solid elements and apply the cyclic symmetry option in NASTRAN.

Negaard, G. R.↗

NASA NTRS1980

On the cause of plasma-sheet thinning during magnetospheric substorms

It is proposed that the thinning of the plasma sheet during magnetospheric substorms is caused by an earthward gradient of the rate of magnetic merging (field annihilation) in the tail current sheet, which is in turn caused by the velocity-dependent access of plasma mantle particles to the current sheet. A simple model calculation based on this effect predicts a thinning time constant of the order of 1 hour, consistent with observations. The mechanism is also consistent with the observed correlation between plasma-sheet thinning and southward-directed magnetic field components in the solar wind.

Hill, T. W.↗

NASA NTRS1982

An electrostatic parabolic density drift instability

Assuming a uniform magnetic field and using the local approximation, the Vlassov theory for an electrostatic instability driven by a parabolic density gradient is considered. It is found that the instability grows only in the case of a sufficiently large, positive second derivative of the density. Linear growth rate parametric dependences are given, in addition to weakly nonlinear calculations on wave-particle transport due to this instability.

Gary, S. P.↗

NASA NTRS1983

Analysis of shuttle oscillation in the Mach Number = 1.7 to Mach Number = 1.0 range

The first five flights of the Space Transportation System (STS) have exhibited unexpected lateral oscillations in the Mach Number = 1.7 to Mach Number = 1.0 region of the descent trajectory. These oscillations can be split into two parts: a predominantly rolling oscillation referred to as the quarter hertz motion and a long-priod, large-amplitude oscillation in sideslips, roll rate, and yaw rate. These motions are analyzed in this paper in order to determine their source and the mechanism driving them. They will first be examined to determine how much of the motion can be explained using the set of equations that contain linear aerodynamic parameters. Then differences between measured moments and those calculated using linear aerodynamics which are considered to be due to unmodeled moments will be exained. Possible error sources such as not inluding nonlinear aerodynamics in the vehicle model, measurement errors, and the effect of pressure gradients will be considered. Based on these analyses, conclusions as to the nature and cause of the Shuttle lateral oscillations will be drawn.

Suit, W. T.↗

NASA NTRS1985

The theoretical and experimental investigation of cosmic ray Forbush-effects

The theoretical results of analysis of the expected spatial distributions of density, gradients and anisotropy of cosmic rays, obtained on the basis of the numerical solution of anisotropic diffusion equation in the presence of the disturbances of shock wave type in the interplanetary space are presented. The theoretical calculations on the definition of the energy spectrum and anisotropy of galactic cosmic rays during Forbush effect are compared with the experimental data.

Alania, M. V.↗