Partition density functional theory
NASA Astrophysics Data System (ADS)
Nafziger, Jonathan
Partition density functional theory (PDFT) is a method for dividing a molecular electronic structure calculation into fragment calculations. The molecular density and energy corresponding to Kohn Sham density-functional theory (KS-DFT) may be exactly recovered from these fragments. Each fragment acts as an isolated system except for the influence of a global one-body 'partition' potential which deforms the fragment densities. In this work, the developments of PDFT are put into the context of other fragment-based density functional methods. We developed three numerical implementations of PDFT: One within the NWChem computational chemistry package using basis sets, and the other two developed from scratch using real-space grids. It is shown that all three of these programs can exactly reproduce a KS-DFT calculation via fragment calculations. The first of our in-house codes handles non-interacting electrons in arbitrary one-dimensional potentials with any number of fragments. This code is used to explore how the exact partition potential changes for different partitionings of the same system and also to study features which determine which systems yield non-integer PDFT occupations and which systems are locked into integer PDFT occupations. The second in-house code, CADMium, performs real-space calculations of diatomic molecules. Features of the exact partition potential are studied for a variety of cases and an analytical formula determining singularities in the partition potential is derived. We introduce an approximation for the non-additive kinetic energy and show how this quantity can be computed exactly. Finally a PDFT functional is developed to address the issues of static correlation and delocalization errors in approximations within DFT. The functional is applied to the dissociation of H2 + and H2.
Quantum field theory of partitions
Bender, C.M.; Brody, D.C.; Meister, B.K.
1999-07-01
Given a sequence of numbers {l_brace}a{sub n}{r_brace}, it is always possible to find a set of Feynman rules that reproduce that sequence. For the special case of the partitions of the integers, the appropriate Feynman rules give rise to graphs that represent the partitions in a clear pictorial fashion. These Feynman rules can be used to generate the Bell numbers B(n) and the Stirling numbers S(n,k) that are associated with the partitions of the integers. {copyright} {ital 1999 American Institute of Physics.}
A model for partitioning particulate absorption into phytoplanktonic and detrital components
NASA Astrophysics Data System (ADS)
Cleveland, J. S.; Perry, M. J.
1994-01-01
A model for partitioning total particulate absorption, measured on glass fiber filters, into phytoplanktonic and detrital components is developed. The model reconstructs absorption spectra for living phytoplankton using total particulate absorption at the red absorption maxima for chlorophylls a and b, concentrations of chlorophyll a and pheopigment, and mean normalized absorption spectra for laboratory-grown algal cultures. The model was developed in stages for two types of phytoplankton assemblages. Section A of the model applies to waters dominated by eukaryotic algae and is based on absorption spectra for chromophytic (phytoplankton containing chlorophyll c) and chlorophytic (containing chlorophyll b) species. Section B of the model, allowing more variability in spectral shape, was developed for algal communities with more diverse pigmentation. All spectra are processed through Section A, with an internal evaluation determining whether processing continues through Section B. Detrital spectra, generated as the difference between total particulate and modelled phytoplanktonic spectra, included pheopigment absorption and had high blue absorption. Blind tests on samples of known composition predicted absorption within 8-10% at 436 nm and 1-13% when averaged from 400 to 700 nm, which is within the expected accuracy of the glass fiber filter method. No true measure of phytoplankton absorption in field samples is available for testing the model, but results from methanol-extractions were used for comparison despite inclusion of pheopigment absorption as "phytoplankton". For samples collected from coastal waters of Washington State, the Sargasso Sea and coastal waters of Norway, modelled absorption (averaged over 400-700 nm) ranged from 25% lower to 0.5% higher than the methanol-extraction results; pheopigment absorption inappropriately included in the phytoplankton component accounts for the higher phytoplanktonic absorption estimated by the methanol technique
Skeletonization and Partitioning of Digital Images Using Discrete Morse Theory.
Delgado-Friedrichs, Olaf; Robins, Vanessa; Sheppard, Adrian
2015-03-01
We show how discrete Morse theory provides a rigorous and unifying foundation for defining skeletons and partitions of grayscale digital images. We model a grayscale image as a cubical complex with a real-valued function defined on its vertices (the voxel values). This function is extended to a discrete gradient vector field using the algorithm presented in Robins, Wood, Sheppard TPAMI 33:1646 (2011). In the current paper we define basins (the building blocks of a partition) and segments of the skeleton using the stable and unstable sets associated with critical cells. The natural connection between Morse theory and homology allows us to prove the topological validity of these constructions; for example, that the skeleton is homotopic to the initial object. We simplify the basins and skeletons via Morse-theoretic cancellation of critical cells in the discrete gradient vector field using a strategy informed by persistent homology. Simple working Python code for our algorithms for efficient vector field traversal is included. Example data are taken from micro-CT images of porous materials, an application area where accurate topological models of pore connectivity are vital for fluid-flow modelling. PMID:26353267
Short Pulse Laser Absorption and Energy Partition at Relativistic Laser Intensities
Shepherd, R; Chen, H; Ping, Y; Dyer, G; Wilks, S; Chung, H; Kemp, A; Hanson, S; Widmann, K; Fournier, K; Faenov, A; Pikuz, T; Niles, A; Beiersdorfer, P
2007-02-27
We have performed experiments at the COMET and Calisto short pulse laser facilities to make the first comprehensive measurements of the laser absorption and energy partition in solid targets heated with an ultrashort laser pulse focused to relativistic laser intensities (>10 10{sup 17} W/cm{sup 2}). The measurements show an exceedingly high absorption for P polarized laser-target interactions above 10{sup 19} W/cm{sup 2}. Additionally, the hot electron population is observed to markedly increase at the same intensity range. An investigation of the relaxation process was initiated u using time sing time-resolved K{sub {alpha}} spectroscopy. Measurements of the time time-resolved K{sub {alpha}} radiation suggest a 10-20 ps relativistic electron relaxation time. However modeling difficulties of these data are apparent and a more detailed investigation on this subject matter is warranted.
Problems with the process partitioning theory of stratocumulus entrainment
NASA Technical Reports Server (NTRS)
Randall, D. A.
1984-01-01
Three different approaches to partitioning were proposed. Ball (1960), Lilly (1968), and Deardorff et al. (1969, 1974) considered the sign of the net buoyancy flux at each level. If the net flux is positive, it is counted as TKE producing; otherwise, it is counted as TKE consuming. This approach can be called Eulerian partitioning. The second approach can be called process partitioning. It is assumed that the various processes acting in concert each produce and consume the same energy as if they acted independently (Manins and Turner, 1978). The total rates of TKE production and consumption are obtained by summing the effects of all the forcing processes. The third approach is Lagrangian partitioning. Each air parcel is considered as either producing or consuming TKE, according to the sign of the product of its density and vertical velocity anomalies. Stage and Businger (1981a,b) have applied process partitioning to the cloud topped mixed layer. One of the most important processes influencing entrainment into such a layer is cloud top radiative cooling. The production and consumption due to entrainment and radiative cooling are thus closely related. Model results are sensitive to the choice of formulation.
NASA Astrophysics Data System (ADS)
Szumski, Daniel S.
2013-10-01
This research uses classical arguments to develop a blackbody spectral equation that provides useful insights into heat processes. The theory unites in a single equation, the heat radiation theory of Planck and the heat of molecular motion theory of Maxwell and Boltzmann. Light absorption is considered a two-step process. The first is an adiabatic reversible step, wherein one-dimensional light energy is absorbed in a quantum amount, ! h" , by an electron. The absorbed quanta is still 1-dimensional(1-D), and remains within the domain of reversible thermodynamics. There is no recourse to the Second Law during this first step. The absorption process' second step is a dimensional restructuring wherein the electrical and magnetic vectors evolve separately. The 1-D electrical quanta transforms into its 3-D equivalent, electrical charge density. The resulting displacement of the generalized coordinates translates to 3-D motion, the evolution of Joule heat, and irreversible thermodynamics. The magnetic vector has no 3-D equivalent, and can only transform to 1-D paramagnetic spin. Accordingly, photon decoupling distorts time's fabric, giving rise to the characteristic blackbody spectral emittance. This study's spectral equation introduces a new quantity to physics, the radiation temperature. Where it is identical to the classical thermodynamic temperature, the blackbody spectral curves are consistent with Planck's. However, by separating these two temperatures in a stable far-from-equilibrium manner, new energy storage modes become possible at the atomic level, something that could have profound implications in understanding matter's living state.
A Theory of Institutional Change and Control: Tri-Partite Power. Revised.
ERIC Educational Resources Information Center
Shapiro, Arthur
This paper describes the Tri-Partite Theory of institutional change, which proposes that organizations in general and educational institutions in particular pass through three phases, each dominated by a specific personality type: person-orientation (loyalty to a charismatic leader as the basis of motivation); plan-orientation (functions…
NASA Astrophysics Data System (ADS)
Utami, Sentagi Sesotya; Al Rochmadi, Nurwachid; Sarwono, R. Sugeng Joko
2015-09-01
Low partitions are commonly found in open-plan offices as the boundaries of workstation islands or groups of workstations. This room layout often cause excessive speech intelligibility, which creates work distraction and reduce the quality of speech privacy. Sound absorption, distance between workstations, and height of partitions are factors that were investigated on their impact to the room acoustics condition, referred to ISO 3382-3:2012. Observed room acoustics conditions were speech intelligibility, speech privacy, and distraction to concentrate in work using parameters of T30, C50, and RASTI. Parameters of T30, C50, and RASTI were used to evaluate the speech intelligibility. The level of speech privacy was indicated by parameter of privacy distance (rP). Distraction to concentrate in work was indicated by distraction distance (rD). The results from 2 experimental setups show that sound absorption, distance between workstations, and partitions influenced the level of speech intelligibility, speech privacy, and distraction to concentration at work. The value of C50 decline, by 76.9% and 77.4%, each for scenario A and B. RASTI decline, by 18.7% and 14.8%. Difference in percentage of speech privacy, by 6% and 11%. Difference in percentage of distraction to concentration at work, by 79% and 70%.
Geometry of Spin and SPINc Structures in the M-Theory Partition Function
NASA Astrophysics Data System (ADS)
Sati, Hisham
We study the effects of having multiple Spin structures on the partition function of the spacetime fields in M-theory. This leads to a potential anomaly which appears in the eta invariants upon variation of the Spin structure. The main sources of such spaces are manifolds with nontrivial fundamental group, which are also important in realistic models. We extend the discussion to the Spinc case and find the phase of the partition function, and revisit the quantization condition for the C-field in this case. In type IIA string theory in 10 dimensions, the (mod 2) index of the Dirac operator is the obstruction to having a well-defined partition function. We geometrically characterize manifolds with and without such an anomaly and extend to the case of nontrivial fundamental group. The lift to KO-theory gives the α-invariant, which in general depends on the Spin structure. This reveals many interesting connections to positive scalar curvature manifolds and constructions related to the Gromov-Lawson-Rosenberg conjecture. In the 12-dimensional theory bounding M-theory, we study similar geometric questions, including choices of metrics and obtaining elements of K-theory in 10 dimensions by pushforward in K-theory on the disk fiber. We interpret the latter in terms of the families index theorem for Dirac operators on the M-theory circle and disk. This involves superconnections, eta forms, and infinite-dimensional bundles, and gives elements in Deligne cohomology in lower dimensions. We illustrate our discussion with many examples throughout.
NASA Astrophysics Data System (ADS)
Finley, James P.; Chaudhuri, Rajat K.; Freed, Karl F.
1996-07-01
High-order multireference perturbation theory is applied to the 1S states of the beryllium atom using a reference (model) space composed of the \\|1s22s2> and the \\|1s22p2> configuration-state functions (CSF's), a system that is known to yield divergent expansions using Mo/ller-Plesset and Epstein-Nesbet partitioning methods. Computations of the eigenvalues are made through 40th order using forced degeneracy (FD) partitioning and the recently introduced optimization (OPT) partitioning. The former forces the 2s and 2p orbitals to be degenerate in zeroth order, while the latter chooses optimal zeroth-order energies of the (few) most important states. Our methodology employs simple models for understanding and suggesting remedies for unsuitable choices of reference spaces and partitioning methods. By examining a two-state model composed of only the \\|1s22p2> and \\|1s22s3s> states of the beryllium atom, it is demonstrated that the full computation with 1323 CSF's can converge only if the zeroth-order energy of the \\|1s22s3s> Rydberg state from the orthogonal space lies below the zeroth-order energy of the \\|1s22p2> CSF from the reference space. Thus convergence in this case requires a zeroth-order spectral overlap between the orthogonal and reference spaces. The FD partitioning is not capable of generating this type of spectral overlap and thus yields a divergent expansion. However, the expansion is actually asymptotically convergent, with divergent behavior not displayed until the 11th order because the \\|1s22s3s> Rydberg state is only weakly coupled with the \\|1s22p2> CSF and because these states are energetically well separated in zeroth order. The OPT partitioning chooses the correct zeroth-order energy ordering and thus yields a convergent expansion that is also very accurate in low orders compared to the exact solution within the basis.
NASA Astrophysics Data System (ADS)
Parrish, Robert M.; Sherrill, C. David
2014-07-01
We develop a physically-motivated assignment of symmetry adapted perturbation theory for intermolecular interactions (SAPT) into atom-pairwise contributions (the A-SAPT partition). The basic precept of A-SAPT is that the many-body interaction energy components are computed normally under the formalism of SAPT, following which a spatially-localized two-body quasiparticle interaction is extracted from the many-body interaction terms. For electrostatics and induction source terms, the relevant quasiparticles are atoms, which are obtained in this work through the iterative stockholder analysis (ISA) procedure. For the exchange, induction response, and dispersion terms, the relevant quasiparticles are local occupied orbitals, which are obtained in this work through the Pipek-Mezey procedure. The local orbital atomic charges obtained from ISA additionally allow the terms involving local orbitals to be assigned in an atom-pairwise manner. Further summation over the atoms of one or the other monomer allows for a chemically intuitive visualization of the contribution of each atom and interaction component to the overall noncovalent interaction strength. Herein, we present the intuitive development and mathematical form for A-SAPT applied in the SAPT0 approximation (the A-SAPT0 partition). We also provide an efficient series of algorithms for the computation of the A-SAPT0 partition with essentially the same computational cost as the corresponding SAPT0 decomposition. We probe the sensitivity of the A-SAPT0 partition to the ISA grid and convergence parameter, orbital localization metric, and induction coupling treatment, and recommend a set of practical choices which closes the definition of the A-SAPT0 partition. We demonstrate the utility and computational tractability of the A-SAPT0 partition in the context of side-on cation-π interactions and the intercalation of DNA by proflavine. A-SAPT0 clearly shows the key processes in these complicated noncovalent interactions, in
Parrish, Robert M.; Sherrill, C. David
2014-07-28
We develop a physically-motivated assignment of symmetry adapted perturbation theory for intermolecular interactions (SAPT) into atom-pairwise contributions (the A-SAPT partition). The basic precept of A-SAPT is that the many-body interaction energy components are computed normally under the formalism of SAPT, following which a spatially-localized two-body quasiparticle interaction is extracted from the many-body interaction terms. For electrostatics and induction source terms, the relevant quasiparticles are atoms, which are obtained in this work through the iterative stockholder analysis (ISA) procedure. For the exchange, induction response, and dispersion terms, the relevant quasiparticles are local occupied orbitals, which are obtained in this work through the Pipek-Mezey procedure. The local orbital atomic charges obtained from ISA additionally allow the terms involving local orbitals to be assigned in an atom-pairwise manner. Further summation over the atoms of one or the other monomer allows for a chemically intuitive visualization of the contribution of each atom and interaction component to the overall noncovalent interaction strength. Herein, we present the intuitive development and mathematical form for A-SAPT applied in the SAPT0 approximation (the A-SAPT0 partition). We also provide an efficient series of algorithms for the computation of the A-SAPT0 partition with essentially the same computational cost as the corresponding SAPT0 decomposition. We probe the sensitivity of the A-SAPT0 partition to the ISA grid and convergence parameter, orbital localization metric, and induction coupling treatment, and recommend a set of practical choices which closes the definition of the A-SAPT0 partition. We demonstrate the utility and computational tractability of the A-SAPT0 partition in the context of side-on cation-π interactions and the intercalation of DNA by proflavine. A-SAPT0 clearly shows the key processes in these complicated noncovalent interactions, in
NASA Astrophysics Data System (ADS)
Taormina, Anne
1993-05-01
The representation theory of the doubly extended N=4 superconformal algebra is reviewed. The modular properties of the corresponding characters can be derived, using characters sumrules for coset realizations of these N=4 algebras. Some particular combinations of massless characters are shown to transform as affine SU(2) characters under S and T, a fact used to completely classify the massless sector of the partition function.
A theory for optimal heat transfer in a partitioned convection cell
NASA Astrophysics Data System (ADS)
Chen, Jun; Bao, Yun; She, Zhen-Su
2015-11-01
We report a theory explaining recent observation of significant enhancement of heat transfer in a partitioned Rayleigh-Bénard convection (RBC), where vertical adiabatic boards are inserted into the enclosure with narrow channel left open between partition boards and the cooling/heating plates. An enhancement of heat transfer of up to 2.7 times is observed compared to normal RBC cell without partitions. It is found that laminar wall jet is formed in the narrow horizontal channel, which makes the thermal boundary layer thinner. Two asymptotic trends, a channel flow and a boundary layer, describe the motions of the jets in the horizontal channel, and the competition between them gives rise to an optimized state for the global heat transfer, with an optimal width of the sub-cell W/H =0.038-0.083 for Γ = 1, and an optimal spacing of the horizontal channel b/H =0.011 for Γ = 5. The former (channel) yields a heat flux linearly proportional to b for small b, whereas the latter (boundary layer) follows -2/3-law for large b. We suggest that the partitioned RBC provides a vehicle for heat enhancement with a wide range of industrial applications. This work was supported by National Nature Science Fund of China under Grant No. 11372362.
NASA Astrophysics Data System (ADS)
Méliot, Pierre-Loïc
2010-12-01
In this thesis, we investigate the asymptotics of random partitions chosen according to probability measures coming from the representation theory of the symmetric groups S_n and of the finite Chevalley groups GL(n,F_q) and Sp(2n,F_q). More precisely, we prove laws of large numbers and central limit theorems for the q-Plancherel measures of type A and B, the Schur-Weyl measures and the Gelfand measures. Using the RSK algorithm, it also gives results on longest increasing subsequences in random words. We develop a technique of moments (and cumulants) for random partitions, thereby using the polynomial functions on Young diagrams in the sense of Kerov and Olshanski. The algebra of polynomial functions, or observables of Young diagrams is isomorphic to the algebra of partial permutations; in the last part of the thesis, we try to generalize this beautiful construction.
Geometric model from microscopic theory for nuclear absorption
NASA Technical Reports Server (NTRS)
John, Sarah; Townsend, Lawrence W.; Wilson, John W.; Tripathi, Ram K.
1993-01-01
A parameter-free geometric model for nuclear absorption is derived herein from microscopic theory. The expression for the absorption cross section in the eikonal approximation, taken in integral form, is separated into a geometric contribution that is described by an energy-dependent effective radius and two surface terms that cancel in an asymptotic series expansion. For collisions of light nuclei, an expression for the effective radius is derived from harmonic oscillator nuclear density functions. A direct extension to heavy nuclei with Woods-Saxon densities is made by identifying the equivalent half-density radius for the harmonic oscillator functions. Coulomb corrections are incorporated, and a simplified geometric form of the Bradt-Peters type is obtained. Results spanning the energy range from 1 MeV/nucleon to 1 GeV/nucleon are presented. Good agreement with experimental results is obtained.
Mean-field theory of planar absorption of RNA molecules
NASA Astrophysics Data System (ADS)
Nguyen, Toan; Bruinsma, Robijn; Gelbart, William
2006-03-01
Interaction between the viral RNA and the protective protein capsid plays a very important role in the cell infection and self-assembly process of a virus. To better understand this interaction, we study a similar problem of absorption of RNA on an attractive wall. It is known that the secondary structure of a folded RNA molecules without pseudo-knots has the same topology as that of a branched polymer. We use a mean-field theory for branched polymers to analytically calculate the RNA concentration profile. The results are compared to known exact scaling calculations and computer simulations.
Current density partitioning in time-dependent current density functional theory
Mosquera, Martín A.; Wasserman, Adam; Department of Physics, Purdue University, West Lafayette, Indiana 47907
2014-05-14
We adapt time-dependent current density functional theory to allow for a fragment-based solution of the many-electron problem of molecules in the presence of time-dependent electric and magnetic fields. Regarding a molecule as a set of non-interacting subsystems that individually evolve under the influence of an auxiliary external electromagnetic vector-scalar potential pair, the partition 4-potential, we show that there are one-to-one mappings between this auxiliary potential, a sharply-defined set of fragment current densities, and the total current density of the system. The partition electromagnetic (EM) 4-potential is expressed in terms of the real EM 4-potential of the system and a gluing EM 4-potential that accounts for exchange-correlation effects and mutual interaction forces between fragments that are required to yield the correct electron dynamics. We prove the zero-force theorem for the fragmented system, establish a variational formulation in terms of action functionals, and provide a simple illustration for a charged particle in a ring.
Duval, Jérôme F L
2016-04-14
A mechanistic understanding of the processes governing metal toxicity to microorganisms (bacteria, algae) calls for an adequate formulation of metal partitioning at biointerfaces during cell exposure. This includes the account of metal transport dynamics from bulk solution to biomembrane and the kinetics of metal internalisation, both potentially controlling the intracellular and surface metal fractions that originate cell growth inhibition. A theoretical rationale is developed here for such coupled toxicodynamics and interfacial metal partitioning dynamics under non-complexing medium conditions with integration of the defining cell electrostatic properties. The formalism explicitly considers intertwined metal adsorption at the biointerface, intracellular metal excretion, cell growth and metal depletion from bulk solution. The theory is derived under relevant steady-state metal transport conditions on the basis of coupled Nernst-Planck equation and continuous logistic equation modified to include metal-induced cell growth inhibition and cell size changes. Computational examples are discussed to identify limitations of the classical Biotic Ligand Model (BLM) in evaluating metal toxicity over time. In particular, BLM is shown to severely underestimate metal toxicity depending on cell exposure time, metal internalisation kinetics, cell surface electrostatics and initial cell density. Analytical expressions are provided for the interfacial metal concentration profiles in the limit where cell-growth is completely inhibited. A rigorous relationship between time-dependent cell density and metal concentrations at the biosurface and in bulk solution is further provided, which unifies previous equations formulated by Best and Duval under constant cell density and cell size conditions. The theory is sufficiently flexible to adapt to toxicity scenarios with involved cell survival-death processes. PMID:26980542
Light absorption and partitioning in Arctic Ocean surface waters: impact of multiyear ice melting
NASA Astrophysics Data System (ADS)
Bélanger, S.; Cizmeli, S. A.; Ehn, J.; Matsuoka, A.; Doxaran, D.; Hooker, S.; Babin, M.
2013-10-01
Ice melting in the Arctic Ocean exposes the surface water to more radiative energy with poorly understood effects on photo-biogeochemical processes and heat deposition in the upper ocean. In August 2009, we documented the vertical variability of light absorbing components at 37 stations located in the southeastern Beaufort Sea including both Mackenzie River-influenced waters and polar mixed layer waters. We found that melting multiyear ice released significant amount of non-algal particulates (NAP) near the sea surface relative to subsurface waters. NAP absorption coefficients at 440 nm (aNAP(440)) immediately below the sea surface were on average 3-fold (up to 10-fold) higher compared to subsurface values measured at 2-3 m depth. The impact of this unusual feature on the light transmission and remote sensing reflectance (Rrs) was further examined using a radiative transfer model. A 10-fold particle enrichment homogeneously distributed in the first meter of the water column slightly reduced photosynthetically available and usable radiation (PAR and PUR) by ∼6 and ∼8%, respectively, relative to a fully homogenous water column with low particle concentration. In terms of Rrs, the particle enrichment significantly flattered the spectrum by reducing the Rrs by up to 20% in the blue-green spectral region (400-550 nm). These results highlight the impact of meltwater on the concentration of particles at sea surface, and the need for considering non-uniform vertical distribution of particles in such systems when interpreting remotely sensed ocean color. Spectral slope of aNAP spectra calculated in the UV (ultraviolet) domain decreased with depth suggesting that this parameter is sensitive to detritus composition and/or diagenesis state (e.g., POM (particulate organic matter) photobleaching).
Light absorption and partitioning in Arctic Ocean surface waters: impact of multi year ice melting
NASA Astrophysics Data System (ADS)
Bélanger, S.; Cizmeli, S. A.; Ehn, J.; Matsuoka, A.; Doxaran, D.; Hooker, S.; Babin, M.
2013-03-01
Ice melting in the Arctic Ocean exposes the surface water to more radiative energy with poorly understood effects on photo-biogeochemical processes and heat deposition in the upper ocean. In August 2009, we documented the vertical variability of light absorbing components at 37 stations located in the southeastern Beaufort Sea including both Mackenzie river-influenced waters and polar mixed layer waters. We found that melting multi-year ice released significant amount of non-algal particulates (NAP) near the sea surface relative to sub-surface waters. NAP absorption coefficients at 440 nm (aNAP(440)) immediately below the sea surface (0-) were on average 3-fold (up to 10-fold) higher compared to sub-surface values measured at 2-3 m depth. The impact of this unusual feature on the light transmission and remote sensing reflectance (Rrs) was further examined using a radiative transfer model. A 10-fold particle enrichment homogeneously distributed in the first meter of the water column slightly reduced photosynthetically available and usable radiation (PAR and PUR) by ~6% and ~8%, respectively, relative to a fully homogenous water column with low particles concentration. In terms of Rrs, the particle enrichment significantly flattered the spectrum by reducing the Rrs by up to 20% in the blue-green spectral region (400-550 nm). These results highlight the impact of melt water on the concentration of particles at sea surface, and the need for considering nonuniform vertical distribution of particles in such systems when interpreting remotely sensed ocean color. Spectral slope of aNAP spectra calculated in the UV domain decreased with depth suggesting that this parameter is sensitive to detritus composition and/or diagenesis state (e.g., POM photobleaching).
NASA Astrophysics Data System (ADS)
Mkrtchyan, R. L.
2014-12-01
We show that partition function of Chern-Simons theory on three-sphere with classical and exceptional groups (actually on the whole corresponding lines in Vogel's plane) can be represented as ratio of respectively triple and double sine functions (last function is essentially a modular quantum dilogarithm). The product representation of sine functions gives Gopakumar-Vafa structure form of partition function, which in turn gives a corresponding integer invariants of manifold after geometrical transition. In this way we suggest to extend gauge/string duality to exceptional groups, although one still have to resolve few problems. In both classical and exceptional cases an additional terms, non-perturbative w.r.t. the string coupling constant, appear. The full universal partition function of ChernSimons theory on three-sphere is shown to be the ratio of quadruple sine functions. We also briefly discuss the matrix model for exceptional line.
Levnajić, Zoran; Mezić, Igor
2010-09-01
We present a computational study of a visualization method for invariant sets based on ergodic partition theory, first proposed by Mezić (Ph.D. thesis, Caltech, 1994) and Mezić and Wiggins [Chaos 9, 213 (1999)]. The algorithms for computation of the time averages of observables on phase space are developed and used to provide an approximation of the ergodic partition of the phase space. We term the graphical representation of this approximation--based on time averages of observables--a mesochronic plot (from Greek: meso--mean, chronos--time). The method is useful for identifying low-dimensional projections (e.g., two-dimensional slices) of invariant structures in phase spaces of dimensionality bigger than two. We also introduce the concept of the ergodic quotient space, obtained by assigning a point to every ergodic set, and provide an embedding method whose graphical representation we call the mesochronic scatter plot. We use the Chirikov standard map as a well-known and dynamically rich example in order to illustrate the implementation of our methods. In addition, we expose applications to other higher dimensional maps such as the Froéschle map for which we utilize our methods to analyze merging of resonances and, the three-dimensional extended standard map for which we study the conjecture on its ergodicity [I. Mezić, Physica D 154, 51 (2001)]. We extend the study in our next paper [Z. Levnajić and I. Mezić, e-print arXiv:0808.2182] by investigating the visualization of periodic sets using harmonic time averages. Both of these methods are related to eigenspace structure of the Koopman operator [I. Mezić and A. Banaszuk, Physica D 197, 101 (2004)]. PMID:20887054
Exact partition functions for the Ω-deformed {N}={2}^{ast } SU(2) gauge theory
NASA Astrophysics Data System (ADS)
Beccaria, Matteo; Macorini, Guido
2016-07-01
We study the low energy effective action of the Ω-deformed {N}={2}^{ast } SU(2) gauge theory. It depends on the deformation parameters ɛ 1, ɛ 2, the scalar field expectation value a, and the hypermultiplet mass m. We explore the plane (m/ɛ_1,ɛ_2/ɛ_1) looking for special features in the multi-instanton contributions to the prepotential, motivated by what happens in the Nekrasov-Shatashvili limit ɛ 2 → 0. We propose a simple condition on the structure of poles of the k-instanton prepotential and show that it is admissible at a finite set of points in the above plane. At these special points, the prepotential has poles at fixed positions independent on the instanton number. Besides and remarkably, both the instanton partition function and the full prepotential, including the perturbative contribution, may be given in closed form as functions of the scalar expectation value a and the modular parameter q appearing in special combinations of Eisenstein series and Dedekind η function. As a byproduct, the modular anomaly equation can be tested at all orders at these points. We discuss these special features from the point of view of the AGT correspondence and provide explicit toroidal 1-blocks in non-trivial closed form. The full list of solutions with 1, 2, 3, and 4 poles is determined and described in details.
Liudchik, Alexander M
2014-08-10
A modified version of the differential optical absorption spectroscopy (DOAS) method is presented. The technique is called orthogonal optical absorption spectroscopy (OOAS). A widespread variant of DOAS with smoothing of the registered spectrum and absorption cross sections being made employing a polynomial regression is a particular case of OOAS. The concept of OOAS provides a variety of new possibilities for constructing computational schemes and analyzing the influence of different error sources on calculated concentrations. PMID:25320931
Microscopic Theory and Simulation of Quantum-Well Intersubband Absorption
NASA Technical Reports Server (NTRS)
Li, Jianzhong; Ning, C. Z.
2004-01-01
We study the linear intersubband absorption spectra of a 15 nm InAs quantum well using the intersubband semiconductor Bloch equations with a three-subband model and a constant dephasing rate. We demonstrate the evolution of intersubband absorption spectral line shape as a function of temperature and electron density. Through a detailed examination of various contributions, such as the phase space filling effects, the Coulomb many-body effects and the non-parabolicity effect, we illuminate the underlying physics that shapes the spectra. Keywords: Intersubband transition, linear absorption, semiconductor heterostructure, InAs quantum well
Theory of strong-field attosecond transient absorption
NASA Astrophysics Data System (ADS)
Wu, Mengxi; Chen, Shaohao; Camp, Seth; Schafer, Kenneth J.; Gaarde, Mette B.
2016-03-01
Attosecond transient absorption is one of the promising new techniques being developed to exploit the availability of sub-femtosecond extreme ultraviolet (XUV) pulses to study the dynamics of the electron on its natural time scale. The temporal resolution in a transient absorption setup comes from the control of the relative delay and coherence between pump and probe pulses, while the spectral resolution comes from the characteristic width of the features that are being probed. In this review we focus on transient absorption scenarios where an attosecond pulse of XUV radiation creates a broadband excitation that is subsequently probed by a few cycle infrared (IR) laser. Because the attosecond XUV pulses are locked to the IR field cycle, the exchange of energy in the laser-matter interaction can be studied with unprecedented precision. We focus on the transient absorption by helium atoms of XUV radiation around the first ionization threshold, where we can simultaneoulsy solve the time-dependent Schrödinger equation for the single atom response and the Maxwell wave equation for the collective response of the nonlinear medium. We use a time-domain method that allows us to treat on an equal footing all the different linear and nonlinear processes by which the medium can exchange energy with the fields. We present several simple models, based on a few-level system interacting with a strong IR field, to explain many of the novel features found in attosecond transient absorption spectrograms. These include the presence of light-induced states, which demonstrate the ability to probe the dressed states of the atom. We also present a time-domain interpretation of the resonant pulse propagation features that appear in absorption spectra in dense, macroscopic media. We close by reviewing several recent experimental results that can be explained in terms of the models we discuss. Our aim is to present a road map for understanding future attosecond transient absorption
Determination of the water vapor continuum absorption by THz-TDS and Molecular Response Theory.
Yang, Yihong; Mandehgar, Mahboubeh; Grischkowsky, D
2014-02-24
Determination of the water vapor continuum absorption from 0.35 to 1 THz is reported. The THz pulses propagate though a 137 m long humidity-controlled chamber and are measured by THz time-domain spectroscopy (THz-TDS). The average relative humidity along the entire THz path is precisely obtained by measuring the difference between transit times of the sample and reference THz pulses to an accuracy of 0.1 ps. Using the measured total absorption and the calculated resonance line absorption with the Molecular Response Theory lineshape, based on physical principles and measurements, an accurate continuum absorption is obtained within four THz absorption windows, that agrees well with the empirical theory. The absorption is significantly smaller than that obtained using the van Vleck-Weisskopf lineshape with a 750 GHz cut-off. PMID:24663762
Application of Equilibrium Partitioning Theory to Soil PAH Contamination (External Review Draft)
In March 2004, ORD's Ecological Risk Assessment Support Center (ERASC) received a request from the Ecological Risk Assessment Forum (ERAF) to provide insight into the issue of whether equilibrium partitioning (EqP) techniques can be used to predict the toxicity of polycyclic arom...
Technology Transfer Automated Retrieval System (TEKTRAN)
Separation of the photosynthetic (Fp) and respiratory (Fr) fluxes of net CO2 exchange (Fn)remains a necessary step toward understanding the biological and physical controls on carbon cycling between the soil, biomass, and atmosphere. Despite recent advancements in stable carbon isotope partitioning ...
Single-dot absorption spectroscopy and theory of silicon nanocrystals
NASA Astrophysics Data System (ADS)
Sychugov, Ilya; Pevere, Federico; Luo, Jun-Wei; Zunger, Alex; Linnros, Jan
2016-04-01
Photoluminescence excitation measurements have been performed on single, unstrained oxide-embedded Si nanocrystals. Having overcome the challenge of detecting weak emission, we observe four broad peaks in the absorption curve above the optically emitting state. Atomistic calculations of the Si nanocrystal energy levels agree well with the experimental results and allow identification of some of the observed transitions. An analysis of their physical nature reveals that they largely retain the indirect band-gap structure of the bulk material with some intermixing of direct band-gap character at higher energies.
Unified theory of electron-phonon renormalization and phonon-assisted optical absorption
NASA Astrophysics Data System (ADS)
Patrick, Christopher E.; Giustino, Feliciano
2014-09-01
We present a theory of electronic excitation energies and optical absorption spectra which incorporates energy-level renormalization and phonon-assisted optical absorption within a unified framework. Using time-independent perturbation theory we show how the standard approaches for studying vibronic effects in molecules and those for addressing electron-phonon interactions in solids correspond to slightly different choices for the non-interacting Hamiltonian. Our present approach naturally leads to the Allen-Heine theory of temperature-dependent energy levels, the Franck-Condon principle, the Herzberg-Teller effect and to phonon-assisted optical absorption in indirect band gap materials. In addition, our theory predicts sub-gap phonon-assisted optical absorption in direct gap materials, as well as an exponential edge which we tentatively assign to the Urbach tail. We also consider a semiclassical approach to the calculation of optical absorption spectra which simultaneously captures energy-level renormalization and phonon-assisted transitions and is especially suited to first-principles electronic structure calculations. We demonstrate this approach by calculating the phonon-assisted optical absorption spectrum of bulk silicon.
Dipole Theory of Heat Production and Absorption in Nerve Axon
Wei, Ling Y.
1972-01-01
Exact formulas are derived for the energy change of a dipole system with two energy states (or bands) in a changing field in two cases: (a) no dipole flip-flop and (b) dipole flip-flop caused by stimulation. Based on these formulas, the positive and negative heats are calculated. The results are in good agreement with experiment in case b but are 60-180% larger in case a. Furthermore, the theory shows that the negative heat cannot be less than the positive heat in case a but can be either way in case b, the latter result being found prevalent in experiment. It is concluded that nerve excitation is most likely to involve dipole flip-flop at the membrane surface. The theory is consistent in the interpretations and correlations of the electrical, optical, and thermal effects observed in nerve axon. PMID:5056960
Absolute absorption on the potassium D lines: theory and experiment
NASA Astrophysics Data System (ADS)
Hanley, Ryan K.; Gregory, Philip D.; Hughes, Ifan G.; Cornish, Simon L.
2015-10-01
We present a detailed study of the absolute Doppler-broadened absorption of a probe beam scanned across the potassium D lines in a thermal vapour. Spectra using a weak probe were measured on the 4S \\to 4P transition and compared to the theoretical model of the electric susceptibility detailed by Zentile et al (2015 Comput. Phys. Commun. 189 162-74) in the code named ElecSus. Comparisons were also made on the 4S \\to 5P transition with an adapted version of ElecSus. This is the first experimental test of ElecSus on an atom with a ground state hyperfine splitting smaller than that of the Doppler width. An excellent agreement was found between ElecSus and experimental measurements at a variety of temperatures with rms errors ˜ {10}-3. We have also demonstrated the use of ElecSus as an atomic vapour thermometry tool, and present a possible new measurement technique of transition decay rates which we predict to have a precision of ˜3 {kHz}.
Theory of absorption rate of carriers in fused silica under intense laser irradiation
Deng, Hongxiang; Xiang, Xia; Zheng, WG; Yuan, XD; Wu, SY; Jiang, XD; Gao, Fei; Zu, Xiaotao T.; Sun, Kai
2010-11-15
A quantum non-perturbation theory for phonon-assisted photon absorption of conduction band electron in intense laser was developed. By carrying out the calculation in fused silica at wavelengths from ultraviolet to infrared in terawatt intensity laser, we show that the Non-perturbation approach can make a uniform description of energy absorption rate at both short wavelengths and long wavelengths on TW / cm2 intensity laser.
Ma, W.; Kleunen, A. van; Immerzeel, J.; Maagd, P.G.J. de
1998-09-01
The purpose of this study was to assess the suitability of applying equilibrium partitioning (EqP) theory to predict the bioaccumulation of polycyclic aromatic hydrocarbons (PAHs) by earthworms when these are exposed to contaminated soils in the field. Studies carried out in situ in various contaminated floodplain sites showed the presence of linear relationships with intercept zero between the lipid-normalized concentration of different PAHs in the earthworm, Lumbricus rubellus and the organic-matter-normalized concentration of the compounds in soil. The demonstration of such an isometric relationship is in agreement with the prediction of EqP theory that the biota-soil accumulation factor (BSAF) should be independent of the octanol/water partition coefficient, log K{sub ow}. The average BSAF of PAH compounds in the sampled 20-cm top layer of soil was 0.10. The present study also investigated the route of uptake of PAHs for earthworms in soil. The bioconcentration factor of low-molecular-weight PAHs, such as phenanthrene, fluoranthene, and pyrene, was derived from bioconcentration kinetic modeling of water-only experiments and found to be of the same order of magnitude as the bioaccumulation factor in the field when the latter was normalized to calculated concentrations in soil pore water. The results indicated that the exposure of earthworms to PAHs in soil is mediated through direct contact of the worms with the dissolved interstitial soil-water phase, further supporting the applicability of EqP theory to PAHs. The experimental data on the biotransformation of PAHs suggest that earthworms possess some capacity of metabolization, although this does not seem to be a major factor in the total elimination of these compounds. Even though the EqP approach was found to be applicable to low-molecular-weight PAHs with respect to the prediction of bioaccumulation by earthworms in the field, the results were less conclusive for high-molecular-weight compounds, such as
Varied absorption peaks of dual-band metamaterial absorber analysis by using reflection theory
NASA Astrophysics Data System (ADS)
Xiong, Han; Yu, Yan-Tao; Tang, Ming-Chun; Chen, Shi-Yong; Liu, Dan-Ping; Ou, Xiang; Zeng, Hao
2016-03-01
Cross-resonator metamaterial absorbers (MMA) have been widely investigated from microwave to optical frequencies. However, only part of the factors influencing the absorption properties were analyzed in previous works at the same time. In order to completely understand how the spacer thickness, dielectric parameter and incidence angle affect the absorption properties of the dual-band MMA, two sets of simulation were performed. It was found that with increasing incident angles, the low-frequency absorption peak showed a blue shift, while the high-frequency absorption peaks showed a red shift. However, with the increase in spacer thickness, both of the absorption peaks showed a red shift. By using the reflection theory expressions, the physical mechanism of the cross-resonator MMA was well explained. This method provides an effective way to analyze multi-band absorber in technology.
Dafoe, Julian T; Daugulis, Andrew J
2014-03-01
The biotransformation of levulinic acid to 4-valerolactone (4VL) is pH-dependent and equilibrium limited, distinct from the more common irreversible biotransformations that are constrained by product toxicity or biocatalyst inhibition. Our processing strategy for this system was to selectively remove the product, 4VL, which is in equilibrium with its precursor, 4-hydroxyvalerate (4HV), to pull the reaction to a greater extent of conversion. 4VL is challenging to separate from the aqueous phase due to its water miscibility, necessitating the use of water-absorbing polymers to provide affinity toward the hydrophilic product. Manipulating the composition of copolymers, thereby varying the architecture of polymer chains, conferred drastically different extents of water absorption and caused different biotransformation outcomes. A custom-synthesized random copolymer designed to maximize the proportion of material with affinity for the solute had high water uptake, which resulted in the poor selectivity for the target molecule relative to its precursor. Conversely, a moderately water-absorbing commercial segmented block copolymer, Hytrel(®) 8206, demonstrated selectivity toward 4VL relative to its precursor, 4HV, and increased 4VL production by approximately 30 % by shifting the equilibrium toward the product. This work has shown that water absorption is an important, previously neglected criterion in evaluating polymer affinity and selectivity toward hydrophilic target molecules. PMID:23907719
Cross section calculations of astrophysical interest. [for theories of absorption and emission lines
NASA Technical Reports Server (NTRS)
Gerjuoy, E.
1974-01-01
Cross sections are discussed for rotational excitation associated with theories of absorption and emission lines from molecules in space with emphasis on H2CO, CO, and OH by collisions with neutral particles such H, H2, and He. The sensitivity of the Thaddeus equation for the H2CO calculation is examined.
Theory of x-ray absorption by laser-aligned symmetric-top molecules.
Buth, C.; Santra, R.; Chemical Sciences and Engineering Division
2008-01-01
We devise a theory of x-ray absorption by symmetric-top molecules which are aligned by an intense optical laser. Initially, the density matrix of the system is composed of the electronic ground state of the molecules and a thermal ensemble of rigid-rotor eigenstates. We formulate equations of motion of the two-color (laser plus x rays) rotational-electronic problem. The interaction with the laser is assumed to be nonresonant; it is described by an electric dipole polarizability tensor. X-ray absorption is approximated as a one-photon process. It is shown that the equations can be separated such that the interaction with the laser can be treated independently of the x rays. The laser-only density matrix is propagated numerically. After each time step, the x-ray absorption is calculated. We apply our theory to study adiabatic alignment of bromine molecules (Br2). The required dynamic polarizabilities are determined using the ab initio linear response methods coupled-cluster singles (CCS), second-order approximate coupled-cluster singles and doubles (CC2), and coupled-cluster singles and doubles (CCSD). For the description of x-ray absorption on the {sigma}g1s-->{sigma}u4p resonance, a parameter-free two-level model is used for the electronic structure of the molecules. Our theory opens up novel perspectives for the quantum control of x-ray radiation.
Avetissian, H K; Ghazaryan, A G; Matevosyan, H H; Mkrtchian, G F
2015-10-01
The microscopic quantum theory of plasma nonlinear interaction with the coherent shortwave electromagnetic radiation of arbitrary intensity is developed. The Liouville-von Neumann equation for the density matrix is solved analytically considering a wave field exactly and a scattering potential of plasma ions as a perturbation. With the help of this solution we calculate the nonlinear inverse-bremsstrahlung absorption rate for a grand canonical ensemble of electrons. The latter is studied in Maxwellian, as well as in degenerate quantum plasma for x-ray lasers at superhigh intensities and it is shown that one can achieve the efficient absorption coefficient in these cases. PMID:26565352
Bremmer, Rolf H; van Gemert, Martin J C; Faber, Dirk J; van Leeuwen, Ton G; Aalders, Maurice C G
2013-08-01
Diffuse reflectance spectra are used to determine the optical properties of biological samples. In medicine and forensic science, the turbid objects under study often possess large absorption and/or scattering properties. However, data analysis is frequently based on the diffusion approximation to the radiative transfer equation, implying that it is limited to tissues where the reduced scattering coefficient dominates over the absorption coefficient. Nevertheless, up to absorption coefficients of 20 mm-1 at reduced scattering coefficients of 1 and 11.5 mm-1, we observed excellent agreement (r2=0.994) between reflectance measurements of phantoms and the diffuse reflectance equation proposed by Zonios et al. [Appl. Opt.38, 6628-6637 (1999)], derived as an approximation to one of the diffusion dipole equations of Farrell et al. [Med. Phys.19, 879-888 (1992)]. However, two parameters were fitted to all phantom experiments, including strongly absorbing samples, implying that the reflectance equation differs from diffusion theory. Yet, the exact diffusion dipole approximation at high reduced scattering and absorption also showed agreement with the phantom measurements. The mathematical structure of the diffuse reflectance relation used, derived by Zonios et al. [Appl. Opt.38, 6628-6637 (1999)], explains this observation. In conclusion, diffuse reflectance relations derived as an approximation to the diffusion dipole theory of Farrell et al. can analyze reflectance ratios accurately, even for much larger absorption than reduced scattering coefficients. This allows calibration of fiber-probe set-ups so that the object's diffuse reflectance can be related to its absorption even when large. These findings will greatly expand the application of diffuse reflection spectroscopy. In medicine, it may allow the use of blue/green wavelengths and measurements on whole blood, and in forensic science, it may allow inclusion of objects such as blood stains and cloth at crime
NASA Astrophysics Data System (ADS)
Bremmer, Rolf H.; van Gemert, Martin J. C.; Faber, Dirk J.; van Leeuwen, Ton G.; Aalders, Maurice C. G.
2013-08-01
Diffuse reflectance spectra are used to determine the optical properties of biological samples. In medicine and forensic science, the turbid objects under study often possess large absorption and/or scattering properties. However, data analysis is frequently based on the diffusion approximation to the radiative transfer equation, implying that it is limited to tissues where the reduced scattering coefficient dominates over the absorption coefficient. Nevertheless, up to absorption coefficients of 20 m at reduced scattering coefficients of 1 and 11.5 mm-1, we observed excellent agreement (r2=0.994) between reflectance measurements of phantoms and the diffuse reflectance equation proposed by Zonios et al. [Appl. Opt.
NASA Astrophysics Data System (ADS)
Spinei, E.; Cede, A.; Swartz, W. H.; Herman, J.; Mount, G. H.
2014-06-01
This paper presents a TEmperature SEnsitivity Method (TESEM) to accurately calculate total vertical NO2 column, atmospheric slant NO2 profile-weighted temperature (T), and to separate stratospheric and tropospheric columns from direct-sun (DS) ground-based measurements using the retrieved T. TESEM is based on Differential Optical Absorption Spectroscopy (DOAS) fitting of the linear temperature-dependent NO2 absorption cross section, σ (T), regression model (Vandaele et al., 2003). The direct result of the DOAS spectral fitting retrieval is NO2 differential slant column density (Δ SCD) at the actual atmospheric NO2 T. Atmospheric NO2 T is determined from the DOAS fitting results after SCD in the reference spectrum is estimated using the Minimum Langley Extrapolation method (MLE). Since NO2 is mostly distributed between the lower troposphere and middle stratosphere and direct sun measurements have almost equal sensitivity to stratospheric and tropospheric absorption at solar zenith angles < 75° with a well known photon path, we assume that the retrieved total column NO2 T can be represented as a sum of the NO2 stratospheric and tropospheric Ts multiplied by the corresponding stratospheric and tropospheric fractions of the total SCDNO2. We use Global Modeling Initiative (GMI) chemistry-transport model (CTM) simulations to evaluate diurnal and seasonal variability of stratospheric and tropospheric NO2 T over two northern middle latitude sites in 2011. GMI simulations reveal that stratospheric NO2 T over northern middle latitudes can be estimated with an error of less than 3 K by the simulated temperature at 27 km from April to October. During November-March months the error can reach as high as 10 K. The tropospheric NO2 T can be approximated by the surface temperature within 3-5 K according to GMI simulations. Traditionally, either σ (NO2) is fitted at a single estimated NO2 T, or two predetermined (stratospheric and tropospheric) temperatures. Use of a single T
NASA Astrophysics Data System (ADS)
Draper, David S.; van Westrenen, Wim
2007-12-01
As a complement to our efforts to update and revise the thermodynamic basis for predicting garnet-melt trace element partitioning using lattice-strain theory (van Westrenen and Draper in Contrib Mineral Petrol, this issue), we have performed detailed statistical evaluations of possible correlations between intensive and extensive variables and experimentally determined garnet-melt partitioning values for trivalent cations (rare earth elements, Y, and Sc) entering the dodecahedral garnet X-site. We applied these evaluations to a database containing over 300 partition coefficient determinations, compiled both from literature values and from our own work designed in part to expand that database. Available data include partitioning measurements in ultramafic to basaltic to intermediate bulk compositions, and recent studies in Fe-rich systems relevant to extraterrestrial petrogenesis, at pressures sufficiently high such that a significant component of majorite, the high-pressure form of garnet, is present. Through the application of lattice-strain theory, we obtained best-fit values for the ideal ionic radius of the dodecahedral garnet X-site, r 0(3+), its apparent Young’s modulus E(3+), and the strain-free partition coefficient D 0(3+) for a fictive REE element J of ionic radius r 0(3+). Resulting values of E, D 0, and r 0 were used in multiple linear regressions involving sixteen variables that reflect the possible influence of garnet composition and stoichiometry, melt composition and structure, major-element partitioning, pressure, and temperature. We find no statistically significant correlations between fitted r 0 and E values and any combination of variables. However, a highly robust correlation between fitted D 0 and garnet-melt Fe Mg exchange and D Mg is identified. The identification of more explicit melt-compositional influence is a first for this type of predictive modeling. We combine this statistically-derived expression for predicting D 0 with the new
NASA Astrophysics Data System (ADS)
Andrzejak, Marcin; Sterzel, Mariusz; Pawlikowski, Marek T.
2005-07-01
The absorption spectra of the N-(2,5-di- tert-butylphenyl) phthalimide ( 1-), N-(2,5-di- tert-butylphenyl)-1,8-naphthalimide ( 2-) and N-(2,5-di- tert-butylphenyl)-perylene-3,4-dicarboximide ( 3-) anion radicals are studied in terms of time dependent density functional theory (TDDFT). For these anion radicals a large number electronic states (from 30 to 60) was found in the visible and near-IR regions (5000-45000 cm -1). In these regions the TD/B3LYP treatment at the 6-1+G* level is shown to reproduce satisfactorily the empirical absorption spectra of all three anion radicals studied. The most apparent discrepancies between purely electronic theory and the experiment could be found in the excitation region corresponding to D0→ D1 transitions in the 2- and 3- molecules. For these species we argue that the structures seen in the lowest energy part of the absorptions of the 2- and 3- species are very likely due to Franck-Condon (FC) activity of the totally symmetric vibrations not studied in this Letter.
Baldacci, L; Zanotto, S; Biasiol, G; Sorba, L; Tredicucci, A
2015-04-01
In order to extend the Coherent Perfect Absorption (CPA) phenomenology to broadband operation, the interferometric control of absorption is investigated in two-port systems without port permutation symmetry. Starting from the two-port theory of CPA treated within the Scattering Matrix formalism, we demonstrate that for all linear two-port systems with reciprocity the absorption is represented by an ellipse as function of the relative phase and intensity of the two input beams, and it is uniquely determined by the device single-beam reflectance and transmittance, and by the dephasing of the output beams. The basic properties of the phenomenon in systems without port permutation symmetry show that CPA conditions can still be found in such asymmetric devices, while the asymmetry can be beneficial for broadband operation. As experimental proof, we performed transmission measurements on a metal-semiconductor metamaterial, employing a Mach-Zehnder interferometer. The experimental results clearly evidence the elliptical feature of absorption and trace a route towards broadband operation. PMID:25968754
Optical absorption in lithiated tungsten oxide thin films: Experiment and theory
NASA Astrophysics Data System (ADS)
Berggren, Lars; Jonsson, Jacob C.; Niklasson, Gunnar A.
2007-10-01
Amorphous tungsten oxide exhibits electrochromism when intercalated with protons, lithium, sodium, and other ions. Thin films of the material were prepared by dc magnetron sputtering and then electrochemically intercalated with lithium. The optical absorption in the wavelength range of 300-2500nm was measured for a number of lithium concentrations. The optical absorption shows a maximum for lithium/tungsten ratios of 0.3-0.5. The optical spectra can be fitted by a superposition of three Gaussian peaks, representing the three possible electronic transitions between W6+, W5+, and W4+ sites. The variation of the peak strength with lithium concentration is consistent with an extended site-saturation theory.
Quantitative first-principles theory of interface absorption in multilayer heterostructures
Hachtel, Jordan A.; Sachan, Ritesh; Mishra, Rohan; Pantelides, Sokrates T.
2015-08-31
The unique chemical bonds and electronic states of interfaces result in optical properties that are different from those of the constituting bulk materials. In the nanoscale regime, the interface effects can be dominant and impact the optical response of devices. Using density functional theory (DFT), the interface effects can be calculated, but DFT is computationally limited to small systems. We describe a method to combine DFT with macroscopic methodologies to extract the interface effect on absorption in a consistent and quantifiable manner. The extracted interface effects are an independent parameter and can be applied to more complicated systems. We demonstrate, using NiSi{sub 2}/Si heterostructures, that by varying the relative volume fractions of interface and bulk, we can tune the spectral range of the heterostructure absorption.
Absorption microspectroscopy, theory and applications in the case of the photosynthetic compartment.
Barsanti, Laura; Evangelista, Valtere; Frassanito, Anna Maria; Vesentini, Nicoletta; Passarelli, Vincenzo; Gualtieri, Paolo
2007-01-01
We performed microspectroscopic evaluation of the pigment composition of the photosynthetic compartments of both algae and higher plants. The feasibility of microspectroscopy for discriminating among species and/or phylogenetic groups was tested on laboratory cultures. Gaussian bands decompositions, and a fitting algorithm, together with fourth-derivative transformation of absorbance spectra, provided a reliable discrimination among chlorophylls, phycobiliproteins and carotenoids. Comparative analysis of absorption spectra highlighted the evolutionary grouping of the algae into three main lineages in accordance with the most recent endosymbiotic theories. PMID:16904900
X-ray absorption spectroscopy study of prototype chemical systems: Theory vs. experiment
NASA Astrophysics Data System (ADS)
Schwartz, Craig Philip
Understanding the details of the intensities and spectral shapes of x-ray absorption spectra is a long-standing problem in chemistry and physics. Here, I present detailed studies of x-ray absorption for prototypical liquids, solids and gases with the goal of enhancing our general understanding of core-level spectroscopy via comparisons of modern theory and experiment. In Chapter 2, I investigate the importance of quantum motions in the x-ray absorption spectra of simple gases. It is found that rare fluctuations in atomic positions can be a cause of features in the spectra of gaseous molecules. In Chapter 3, I explore a novel quantization scheme for the excited and ground state potential surfaces for an isolated nitrogen molecule. This allows for the explicit calculation of the "correct" transition energies and peak widths (i.e. without any adjustable parameters). In Chapter 4, the importance of nuclear motion in molecular solids is investigated for glycine. We find that the inclusion of these motions permits the spectrum to be accurately calculated without any additional adjustable parameters. In Chapter 5, I provide a detailed study of the hydroxide ion solvated in water. There has been recent controversy as to how hydroxide is solvated, with two principal models invoked. I show that some of the computational evidence favoring one model of solvation over the other has been either previously obtained with inadequate precision or via a method that is systematically biased. In Chapter 6, the measured and computed x-ray absorption spectra of pyrrole in both the gas phase and when solvated by water are compared. We are able to accurately predict the spectra in both cases. In Chapter 7, the measured x-ray absorption of a series of highly charged cationic salts (YBr3, CrCl3, SnCl4 , LaCl3 and InCl3) solvated in water are presented and explained. In Chapter 8, the measured x-ray absorption spectrum at the nitrogen K-edge of aqueous triglycine is presented, including
NASA Technical Reports Server (NTRS)
Ma, Q.; Tipping, R. H.
1991-01-01
The present theory for the continuous absorption that is due to the far-wing contribution of allowed lines is based on the quasistatic approximation for the far wing limit and the binary collision approximation of one absorber molecule and one bath molecule. The validity of the theory is discussed, and numerical results of the water-continuum absorption in the IR region are presented for comparison with experimental data. Good agreement is obtained for both the magnitude and temperature dependence of the absorption coefficients.
Ginsberg, M.L.
1996-12-31
We introduce a new form of game search called partition search that incorporates dependency analysis, allowing substantial reductions in the portion of the tree that needs to be expanded. Both theoretical results and experimental data are presented. For the game of bridge, partition search provides approximately as much of an improvement over existing methods as {alpha}-{beta} pruning provides over minimax.
Theory of x-ray absorption: a Bethe-Salpeter approach
NASA Astrophysics Data System (ADS)
Shirley, Eric L.
2002-03-01
First-principles calculations of x-ray absorption spectra of solids is a well-established field. The best known and most used treatments are probably those based on real-space multiple-scattering theory. Such Green's Function approaches are particular useful for incorporating electron damping effects (self-energy effects) that broaden spectral features at high electron kinetic energy. Near-edge structure can also be treated, and it can also be treated in super-cell calculations. In this talk, I will present results obtained using an alternative, reciprocal-space approach based on solving the Bethe-Salpeter equation, which is related to the Bethe-Salpeter method used to treat valence excitation signatures in optical absorption spectra. This amounts to solving the coupling equations of motion for the electron-core hole pair that is produced by x-ray absorption. Mutual localization of the electron and core hole in real space is realized by permitting the electron to exist as a wave-packet of Bloch states peaked near the core hole, governed by the excitation process and ensuing electron core-hole attraction. Because this approach permits state-of-the-art electron band structure calculations to be used to evaluate the electron wave function, this approach is particularly well suited for detailed near-edge structure. In presenting the approach and results obtained, particular attention is focused on (1) the role of the electron-hole interaction, (2) the need to deal with core-hole screening accurately, (3) the evaluation of accurate transition matrix elements between core states and Bloch states, and (4) computational-time scaling issues. This work has been done in collaboration with J.A. Soininen, J.J. Rehr, E.K. Chang, and others. This work was supported in part by the U.S. Deparment of Energy (DOE) Grant DE-FG03-97ER45623 and facilitated by the DOE Computational Materials Science Network (CMSN).
NASA Astrophysics Data System (ADS)
Andruniow, T.; Pawlikowski, M.
2000-05-01
The electronic structure of the low-energy states of the pyromellitic diahydride (PMDA) anion is investigated in terms of the VWN (Vosco-Wilk-Nusair) the BP (Becke-Perdew) and the B3LYP density functional (DF) methods employed with 6-31G * basis sets. All the methods are shown to reproduce correctly the absorption and resonance Raman spectra in the region corresponding to the low-energy 1 2Au→1 2B3g transition. The discrepancies between the theory and experiment are attributed to a (weak) Dushinsky effect predominately due to a mixing of the ν3=1593 cm -1 and ν4=1342 cm -1 vibrations in the 1 2B3 g state of the PMDA radical.
Absorption of scalars by nonextremal charged black holes in string theory
NASA Astrophysics Data System (ADS)
Moura, Filipe
2015-12-01
We analyze the low frequency absorption cross section of minimally coupled massless scalar fields by different kinds of charged static black holes in string theory, namely the D1-D5 system in d=5 and a four dimensional dyonic four-charged black hole. In each case we show that this cross section always has the form of some parameter of the solution divided by the black hole Hawking temperature. We also verify in each case that, despite its explicit temperature dependence, such quotient is finite in the extremal limit, giving a well defined cross section. We show that this precise explicit temperature dependence also arises in the same cross section for black holes with string α ' corrections: it is actually induced by them.
Ackerman, J.P.; Johnson, T.R.
1993-10-01
The chemical basis of Integral Fast Reactor fuel reprocessing (pyroprocessing) is partition of fuel, cladding, and fission product elements between molten LiCl-KCl and either a solid metal phase or a liquid cadmium phase. The partition reactions are described herein, and the thermodynamic basis for predicting distributions of actinides and fission products in the pyroprocess is discussed. The critical role of metal-phase activity coefficients, especially those of rare earth and the transuranic elements, is described. Measured separation factors, which are analogous to equilibrium constants but which involve concentrations rather than activities, are presented. The uses of thermodynamic calculations in process development are described, as are computer codes developed for calculating material flows and phase compositions in pyroprocessing.
Theory and interpretation of L-shell X-ray absorption spectra
NASA Astrophysics Data System (ADS)
Nesvizhskii, Alexey I.
X-ray absorption near edge structure (XANES) directly reflects the electronic structure in a material. However, despite significant progress in XANES theory, the quantitative analysis of XANES is not fully developed and remains a challenge. In this work, a detailed analysis of the L2,3 edge XANES in transition metals was performed using relativistic, self-consistent real space Green's function code FEFFS. Several prescriptions for taking into account core hole in calculations of x-ray absorption spectra (XAS) were discussed. It was found that in most cases of L2,3 edge XANES in transition metals, the initial state (ground state) calculations were in the best agreement with experimental data. A procedure was developed for quantitative applications of the sum rules for XAS, e.g., for x-ray magnetic circular dichroism and for obtaining hole counts. The approach is based on theoretical atomic calculations of transformations relating various experimental spectra to corresponding operator-spectral densities. This approach overcomes the difficulties of background subtraction and hole-count normalization of other sum rule analysis methods and yields quantitative values for spin- and orbital-moments from experimental absorption spectra. The developed approach was theoretically tested and applied to experimental XAS data in Cu, Ni, Co, Fe, and other materials. Hole counts obtained from XAS are often interpreted in terms of free-atom occupation numbers or Mulliken counts. We demonstrated that renormalized-atom (RA) counts are a better choice to characterize the configuration of occupied electron states in molecules and condensed matter. A projection-operator approach was introduced to subtract delocalized states and to determine such hole counts from XAS quantitatively. Theoretical tests for the s- and d-electrons in transition metals showed that the approach works well. A formalism was developed based on time dependent local density approximation (TDLDA) theory that takes
Polarized x-ray-absorption spectroscopy of the uranyl ion: Comparison of experiment and theory
Hudson, E.A.; Allen, P.G.; Terminello, L.J.; Denecke, M.A.; Reich, T.
1996-07-01
The x-ray linear dichroism of the uranyl ion (UO{sub 2}{sup 2+}) in uranium {ital L}{sub 3}-edge extended x-ray-absorption fine structure (EXAFS), and {ital L}{sub 1}- and {ital L}{sub 3}-edge x-ray-absorption near-edge structure (XANES), has been investigated both by experiment and theory. A striking polarization dependence is observed in the experimental XANES and EXAFS for an oriented single crystal of uranyl acetate dihydrate [UO{sub 2}(CH{sub 3}CO{sub 2}){sub 2}{center_dot}2H{sub 2}O], with the x-ray polarization vector aligned either parallel or perpendicular to the bond axis of the linear uranyl cation (O-U-O). Single-crystal results are compared to experimental spectra for a polycrystalline uranyl acetate sample and to calculations using the {ital ab} {ital initio} multiple-scattering (MS) code FEFF 6. Theoretical XANES spectra for uranyl fluoride (UO{sub 2}F{sub 2}) reproduce all the features of the measured uranyl acetate spectra. By identifying scattering paths which contribute to individual features in the calculated spectrum, a detailed understanding of the {ital L}{sub 1}-edge XANES is obtained. MS paths within the uranyl cation have a notable influence upon the XANES. The measured {ital L}{sub 3}-edge EXAFS is also influenced by MS, especially when the x-ray polarization is parallel to the uranyl species. These MS contributions are extracted from the total EXAFS and compared to calculations. The best agreement with the isolated MS signal is obtained by using nonoverlapped muffin-tin spheres in the FEFF 6 calculation. This contrasts the {ital L}{sub 1}-edge XANES calculations, in which overlapping was required for the best agreement with experiment. {copyright} {ital 1996 The American Physical Society.}
Polarized x-ray-absorption spectroscopy of the uranyl ion: Comparison of experiment and theory
NASA Astrophysics Data System (ADS)
Hudson, E. A.; Allen, P. G.; Terminello, L. J.; Denecke, M. A.; Reich, T.
1996-07-01
The x-ray linear dichroism of the uranyl ion (UO2+2) in uranium L3-edge extended x-ray-absorption fine structure (EXAFS), and L1- and L3-edge x-ray-absorption near-edge structure (XANES), has been investigated both by experiment and theory. A striking polarization dependence is observed in the experimental XANES and EXAFS for an oriented single crystal of uranyl acetate dihydrate [UO2(CH3CO2)2.2H2O], with the x-ray polarization vector aligned either parallel or perpendicular to the bond axis of the linear uranyl cation (O-U-O). Single-crystal results are compared to experimental spectra for a polycrystalline uranyl acetate sample and to calculations using the ab initio multiple-scattering (MS) code FEFF 6. Theoretical XANES spectra for uranyl fluoride (UO2F2) reproduce all the features of the measured uranyl acetate spectra. By identifying scattering paths which contribute to individual features in the calculated spectrum, a detailed understanding of the L1-edge XANES is obtained. MS paths within the uranyl cation have a notable influence upon the XANES. The measured L3-edge EXAFS is also influenced by MS, especially when the x-ray polarization is parallel to the uranyl species. These MS contributions are extracted from the total EXAFS and compared to calculations. The best agreement with the isolated MS signal is obtained by using nonoverlapped muffin-tin spheres in the FEFF 6 calculation. This contrasts the L1-edge XANES calculations, in which overlapping was required for the best agreement with experiment.
Wong, Kin-Yiu; Gao, Jiali
2009-01-01
In this paper, we describe an automated integration-free path-integral (AIF-PI) method, based on Kleinert’s variational perturbation (KP) theory, to treat internuclear quantum-statistical effects in molecular systems. We have developed an analytical method to obtain the centroid potential as a function of the variational parameter in the KP theory, which avoids numerical difficulties in path-integral Monte Carlo or molecular dynamics simulations, especially at the limit of zero-temperature. Consequently, the variational calculations using the KP theory can be efficiently carried out beyond the first order, i.e., the Giachetti-Tognetti-Feynman-Kleinert variational approach, for realistic chemical applications. By making use of the approximation of independent instantaneous normal modes (INM), the AIF-PI method can readily be applied to many-body systems. Previously, we have shown that in the INM approximation, the AIF-PI method is accurate for computing the quantum partition function of a water molecule (3 degrees of freedom) and the quantum correction factor for the collinear H3 reaction rate (2 degrees of freedom). In this work, the accuracy and properties of the KP theory are further investigated by using the first three order perturbations on an asymmetric double-well potential, the bond vibrations of H2, HF, and HCl represented by the Morse potential, and a proton-transfer barrier modeled by the Eckart potential. The zero-point energy, quantum partition function, and tunneling factor for these systems have been determined and are found to be in excellent agreement with the exact quantum results. Using our new analytical results at the zero-temperature limit, we show that the minimum value of the computed centroid potential in the KP theory is in excellent agreement with the ground state energy (zero-point energy) and the position of the centroid potential minimum is the expectation value of particle position in wave mechanics. The fast convergent property of
NASA Astrophysics Data System (ADS)
Zhang, Changjian; Wang, Haining; Chan, Weimin; Manolatou, Christina; Rana, Farhan
2014-05-01
We measure the optical-absorption spectra and optical conductivities of excitons and trions in monolayers of metal dichalcogenide MoS2 and compare the results with theoretical models. Our results show that the Wannier-Mott model for excitons with modifications to account for small exciton radii and large exciton relative wave function spread in momentum space, phase space blocking due to Pauli exclusion in doped materials, and wave-vector-dependent dielectric constant gives results that agree well with experiments. The measured exciton optical-absorption spectra are used to obtain experimental estimates for the exciton radii that fall in the 7-10Å range and agree well with theory. The measured trion optical-absorption spectra are used to obtain values for the trion radii that also agree well with theory. The measured values of the exciton and trion radii correspond to binding energies that are in good agreement with values obtained from first-principles calculations.
Prediction of Iron K-Edge Absorption Spectra Using Time-Dependent Density Functional Theory
George, S.DeBeer; Petrenko, T.; Neese, F.
2009-05-14
Iron K-edge X-ray absorption pre-edge features have been calculated using a time-dependent density functional approach. The influence of functional, solvation, and relativistic effects on the calculated energies and intensities has been examined by correlation of the calculated parameters to experimental data on a series of 10 iron model complexes, which span a range of high-spin and low-spin ferrous and ferric complexes in O{sub h} to T{sub d} geometries. Both quadrupole and dipole contributions to the spectra have been calculated. We find that good agreement between theory and experiment is obtained by using the BP86 functional with the CP(PPP) basis set on the Fe and TZVP one of the remaining atoms. Inclusion of solvation yields a small improvement in the calculated energies. However, the inclusion of scalar relativistic effects did not yield any improved correlation with experiment. The use of these methods to uniquely assign individual spectral transitions and to examine experimental contributions to backbonding is discussed.
Theory of the electronic states and absorption spectrum of the LiCl:Ag+ impurity system
NASA Astrophysics Data System (ADS)
Jackson, Koblar A.; Lin, Chun C.
1990-01-01
The impurity absorption spectra of Ag+ and Cu+ impurities in alkali halide hosts show characteristically different features, despite the similar nature of the corresponding free ions. We use the self-interaction-corrected local-spin-density (SIC-LSD) theory to calculate the electronic structure of the ground state (4d) and the 5s and 5p excited states of the LiCl:Ag+ impurity ion. The method of linear combinations of atomic orbitals is used to determine the wave functions and energy levels. By comparing with previous calculations for LiCl:Cu+, we are able to attribute the differences in the d-->s and d-->p transitions in the ultraviolet spectra of these systems to the increased bonding between host crystal and impurity orbitals in LiCl:Ag+, due to the more extensive nature of the Ag+ 4d orbitals. A modification of the earlier SIC-LSD impurity-crystal procedure is introduced to treat the strongly mixed impurity states.
NASA Astrophysics Data System (ADS)
Feldman, Michal; Tennenholtz, Moshe
We introduce partition equilibrium and study its existence in resource selection games (RSG). In partition equilibrium the agents are partitioned into coalitions, and only deviations by the prescribed coalitions are considered. This is in difference to the classical concept of strong equilibrium according to which any subset of the agents may deviate. In resource selection games, each agent selects a resource from a set of resources, and its payoff is an increasing (or non-decreasing) function of the number of agents selecting its resource. While it has been shown that strong equilibrium exists in resource selection games, these games do not possess super-strong equilibrium, in which a fruitful deviation benefits at least one deviator without hurting any other deviator, even in the case of two identical resources with increasing cost functions. Similarly, strong equilibrium does not exist for that restricted two identical resources setting when the game is played repeatedly. We prove that for any given partition there exists a super-strong equilibrium for resource selection games of identical resources with increasing cost functions; we also show similar existence results for a variety of other classes of resource selection games. For the case of repeated games we identify partitions that guarantee the existence of strong equilibrium. Together, our work introduces a natural concept, which turns out to lead to positive and applicable results in one of the basic domains studied in the literature.
NASA Technical Reports Server (NTRS)
Ma, Q.; Tipping, R. H.
1992-01-01
The far wing line shape theory developed previously and applied to the calculation of the continuum absorption of pure water vapor is extended to foreign-broadened continua. Explicit results are presented for H2O-N2 and H2O-CO2 in the frequency range from 0 to 10,000/cm. For H2O-N2 the positive and negative resonant frequency average line shape functions and absorption coefficients are computed for a number of temperatures between 296 and 430 K for comparison with available laboratory data. In general the agreement is very good.
Fischer, Sean A; Cramer, Christopher J; Govind, Niranjan
2016-04-01
Optical-limiting materials are capable of attenuating light to protect delicate equipment from high-intensity light sources. Phthalocyanines have attracted a lot of attention for optical-limiting applications due to their versatility and large nonlinear absorption. With excited-state absorption (ESA) being the primary mechanism for optical limiting behavior in phthalocyanines, the ability to tune the optical absorption of ground and excited states in phthalocyanines would allow for the development of advanced optical limiters. We recently developed a method for the calculation of ESA based on real-time time-dependent density functional theory propagation of an excited-state density. In this work, we apply the approach to zinc phthalocyanine, demonstrating the ability of our method to efficiently identify the optical limiting potential of a molecular complex. PMID:27007445
NASA Astrophysics Data System (ADS)
To, Tran Thinh; Adams, Stefan
2012-06-01
A simple first principle model was developed based on extended Hückel-type orbital calculation, Marcus electron transport theory and two-dimensional-electron-gas model for the treatment of charge transport in conjugated polymers. Though simple and easy to compute, the effect of the applied electric-field is factored in. Based on this, a complete one-dimensional device model with a single layer of conjugated polymer sandwiched between two electrodes was developed with poly(3-hexylthiophene) (P3HT) as a case study. Simulated J-V curves show that π-π charge transport is much more pronounced than intra-chain transport, hence agree with previous findings. Using the same framework, we also calculated the absorption spectra of P3HT by considering the electronic energy barrier for electronic transitions that would satisfy Franck-Condon principle. Absorption spectra closely harmonize to experimental UV-Vis result. The model also reveals intra-chain electronic transitions to be the dominant absorption mechanism. All parameters of the model are obtained from either ab-initio Density Functional Theory (DFT) or Molecular Dynamics (MD) calculations, so that this model is capable of predicting charge transport and light absorption properties of new conjugated polymers without introducing fit parameters.
Bordage, Amélie; Rossano, Stéphanie; Horn, Adolf Heinrich; Fuchs, Yves
2012-06-01
X-ray absorption spectroscopy measurements at the Cr K-edge of a trichroic crystal of alexandrite BeAl(2)O(4):Cr(3+) for different orientations of the crystal with respect to the polarization and direction of the x-ray incident beam have been performed. Analysis of the experimental spectra with the help of first-principles calculations of x-ray absorption spectra allowed us to estimate the proportion of chromium Cr(3+) cations among the two different octahedral sites of the alexandrite structure (70% in the C(s) site-30% in the C(i) site). The methodology presented in this work opens up new possibilities in the field of mineralogy for the study of complex minerals containing several sites potentially occupied by several transition elements or for solid solutions. PMID:22551549
NASA Astrophysics Data System (ADS)
Bordage, Amélie; Rossano, Stéphanie; Horn, Adolf Heinrich; Fuchs, Yves
2012-06-01
X-ray absorption spectroscopy measurements at the Cr K-edge of a trichroic crystal of alexandrite BeAl2O4:Cr3+ for different orientations of the crystal with respect to the polarization and direction of the x-ray incident beam have been performed. Analysis of the experimental spectra with the help of first-principles calculations of x-ray absorption spectra allowed us to estimate the proportion of chromium Cr3+ cations among the two different octahedral sites of the alexandrite structure (70% in the Cs site-30% in the Ci site). The methodology presented in this work opens up new possibilities in the field of mineralogy for the study of complex minerals containing several sites potentially occupied by several transition elements or for solid solutions.
Theory of x-ray absorption and linear dichroism at the Ca L23-edge of CaCO3
NASA Astrophysics Data System (ADS)
Krüger, Peter; Natoli, Calogero R.
2016-05-01
X-ray absorption calculations of Ca L23-edge spectra of calcium carbonate in its two main crystal phases, calcite and aragonite, are reported. The multichannel multiple scattering theory with a correlated particle-hole wave function and a partially screened core-hole potential is used. Very good agreement with experiment for both CaCO3 phases is obtained, while the independent particle approximation completely fails. For aragonite, appreciable linear dichroism is predicted in agreement with recent observations.
Hoge, F E; Wright, C W; Lyon, P E; Swift, R N; Yungel, J K
1999-12-20
Oceanic radiance model inversion methods are used to develop a comprehensive algorithm for retrieval of the absorption coefficients of phycourobilin (PUB) pigment, type I phycoerythrobilin (PEB) pigment rich in PUB, and type II PEB deficient in PUB pigment (together with the usual "big three" inherent optical properties: the total backscattering coefficient and the absorption coefficients of chromophoric dissolved organic matter (CDOM)-detritus and phytoplankton). This fully modeled inversion algorithm is then simplified to yield a hybrid modeled-unmodeled inversion algorithm in which the phycoerythrin (PE) absorption coefficient is retrieved as unmodeled 488-nm absorption (which exceeds the modeled phytoplankton and the CDOM-detritus absorption coefficients). Each algorithm was applied to water-leaving radiances, but only hybrid modeled-unmodeled inversions yielded viable retrievals of the PE absorption coefficient. Validation of the PE absorption coefficient retrieval was achieved by relative comparison with airborne laser-induced PEB fluorescence. The modeled-unmodeled retrieval of four inherent optical properties by direct matrix inversion is rapid and well conditioned, but the accuracy is strongly limited by the accuracy of the three principal inherent optical property models across all four spectral bands. Several research areas are identified to enhance the radiance-model-based retrievals: (a) improved PEB and PUB absorption coefficient models, (b) PE spectral shifts induced by PUB chromophore substitution at chromophore binding sites, (c) specific absorption-sensitive phytoplankton absorption modeling, (d) total constituent backscattering modeling, (e) unmodeled carotinoid and phycocyanin absorption that are not now accounted for in the chlorophyll-dominated phytoplankton absorption coefficient model, and (f) iterative inversion techniques to solve for six constituents with only five radiances. Although considerable progress has been made toward the
NASA Astrophysics Data System (ADS)
Hoge, Frank E.; Wright, C. Wayne; Lyon, Paul E.; Swift, Robert N.; Yungel, James K.
1999-12-01
Oceanic radiance model inversion methods are used to develop a comprehensive algorithm for retrieval of the absorption coefficients of phycourobilin (PUB) pigment, type I phycoerythrobilin (PEB) pigment rich in PUB, and type II PEB deficient in PUB pigment (together with the usual big three inherent optical properties: the total backscattering coefficient and the absorption coefficients of chromophoric dissolved organic matter (CDOM) detritus and phytoplankton). This fully modeled inversion algorithm is then simplified to yield a hybrid modeled unmodeled inversion algorithm in which the phycoerythrin (PE) absorption coefficient is retrieved as unmodeled 488-nm absorption (which exceeds the modeled phytoplankton and the CDOM detritus absorption coefficients). Each algorithm was applied to water-leaving radiances, but only hybrid modeled unmodeled inversions yielded viable retrievals of the PE absorption coefficient. Validation of the PE absorption coefficient retrieval was achieved by relative comparison with airborne laser-induced PEB fluorescence. The modeled unmodeled retrieval of four inherent optical properties by direct matrix inversion is rapid and well conditioned, but the accuracy is strongly limited by the accuracy of the three principal inherent optical property models across all four spectral bands. Several research areas are identified to enhance the radiance-model-based retrievals: (a) improved PEB and PUB absorption coefficient models, (b) PE spectral shifts induced by PUB chromophore substitution at chromophore binding sites, (c) specific absorption-sensitive phytoplankton absorption modeling, (d) total constituent backscattering modeling, (e) unmodeled carotinoid and phycocyanin absorption that are not now accounted for in the chlorophyll-dominated phytoplankton absorption coefficient model, and (f) iterative inversion techniques to solve for six constituents with only five radiances. Although considerable progress has been made toward the satellite
NASA Astrophysics Data System (ADS)
Aryanpour, Karan; Roberts, Adam; Sandhu, Arvinder; Shukla, Alok; Mazumdar, Sumit
2013-03-01
Historically, the occurrence of the lowest two-photon state below the optical one-photon state in linear polyenes, polyacetylenes and polydiacetylenes provided the strongest evidence for strong electron correlations in these linear π-conjugated systems. We demonstrate similar behavior in several molecular fragments of graphene with D6 h symmetry, theoretically and experimentally. Theoretically, we have calculated one versus two-photon absorptions in coronene, two different hexabenzocoronenes and circumcoronene, within the Pariser-Parr-Pople π-electron Hamiltonian using high order configuration interaction. Experimentally, we have performed z-scan measurements using a white light super-continuum source on coronene and hexa-peri-hexabenzocoronene to determine frequency-dependent two-photon absorption coefficients, for comparison to the ground state absorptions. Excellent agreement between experiment and theory in our work gives strong evidence for significant electron correlations between the π-electrons in the graphene molecular fragments. We particularly benchmark high order electron-hole excitations in graphene fragments as a key element behind the agreement between theory and experiment in this work. We acknowledge NSF-CHE-1151475 grant as our funding source.
NASA Astrophysics Data System (ADS)
Sims, D. A.; Kwon, H.; Luo, H.; Oechel, W.; Gamon, J.
2001-12-01
Comparisons between eddy covariance measurements of CO2 flux and remotely sensed spectral reflectance are often limited by mis-matches in temporal and spatial scales. Eddy flux measurements are made continuously through time whereas satellite sensors typically measure only once per day or less and many days may be lost because of cloud cover. In addition, satellite sensors such as MODIS have pixel sizes as large as a whole eddy flux footprint, making precise spatial correlation difficult. In order to better match the temporal and spatial scales of remote sensing measurements to those of eddy flux, we installed automated systems (optical sampling instruments on a tram system) within eddy covariance tower footprints at Sky Oaks field station near San Diego, CA. This system measured hyperspectral (narrow-band) reflectance over a 100 m transect throughout diurnal and seasonal cycles. These data were used to explore the controls on carbon flux and to develop models for scaling eddy flux measurements to the surrounding region. Fractional absorbed radiation (estimated from NDVI) varied dramatically over the diurnal cycle but was relatively constant across seasons in this evergreen shrub dominated system. By contrast, seasonal carbon flux varied more closely with optical signals of light-use efficiency. Consequently, large seasonal changes in carbon flux were primarily a function of light-use efficiency rather than light absorption. These data suggest that models based solely on light absorption by vegetation may miss large fluctuations in carbon exchange resulting from downregulation of photosynthesis. Although this ecosystem may be an extreme case, there are many evergreen ecosystems in which photosynthetic downregulation could play a large role. Application of this optical measuring system at other FLUXNET sites would greatly increase our understanding of the role of photosynthetic downregulation in global carbon cycles.
Rate- and Extent-Limiting Factors of Oral Drug Absorption: Theory and Applications.
Sugano, Kiyohiko; Terada, Katsuhide
2015-09-01
The oral absorption of drugs has been represented by various concepts such as the absorption potential, the maximum absorbable dose, the biopharmaceutics classification system, and in vitro-in vivo correlation. The aim of this article is to provide an overview of the theoretical relationships between these concepts. It shows how a simple analytical solution for the fraction of a dose absorbed (Fa equation) can offer a theoretical base to tie together the various concepts, and discusses how this solution relates to the rate-limiting cases of oral drug absorption. The article introduces the Fa classification system as a framework in which all the above concepts were included, and discusses its applications for food effect prediction, active pharmaceutical ingredient form selection, formulation design, and biowaiver strategy. PMID:25712830
NASA Technical Reports Server (NTRS)
Eparvier, F. G.; Barth, C. A.
1992-01-01
Observations of the UV fluorescent emissions of the NO (1, 0) and (0, 1) gamma bands in the lower-thermospheric dayglow, made with a sounding rocket launched on March 7, 1989 from Poker Flat, Alaska, were analyzed. The resonant (1, 0) gamma band was found to be attenuated below an altitude of about 120 km. A self-absorption model based on Holstein transmission functions was developed for the resonant (1, 0) gamma band under varying conditions of slant column density and temperature and was applied for the conditions of the rocket flight. The results of the model agreed with the measured attenuation of the band, indicating the necessity of including self-absorption theory in the analysis of satellite and rocket limb data of NO.
2014-01-01
Atomistic level understanding of interaction of α,β-unsaturated carbonyls with late transition metals is a key prerequisite for rational design of new catalytic materials with the desired selectivity toward C=C or C=O bond hydrogenation. The interaction of this class of compounds with transition metals was investigated on α,β-unsaturated ketone isophorone on Pd(111) as a prototypical system. In this study, infrared reflection–absorption spectroscopy (IRAS), near-edge X-ray absorption fine structure (NEXAFS) experiments, and density functional theory calculations including van der Waals interactions (DFT+vdW) were combined to obtain detailed information on the binding of isophorone to palladium at different coverages and on the effect of preadsorbed hydrogen on the binding and adsorption geometry. According to these experimental observations and the results of theoretical calculations, isophorone adsorbs on Pd(111) in a flat-lying geometry at low coverages. With increasing coverage, both C=C and C=O bonds of isophorone tilt with respect to the surface plane. The tilting is considerably more pronounced for the C=C bond on the pristine Pd(111) surface, indicating a prominent perturbation and structural distortion of the conjugated π system upon interaction with Pd. Preadsorbed hydrogen leads to higher tilting angles of both π bonds, which points to much weaker interaction of isophorone with hydrogen-precovered Pd and suggests the conservation of the in-plane geometry of the conjugated π system. The results of the DFT+vdW calculations provide further insights into the perturbation of the molecular structure of isophorone on Pd(111). PMID:26089998
De Vrieze, Mike; Janssens, Pieter; Szucs, Roman; Van der Eycken, Johan; Lynen, Frédéric
2015-09-01
Over the past decades, several in vitro methods have been tested for their ability to predict either human intestinal absorption (HIA) or penetration across the blood-brain barrier (BBB) of drugs. Micellar liquid chromatography (MLC) has been a successful approach for retention time measurements of drugs to establish models together with other molecular descriptors. Thus far, MLC approaches have only made use of commercial surfactants such as sodium dodecyl sulfate (SDS) and polyoxyethylene (23) lauryl ether (Brij35), which are not representative for the phospholipids present in human membranes. Miltefosine, a phosphocholine-based lipid, is presented here as an alternative surfactant for MLC measurements. By using the obtained retention factors and several computed descriptors for a set of 48 compounds, two models were constructed: one for the prediction of HIA and another for the prediction of penetration across the BBB expressed as log BB. All data were correlated to experimental HIA and log BB values, and the performance of the models was evaluated. Log BB prediction performed better than HIA prediction, although HIA prediction was also improved a lot (from 0.5530 to 0.7175) compared to in silico predicted HIA values. PMID:26277183
Absorption and diffusion of hydrogen in palladium-silver alloys by density functional theory
NASA Astrophysics Data System (ADS)
Ke, Xuezhi; Kramer, Gert Jan
2002-11-01
The vibrational states, absorption energies, and diffusions of H in Pd and Pd1-xAgx(0<~x<~1) have been studied by first-principle calculations. All results compare favorably to experiment. The zero-point motion of H is important in the determination of the H site occupation, in the estimation of the diffusion barrier, and in the explanation of the reversed isotope effect. The interesting anomalous isotope effect is explored, and a diffusion mechanism is proposed for tritium. The preferred diffusion paths of H in Pd and Pd1-xAgx are “indirect” paths. According to the absorption energies and diffusion barriers, H diffusion in Pd-Ag alloys should avoid the Ag-rich areas.
Theory of the anomalous resonant absorption of DNA at microwave frequencies.
Van Zandt, L L; Davis, M E
1986-04-01
Aqueous solutions of oligopolymer DNA have been observed by Edwards, Davis, Swicord & Saffer to show structured absorption of microwave energy in the region of several gigahertz characteristic of an ordered series of compressional normal mode vibrations propagating on the polymer chain. Hydrodynamic coupling of such vibrations to the surrounding solvent would preclude the existence of sharp resonances. The inclusion of electromagnetic interactions with surrounding counter ions yields a richer space of possibilities for complex behavior of the combined system. A well defined resonant absorption peak appears when the molecular motion and the nearby solvent motion are even slightly decoupled. The microwave electric fields in the vicinity of the molecule provide a mechanism for such a decoupling not present for the case of electrically neutral solvent. PMID:3271413
NASA Astrophysics Data System (ADS)
Walkenhorst, Jessica; De Giovannini, Umberto; Castro, Alberto; Rubio, Angel
2016-05-01
Recent advances in laser technology allow us to follow electronic motion at its natural time-scale with ultra-fast time resolution, leading the way towards attosecond physics experiments of extreme precision. In this work, we assess the use of tailored pumps in order to enhance (or reduce) some given features of the probe absorption (for example, absorption in the visible range of otherwise transparent samples). This type of manipulation of the system response could be helpful for its full characterization, since it would allow us to visualize transitions that are dark when using unshaped pulses. In order to investigate these possibilities, we perform first a theoretical analysis of the non-equilibrium response function in this context, aided by one simple numerical model of the hydrogen atom. Then, we proceed to investigate the feasibility of using time-dependent density-functional theory as a means to implement, theoretically, this absorption-optimization idea, for more complex atoms or molecules. We conclude that the proposed idea could in principle be brought to the laboratory: tailored pump pulses can excite systems into light-absorbing states. However, we also highlight the severe numerical and theoretical difficulties posed by the problem: large-scale non-equilibrium quantum dynamics are cumbersome, even with TDDFT, and the shortcomings of state-of-the-art TDDFT functionals may still be serious for these out-of-equilibrium situations.
Pollard, W.T.; Peteanu, L.A.; Mathies, R.A.
1992-07-23
A time-dependent theory for femtosecond dynamic absorption spectroscopy is used to describe the creation and observation of molecular ground-state vibrational coherence through the resonance impulsive stimulated Raman mechanism. Model calculations show that the oscillatory absorption signal that arises from this ground-state coherence is maximized for a limited range of pulse lengths and that there is a complex relationship between the probe wavelength and the strength of the spectral oscillations. The generalized time-dependent linear susceptibility of the nonstationary system created by the impulsive pump pulse is defined and used to discuss the strong dependence of the measured signals on the properties of the probe pulse. Finally, calculations are presented to analyze the high-frequency oscillations ({approximately}20-fs period) recently observed in the transient absorption spectra of light-adapted bacteriorhodopsin (BR{sub 568}) following excitation with a 12-fs optical pulse. At the probe wavelengths used in this experiment, the contribution of stimulated emission is negligible at long times because of the extremely rapid excited-state isomerization; as a result, the spectral oscillations observed after this time are due to the impulsive excitation of coherent vibrations in the ground state. The transient response observed for BR{sub 568} is calculated using a 29-mode harmonic potential surface derived from a prior resonance Raman intensity analysis. Both the oscillatory signals and their dependence on the probe wavelength are satisfactorily reproduced. 68 refs., 11 figs.
NASA Astrophysics Data System (ADS)
Carati, Andrea; Galgani, Luigi
2014-10-01
This paper is a continuation of a recent one in which, apparently for the first time, the existence of polaritons in ionic crystals was proven in a microscopic electrodynamic theory. This was obtained through an explicit computation of the dispersion curves. Here the main further contribution consists in studying electric susceptibility, from which the spectrum can be inferred. We show how susceptibility is obtained by the Green-Kubo methods of Hamiltonian statistical mechanics, and give for it a concrete expression in terms of time-correlation functions. As in the previous paper, here too we work in a completely classical framework, in which the electrodynamic forces acting on the charges are all taken into account, both the retarded forces and the radiation reaction ones. So, in order to apply the methods of statistical mechanics, the system has to be previously reduced to a Hamiltonian one. This is made possible in virtue of two global properties of classical electrodynamics, namely, the Wheeler-Feynman identity and the Ewald resummation properties, the proofs of which were already given for ordered system. The second contribution consists in formulating the theory in a completely general way, so that in principle it applies also to disordered systems such as glasses, or liquids or gases, provided the two general properties mentioned above continue to hold. A first step in this direction is made here by providing a completely general proof of the Wheeler-Feynman identity, which is shown to be the counterpart of a general causality property of classical electrodynamics. Finally it is shown how a line spectrum can appear at all in classical systems, as a counterpart of suitable stability properties of the motions, with a broadening due to a coexistence of chaoticity. The relevance of some recent results of the theory of dynamical systems in this connection is also pointed out.
The energy of the vacuum related to the theory of energy absorption
NASA Astrophysics Data System (ADS)
Danilov, A. P.
2016-07-01
The primary objective in this article is to investigate a new source of renewable energy, the existence of the vacuum in five environments, and the possibility of absorption of the explosion. The study has also addressed the development of new principles in the motor industry, protection against explosions, new principles of mineral processing and new types of explosives. Also, this study may offer some insight into new approaches in solving problems in thermodynamics, the development of gravity waves, the basis of renewable energy source, and the mechanism of the emergence of gravitational waves.
Near-Edge X-ray Absorption Fine Structure within Multilevel Coupled Cluster Theory.
Myhre, Rolf H; Coriani, Sonia; Koch, Henrik
2016-06-14
Core excited states are challenging to calculate, mainly because they are embedded in a manifold of high-energy valence-excited states. However, their locality makes their determination ideal for local correlation methods. In this paper, we demonstrate the performance of multilevel coupled cluster theory in computing core spectra both within the core-valence separated and the asymmetric Lanczos implementations of coupled cluster linear response theory. We also propose a visualization tool to analyze the excitations using the difference between the ground-state and excited-state electron densities. PMID:27182829
NASA Technical Reports Server (NTRS)
Borel, Christoph C.; Schlaepfer, Daniel
1996-01-01
Two different approaches exist to retrieve columnar water vapor from imaging spectrometer data: (1) Differential absorption techniques based on: (a) Narrow-Wide (N/W) ratio between overlapping spectrally wide and narrow channels; (b) Continuum Interpolated Band Ratio (CIBR) between a measurement channel and the weighted sum of two reference channels. (2) Non-linear fitting techniques which are based on spectral radiative transfer calculations. The advantage of the first approach is computational speed and of the second, improved retrieval accuracy. Our goal was to improve the accuracy of the first technique using physics based on radiative transfer. Using a modified version of the Duntley equation, we derived an "Atmospheric Pre-corrected Differential Absorption" (APDA) technique and described an iterative scheme to retrieve water vapor on a pixel-by-pixel basis. Next we compared both, the CIBR and the APDA using the Duntley equation for MODTRAN3 computed irradiances, transmissions and path radiance (using the DISORT option). This simulation showed that the CIBR is very sensitive to reflectance effects and that the APDA performs much better. An extensive data set was created with the radiative transfer code 6S over 379 different ground reflectance spectra. The calculated relative water vapor error was reduced significantly for the APDA. The APDA technique had about 8% (vs. over 35% for the CIBR) of the 379 spectra with a relative water vapor error of greater than +5%. The APDA has been applied to 1991 and 1995 AVIRIS scenes which visually demonstrate the improvement over the CIBR technique.
Theory of microwave absorption by the spin-1/2 Heisenberg-Ising magnet.
Brockmann, Michael; Göhmann, Frank; Karbach, Michael; Klümper, Andreas; Weisse, Alexander
2011-07-01
We analyze the problem of microwave absorption by the Heisenberg-Ising magnet in terms of shifted moments of the imaginary part of the dynamical susceptibility. When both the Zeeman field and the wave vector of the incident microwave are parallel to the anisotropy axis, the first four moments determine the shift of the resonance frequency and the linewidth in a situation where the frequency is varied for fixed Zeeman field. For the one-dimensional model we can calculate the moments exactly. This provides exact data for the resonance shift and the linewidth at arbitrary temperatures and magnetic fields. In current ESR experiments the Zeeman field is varied for fixed frequency. We show how in this situation the moments give perturbative results for the resonance shift and for the integrated intensity at small anisotropy as well as an explicit formula connecting the linewidth with the anisotropy parameter in the high-temperature limit. PMID:21797567
Borel, C.C.; Schlaepfer, D.
1996-03-01
Two different approaches exist to retrieve columnar water vapor from imaging spectrometer data: (1) Differential absorption techniques based on: (a) Narrow-Wide (N/W) ratio between overlapping spectrally wide and narrow channels (b) Continuum Interpolated Band Ratio (CIBR) between a measurement channel and the weighted sum of two reference channels; and (2) Non-linear fitting techniques which are based on spectral radiative transfer calculations. The advantage of the first approach is computational speed and of the second, improved retrieval accuracy. Our goal was to improve the accuracy of the first technique using physics based on radiative transfer. Using a modified version of the Duntley equation, we derived an {open_quote}Atmospheric Pre-corrected Differential Absorption{close_quote} (APDA) technique and described an iterative scheme to retrieve water vapor on a pixel-by-pixel basis. Next we compared both, the CIBR and the APDA using the Duntley equation for MODTRAN3 computed irradiances, transmissions and path radiance (using the DISORT option). This simulation showed that the CIBR is very sensitive to reflectance effects and that the APDA performs much better. An extensive data set was created with the radiative transfer code 6S over 379 different ground reflectance spectra. The calculated relative water vapor error was reduced significantly for the APDA. The APDA technique had about 8% (vs. over 35% for the CIBR) of the 379 spectra with a relative water vapor error of greater than {+-}5%. The APDA has been applied to 1991 and 1995 AVIRIS scenes which visually demonstrate the improvement over the CIBR technique.
Theory of x-ray absorption by laser-dressed atoms
Buth, Christian; Santra, Robin
2007-03-15
An ab initio theory is devised for the x-ray photoabsorption cross section of atoms in the field of a moderately intense optical laser (800 nm, 10{sup 13} W/cm{sup 2}). The laser dresses the core-excited atomic states, which introduces a dependence of the cross section on the angle between the polarization vectors of the two linearly polarized radiation sources. We use the Hartree-Fock-Slater approximation to describe the atomic many-particle problem in conjunction with a nonrelativistic quantum-electrodynamic approach to treat the photon-electron interaction. The continuum wave functions of ejected electrons are treated with a complex absorbing potential that is derived from smooth exterior complex scaling. The solution to the two-color (x-ray plus laser) problem is discussed in terms of a direct diagonalization of the complex symmetric matrix representation of the Hamiltonian. Alternative treatments with time-independent and time-dependent non-Hermitian perturbation theories are presented that exploit the weak interaction strength between x rays and atoms. We apply the theory to study the photoabsorption cross section of krypton atoms near the K edge. A pronounced modification of the cross section is found in the presence of the optical laser.
Gas/particle partitioning of 2-methyltetrols and levoglucosan at an urban site in Denver.
Xie, Mingjie; Hannigan, Michael P; Barsanti, Kelley C
2014-01-01
In this study, a medium volume sampler incorporating quartz fiber filters (QFFs) and a polyurethane foam (PUF)/XAD/PUF sandwich (PXP) was used to collect 2-methyltetrols (isoprene tracer) and levoglucosan (biomass burning tracer) in gaseous and particle (PM2.5) phases. The measured gas/particle (G/P) partitioning coefficients (Kp,OMm) of 2-methyltetrols and levoglucosan were calculated and compared to their predicted G/P partitioning coefficients (Kp,OMt) based on an absorptive partitioning theory. The breakthrough experiments showed that gas-phase 2-methyltetrols and levoglucosan could be collected using the PXP or PUF adsorbent alone, with low breakthrough; however, the recoveries of levoglucosan in PXP samples were lower than 70% (average of 51.9–63.3%). The concentration ratios of 2-methyltetrols and levoglucosan in the gas phase to those in the particle phase were often close to or higher than unity in summer, indicating that these polar species are semi-volatile and their G/P partitioning should be considered when applying particle-phase data for source apportionment. The Kp,OMm values of 2-methyltetrols had small variability in summer Denver, which was ascribed to large variations in concentrations of particulate organic matter (5.14 ± 3.29 μg m–3) and small changes in ambient temperature (21.8 ± 4.05 °C). The regression between log Kp,OMm and log Kp,OMt suggested that the absorptive G/P partitioning theory could reasonably predict the measured G/P partitioning of levoglucosan in ambient samples. PMID:24517510
NASA Astrophysics Data System (ADS)
Dimakis, Nicholas; Farooqi, Mohammed Junaid; Garza, Emily Sofia; Bunker, Grant
2008-03-01
Density functional theory (DFT) and x-ray absorption fine structure (XAFS) spectroscopy are complementary tools for the biophysical study of active sites in metalloproteins. DFT is used to compute XAFS multiple scattering Debye Waller factors, which are then employed in genetic algorithm-based fitting process to obtain a global fit to the XAFS in the space of fitting parameters. Zn-Cys sites, which serve important functions as transcriptional switches in Zn finger proteins and matrix metalloproteinases, previously have proven intractable by this method; here these limitations are removed. In this work we evaluate optimal DFT nonlocal functionals and basis sets for determining optimal geometries and vibrational densities of states of mixed ligation Zn(His)4-n(Cys)n sites. Theoretical results are compared to experimental XAFS measurements and Raman spectra from the literature and tabulated for use.
NASA Astrophysics Data System (ADS)
Zanatta, G.; Gottfried, C.; Silva, A. M.; Caetano, E. W. S.; Sales, F. A. M.; Freire, V. N.
2014-03-01
Results of optical absorption measurements are presented together with calculated structural, electronic, and optical properties for the anhydrous monoclinic L-asparagine crystal. Density functional theory (DFT) within the generalized gradient approximation (GGA) including dispersion effects (TS, Grimme) was employed to perform the calculations. The optical absorption measurements revealed that the anhydrous monoclinic L-asparagine crystal is a wide band gap material with 4.95 eV main gap energy. DFT-GGA+TS simulations, on the other hand, produced structural parameters in very good agreement with X-ray data. The lattice parameter differences Δa, Δb, Δc between theory and experiment were as small as 0.020, 0.051, and 0.022 Å, respectively. The calculated band gap energy is smaller than the experimental data by about 15%, with a 4.23 eV indirect band gap corresponding to Z → Γ and Z → β transitions. Three other indirect band gaps of 4.30 eV, 4.32 eV, and 4.36 eV are assigned to α3 → Γ, α1 → Γ, and α2 → Γ transitions, respectively. Δ-sol computations, on the other hand, predict a main band gap of 5.00 eV, just 50 meV above the experimental value. Electronic wavefunctions mainly originating from O 2p-carboxyl, C 2p-side chain, and C 2p-carboxyl orbitals contribute most significantly to the highest valence and lowest conduction energy bands, respectively. By varying the lattice parameters from their converged equilibrium values, we show that the unit cell is less stiff along the b direction than for the a and c directions. Effective mass calculations suggest that hole transport behavior is more anisotropic than electron transport, but the mass values allow for some charge mobility except along a direction perpendicular to the molecular layers of L-asparagine which form the crystal, so anhydrous monoclinic L-asparagine crystals could behave as wide gap semiconductors. Finally, the calculations point to a high degree of optical anisotropy for the
Zanatta, G.; Gottfried, C.; Silva, A. M.; Caetano, E. W. S.; Sales, F. A. M.; Freire, V. N.
2014-03-28
Results of optical absorption measurements are presented together with calculated structural, electronic, and optical properties for the anhydrous monoclinic L-asparagine crystal. Density functional theory (DFT) within the generalized gradient approximation (GGA) including dispersion effects (TS, Grimme) was employed to perform the calculations. The optical absorption measurements revealed that the anhydrous monoclinic L-asparagine crystal is a wide band gap material with 4.95 eV main gap energy. DFT-GGA+TS simulations, on the other hand, produced structural parameters in very good agreement with X-ray data. The lattice parameter differences Δa, Δb, Δc between theory and experiment were as small as 0.020, 0.051, and 0.022 Å, respectively. The calculated band gap energy is smaller than the experimental data by about 15%, with a 4.23 eV indirect band gap corresponding to Z → Γ and Z → β transitions. Three other indirect band gaps of 4.30 eV, 4.32 eV, and 4.36 eV are assigned to α3 → Γ, α1 → Γ, and α2 → Γ transitions, respectively. Δ-sol computations, on the other hand, predict a main band gap of 5.00 eV, just 50 meV above the experimental value. Electronic wavefunctions mainly originating from O 2p–carboxyl, C 2p–side chain, and C 2p–carboxyl orbitals contribute most significantly to the highest valence and lowest conduction energy bands, respectively. By varying the lattice parameters from their converged equilibrium values, we show that the unit cell is less stiff along the b direction than for the a and c directions. Effective mass calculations suggest that hole transport behavior is more anisotropic than electron transport, but the mass values allow for some charge mobility except along a direction perpendicular to the molecular layers of L-asparagine which form the crystal, so anhydrous monoclinic L-asparagine crystals could behave as wide gap semiconductors. Finally, the calculations point to a high degree of optical
Theory of Jahn Teller signatures in the infrared absorption of C603-
NASA Astrophysics Data System (ADS)
Naghavi, S. Shahab; Fabrizio, Michele; Tosatti, Erio; Condensed Matter Physics Team
2014-03-01
Among the molecular superconductors, trivalent fullerides such as Cs3C60, with three folded degenerate HOMO and a fully ordered pressure induced superconductor-insulator are still intriguing. The orbital degeneracy of the fulleride ion C60-3 implies that besides a Jahn-Teller distorted state with S=1/2 and high-lying spin (S=3/2) excitation known from NMR, another undetected orbital excitation with S=1/2 should exist. Building upon accurate density hybrid functional theory calculations where properties such as the infrared (IR) spectrum and its Jahn-Teller features are well described, we extracted the ab-initio orbital and spin spectrum of a C60-3 ion in different spin and orbital states including a new low lying L=2 S=1/2 excitation. Despite a Jahn-Teller distortion so small to be observable in its IR spectrum, this state is found to gain a large zero-point energy, placing it just above the L=1, S=1/2 ion ground state, and way below the L=0, S=3/2 high lying excitation. We can now elegantly explain the surprising early thermal disappearance of the low-temperature Jahn-Teller IR spectral features and splitting without a concurrent rise of spin susceptibility that would instead be required by population of the high spin S=3/2 excitation. Sponsored by EU LEMSUPER Grant 283214.
Ansari, Seraj A; Bhattacharyya, Arunasis; Zhang, Zhicheng; Rao, Linfeng
2015-09-01
Complexation of NpO2(+) ions with glutaroimide dioxime (H2L), a cyclic imide dioxime ligand that has been shown to form strong complexes with UO2(2+) in aqueous solutions, was studied by absorption spectroscopy and microcalorimetry in 1.0 M NaClO4 aqueous solutions. NpO2(+) forms two successive complexes, NpO2(HL)(aq) and NpO2(HL)2(-) (where HL(-) stands for the partially deprotonated glutaroimide dioxime ligand), with stability constants of log β111 = 17.8 ± 0.1 and log β122 = 33.0 ± 0.2, respectively. The complexation is both enthalpy- and entropy-driven, with negative enthalpies (ΔH111 = -52.3 ± 1.0 kJ/mol and ΔH122 = -96.1 ± 1.4 kJ/mol) and positive entropies (ΔS111 = 164 ± 3 J/mol/K and ΔS122 = 310 ± 4 J/mol/K). The thermodynamic parameters suggest that, similar to complexation of UO2(2+), the ligand coordinates with NpO2(+) in a tridentate mode, via the two oxygen atoms of the oxime groups and the nitrogen atom of the imide group. Density functional theory calculations have helped to interpret the optical absorption properties of the NpO2(HL)2(-) complex, by showing that the cis and trans configurations of the complex have very similar energies so that both configurations could be present in the aqueous solutions. It is the noncentrosymmetric cis configuration that makes the 5f → 5f transition allowable so that the NpO2(HL)2(-) complex absorbs in the near-IR region. PMID:26263050
NASA Astrophysics Data System (ADS)
Gaebler, Peter J.; Eulenfeld, Tom; Wegler, Ulrich
2015-12-01
In this study, frequency-dependent seismic scattering and intrinsic attenuation parameters for the crustal structure beneath the W-Bohemia/Vogtland swarm earthquake region close to the border of Czech Republic and Germany are estimated. Synthetic seismogram envelopes are modelled using elastic and acoustic radiative transfer theory. Scattering and absorption parameters are determined by fitting these synthetic envelopes to observed seismogram envelopes from 14 shallow local events from the October 2008 W-Bohemia/Vogtland earthquake swarm. The two different simulation approaches yield similar results for the estimated crustal parameters and show a comparable frequency dependence of both transport mean free path and intrinsic absorption path length. Both methods suggest that intrinsic attenuation is dominant over scattering attenuation in the W-Bohemia/Vogtland region for the investigated epicentral distance range and frequency bands from 3 to 24 Hz. Elastic simulations of seismogram envelopes suggest that forward scattering is required to explain the data, however, the degree of forward scattering is not resolvable. Errors in the parameter estimation are smaller in the elastic case compared to results from the acoustic simulations. The frequency decay of the transport mean free path suggests a random medium described by a nearly exponential autocorrelation function. The fluctuation strength and correlation length of the random medium cannot be estimated independently, but only a combination of the parameters related to the transport mean free path of the medium can be computed. Furthermore, our elastic simulations show, that using our numerical method, it is not possible to resolve the value of the mean free path of the random medium.
Karman, Tijs; Avoird, Ad van der; Groenenboom, Gerrit C.
2015-02-28
We discuss three quantum mechanical formalisms for calculating collision-induced absorption spectra. First, we revisit the established theory of collision-induced absorption, assuming distinguishable molecules which interact isotropically. Then, the theory is rederived incorporating exchange effects between indistinguishable molecules. It is shown that the spectrum can no longer be written as an incoherent sum of the contributions of the different spherical components of the dipole moment. Finally, we derive an efficient method to include the effects of anisotropic interactions in the computation of the absorption spectrum. This method calculates the dipole coupling on-the-fly, which allows for the uncoupled treatment of the initial and final states without the explicit reconstruction of the many-component wave functions. The three formalisms are applied to the collision-induced rotation-translation spectra of hydrogen molecules in the far-infrared. Good agreement with experimental data is obtained. Significant effects of anisotropic interactions are observed in the far wing.
NASA Astrophysics Data System (ADS)
Rasulov, R. Ya.; Rasulov, V. R.; Eshboltaev, I.
2016-05-01
An occurrence of the current of the shift linear photovoltaic effect under two-photon absorption of light in semiconductors without a center of symmetry with a complex band structure is theoretically analyzed. The contributions both from the simultaneous absorption of two photons and successive absorption of two single photons to the photocurrent are taken into account.
Inner-Shell Absorption Lines of Fe 6-Fe 16: a Many-Body Perturbation Theory Approach
Gu, Ming F.; Holczer, Tomer; Behar, Ehud; Kahn, Steven M.; /KIPAC, Menlo Park
2006-01-17
We provide improved atomic calculation of wavelengths, oscillator strengths, and autoionization rates relevant to the 2 -> 3 inner-shell transitions of Fe VI-XVI, the so-called Fe M-shell unresolved transition array (UTA). A second order many-body perturbation theory is employed to obtain accurate transition wavelengths, which are systematically larger than previous theoretical results by 15-45 mA. For a few transitions of Fe XVI and Fe XV where laboratory measurements exist, our new wavelengths are accurate to within a few mA. Using these new calculations, the apparent discrepancy in the velocities between the Fe M-shell UTA and other highly ionized absorption lines in the outflow of NGC 3783 disappears. The oscillator strengths in our new calculation agree well with the previous theoretical data, while the new autoionization rates are significantly larger, especially for lower charge states. We attribute this discrepancy to the missing autoionization channels in the previous calculation. The increased autoionization rates may slightly affect the column density analysis of the Fe M-shell UTA for sources with high column density and very low turbulent broadening. The complete set of atomic data is provided as an electronic table.
Lima, Frederico A; Bjornsson, Ragnar; Weyhermüller, Thomas; Chandrasekaran, Perumalreddy; Glatzel, Pieter; Neese, Frank; DeBeer, Serena
2013-12-28
X-ray absorption spectroscopy (XAS) is a widely used experimental technique capable of selectively probing the local structure around an absorbing atomic species in molecules and materials. When applied to heavy elements, however, the quantitative interpretation can be challenging due to the intrinsic spectral broadening arising from the decrease in the core-hole lifetime. In this work we have used high-energy resolution fluorescence detected XAS (HERFD-XAS) to investigate a series of molybdenum complexes. The sharper spectral features obtained by HERFD-XAS measurements enable a clear assignment of the features present in the pre-edge region. Time-dependent density functional theory (TDDFT) has been previously shown to predict K-pre-edge XAS spectra of first row transition metal compounds with a reasonable degree of accuracy. Here we extend this approach to molybdenum K-edge HERFD-XAS and present the necessary calibration. Modern pure and hybrid functionals are utilized and relativistic effects are accounted for using either the Zeroth Order Regular Approximation (ZORA) or the second order Douglas-Kroll-Hess (DKH2) scalar relativistic approximations. We have found that both the predicted energies and intensities are in excellent agreement with experiment, independent of the functional used. The model chosen to account for relativistic effects also has little impact on the calculated spectra. This study provides an important calibration set for future applications of molybdenum HERFD-XAS to complex catalytic systems. PMID:24197060
High-temperature asymptotics of supersymmetric partition functions
NASA Astrophysics Data System (ADS)
Ardehali, Arash Arabi
2016-07-01
We study the supersymmetric partition function of 4d supersymmetric gauge theories with a U(1) R-symmetry on Euclidean S 3 × S β 1 , with S 3 the unit-radius squashed three-sphere, and β the circumference of the circle. For superconformal theories, this partition function coincides (up to a Casimir energy factor) with the 4d superconformal index.
NASA Astrophysics Data System (ADS)
Rasulov, R. Ya.; Rasulov, V. R.; Eshboltaev, I.
2016-07-01
The ballistic contribution to the current of linear photovoltaic effect under two-photon absorption of light is calculated and theoretically analyzed for the semiconductors of a tetrahedral symmetry with a complex band structure consisting of two closely spaced subbands. The transitions between the branches of one band in cases of the simultaneous absorption of two photons and successive absorption of two single photons are taken into account.
Partitioning ecosystems for sustainability.
Murray, Martyn G
2016-03-01
Decline in the abundance of renewable natural resources (RNRs) coupled with increasing demands of an expanding human population will greatly intensify competition for Earth's natural resources during this century, yet curiously, analytical approaches to the management of productive ecosystems (ecological theory of wildlife harvesting, tragedy of the commons, green economics, and bioeconomics) give only peripheral attention to the driving influence of competition on resource exploitation. Here, I apply resource competition theory (RCT) to the exploitation of RNRs and derive four general policies in support of their sustainable and equitable use: (1) regulate resource extraction technology to avoid damage to the resource base; (2) increase efficiency of resource use and reduce waste at every step in the resource supply chain and distribution network; (3) partition ecosystems with the harvesting niche as the basic organizing principle for sustainable management of natural resources by multiple users; and (4) increase negative feedback between consumer and resource to bring about long-term sustainable use. A simple policy framework demonstrates how RCT integrates with other elements of sustainability science to better manage productive ecosystems. Several problem areas of RNR management are discussed in the light of RCT, including tragedy of the commons, overharvesting, resource collapse, bycatch, single species quotas, and simplification of ecosystems. PMID:27209800
Modular properties of full 5D SYM partition function
NASA Astrophysics Data System (ADS)
Qiu, Jian; Tizzano, Luigi; Winding, Jacob; Zabzine, Maxim
2016-03-01
We study properties of the full partition function for the U(1) 5D N = {2}^{ast } gauge theory with adjoint hypermultiplet of mass M . This theory is ultimately related to abelian 6D (2,0) theory. We construct the full non-perturbative partition function on toric Sasaki-Einstein manifolds by gluing flat copies of the Nekrasov partition function and we express the full partition function in terms of the generalized double elliptic gamma function G 2 C associated with a certain moment map cone C. The answer exhibits a curious SL(4 , ℤ) modular property. Finally, we propose a set of rules to construct the partition function that resembles the calculation of 5d supersymmetric partition function with the insert ion of defects of various co-dimensions.
Donahue, Courtney M; Pacheco, Juan S Lezama; Keith, Jason M; Daly, Scott R
2014-06-28
S K-edge X-ray absorption spectroscopy (XAS) and time-dependent density functional theory (TDDFT) calculations were performed on a series of As[S2CNR2]3 complexes, where R2 = Et2, (CH2)5 and Ph2, to determine how dithiocarbamate substituents attached to N affect As[S2CNR2]3 electronic structure. Complimentary [PPh4][S2CNR2] salts were also studied to compare dithiocarbamate bonding in the absence of As. The XAS results indicate that changing the orientation of the alkyl substituents from trans to cis (R2 = Et2vs. (CH2)5) yields subtle variations whereas differences associated with a change from alkyl to aryl are much more pronounced. For example, despite the differences in As 4p mixing, the first features in the S K-edge XAS spectra of [PPh4][S2CNPh2] and As[S2CNPh2]3 were both shifted by 0.3 eV compared to their alkyl-substituted derivatives. DFT calculations revealed that the unique shift observed for [PPh4][S2CNPh2] is due to phenyl-induced splitting of the π* orbitals delocalized over N, C and S. A similar phenomenon accounts for the shift observed for As[S2CNPh2]3, but the presence of two unique S environments (As-S and As···S) prevented reliable analysis of As-S covalency from the XAS data. In the absence of experimental values, DFT calculations revealed a decrease in As-S orbital mixing in As[S2CNPh2]3 that stems from a redistribution of electron density to S atoms participating in weaker As···S interactions. Simulated spectra obtained from TDDFT calculations reproduce the experimental differences in the S K-edge XAS data, which suggests that the theory is accurately modeling the experimental differences in As-S orbital mixing. The results highlight how S K-edge XAS and DFT can be used cooperatively to understand the electronic structure of low symmetry coordination complexes containing S atoms in different chemical environments. PMID:24811926
Debeer George, Serena; Neese, Frank
2010-02-15
Sulfur K-edge X-ray absorption spectroscopy has been proven to be a powerful tool for investigating the electronic structures of sulfur-containing coordination complexes. The full information content of the spectra can be developed through a combination of experiment and time-dependent density functional theory (TD-DFT). In this work, the necessary calibration is carried out for a range of contemporary functionals (BP86, PBE, OLYP, OPBE, B3LYP, PBE0, TPSSh) in a scalar relativistic (0(th) order regular approximation, ZORA) DFT framework. It is shown that with recently developed segmented all-electron scalar relativistic (SARC) basis sets one obtains results that are as good as with large, uncontracted basis sets. The errors in the calibrated transition energies are on the order of 0.1 eV. The error in calibrated intensities is slightly larger, but the calculations are still in excellent agreement with experiment. The behavior of full TD-DFT linear response versus the Tamm-Dancoff approximation has been evaluated with the result that two methods are almost indistinguishable. The inclusion of relativistic effects barely changes the results for first row transition metal complexes, however, the contributions become visible for second-row transition metals and reach a maximum (of an approximately 10% change in the calibration parameters) for third row transition metal species. The protocol developed here is approximately 10 times more efficient than the previously employed protocol, which was based on large, uncontracted basis sets. The calibration strategy followed here may be readily extended to other edges. PMID:20092349
NASA Astrophysics Data System (ADS)
Pena, J.; Kwon, K.; Refson, K.; Bargar, J. R.; Sposito, G.
2008-12-01
Bacteriogenic Mn oxides are ubiquitous, highly reactive minerals with a remarkable capacity to scavenge metals due to their nanoparticulate dimensions and abundant structural defects. These minerals are commonly deposited in a matrix of bacterial cells and extracellular polymeric substances, forming geosymbiotic systems whose reactivity with contaminant metals is not fully characterized. In the current study, a synergistic experimental-computational approach was used to study the mechanism of Ni adsorption at varying loadings and at pH 6-8 using the Mn oxide produced by Pseudomonas putida GB-1. Extended X-ray absorption fine structure (EXAFS) spectra showed two dominant coordination environments: Ni bound as a triple corner sharing (TCS) complex at octahedral vacancy sites and Ni incorporated into the octahedral sheet. The proportion of adsorbed and incorporated Ni varied as a function of surface coverage and pH, with the latter form of Ni being favored at higher loadings and decreased proton activity. These two coordination environments, although consistent with data published for Ni sorbed by synthetic MnO2(s), did not describe fully all of our EXAFS spectra, leading us to consider the binding of Ni at particle edges or via a non-specific sorption mechanism. In parallel to the spectral analysis, density functional theory (DFT) calculations were performed to test different adsorbate-adsorbent configurations and the pH dependence of the adsorption mechanism. Geometry optimized structures for Ni sorbed above vacancies (i.e., TCS) or incorporated into the Mn oxide structure were in excellent agreement with corresponding structural parameters obtained from EXAFS analysis. The calculated energy barriers for the transition from adsorbed TCS to incorporated Ni were consistent with the hypothesis that the TCS complex is a precursor for Ni incorporation and that incorporation is favored by decreased proton activity. The combined perspectives obtained from these two
NASA Astrophysics Data System (ADS)
Cappa, C. D.; Wilson, K. R.; Smith, J. D.; Kolesar, K.
2010-12-01
VUV mass spectra for two distinct aerosol types as they are passed through a thermodenuder at different temperatures have been measured. The two aerosol types considered are primary lubricating oil (LO) aerosol and secondary aerosol from the α-pinene + O3 reaction (αP). The evolution of the VUV mass spectra for the two aerosol types with temperature are observed to differ dramatically. For LO particles, the spectra exhibit distinct, T-dependent changes in which the lower m/z peaks, corresponding to compounds with higher vapor pressures, disappear more rapidly than the high m/z peaks. In stark contrast, the αP aerosol spectrum is essentially unchanged by temperature even though the particles experience significant mass loss due to evaporation. The variations in the LO spectra are found to be quantitatively in good agreement with expectations from absorptive partitioning theory whereas the αP spectra suggest that the evaporation of αP particles is not governed by partitioning theory. We postulate that this difference arises from the αP particles existing as a glass instead of having the expected liquid-like behavior. To reconcile these observations with decades of aerosol growth experiments, which indicate that OA formation is describable through equilibrium partitioning, we put forward a sequential partitioning model wherein secondary OA is rapidly converted from an absorbing form to a non-absorbing form. The results suggest that although OA growth may be describable through equilibrium partitioning theory, the thermodynamic properties of formed OA particles may differ significantly from the properties determined in the equilibrium framework.
Dense Subgraph Partition of Positive Hypergraphs.
Liu, Hairong; Latecki, Longin Jan; Yan, Shuicheng
2015-03-01
In this paper, we present a novel partition framework, called dense subgraph partition (DSP), to automatically, precisely and efficiently decompose a positive hypergraph into dense subgraphs. A positive hypergraph is a graph or hypergraph whose edges, except self-loops, have positive weights. We first define the concepts of core subgraph, conditional core subgraph, and disjoint partition of a conditional core subgraph, then define DSP based on them. The result of DSP is an ordered list of dense subgraphs with decreasing densities, which uncovers all underlying clusters, as well as outliers. A divide-and-conquer algorithm, called min-partition evolution, is proposed to efficiently compute the partition. DSP has many appealing properties. First, it is a nonparametric partition and it reveals all meaningful clusters in a bottom-up way. Second, it has an exact and efficient solution, called min-partition evolution algorithm. The min-partition evolution algorithm is a divide-and-conquer algorithm, thus time-efficient and memory-friendly, and suitable for parallel processing. Third, it is a unified partition framework for a broad range of graphs and hypergraphs. We also establish its relationship with the densest k-subgraph problem (DkS), an NP-hard but fundamental problem in graph theory, and prove that DSP gives precise solutions to DkS for all kin a graph-dependent set, called critical k-set. To our best knowledge, this is a strong result which has not been reported before. Moreover, as our experimental results show, for sparse graphs, especially web graphs, the size of critical k-set is close to the number of vertices in the graph. We test the proposed partition framework on various tasks, and the experimental results clearly illustrate its advantages. PMID:26353260
Gilbert, Dorothea; Witt, Gesine; Smedes, Foppe; Mayer, Philipp
2016-06-01
Polymers are increasingly applied for the enrichment of hydrophobic organic chemicals (HOCs) from various types of samples and media in many analytical partitioning-based measuring techniques. We propose using polymers as a reference partitioning phase and introduce polymer-polymer partitioning as the basis for a deeper insight into partitioning differences of HOCs between polymers, calibrating analytical methods, and consistency checking of existing and calculation of new partition coefficients. Polymer-polymer partition coefficients were determined for polychlorinated biphenyls (PCBs), polycyclic aromatic hydrocarbons (PAHs), and organochlorine pesticides (OCPs) by equilibrating 13 silicones, including polydimethylsiloxane (PDMS) and low-density polyethylene (LDPE) in methanol-water solutions. Methanol as cosolvent ensured that all polymers reached equilibrium while its effect on the polymers' properties did not significantly affect silicone-silicone partition coefficients. However, we noticed minor cosolvent effects on determined polymer-polymer partition coefficients. Polymer-polymer partition coefficients near unity confirmed identical absorption capacities of several PDMS materials, whereas larger deviations from unity were indicated within the group of silicones and between silicones and LDPE. Uncertainty in polymer volume due to imprecise coating thickness or the presence of fillers was identified as the source of error for partition coefficients. New polymer-based (LDPE-lipid, PDMS-air) and multimedia partition coefficients (lipid-water, air-water) were calculated by applying the new concept of a polymer as reference partitioning phase and by using polymer-polymer partition coefficients as conversion factors. The present study encourages the use of polymer-polymer partition coefficients, recognizing that polymers can serve as a linking third phase for a quantitative understanding of equilibrium partitioning of HOCs between any two phases. PMID:27115830
Björner, Anders
1987-01-01
A continuous analogue to the partition lattices is presented. This is the metric completion of the direct limit of a system of embeddings of the finite partition lattices. The construction is analogous to von Neumann's construction of a continuous geometry over a field F from the finite-dimensional projective geometries over F. PMID:16593874
Zhao, Yunliang; Kreisberg, Nathan M; Worton, David R; Isaacman, Gabriel; Weber, Robin J; Liu, Shang; Day, Douglas A; Russell, Lynn M; Markovic, Milos Z; VandenBoer, Trevor C; Murphy, Jennifer G; Hering, Susanne V; Goldstein, Allen H
2013-04-16
In situ measurements of organic compounds in both gas and particle phases were made with a thermal desorption aerosol gas chromatography (TAG) instrument. The gas/particle partitioning of phthalic acid, pinonaldehyde, and 6,10,14-trimethyl-2-pentadecanone is discussed in detail to explore secondary organic aerosol (SOA) formation mechanisms. Measured fractions in the particle phase (f(part)) of 6,10,14-trimethyl-2-pentadecanone were similar to those expected from the absorptive gas/particle partitioning theory, suggesting that its partitioning is dominated by absorption processes. However, f(part) of phthalic acid and pinonaldehyde were substantially higher than predicted. The formation of low-volatility products from reactions of phthalic acid with ammonia is proposed as one possible mechanism to explain the high f(part) of phthalic acid. The observations of particle-phase pinonaldehyde when inorganic acids were fully neutralized indicate that inorganic acids are not required for the occurrence of reactive uptake of pinonaldehyde on particles. The observed relationship between f(part) of pinonaldehyde and relative humidity suggests that the aerosol water plays a significant role in the formation of particle-phase pinonaldehyde. Our results clearly show it is necessary to include multiple gas/particle partitioning pathways in models to predict SOA and multiple SOA tracers in source apportionment models to reconstruct SOA. PMID:23448102
Parameters of photosynthetic energy partitioning.
Lazár, Dušan
2015-03-01
Almost every laboratory dealing with plant physiology, photosynthesis research, remote sensing, and plant phenotyping possesses a fluorometer to measure a kind of chlorophyll (Chl) fluorescence induction (FLI). When the slow Chl FLI is measured with addition of saturating pulses and far-red illumination, the so-called quenching analysis followed by the so-called relaxation analysis in darkness can be realized. These measurements then serve for evaluation of the so-called energy partitioning, that is, calculation of quantum yields of photochemical and of different types of non-photochemical processes. Several theories have been suggested for photosynthetic energy partitioning. The current work aims to summarize all the existing theories, namely their equations for the quantum yields, their meaning and their assumptions. In the framework of these theories it is also found here that the well-known NPQ parameter ( [Formula: see text] ; Bilger and Björkman, 1990) equals the ratio of the quantum yield of regulatory light-induced non-photochemical quenching to the quantum yield of constitutive non-regulatory non-photochemical quenching (ΦNPQ/Φf,D). A similar relationship is also found here for the PQ parameter (ΦP/Φf,D). PMID:25569797
Silverstein, Daniel W.; Govind, Niranjan; van Dam, Hubertus J. J.; Jensen, Lasse
2013-12-10
A parallel implementation of analytical time-dependent density functional theory gradients is presented for the quantum chemistry program NWChem. The implementation is based on the Lagrangian approach developed by Furche and Ahlrichs. To validate our implementation, we first calculate the Stokes shifts for a range of organic dye molecules using a diverse set of exchange-correlation functionals (traditional density functionals, global hybrids, and range-separated hybrids) followed by simulations of the one-photon absorption and resonance Raman scattering spectrum of the phenoxyl radical, the well-studied dye molecule rhodamine 6G, and a molecular host–guest complex (TTFcCBPQT^{4+}). The study of organic dye molecules illustrates that B3LYP and CAM-B3LYP generally give the best agreement with experimentally determined Stokes shifts unless the excited state is a charge transfer state. Absorption, resonance Raman, and fluorescence simulations for the phenoxyl radical indicate that explicit solvation may be required for accurate characterization. For the host–guest complex and rhodamine 6G, it is demonstrated that absorption spectra can be simulated in good agreement with experimental data for most exchange-correlation functionals. Finally, however, because one-photon absorption spectra generally lack well-resolved vibrational features, resonance Raman simulations are necessary to evaluate the accuracy of the exchange-correlation functional for describing a potential energy surface.
Levine, Zachary H.; Grantham, Steven; Tarrio, Charles; Paterson, David J.; McNulty, Ian; Levin, T. M.; Ankudinov, Alexei L.; Rehr, John J.
2003-01-01
The mass absorption coefficients of tungsten and tantalum were measured with soft x-ray photons from 1450 eV to 2350 eV using an undulator source. This region includes the M3, M4, and M5 absorption edges. X-ray absorption fine structure was calculated within a real-space multiple scattering formalism; the predicted structure was observed for tungsten and to a lesser degree tantalum as well. Separately, the effects of dynamic screening were observed as shown by an atomic calculation within the relativistic time-dependent local-density approximation. Dynamic screening effects influence the spectra at the 25 % level and are observed for both tungsten and tantalum. We applied these results to characterize spatially-resolved spectra of a tungsten integrated circuit interconnect obtained using a scanning transmission x-ray microscope. The results indicate tungsten fiducial markers were deposited into silica trenches with a depths of 50 % and 60 % of the markers’ heights.
Novoderezhkin, Vladimir I; Doust, Alexander B; Curutchet, Carles; Scholes, Gregory D; van Grondelle, Rienk
2010-07-21
We model the spectra and excitation dynamics in the phycobiliprotein antenna complex PE545 isolated from the unicellular photosynthetic cryptophyte algae Rhodomonas CS24. The excitonic couplings between the eight bilins are calculated using the CIS/6-31G method. The site energies are extracted from a simultaneous fit of the absorption, circular dichroism, fluorescence, and excitation anisotropy spectra together with the transient absorption kinetics using the modified Redfield approach. Quantitative fit of the data enables us to assign the eight exciton components of the spectra and build up the energy transfer picture including pathways and timescales of energy relaxation, thus allowing a visualization of excitation dynamics within the complex. PMID:20643051
NASA Astrophysics Data System (ADS)
Li, Xuan; Bernhardt, Birgitta; Beck, Annelise R.; Warrick, Erika R.; Pfeiffer, Adrian N.; Justine Bell, M.; Haxton, Daniel J.; McCurdy, C. William; Neumark, Daniel M.; Leone, Stephen R.
2015-06-01
Attosecond transient absorption spectra near the energies of autoionizing states are analyzed in terms of the photon coupling mechanisms to other states. In a recent experiment, the autoionization lifetimes of highly excited states of xenon were determined and compared to a simple expression based on a model of how quantum coherence determines the decay of a metastable state in the transient absorption spectrum. Here it is shown that this procedure for extracting lifetimes is more general and can be used in cases involving either resonant or nonresonant coupling of the attosecond-probed autoionizing state to either continua or discrete states by a time-delayed near infrared (NIR) pulse. The fits of theoretically simulated absorption signals for the 6p resonance in xenon (lifetime = 21.1 fs) to this expression yield the correct decay constant for all the coupling mechanisms considered, properly recovering the time signature of twice the autoionization lifetime due to the coherent nature of the transient absorption experiment. To distinguish between these two coupling cases, the characteristic dependencies of the transient absorption signals on both the photon energy and time delay are investigated. Additional oscillations versus delay-time in the measured spectrum are shown and quantum beat analysis is used to pinpoint the major photon-coupling mechanism induced by the NIR pulse in the current xenon experiment: the NIR pulse resonantly couples the attosecond-probed state, 6p, to an intermediate 8s (at 22.563 eV), and this 8s state is also coupled to a neighboring state (at 20.808 eV).
Fuzzy Partition Models for Fitting a Set of Partitions.
ERIC Educational Resources Information Center
Gordon, A. D.; Vichi, M.
2001-01-01
Describes methods for fitting a fuzzy consensus partition to a set of partitions of the same set of objects. Describes and illustrates three models defining median partitions and compares these methods to an alternative approach to obtaining a consensus fuzzy partition. Discusses interesting differences in the results. (SLD)
A Framework for Parallel Nonlinear Optimization by Partitioning Localized Constraints
Xu, You; Chen, Yixin
2008-06-28
We present a novel parallel framework for solving large-scale continuous nonlinear optimization problems based on constraint partitioning. The framework distributes constraints and variables to parallel processors and uses an existing solver to handle the partitioned subproblems. In contrast to most previous decomposition methods that require either separability or convexity of constraints, our approach is based on a new constraint partitioning theory and can handle nonconvex problems with inseparable global constraints. We also propose a hypergraph partitioning method to recognize the problem structure. Experimental results show that the proposed parallel algorithm can efficiently solve some difficult test cases.
Partitioning and parallel radiosity
NASA Astrophysics Data System (ADS)
Merzouk, S.; Winkler, C.; Paul, J. C.
1996-03-01
This paper proposes a theoretical framework, based on domain subdivision for parallel radiosity. Moreover, three various implementation approaches, taking advantage of partitioning algorithms and global shared memory architecture, are presented.
NASA Astrophysics Data System (ADS)
Cappa, C. D.; Wilson, K. R.
2011-03-01
Vacuum Ultraviolet (VUV) photoionization mass spectrometry has been used to measure the evolution of chemical composition for two distinct organic aerosol types as they are passed through a thermodenuder at different temperatures. The two organic aerosol types considered are primary lubricating oil (LO) aerosol and secondary aerosol from the α-pinene + O3 reaction (αP). The evolution of the VUV mass spectra for the two aerosol types with temperature are observed to differ dramatically. For LO particles, the spectra exhibit distinct changes with temperature in which the lower m/z peaks, corresponding to compounds with higher vapor pressures, disappear more rapidly than the high m/z peaks. In contrast, the αP aerosol spectrum is essentially unchanged by temperature even though the particles experience significant mass loss due to evaporation. The variations in the LO spectra are found to be quantitatively in agreement with expectations from absorptive partitioning theory whereas the αP spectra suggest that the evaporation of αP derived aerosol appears to not be governed by partitioning theory. We postulate that this difference arises from diffusivity within the αP particles being sufficiently slow that they do not exhibit the expected liquid-like behavior and perhaps exist in a glassy state. To reconcile these observations with decades of aerosol growth measurements, which indicate that OA formation is described by equilibrium partitioning, we present a conceptual model wherein the secondary OA is formed and then rapidly converted from an absorbing form to a non-absorbing form. The results suggest that, although OA growth may be describable by equilibrium partitioning theory, the properties of organic aerosol once formed may differ significantly from the properties determined in the equilibrium framework.
NASA Astrophysics Data System (ADS)
Cappa, C. D.; Wilson, K. R.
2010-11-01
Vacuum Ultraviolet (VUV) photoionization mass spectrometry has been used to measure the evolution of chemical composition for two distinct organic aerosol types as they are passed through a thermodenuder at different temperatures. The two organic aerosol types considered are primary lubricating oil (LO) aerosol and secondary aerosol from the α-pinene + O3 reaction (αP). The evolution of the VUV mass spectra for the two aerosol types with temperature are observed to differ dramatically. For LO particles, the spectra exhibit distinct changes with temperature in which the lower m/z peaks, corresponding to compounds with higher vapor pressures, disappear more rapidly than the high m/z peaks. In contrast, the αP aerosol spectrum is essentially unchanged by temperature even though the particles experience significant mass loss due to evaporation. The variations in the LO spectra are found to be quantitatively in agreement with expectations from absorptive partitioning theory whereas the αP spectra suggest that the evaporation of αP derived aerosol appears to not be governed by partitioning theory. We postulate that this difference arises from the αP particles existing as in a glassy state instead of having the expected liquid-like behavior. To reconcile these observations with decades of aerosol growth measurements, which indicate that OA formation is described by equilibrium partitioning, we present a conceptual model wherein the secondary OA is formed and then rapidly converted from an absorbing form to a non-absorbing form. The results suggest that although OA growth may be describable by equilibrium partitioning theory, the properties of organic aerosol once formed may differ significantly from the properties determined in the equilibrium framework.
UC Davis; Cappa, Christopher D.; Wilson, Kevin R.
2010-10-28
Vacuum Ultraviolet (VUV) photoionization mass spectrometry has been used to measure the evolution of chemical composition for two distinct organic aerosol types as they are passed through a thermodenuder at different temperatures. The two organic aerosol types considered are primary lubricating oil (LO) aerosol and secondary aerosol from the alpha-pinene + O3 reaction (alphaP). The evolution of the VUV mass spectra for the two aerosol types with temperature are observed to differ dramatically. For LO particles, the spectra exhibit distinct changes with temperature in which the lower m/z peaks, corresponding to compounds with higher vapor pressures, disappear more rapidly than the high m/z peaks. In contrast, the alphaP aerosol spectrum is essentially unchanged by temperature even though the particles experience significant mass loss due to evaporation. The variations in the LO spectra are found to be quantitatively in agreement with expectations from absorptive partitioning theory whereas the alphaP spectra suggest that the evaporation of alphaP derived aerosol appears to not be governed by partitioning theory. We postulate that this difference arises from the alphaP particles existing as in a glassy state instead of having the expected liquid-like behavior. To reconcile these observations with decades of aerosol growth measurements, which indicate that OA formation is described by equilibrium partitioning, we present a conceptual model wherein the secondary OA is formed and then rapidly converted from an absorbing form to a non-absorbing form. The results suggest that although OA growth may be describable by equilibrium partitioning theory, the properties of organic aerosol once formed may differ significantly from the properties determined in the equilibrium framework.
Xie, Rui-Hua; Bryant, Garnett W; Sun, Guangyu; Nicklaus, Marc C; Heringer, David; Frauenheim, Th; Manaa, M Riad; Smith, Vedene H; Araki, Yasuyuki; Ito, Osamu
2004-03-15
Low-energy excitations and optical absorption spectrum of C(60) are computed by using time-dependent (TD) Hartree-Fock, TD-density functional theory (TD-DFT), TD DFT-based tight-binding (TD-DFT-TB), and a semiempirical Zerner intermediate neglect of diatomic differential overlap method. A detailed comparison of experiment and theory for the excitation energies, optical gap, and absorption spectrum of C(60) is presented. It is found that electron correlations and correlation of excitations play important roles in accurately assigning the spectral features of C(60), and that the TD-DFT method with nonhybrid functionals or a local spin density approximation leads to more accurate excitation energies than with hybrid functionals. The level of agreement between theory and experiment for C(60) justifies similar calculations of the excitations and optical absorption spectrum of a monomeric azafullerene cation C(59)N(+), to serve as a spectroscopy reference for the characterization of carborane anion salts. Although it is an isoelectronic analogue to C(60), C(59)N(+) exhibits distinguishing spectral features different from C(60): (1) the first singlet is dipole-allowed and the optical gap is redshifted by 1.44 eV; (2) several weaker absorption maxima occur in the visible region; (3) the transient triplet-triplet absorption at 1.60 eV (775 nm) is much broader and the decay of the triplet state is much faster. The calculated spectra of C(59)N(+) characterize and explain well the measured ultraviolet-visible (UV-vis) and transient absorption spectra of the carborane anion salt [C(59)N][Ag(CB(11)H(6)Cl(6))(2)] [Kim et al., J. Am. Chem. Soc. 125, 4024 (2003)]. For the most stable isomer of C(48)N(12), we predict that the first singlet is dipole-allowed, the optical gap is redshifted by 1.22 eV relative to that of C(60), and optical absorption maxima occur at 585, 528, 443, 363, 340, 314, and 303 nm. We point out that the characterization of the UV-vis and transient absorption
DNA Partitioning in Confining Nanofluidic Slits
NASA Astrophysics Data System (ADS)
Greenier, Madeline; Levy, Stephen
We measure the partitioning of double stranded DNA molecules in moderately and strongly confining nanofluidic slit-like structures. Using fluorescent microscopy, the free energy penalty of confinement is inferred by comparing the concentration of DNA molecules in adjoining slits of different depths. These depths range in size from several persistence lengths to the DNA molecule's radius of gyration. The partition coefficient is determined as a function of the slit depth, DNA contour length, and DNA topology. We compare our results to theory and Monte Carlo simulations that predict the loss of free energy for ideal and semiflexible excluded volume polymers confined between parallel plates.
List, Nanna Holmgaard Jensen, Hans Jørgen Aagaard; Kauczor, Joanna; Norman, Patrick; Saue, Trond
2015-06-28
We present a formulation of molecular response theory for the description of a quantum mechanical molecular system in the presence of a weak, monochromatic, linearly polarized electromagnetic field without introducing truncated multipolar expansions. The presentation focuses on a description of linear absorption by adopting the energy-loss approach in combination with the complex polarization propagator formulation of response theory. Going beyond the electric-dipole approximation is essential whenever studying electric-dipole-forbidden transitions, and in general, non-dipolar effects become increasingly important when addressing spectroscopies involving higher-energy photons. These two aspects are examined by our study of the near K-edge X-ray absorption fine structure of the alkaline earth metals (Mg, Ca, Sr, Ba, and Ra) as well as the trans-polyenes. In following the series of alkaline earth metals, the sizes of non-dipolar effects are probed with respect to increasing photon energies and a detailed assessment of results is made in terms of studying the pertinent transition electron densities and in particular their spatial extension in comparison with the photon wavelength. Along the series of trans-polyenes, the sizes of non-dipolar effects are probed for X-ray spectroscopies on organic molecules with respect to the spatial extension of the chromophore.
Jun, Ye
2015-12-24
Low-lying band shapes of absorption and fluorescence spectra for a member of a newly synthesized family of phenylene-containing oligoacenes (POA 6) reported in J. Am. Chem. Soc. 2012 , 134 , 15351 are studied theoretically with two different approaches with TIPS-anthracene as a comparison. Underlying photophysics and exciton-phonon interactions in both molecules are investigated in details with the aid of the time-dependent density functional theory and multimode Brownian oscillator model. The first two low-lying excited-states of POA 6 were found to exhibit excitation characteristics spanning entire conjugated backbone despite the presence of antiaromatic phenylene section. Absorption and fluorescence spectra calculated from both time-dependent density functional theory and multimode Brownian oscillator model are shown to reach good agreement with experimental ones. The coupling between phonon modes and optical transitions is generally weak as suggested by the multimode Brownian oscillator model. Broader peaks of POA 6 spectra are found to relate to stronger coupling between low frequency phonon modes such as backbone twisting (with frequency <300 cm(-1)) and optical transitions. Furthermore, POA 6 exhibits weaker exciton-phonon coupling for the phonon modes above 1000 cm(-1) compared to TIPS-anthracene owing to extended conjugated backbone. A significant coupling between an in-plane breathing mode localized around the antiaromatic phenylene segment with frequency at 1687 cm(-1) and optical transitions for the first two excited-states of POA 6 is also observed. PMID:26611665
List, Nanna Holmgaard; Kauczor, Joanna; Saue, Trond; Jensen, Hans Jørgen Aagaard; Norman, Patrick
2015-06-28
We present a formulation of molecular response theory for the description of a quantum mechanical molecular system in the presence of a weak, monochromatic, linearly polarized electromagnetic field without introducing truncated multipolar expansions. The presentation focuses on a description of linear absorption by adopting the energy-loss approach in combination with the complex polarization propagator formulation of response theory. Going beyond the electric-dipole approximation is essential whenever studying electric-dipole-forbidden transitions, and in general, non-dipolar effects become increasingly important when addressing spectroscopies involving higher-energy photons. These two aspects are examined by our study of the near K-edge X-ray absorption fine structure of the alkaline earth metals (Mg, Ca, Sr, Ba, and Ra) as well as the trans-polyenes. In following the series of alkaline earth metals, the sizes of non-dipolar effects are probed with respect to increasing photon energies and a detailed assessment of results is made in terms of studying the pertinent transition electron densities and in particular their spatial extension in comparison with the photon wavelength. Along the series of trans-polyenes, the sizes of non-dipolar effects are probed for X-ray spectroscopies on organic molecules with respect to the spatial extension of the chromophore. PMID:26133414
Brandbyge, Mads
2014-05-07
In a recent paper Reuter and Harrison [J. Chem. Phys. 139, 114104 (2013)] question the widely used mean-field electron transport theories, which employ nonorthogonal localized basis sets. They claim these can violate an “implicit decoupling assumption,” leading to wrong results for the current, different from what would be obtained by using an orthogonal basis, and dividing surfaces defined in real-space. We argue that this assumption is not required to be fulfilled to get exact results. We show how the current/transmission calculated by the standard Greens function method is independent of whether or not the chosen basis set is nonorthogonal, and that the current for a given basis set is consistent with divisions in real space. The ambiguity known from charge population analysis for nonorthogonal bases does not carry over to calculations of charge flux.
X-ray absorption and reflection as probes of the GaN conduction bands: Theory and experiments
Lambrecht, W.R.L.; Rashkeev, S.N.; Segall, B.
1997-04-01
X-ray absorption measurements are a well-known probe of the unoccupied states in a material. The same information can be obtained by using glancing angle X-ray reflectivity. In spite of several existing band structure calculations of the group III nitrides and previous optical studies in UV range, a direct probe of their conduction band densities of states is of interest. The authors performed a joint experimental and theoretical investigation using both of these experimental techniques for wurtzite GaN.
A brief history of partitions of numbers, partition functions and their modern applications
NASA Astrophysics Data System (ADS)
Debnath, Lokenath
2016-04-01
Partitioning Breaks Communities
NASA Astrophysics Data System (ADS)
Reid, Fergal; McDaid, Aaron; Hurley, Neil
Considering a clique as a conservative definition of community structure, we examine how graph partitioning algorithms interact with cliques. Many popular community-finding algorithms partition the entire graph into non-overlapping communities. We show that on a wide range of empirical networks, from different domains, significant numbers of cliques are split across the separate partitions produced by these algorithms. We then examine the largest connected component of the subgraph formed by retaining only edges in cliques, and apply partitioning strategies that explicitly minimise the number of cliques split. We further examine several modern overlapping community finding algorithms, in terms of the interaction between cliques and the communities they find, and in terms of the global overlap of the sets of communities they find. We conclude that, due to the connectedness of many networks, any community finding algorithm that produces partitions must fail to find at least some significant structures. Moreover, contrary to traditional intuition, in some empirical networks, strong ties and cliques frequently do cross community boundaries; much community structure is fundamentally overlapping and unpartitionable in nature.
NASA Astrophysics Data System (ADS)
Refaely-Abramson, Sivan; Jain, Manish; Sharifzadeh, Sahar; Neaton, Jeffrey B.; Kronik, Leeor
2015-08-01
We present a framework for obtaining reliable solid-state charge and optical excitations and spectra from optimally tuned range-separated hybrid density functional theory. The approach, which is fully couched within the formal framework of generalized Kohn-Sham theory, allows for the accurate prediction of exciton binding energies. We demonstrate our approach through first principles calculations of one- and two-particle excitations in pentacene, a molecular semiconducting crystal, where our work is in excellent agreement with experiments and prior computations. We further show that with one adjustable parameter, set to produce the known band gap, this method accurately predicts band structures and optical spectra of silicon and lithium fluoride, prototypical covalent and ionic solids. Our findings indicate that for a broad range of extended bulk systems, this method may provide a computationally inexpensive alternative to many-body perturbation theory, opening the door to studies of materials of increasing size and complexity.
Shawahna, R.; Rahman, NU.
2011-01-01
Background and the purpose of the study Partition coefficients (log D and log P) and molecular surface area (PSA) are potential predictors of the intestinal permeability of drugs. The aim of this investigation was to evaluate and compare these intestinal permeability indicators. Methods Aqueous solubility data were obtained from literature or calculated using ACD/Labs and ALOGPS. Permeability data were predicted based on log P, log D at pH 6.0 (log D6.0), and PSA. Results Metoprolol's log P, log D6.0, and a PSA of <65 Å correctly predicted 55.9%, 50.8% and 54.2% of permeability classes, respectively. Labetalol's log P, log D6.0 and PSA correctly predicted 54.2%, 64.4% and 61% of permeability classes, respectively. Log D6.0 correlated well (81%) with Caco-2 permeability (Papp). Of the list of national essential medicines, 135 orally administered drugs were classified into biopharmaceutical classification system (BCS). Of these, 57 (42.2%), 28 (20.7%), 44 (32.6%), and 6 (4.4%) were class I, II, III and IV respectively. Conclusion Log D6.0 showed better prediction capability than log P. Metoprolol as permeability internal standard was more conservative than labetalol. PMID:22615645
Partitioning technique for open systems
NASA Astrophysics Data System (ADS)
Brändas, Erkki J.
2010-11-01
The focus of the present contribution is essentially confined to three research areas carried out during the author's turns as visiting (assistant, associate and full) professor at the University of Florida's Quantum Theory Project, QTP. The first two topics relate to perturbation theory and spectral theory for self-adjoint operators in Hilbert space. The third subject concerns analytic extensions to non-self-adjoint problems, where particular consequences of the occurrence of continuous energy spectra are measured. In these studies general partitioning methods serve as general cover for perturbation-, variational- and general matrix theory. In addition we follow up associated inferences for the time dependent problem as well as recent results and conclusions of a rather general yet surprising character. Although the author spent most of his times at QTP during visits in the 1970s and 1980s, collaborations with department members and shorter stays continued through later decades. Nevertheless the impact must be somewhat fragmentary, yet it is hoped that the present account is sufficiently self-contained to be realistic and constructive.
NASA Technical Reports Server (NTRS)
Vanalstine, James M.
1993-01-01
Project NAS8-36955 D.O. #100 initially involved the following tasks: (1) evaluation of various coatings' ability to control wall wetting and surface zeta potential expression; (2) testing various methods to mix and control the demixing of phase systems; and (3) videomicroscopic investigation of cell partition. Three complementary areas were identified for modification and extension of the original contract. They were: (1) identification of new supports for column cell partition; (2) electrokinetic detection of protein adsorption; and (3) emulsion studies related to bioseparations.
NASA Astrophysics Data System (ADS)
Weiss, Christoph; Block, Martin; Holthaus, Martin; Schmieder, Gerald
2003-02-01
We utilize the formal equivalence between the number-partitioning problem and a harmonically trapped ideal Bose gas within the microcanonical ensemble for characterizing the probability distribution which governs the number of addends occurring in an unrestricted partition of a natural number n. By deriving accurate asymptotic formulae for its coefficients of skewness and excess, it is shown that this distribution remains non-Gaussian even when n is made arbitrarily large. Both skewness and excess vary substantially before settling to their constant-limiting values for n > 1010.
NASA Astrophysics Data System (ADS)
Luo, Q.; Dai, D. C.; Wang, G. Q.; Ninulescu, V.; Yu, X. Y.; Luo, L.; Zhou, J. Y.; Yan, YiJing
2001-01-01
Coherent dynamic property of neodymium yttrium aluminum garnet (Nd:YAG) crystal at 77 K is studied via the conventional absorption, the femtosecond fringe-resolved wave packet interferometry, and the related difference-phase spectrum. The recorded interferogram exhibits beatings in subpicosecond time scale arising from the interferences among various weakly split 4f-electronic states and the coupled vibronic optical phonon sidebands. The electron-phonon coupling in Nd:YAG can be well described by multiple Brownian oscillators model involving in each individual electronic transition. The parameters for characterizing material coherence and relaxation are determined via the theoretical modelings of both the frequency and the time-domain experimental signals.
NASA Astrophysics Data System (ADS)
Refaely-Abramson, Sivan; Jain, Manish; Sharifzadeh, Sahar; Neaton, Jeffrey B.; Kronik, Leeor
We present a framework for obtaining solid-state charge and optical excitations and spectra from optimally tuned range-separated hybrid density functional theory, which allows for the accurate prediction of exciton binding energies. We demonstrate our approach through calculations of one- and two-particle excitations in pentacene, a molecular semiconducting crystal, where we find excellent agreement with experiments and prior computations. We show that with one adjustable parameter, our method accurately predicts band structures and optical spectra of Si and LiF, prototypical covalent and ionic solids. For a range of extended bulk systems, this method may provide a computationally inexpensive alternative to many-body perturbation theory, opening the door to studies of materials of increasing size and complexity [Phys. Rev. B 92, 081204(R), 2015]. This work was supported by DOE.
New Aperture Partitioning Element
NASA Astrophysics Data System (ADS)
Griffin, S.; Calef, B.; Williams, S.
Postprocessing in an optical system can be aided by adding an optical element to partition the pupil into a number of segments. When imaging through the atmosphere, the recorded data are blurred by temperature-induced variations in the index of refraction along the line of sight. Using speckle imaging techniques developed in the astronomy community, this blurring can be corrected to some degree. The effectiveness of these techniques is diminished by redundant baselines in the pupil. Partitioning the pupil reduces the degree of baseline redundancy, and therefore improves the quality of images that can be obtained from the system. It is possible to implement the described approach on an optical system with a segmented primary mirror, but not very practical. This is because most optical systems do not have segmented primary mirrors, and those that do have relatively low bandwidth positioning of segments due to their large mass and inertia. It is much more practical to position an active aperture partitioning element at an aft optics pupil of the optical system. This paper describes the design, implementation and testing of a new aperture partitioning element that is completely reflective and reconfigurable. The device uses four independent, annular segments that can be positioned with a high degree of accuracy without impacting optical wavefront of each segment. This mirror has been produced and is currently deployed and working on the 3.6 m telescope.
NASA Technical Reports Server (NTRS)
Butler, C.
1986-01-01
The improvement of computer hardware and software of the NASA Multipurpose Differential Absorption Lidar (DIAL) system is documented. The NASA DIAL system is undergoing development and experimental deployment at NASA Langley Research Center for the remote measurement of atmospheric trace gas concentrations from ground and aircraft platforms. A viable DIAL system was developed capable of remotely measuring O3 and H2O concentrations from an aircraft platform. Test flights of the DIAL system were successfully performed onboard the NASA Goddard Flight Center Electra aircraft from 1980 to 1985. The DIAL Data Acquisition System has undergone a number of improvements over the past few years. These improvements have now been field tested. The theory behind a real time computer system as it applies to the needs of the DIAL system is discussed. This report is designed to be used as an operational manual for the DIAL DAS.
Govind, Niranjan; De Jong, Wibe A.
2014-02-21
We report simulations of the X-ray absorption near edge structure (XANES) at the Cl K-edge of actinide hexahalides MCl62- (M = U, Np, Pu) and the UOCl5- complex using linear-response time-dependent density functional theory (LR-TDDFT) extended for core excitations. To the best of our knowledge, these are the first calculations of the Cl K-edge spectra of NpCl62- and PuCl62-. In addition, the spectra are simulated with and without the environmental effects of the host crystal as well as ab initio molecular dynamics (AIMD) to capture the dynamical effects due to atomic motion. The calculated spectra are compared with experimental results, where available and the observed trends are discussed.
NASA Astrophysics Data System (ADS)
Li, Junfeng; Rinkevicius, Zilvinas; Cao, Zexing
2014-07-01
Time-dependent density-functional theory (TD-DFT) and complete active space multiconfiguration self-consistent field (CASSCF) calculations have been used to determine equilibrium structures and vibrational frequencies of the ground state and several singlet low-lying excited states of coumarin. Vertical and adiabatic transition energies of S1, S2, and S3 have been estimated by TD-B3LYP and CASSCF/PT2. Calculations predict that the dipole-allowed S1 and S3 states have a character of 1(ππ*), while the dipole-forbidden 1(nπ*) state is responsible for S2. The vibronic absorption and emission spectra of coumarin have been simulated by TD-B3LYP and CASSCF calculations within the Franck-Condon approximation, respectively. The simulated vibronic spectra show good agreement with the experimental observations available, which allow us to reasonably interpret vibronic features in the S0→S1 and S0→S3 absorption and the S0←S1 emission spectra. Based on the calculated results, activity, intensity, and density of the vibronic transitions and their contribution to the experimental spectrum profile have been discussed.
Li, Junfeng; Rinkevicius, Zilvinas; Cao, Zexing
2014-07-01
Time-dependent density-functional theory (TD-DFT) and complete active space multiconfiguration self-consistent field (CASSCF) calculations have been used to determine equilibrium structures and vibrational frequencies of the ground state and several singlet low-lying excited states of coumarin. Vertical and adiabatic transition energies of S1, S2, and S3 have been estimated by TD-B3LYP and CASSCF/PT2. Calculations predict that the dipole-allowed S1 and S3 states have a character of (1)(ππ*), while the dipole-forbidden (1)(nπ*) state is responsible for S2. The vibronic absorption and emission spectra of coumarin have been simulated by TD-B3LYP and CASSCF calculations within the Franck-Condon approximation, respectively. The simulated vibronic spectra show good agreement with the experimental observations available, which allow us to reasonably interpret vibronic features in the S0→S1 and S0→S3 absorption and the S0←S1 emission spectra. Based on the calculated results, activity, intensity, and density of the vibronic transitions and their contribution to the experimental spectrum profile have been discussed. PMID:25005288
Fransson, Thomas; Coriani, Sonia; Christiansen, Ove; Norman, Patrick
2013-03-28
Near carbon K-edge X-ray absorption fine structure spectra of a series of fluorine-substituted ethenes and acetone have been studied using coupled cluster and density functional theory (DFT) polarization propagator methods, as well as the static-exchange (STEX) approach. With the complex polarization propagator (CPP) implemented in coupled cluster theory, relaxation effects following the excitation of core electrons are accounted for in terms of electron correlation, enabling a systematic convergence of these effects with respect to electron excitations in the cluster operator. Coupled cluster results have been used as benchmarks for the assessment of propagator methods in DFT as well as the state-specific static-exchange approach. Calculations on ethene and 1,1-difluoroethene illustrate the possibility of using nonrelativistic coupled cluster singles and doubles (CCSD) with additional effects of electron correlation and relativity added as scalar shifts in energetics. It has been demonstrated that CPP spectra obtained with coupled cluster singles and approximate doubles (CC2), CCSD, and DFT (with a Coulomb attenuated exchange-correlation functional) yield excellent predictions of chemical shifts for vinylfluoride, 1,1-difluoroethene, trifluoroethene, as well as good spectral features for acetone in the case of CCSD and DFT. Following this, CPP-DFT is considered to be a viable option for the calculation of X-ray absorption spectra of larger π-conjugated systems, and CC2 is deemed applicable for chemical shifts but not for studies of fine structure features. The CCSD method as well as the more approximate CC2 method are shown to yield spectral features relating to π∗-resonances in good agreement with experiment, not only for the aforementioned molecules but also for ethene, cis-1,2-difluoroethene, and tetrafluoroethene. The STEX approach is shown to underestimate π∗-peak separations due to spectral compressions, a characteristic which is inherent to this
NASA Astrophysics Data System (ADS)
Spinei, E.; Cede, A.; Swartz, W. H.; Herman, J.; Mount, G. H.
2014-12-01
This paper presents a temperature sensitivity method (TESEM) to accurately calculate total vertical NO2 column, atmospheric slant NO2 profile-weighted temperature (T), and to separate stratospheric and tropospheric columns from direct-sun (DS), ground-based measurements using the retrieved T. TESEM is based on differential optical absorption spectroscopy (DOAS) fitting of the linear temperature-dependent NO2 absorption cross section, σ (T), regression model (Vandaele et al., 2003). Separation between stratospheric and tropospheric columns is based on the primarily bimodal vertical distribution of NO2 and an assumption that stratospheric effective temperature can be represented by temperature at 27 km ± 3 K, and tropospheric effective temperature is equal to surface temperature within 3-5 K. These assumptions were derived from the Global Modeling Initiative (GMI) chemistry-transport model (CTM) simulations over two northern midlatitude sites in 2011. TESEM was applied to the Washington State University Multi-Function DOAS instrument (MFDOAS) measurements at four midlatitude locations with low and moderate NO2 anthropogenic emissions: (1) the Jet Propulsion Laboratory's Table Mountain Facility (JPL-TMF), CA, USA (34.38° N/117.68° W); (2) Pullman, WA, USA (46.73° N/117.17° W); (3) Greenbelt, MD, USA (38.99° N/76.84° W); and (4) Cabauw, the Netherlands (51.97° N/4.93° E) during July 2007, June-July 2009, July-August and October 2011, November 2012-May 2013, respectively. NO2 T and total, stratospheric, and tropospheric NO2 vertical columns were determined over each site.
Analysis of fractals with combined partition
NASA Astrophysics Data System (ADS)
Dedovich, T. G.; Tokarev, M. V.
2016-03-01
The space—time properties in the general theory of relativity, as well as the discreteness and non-Archimedean property of space in the quantum theory of gravitation, are discussed. It is emphasized that the properties of bodies in non-Archimedean spaces coincide with the properties of the field of P-adic numbers and fractals. It is suggested that parton showers, used for describing interactions between particles and nuclei at high energies, have a fractal structure. A mechanism of fractal formation with combined partition is considered. The modified SePaC method is offered for the analysis of such fractals. The BC, PaC, and SePaC methods for determining a fractal dimension and other fractal characteristics (numbers of levels and values of a base of forming a fractal) are considered. It is found that the SePaC method has advantages for the analysis of fractals with combined partition.
Keller, Paul E.; Batdorf, Michael T.; Strasburg, Jana D.; Harper, Warren W.
2009-05-28
This paper presents theory of speckle noise for a frequency-modulation differential-absorption LIDAR system along with simulation results. These results show an unexpected relationship between the signal-to-noise ratio (SNR) of the speckle and the distance to the retro-reflector or target. In simulation, the use of an annular aperture in the system results in a higher SNR at midrange distances than at short or long distances. This peak in SNR occurs in the region where the laser’s Gaussian beam profile approximately fills the target. This was unexpected since it does not occur in the theory or simulations of the same system with a circular aperture. By including the autocorrelation of this annular aperture and expanding the complex correlation factor used in speckle models to include conditions not generally covered, a more complete theoretical model is derived for this system. Obscuration of the center of the beam at near distances is also a major factor in this relationship between SNR and distance. We conclude by comparing the resulting SNR as a function of distance from this expanded theoretical model to the simulations of the system over a double-pass horizontal range of 10 meters to 10 km at a wavelength of 1.28 micrometers
On the monogamy of holographic n -partite information
NASA Astrophysics Data System (ADS)
Mirabi, S.; Tanhayi, M. Reza; Vazirian, R.
2016-05-01
We investigate the monogamy of holographic n -partite information for a system consisting of n disjoint parallel strips with the same width and separation in AdS and AdS black brane geometries. More precisely, we study the sign of this quantity, e.g., for n =4 , 5, in various dimensions and for different parameters. Our results show that for quantum field theories with holographic duals, the holographic 4-partite information is always positive, and the sign of holographic 5-partite information is found to be negative in the dual strongly coupled 1 +1 dimensional conformal field theory. This latter result indicates that the holographic 4-partite information is monogamous. We also find the critical points corresponding to the possible phase transitions of these quantities.
Spatially-partitioned many-body vortices
NASA Astrophysics Data System (ADS)
Klaiman, S.; Alon, O. E.
2016-02-01
A vortex in Bose-Einstein condensates is a localized object which looks much like a tiny tornado storm. It is well described by mean-field theory. In the present work we go beyond the current paradigm and introduce many-body vortices. These are made of spatially- partitioned clouds, carry definite total angular momentum, and are fragmented rather than condensed objects which can only be described beyond mean-field theory. A phase diagram based on a mean-field model assists in predicting the parameters where many-body vortices occur. Implications are briefly discussed.
Mattsson, A.; Österlund, L.; Hu, Shuanglin Hermansson, K.
2014-01-21
Formic acid (HCOOH) adsorption on rutile TiO{sub 2} (110) has been studied by s- and p-polarized infrared reflection-absorption spectroscopy (IRRAS) and spin-polarized density functional theory together with Hubbard U contributions (DFT+U) calculations. To compare with IRRAS spectra, the results from the DFT+U calculations were used to simulate IR spectra by employing a three-layer model, where the adsorbate layer was modelled using Lorentz oscillators with calculated dielectric constants. To account for the experimental observations, four possible formate adsorption geometries were calculated, describing both the perfect (110) surface, and surfaces with defects; either O vacancies or hydroxyls. The majority species seen in IRRAS was confirmed to be the bridging bidentate formate species with associated symmetric and asymmetric frequencies of the ν(OCO) modes measured to be at 1359 cm{sup −1} and 1534 cm{sup −1}, respectively. The in-plane δ(C–H) wagging mode of this species couples to both the tangential and the normal component of the incident p-polarized light, which results in absorption and emission bands at 1374 cm{sup −1} and 1388 cm{sup −1}. IRRAS spectra measured on surfaces prepared to be either reduced, stoichiometric, or to contain surplus O adatoms, were found to be very similar. By comparisons with computed spectra, it is proposed that in our experiments, formate binds as a minority species to an in-plane Ti{sub 5c} atom and a hydroxyl, rather than to O vacancy sites, the latter to a large extent being healed even at our UHV conditions. Excellent agreement between calculated and experimental IRRAS spectra is obtained. The results emphasize the importance of protonation and reactive surface hydroxyls – even under UHV conditions – as reactive sites in e.g., catalytic applications.
NASA Astrophysics Data System (ADS)
Yang, Xue-min; Li, Jin-yan; Chai, Guo-ming; Duan, Dong-ping; Zhang, Jian
2016-08-01
A thermodynamic model for predicting phosphorus partition L P between a CaO-based slags and hot metal during hot metal dephosphorization pretreatment process has been developed based on the ion and molecule coexistence theory (IMCT), i.e., the IMCT- L P model. The reaction abilities of structural units or ion couples in the CaO-based slags have been represented by the calculated mass action concentrations N i through the developed IMCT- N i model based on the IMCT. The developed IMCT- L P model has been verified to be valid through comparing with the measured L P as well as the predicted L P by two reported L P models from the literature. Besides the total phosphorus partition L P between the CaO-based slag and hot metal, the respective phosphorus partitions L P, i of nine dephosphorization products as P2O5, 3FeO·P2O5, 4FeO·P2O5, 2CaO·P2O5, 3CaO·P2O5, 4CaO·P2O5, 2MgO·P2O5, 3MgO·P2O5, and 3MnO·P2O5 can also be accurately predicted by the developed IMCT- L P model. The formed 3CaO·P2O5 accounts for 99.20 pct of dephosphorization products comparing with the generated 4CaO·P2O5 for 0.08 pct. The comprehensive effect of CaO+Fe t O, which can be described by the mass percentage ratio (pct Fe t O)/(pct CaO) or the mass action concentration ratio N_{Fe}t O/N_{Fe}t O N_{CaO}. N_{CaO}} as well as the mass percentage product (pct Fe t O) × (pct CaO) or the mass action concentration product N_{{{{Fe}}t {{O}}}}5 × N_{{CaO}}3 , controls dephosphorization ability of the CaO-based slags. A linear relationship of L P against (pct Fe t O)/(pct CaO) can be correlated compared with a parabolic relationship of L P against N_{Fe}t O/N_{Fe}t O N_{CaO}. N_{CaO}, while the linear relationship of L P against (pct Fe t O) × (pct CaO) or N_{Fe}t O5 × N_{CaO}3 can be established. Thus, the mass percentage product (pct Fe t O) × (pct CaO) and the mass action concentration product N_{Fe}t O5 × N_{CaO}3 are recommended to represent the comprehensive effect of CaO+Fe t O on
Over the last decade, several studies reported that the partitioning of PAHs to sediments, in some cases, did not follow predictions based on equilibrium partitioning theory. One explanation for these differences is the presence of a second sedimentary phase with partitioning cha...
Chemical amplification based on fluid partitioning
Anderson, Brian L.; Colston, Jr., Billy W.; Elkin, Chris
2006-05-09
A system for nucleic acid amplification of a sample comprises partitioning the sample into partitioned sections and performing PCR on the partitioned sections of the sample. Another embodiment of the invention provides a system for nucleic acid amplification and detection of a sample comprising partitioning the sample into partitioned sections, performing PCR on the partitioned sections of the sample, and detecting and analyzing the partitioned sections of the sample.
Verma, Prakash; Derricotte, Wallace D; Evangelista, Francesco A
2016-01-12
Orthogonality constrained density functional theory (OCDFT) provides near-edge X-ray absorption (NEXAS) spectra of first-row elements within one electronvolt from experimental values. However, with increasing atomic number, scalar relativistic effects become the dominant source of error in a nonrelativistic OCDFT treatment of core-valence excitations. In this work we report a novel implementation of the spin-free exact-two-component (X2C) one-electron treatment of scalar relativistic effects and its combination with a recently developed OCDFT approach to compute a manifold of core-valence excited states. The inclusion of scalar relativistic effects in OCDFT reduces the mean absolute error of second-row elements core-valence excitations from 10.3 to 2.3 eV. For all the excitations considered, the results from X2C calculations are also found to be in excellent agreement with those from low-order spin-free Douglas-Kroll-Hess relativistic Hamiltonians. The X2C-OCDFT NEXAS spectra of three organotitanium complexes (TiCl4, TiCpCl3, TiCp2Cl2) are in very good agreement with unshifted experimental results and show a maximum absolute error of 5-6 eV. In addition, a decomposition of the total transition dipole moment into partial atomic contributions is proposed and applied to analyze the nature of the Ti pre-edge transitions in the three organotitanium complexes. PMID:26584082
Fransson, Thomas; Saue, Trond; Norman, Patrick
2016-05-10
The influences of group 12 (Zn, Cd, Hg) metal-substitution on the valence spectra and phosphorescence parameters of porphyrins (P) have been investigated in a relativistic setting. In order to obtain valence spectra, this study reports the first application of the damped linear response function, or complex polarization propagator, in the four-component density functional theory framework [as formulated in Villaume et al. J. Chem. Phys. 2010 , 133 , 064105 ]. It is shown that the steep increase in the density of states as due to the inclusion of spin-orbit coupling yields only minor changes in overall computational costs involved with the solution of the set of linear response equations. Comparing single-frequency to multifrequency spectral calculations, it is noted that the number of iterations in the iterative linear equation solver per frequency grid-point decreases monotonously from 30 to 0.74 as the number of frequency points goes from one to 19. The main heavy-atom effect on the UV/vis-absorption spectra is indirect and attributed to the change of point group symmetry due to metal-substitution, and it is noted that substitutions using heavier atoms yield small red-shifts of the intense Soret-band. Concerning phosphorescence parameters, the adoption of a four-component relativistic setting enables the calculation of such properties at a linear order of response theory, and any higher-order response functions do not need to be considered-a real, conventional, form of linear response theory has been used for the calculation of these parameters. For the substituted porphyrins, electronic coupling between the lowest triplet states is strong and results in theoretical estimates of lifetimes that are sensitive to the wave function and electron density parametrization. With this in mind, we report our best estimates of the phosphorescence lifetimes to be 460, 13.8, 11.2, and 0.00155 s for H2P, ZnP, CdP, and HgP, respectively, with the corresponding transition
NASA Astrophysics Data System (ADS)
Dostert, Karl-Heinz; O'Brien, Casey P.; Liu, Wei; Riedel, Wiebke; Savara, Aditya; Tkatchenko, Alexandre; Schauermann, Swetlana; Freund, Hans-Joachim
2016-08-01
Understanding the interaction of α,β-unsaturated carbonyl compounds with late transition metals is a key prerequisite for rational design of new catalysts with desired selectivity towards C = C or C = O bond hydrogenation. The interaction of the α,β-unsaturated ketone isophorone and the saturated ketone TMCH (3,3,5-trimethylcyclohexanone) with Pd(111) was investigated in this study as a prototypical system. Infrared reflection-absorption spectroscopy (IRAS) and density functional theory calculations including van der Waals interactions (DFT + vdWsurf) were combined to form detailed assignments of IR vibrational modes in the range from 3000 cm- 1 to 1000 cm- 1 in order to obtain information on the binding of isophorone and TMCH to Pd(111) as well as to study the effect of co-adsorbed hydrogen. IRAS measurements were performed with deuterium-labeled (d5-) isophorone, in addition to unlabeled isophorone and unlabeled TMCH. Experimentally observed IR absorption features and calculated vibrational frequencies indicate that isophorone and TMCH molecules in multilayers have a mostly unperturbed structure with random orientation. At sub-monolayer coverages, strong perturbation and preferred orientations of the adsorbates were found. At low coverage, isophorone interacts strongly with Pd(111) and adsorbs in a flat-lying geometry with the C = C and C = O bonds parallel, and a CH3 group perpendicular, to the surface. At intermediate sub-monolayer coverage, the C = C bond is strongly tilted, while the C = O bond remains flat-lying, which indicates a prominent perturbation of the conjugated π system. Pre-adsorbed hydrogen leads to significant changes in the adsorption geometry of isophorone, which suggests a weakening of its binding to Pd(111). At low coverage, the structure of the CH3 groups seems to be mostly unperturbed on the hydrogen pre-covered surface. With increasing coverage, a conservation of the in-plane geometry of the conjugated π system was observed in the
Krechmer, Jordan E; Pagonis, Demetrios; Ziemann, Paul J; Jimenez, Jose L
2016-06-01
Partitioning of gas-phase organic compounds to the walls of Teflon environmental chambers is a recently reported phenomenon than can affect the yields of reaction products and secondary organic aerosol (SOA) measured in laboratory experiments. Reported time scales for reaching gas-wall partitioning (GWP) equilibrium (τGWE) differ by up to 3 orders of magnitude, however, leading to predicted effects that vary from substantial to negligible. A new technique is demonstrated here in which semi- and low-volatility oxidized organic compounds (saturation concentration c* < 100 μg m(-3)) were photochemically generated in rapid bursts in situ in an 8 m(3) environmental chamber, and then their decay in the absence of aerosol was measured using a high-resolution chemical ionization mass spectrometer (CIMS) equipped with an "inlet-less" NO3(-) ion source. Measured τGWE were 7-13 min (rel. std. dev. 33%) for all compounds. The fraction of each compound that partitioned to the walls at equilibrium follows absorptive partitioning theory with an equivalent wall mass concentration in the range 0.3-10 mg m(-3). Measurements using a CIMS equipped with a standard ion-molecule reaction region showed large biases due to the contact of compounds with walls. On the basis of these results, a set of parameters is proposed for modeling GWP in chamber experiments. PMID:27138683
NASA Astrophysics Data System (ADS)
Isaacman, G. A.; Kreisberg, N. M.; Yee, L.; Chan, A.; Worton, D. R.; Hering, S. V.; Goldstein, A. H.
2013-12-01
Hourly and bi-hourly time-resolved measurements of organic tracer compounds in ambient aerosols have been successfully used to elucidate sources and formation pathways of atmospheric particulate matter. Here we extend the Semi-Volatile Thermal desorption Aerosol Gas chromatograph (SVTAG), a custom in-situ instrument that collects, desorbs, and analyzes ambient aerosol and semi-volatile compounds with hourly time resolution, to include on-line derivatization and a second, parallel collection cell that provides simultaneous collection of both particle-phase and particle-plus-gas-phase organic compounds. By introducing a silylating agent upon desorption, SVTAG can measure highly oxygenated compounds that are not easily detected using traditional gas chromatography including most of the previously reported oxygenated tracers for biogenic and anthropogenic secondary organic aerosol. The use of a pair of matched collection cells with parallel sampling and serial analysis provides direct gas-particle partitioning information. One cell collects the total organic fraction of compounds with volatilities lower than a C13 hydrocarbon, while the other cell samples through an activated carbon denuder to selectively remove the gas-phase components. Taken together these provide a direct measurement of gas-particle partitioning to yield a check on classical absorption based partitioning theory while deviations from this theory provide constraints on other driving factors in aerosol formation chemistry, such as oligomerization, salt formation, and acidity. We present here the capabilities and utility of the dual cell SVTAG with derivatization, with chemical insights gained from initial tests on ambient Berkeley air and the first results from a rural site in Alabama obtained during the Southern Oxidant and Aerosol Study (SOAS). Tracers for varying isoprene oxidation pathways are used to explore the influence of anthropogenic emissions; concentrations of 2-methyltetrols and 2-methyl
Yano, Junko; Yachandra, Vittal K.
2009-07-09
This review gives a brief description of the theory and application of X-ray absorption spectroscopy, both X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS), especially, pertaining to photosynthesis. The advantages and limitations of the methods are discussed. Recent advances in extended EXAFS and polarized EXAFS using oriented membranes and single crystals are explained. Developments in theory in understanding the XANES spectra are described. The application of X-ray absorption spectroscopy to the study of the Mn4Ca cluster in Photosystem II is presented.
Spencer, Liam P.; Yang, Ping; Minasian, Stefan G.; Jilek, Robert E.; Batista, Enrique R.; Boland, Kevin S.; Boncella, James M.; Conradson, S. D.; Clark, David L.; Hayton, Trevor W.; Kozimor, Stosh A.; Martin, Richard L.; MacInnes, Molly M.; Olson, Angela C.; Scott, Brian L.; Shuh, D. K.; Wilkerson, Marianne P.
2013-02-13
Synthetic routes to salts containing uranium bisimido tetrahalide anions [U(NR)(2)X-4](2-) (X = Cl-, Br-) and non-coordinating NEt4+ and PPh4+ countercations are reported. In general, these compounds can be prepared from U(NR)(2)I-2(THF)(x) (x = 2 and R = 'Bu, Ph; x = 3 and R = Me) upon addition of excess halide. In addition to providing stable coordination complexes with Cl-, the [U(NMe)(2)](2 +) cation also reacts with Br- to form stable [NEt4](2)[U(NMe)(2)Br-4] complexes. These materials were used as a platform to compare electronic structure and bonding in [U(NR)(2)](2+) with [UO2](2+). Specifically, Cl K-edge X-ray absorption spectroscopy (XAS) and both ground-state and time-dependent hybrid density functional theory (DFT and TDDFT) were used to probe U-Cl bonding interactions in [PPh4](2)[U((NBu)-Bu-t)(2)Cl-4] and [PPh4](2)[UO2Cl4]. The DFT and XAS results show the total amount of Cl 3p character mixed with the U 5f orbitals was roughly 7-10% per U-Cl bond for both compounds, which shows that moving from oxo to imido has little effect on orbital mixing between the U 5f and equatorial Cl 3p orbitals. The results are presented in the context of recent Cl K-edge XAS and DFT studies on other hexavalent uranium chloride systems with fewer oxo or imido ligands.
Van Kuiken, Benjamin E.; Valiev, Marat; Daifuku, Stephanie L.; Bannan, Caitlin; Strader, Matthew L.; Cho, Hana; Huse, N.; Schoenlein, R. W.; Govind, Niranjan; Khalil, Munira
2013-05-01
Ruthenium L2,3-edge X-ray absorption (XA) spectroscopy probes transitions from core 2p orbitals to the 4d levels of the atom and is a powerful tool for interrogating the local electronic and molecular structure around the metal atom. However, a molecular-level interpretation of the Ru L2,3-edge spectral lineshapes is often complicated by spin–orbit coupling (SOC) and multiplet effects. In this study, we develop spin-free time-dependent density functional theory (TDDFT) as a viable and predictive tool to simulate the Ru L3-edge spectra. We successfully simulate and analyze the ground state Ru L3-edge XA spectra of a series of RuII and RuIII complexes: [Ru(NH3)6]2+/3+, [Ru(CN)6]4-/3-, [RuCl6]4-/3-, and the ground (1A1) and photoexcited (3MLCT) transient states of [Ru(bpy)3]2+ and Ru(dcbpy)2(NCS)2 (termed N3). The TDDFT simulations reproduce all the experimentally observed features in Ru L3-edge XA spectra. The advantage of using TDDFT to assign complicated Ru L3-edge spectra is illustrated by its ability to identify ligand specific charge transfer features in complex molecules. We conclude that the B3LYP functional is the most reliable functional for accurately predicting the location of charge transfer features in these spectra. Experimental and simulated Ru L3-edge XA spectra are presented for the transition metal mixed-valence dimers [(NC)5MII-CN-RuIII(NH3)5]- (where M = Fe or Ru) dissolved in water. We explore the spectral signatures of electron delocalization in Ru L3-edge XA spectroscopy and our simulations reveal that the inclusion of explicit solvent molecules is crucial for reproducing the experimentally determined valencies, highlighting the importance of the role of the solvent in transition metal charge transfer chemistry.
Kuiken, Benjamin E. Van; Valiev, Marat; Daifuku, Stephanie L.; Bannan, Caitlin; Strader, Matthew L.; Cho, Hana; Huse, Nils; Schoenlein, Robert W.; Govind, Niranjan; Khalil, Munira
2013-04-26
Ruthenium L3-edge X-ray absorption (XA) spectroscopy probes unoccupied 4d orbitals of the metal atom and is increasingly being used to investigate the local electronic structure in ground and excited electronic states of Ru complexes. The simultaneous development of computational tools for simulating Ru L3-edge spectra is crucial for interpreting the spectral features at a molecular level. This study demonstrates that time-dependent density functional theory (TDDFT) is a viable and predictive tool for simulating ruthenium L3-edge XA spectroscopy. We systematically investigate the effects of exchange correlation functional and implicit and explicit solvent interactions on a series of RuII and RuIII complexes in their ground and electronic excited states. The TDDFT simulations reproduce all of the experimentally observed features in Ru L3-edge XA spectra within the experimental resolution (0.4 eV). Our simulations identify ligand-specific charge transfer features in complicated Ru L3-edge spectra of [Ru(CN)6]4- and RuII polypyridyl complexes illustrating the advantage of using TDDFT in complex systems. We conclude that the B3LYP functional most accurately predicts the transition energies of charge transfer features in these systems. We use our TDDFT approach to simulate experimental Ru L3-edge XA spectra of transition metal mixed-valence dimers of the form [(NC)5MII-CN-RuIII(NH3)5] (where M = Fe or Ru) dissolved in water. Our study determines the spectral signatures of electron delocalization in Ru L3-edge XA spectra. We find that the inclusion of explicit solvent molecules is necessary for reproducing the spectral features and the experimentally determined valencies in these mixed-valence complexes. This study validates the use of TDDFT for simulating Ru 2p excitations using popular quantum chemistry codes and providing a powerful interpretive tool for equilibrium and ultrafast Ru L3-edge XA spectroscopy.
Murphy, M. W.; Yiu, Y. M. Sham, T. K.; Ward, M. J.; Liu, L.; Hu, Y.; Zapien, J. A.; Liu, Yingkai
2014-11-21
The electronic structure and optical properties of a series of iso-electronic and iso-structural CdS{sub x}Se{sub 1−x} solid solution nanostructures have been investigated using X-ray absorption near edge structure, extended X-ray absorption fine structure, and X-ray excited optical luminescence at various absorption edges of Cd, S, and Se. It is found that the system exhibits compositions, with variable local structure in-between that of CdS and CdSe accompanied by tunable optical band gap between that of CdS and CdSe. Theoretical calculation using density functional theory has been carried out to elucidate the observations. It is also found that luminescence induced by X-ray excitation shows new optical channels not observed previously with laser excitation. The implications of these observations are discussed.
The conventional Junge-Pankow adsorption model uses the sub-cooled liquid vapor pressure (pLo) as a correlation parameter for gas/particle interactions. An alternative is the octanol-air partition coefficient (Koa) absorption model. Log-log plots of the particle-gas partition c...
Probabilistic framework for network partition
NASA Astrophysics Data System (ADS)
Li, Tiejun; Liu, Jian; E, Weinan
2009-08-01
Given a large and complex network, we would like to find the partition of this network into a small number of clusters. This question has been addressed in many different ways. In a previous paper, we proposed a deterministic framework for an optimal partition of a network as well as the associated algorithms. In this paper, we extend this framework to a probabilistic setting, in which each node has a certain probability of belonging to a certain cluster. Two classes of numerical algorithms for such a probabilistic network partition are presented and tested. Application to three representative examples is discussed.
Inquiry Calculus and Information Theory
NASA Astrophysics Data System (ADS)
Center, Julian L.
2009-12-01
We consider the relationship between information theory and a calculus of inquiries. We show how an inquiry calculus can be constructed using lattice theory, and how the inquiry calculus relates to information theory. The key idea is to identify both inquiries and variables with partitions of the state space. We also show an approach to extending information theory that deals with the problem of negative entropies on questions that do not correspond to partitions.
Optimal Partitioning of Testing Time: Theoretical Properties and Practical Implications
ERIC Educational Resources Information Center
Wang, Tianyou; Zhang, Jiawei
2006-01-01
This paper deals with optimal partitioning of limited testing time in order to achieve maximum total test score. Nonlinear optimization theory was used to analyze this problem. A general case using a generic item response model is first presented. A special case that applies a response time model proposed by Wang and Hanson (2005) is also…
Graph Partitioning and Sequencing Software
Energy Science and Technology Software Center (ESTSC)
1995-09-19
Graph partitioning is a fundemental problem in many scientific contexts. CHACO2.0 is a software package designed to partition and sequence graphs. CHACO2.0 allows for recursive application of several methods for finding small edge separators in weighted graphs. These methods include inertial, spectral, Kernighan Lin and multilevel methods in addition to several simpler strategies. Each of these approaches can be used to partition the graph into two, four, or eight pieces at each level of recursion.more » In addition, the Kernighan Lin method can be used to improve partitions generated by any of the other algorithms. CHACO2.0 can also be used to address various graph sequencing problems, with applications to scientific computing, database design, gene sequencing and other problems.« less
A diffusion-diffusion model for percutaneous drug absorption.
Kubota, K; Ishizaki, T
1986-08-01
Several theories describing percutaneous drug absorption have been proposed, incorporating the mathematical solutions of differential equations describing percutaneous drug absorption processes where the vehicle and skin are regarded as simple diffusion membranes. By a solution derived from Laplace transforms, the mean residence time MRT and the variance of the residence time VRT in the vehicle are expressed as simple elementary functions of the following five pharmacokinetic parameters characterizing the percutaneous drug absorption: kd, which is defined as the normalized diffusion coefficient of the skin, kc, which is defined as the normalized skin-capillary boundary clearance, the apparent length of diffusion of the skin 1d, the effective length of the vehicle lv, and the diffusion coefficient of the vehicle Dv. All five parameters can be obtained by the methods proposed here. Results of numerical computation indicate that: concentration-distance curves in the vehicle and skin approximate two curves which are simply expressed using trigonometric functions when sufficient time elapses after an ointment application; the most suitable condition for the assumption that the concentration of a drug in the uppermost epidermis can be considered unchanged is the case where the partition coefficient between vehicle and skin is small, and the constancy of drug concentration is even more valid when the effective length of the vehicle is large; and the amount of a drug in the vehicle or skin and the flow rate of the drug from vehicle into skin or from skin into blood becomes linear on a semilogarithmic scale, and the slopes of those lines are small when Dv is small, when the partition coefficient between vehicle and skin is small, when lv is large, or when kc is small. A simple simulation method is also proposed using a biexponential for the concentration-time curve for the skin near the skin-capillary boundary, that is, the flow rate-time curve for drug passing from skin
Ostlund, Richard E
2002-03-01
Cholesterol absorption is a key regulatory point in human lipid metabolism because it determines the amount of endogenous biliary as well as dietary cholesterol that is retained, thereby influencing whole body cholesterol balance. Plant sterols (phytosterols) and the drug ezetimibe reduce cholesterol absorption and low-density lipoprotein cholesterol in clinical trials, complementing the statin drugs, which inhibit cholesterol biosynthesis. The mechanism of cholesterol absorption is not completely known but involves the genes ABC1, ABCG5, and ABCG8, which are members of the ATP-binding cassette protein family and appear to remove unwanted cholesterol and phytosterols from the enterocyte. ABC1 is upregulated by the liver X (LXR) and retinoid X (RXR) nuclear receptors. Acylcholesterol acytransferase-2 is an intestinal enzyme that esterifies absorbed cholesterol and increases cholesterol absorption when dietary intake is high. New clinical treatments based on better understanding of absorption physiology are likely to substantially improve clinical cholesterol management in the future. PMID:17033296
NASA Astrophysics Data System (ADS)
Glebov, L. B.; Dokuchaev, V. G.; Petrovskiĭ, G. T.
1987-06-01
A theoretical analysis is made of a polarization calorimetric method for the determination of weak absorption in optical materials. Several variants of the method are considered and the optimal conditions for its application are identified. The sensitivity of the method is ~1 dB/km for a sample 1 cm thick. It is shown that the method can be used to determine absorption in optically anisotropic materials.
Line defects and 5d instanton partition functions
NASA Astrophysics Data System (ADS)
Kim, Hee-Cheol
2016-03-01
We consider certain line defect operators in five-dimensional SUSY gauge theories, whose interaction with the self-dual instantons is described by 1d ADHM-like gauged quantum mechanics constructed by Tong and Wong. The partition function in the presence of these operators is known to be a generating function of BPS Wilson loops in skew symmetric tensor representations of the gauge group. We calculate the partition function and explicitly prove that it is a finite polynomial of the defect mass parameter x, which is an essential property of the defect operator and the Wilson loop generating function. The relation between the line defect partition function and the qq-character defined by N . Nekrasov is briefly discussed.
Supersymmetric partition functions in the AdS/CFT conjecture
NASA Astrophysics Data System (ADS)
Raju, Suvrat
We study supersymmetric partition functions in several versions of the AdS/CFT correspondence. We present an Index for superconformal field theories in d = 3, 4, 5, 6. This captures all information about the spectrum that is protected, under continuous deformations of the theory, purely by group theory. We compute our Index in N = 4 SYM at weak coupling using gauge theory and at strong coupling using supergravity and find perfect agreement at large N. We also compute this Index for supergravity on AdS4 x S7 and AdS7 x S4 and for the recently constructed Chern Simons matter theories. We count 1/16 BPS states in the free gauge theory and find qualitative agreement with the entropy of big black holes in AdS5. We note that the near horizon geometry of some small supersymmetric black holes is an extremal BTZ black holes fibered on a compact base and propose a possible explanation for this, based on giant gravitons. We also find the partition function of the chiral ring of the N = 4 SYM theory at finite coupling and finite N. Turning to AdS3, we study the low energy 1/4 and 1/2 BPS partition functions by finding all classical supersymmetric probe brane solutions of string theory on this background. If the background BNS field and theta angle vanish, AdS3 x S 3 x T4/K3 supports supersymmetric probes: D1 branes, D5 branes and bound states of D5 and D1 branes. In global AdS, upon quantization, these solutions give rise to states in discrete representations of the SL(2,R) WZW model on AdS 3. We conclude that (a) the 1/4 BPS partition function jumps if we turn on a theta angle or NS-NS field (b) generic 1/2 BPS states are protected. We successfully compare our 1/2 BPS partition function with that of the symmetric product. We also discuss puzzles, and their possible resolutions, in reproducing the elliptic genus of the symmetric product. Finally, we comment on the spectrum of particles in the theory of gravity dual to non-supersymmetric Yang Mills theory on S3 x time.
Revisiting noninteracting string partition functions in Rindler space
NASA Astrophysics Data System (ADS)
Mertens, Thomas G.; Verschelde, Henri; Zakharov, Valentin I.
2016-05-01
We revisit noninteracting string partition functions in Rindler space by summing over fields in the spectrum. In field theory, the total partition function splits in a natural way into a piece that does not contain surface terms and a piece consisting of solely the so-called edge states. For open strings, we illustrate that surface contributions to the higher-spin fields correspond to open strings piercing the Rindler origin, unifying the higher-spin surface contributions in string language. For closed strings, we demonstrate that the string partition function is not quite the same as the sum over the partition functions of the fields in the spectrum: an infinite overcounting is present for the latter. Next we study the partition functions obtained by excluding the surface terms. Using recent results of He et al. [J. High Energy Phys. 05 (2015) 106], this construction, first done by Emparan [arXiv:hep-th/9412003], can be put on much firmer ground. We generalize to type II and heterotic superstrings and demonstrate modular invariance. All of these exhibit an IR divergence that can be interpreted as a maximal acceleration close to the black hole horizon. Ultimately, since these partition functions are only part of the full story, divergences here should not be viewed as a failure of string theory: maximal acceleration is a feature of a faulty treatment of the higher-spin fields in the string spectrum. We comment on the relevance of this to Solodukhin's recent proposal [Phys. Rev. D 91, 084028 (2015)]. A possible link with the firewall paradox is apparent.
Mechanism and kinetics of peptide partitioning into membranes
Ulmschneider, Martin; Killian, J Antoinette; Doux, Jacques P. F.; Smith, Jeremy C; Ulmschneider, Jakob
2010-02-01
Partitioning properties of transmembrane (TM) polypeptide segments directly determine membrane protein folding, stability, and function, and their understanding is vital for rational design of membrane active peptides. However, direct determination of water-to-bilayer transfer of TM peptides has proved difficult. Experimentally, sufficiently hydrophobic peptides tend to aggregate, while atomistic computer simulations at physiological temperatures cannot yet reach the long time scales required to capture partitioning. Elevating temperatures to accelerate the dynamics has been avoided, as this was thought to lead to rapid denaturing. However, we show here that model TM peptides (WALP) are exceptionally thermostable. Circular dichroism experiments reveal that the peptides remain inserted into the lipid bilayer and are fully helical, even at 90 C. At these temperatures, sampling is 50 500 times faster, sufficient to directly simulate spontaneous partitioning at atomic resolution. A folded insertion pathway is observed, consistent with three-stage partitioning theory. Elevated temperature simulation ensembles further allow the direct calculation of the insertion kinetics, which is found to be first-order for all systems. Insertion barriers are Hin = 15 kcal/mol for a general hydrophobic peptide and 23 kcal/mol for the tryptophan-flanked WALP peptides. The corresponding insertion times at room temperature range from 8.5 s to 163 ms. High-temperature simulations of experimentally validated thermostable systems suggest a new avenue for systematic exploration of peptide partitioning properties.
New Instrumentation for Phase Partitioning
NASA Technical Reports Server (NTRS)
Harris, J. M.
1985-01-01
Cells and molecules can be purified by partitioning between the two immiscible liquid phases formed by aqueous solutions of poly/ethylene glycol and dextran. Such purification can be more selective, higher yielding, and less destructive to sensitive biological materials than other available techniques. Earth's gravitational field is a hindering factor as it causes sedimentation of particles to be purified and shear-induced particle randomization. The present proposal is directed toward developing new instrumentation for performing phase partitioning both on Earth and in microgravity.
New parallel SOR method by domain partitioning
Xie, Dexuan
1996-12-31
In this paper, we propose and analyze a new parallel SOR method, the PSOR method, formulated by using domain partitioning together with an interprocessor data-communication technique. For the 5-point approximation to the Poisson equation on a square, we show that the ordering of the PSOR based on the strip partition leads to a consistently ordered matrix, and hence the PSOR and the SOR using the row-wise ordering have the same convergence rate. However, in general, the ordering used in PSOR may not be {open_quote}consistently ordered{close_quotes}. So, there is a need to analyze the convergence of PSOR directly. In this paper, we present a PSOR theory, and show that the PSOR method can have the same asymptotic rate of convergence as the corresponding sequential SOR method for a wide class of linear systems in which the matrix is {open_quotes}consistently ordered{close_quotes}. Finally, we demonstrate the parallel performance of the PSOR method on four different message passing multiprocessors (a KSR1, the Intel Delta, an Intel Paragon and an IBM SP2), along with a comparison with the point Red-Black and four-color SOR methods.
Ferrous iron partitioning in the lower mantle
NASA Astrophysics Data System (ADS)
Muir, Joshua M. R.; Brodholt, John P.
2016-08-01
We used density functional theory (DFT) to examine the partitioning of ferrous iron between periclase and bridgmanite under lower mantle conditions. To study the effects of the three major variables - pressure, temperature and concentration - these have been varied from 0 to 150 GPa, from 1000 to 4000 K and from 0 to 100% total iron content. We find that increasing temperature increases KD, increasing iron concentration decreases KD, while pressure can both increase and decrease KD. We find that KD decreases slowly from about 0.32 to 0.06 with depth under lower mantle conditions. We also find that KD increases sharply to 0.15 in the very lowermost mantle due to the strong temperature increases near the CMB. Spin transitions have a large effect on the activity of ferropericlase which causes KD to vary with pressure in a peak-like fashion. Despite the apparently large changes in KD through the mantle, this actually results in relatively small changes in total iron content in the two phases, with XFefp ranging from about 0.20 to 0.35, before decreasing again to about 0.28 at the CMB, and XFebd has a pretty constant value of about 0.04-0.07 throughout the lower mantle. For the very high Fe concentrations suggested for ULVZs, Fe partitions very strongly into ferropericlase.
Rectilinear partitioning of irregular data parallel computations
NASA Technical Reports Server (NTRS)
Nicol, David M.
1991-01-01
New mapping algorithms for domain oriented data-parallel computations, where the workload is distributed irregularly throughout the domain, but exhibits localized communication patterns are described. Researchers consider the problem of partitioning the domain for parallel processing in such a way that the workload on the most heavily loaded processor is minimized, subject to the constraint that the partition be perfectly rectilinear. Rectilinear partitions are useful on architectures that have a fast local mesh network. Discussed here is an improved algorithm for finding the optimal partitioning in one dimension, new algorithms for partitioning in two dimensions, and optimal partitioning in three dimensions. The application of these algorithms to real problems are discussed.
NASA Technical Reports Server (NTRS)
Halasinski, Thomas M.; Weisman, Jennifer L.; Lee, Timothy J.; Salama, Farid; Head-Gordon, Martin; Kwak, Dochan (Technical Monitor)
2002-01-01
We present a full experimental and theoretical study of an interesting series of polycyclic aromatic hydrocarbons, the oligorylenes. The absorption spectra of perylene, terrylene and quaterrylene in neutral, cationic and anionic charge states are obtained by matrix-isolation spectroscopy in Ne. The experimental spectra are dominated by a bright state that red shifts with growing molecular size. Excitation energies and state symmetry assignments are supported by calculations using time dependent density functional theory methods. These calculations also provide new insight into the observed trends in oscillator strength and excitation energy for the bright states: the oscillator strength per unit mass of carbon increases along the series.
Irradiation of linear polyethylene - Partitioning between sol and gel.
NASA Technical Reports Server (NTRS)
Rijke, A. M.; Mandelkern, L.
1971-01-01
Investigation of the importance of chain-scission processes and of the applicability of the general theory of network formation to polyethylene with respect to critical conditions for gelation, using molecular weight fractions of linear polyethylene irradiated at 133 C. The partitioning between sol and gel was found to adhere to the theory just beyond the gel point. Deviations from theory occurred as the irradiation dosage was increased. It was concluded that main-chain scission at the temperatures concerned is not a significant process.
Petawatt laser absorption bounded
NASA Astrophysics Data System (ADS)
Levy, Matthew; Wilks, Scott; Tabak, Max; Libby, Stephen; Baring, Matthew
2014-10-01
The interaction of petawatt (1015 W) lasers with solid matter forms the basis for advanced scientific applications such as table-top relativistic particle accelerators, ultrafast charged particle imaging systems and fast ignition inertial confinement fusion. Key metrics for these applications relate to absorption, yet conditions in this regime are so nonlinear that it is often impossible to know the fraction of absorbed light f, and even the range of f is unknown. In this presentation, using a relativistic Rankine-Hugoniot-like analysis, we show how to derive the theoretical maximum and minimum of f. These boundaries constrain nonlinear absorption mechanisms across the petawatt regime, forbidding high absorption values at low laser power and low absorption values at high laser power. Close agreement is shown with several dozens of published experimental data points and simulation results, helping to confirm the theory. For applications needing to circumvent the absorption bounds, these results will accelerate a shift from solid targets, towards structured and multilayer targets, and lead the development of new materials.
Monomial Crystals and Partition Crystals
NASA Astrophysics Data System (ADS)
Tingley, Peter
2010-04-01
Recently Fayers introduced a large family of combinatorial realizations of the fundamental crystal B(Λ0) for ^sln, where the vertices are indexed by certain partitions. He showed that special cases of this construction agree with the Misra-Miwa realization and with Berg's ladder crystal. Here we show that another special case is naturally isomorphic to a realization using Nakajima's monomial crystal.
Set covering, partition and packing
Hulme, B.L.; Baca, L.S.
1984-03-01
Set covering problems are known to be solvable by Boolean algebraic methods. This report shows that set partition and set packing problems can be solved by the same algebraic methods because these problems can be converted into covering problems. Many applications are possible including security patrol assignment which is used as an example.
METAL PARTITIONING IN COMBUSTION PROCESSES
This article summarizes ongoing research efforts at the National Risk Management Research Laboratory of the U.S. Environmental Protection Agency examining [high temperature] metal behavior within combustion environments. The partitioning of non-volatile (Cr and Ni), semi-volatil...
Some trees with partition dimension three
NASA Astrophysics Data System (ADS)
Fredlina, Ketut Queena; Baskoro, Edy Tri
2016-02-01
The concept of partition dimension of a graph was introduced by Chartrand, E. Salehi and P. Zhang (1998) [2]. Let G(V, E) be a connected graph. For S ⊆ V (G) and v ∈ V (G), define the distance d(v, S) from v to S is min{d(v, x)|x ∈ S}. Let Π be an ordered partition of V (G) and Π = {S1, S2, ..., Sk }. The representation r(v|Π) of vertex v with respect to Π is (d(v, S1), d(v, S2), ..., d(v, Sk)). If the representations of all vertices are distinct, then the partition Π is called a resolving partition of G. The partition dimension of G is the minimum k such that G has a resolving partition with k partition classes. In this paper, we characterize some classes of trees with partition dimension three, namely olive trees, weeds, and centipedes.
Terminology for trace-element partitioning
Beattie, P. ); Drake, M. ); Jones, J.; McKay, G. ); Leeman, W. ); Longhi, J. ); Nielsen, R. ); Palme, H. ); Shaw, D. ); Takahashi, E. ); Watson, B. )
1993-04-01
A self-consistent terminology for partitioning data is presented. Ratios of the concentration of a component in two phases are termed partition coefficients and given the symbol D. Ratios of partition coefficients are termed exchange coefficients and given the symbol K[sub D]. The prefix bulk implies that these coefficients are weighted according to the proportions of coexisting phases. Bulk partition and bulk exchange coefficients are denoted by [bar D] and [ovr K[sub D
ERIC Educational Resources Information Center
Brusco, Michael; Steinley, Douglas
2010-01-01
Structural balance theory (SBT) has maintained a venerable status in the psychological literature for more than 5 decades. One important problem pertaining to SBT is the approximation of structural or generalized balance via the partitioning of the vertices of a signed graph into "K" clusters. This "K"-balance partitioning problem also has more…
Metaporous layer to overcome the thickness constraint for broadband sound absorption
Yang, Jieun; Lee, Joong Seok; Kim, Yoon Young
2015-05-07
The sound absorption of a porous layer is affected by its thickness, especially in a low-frequency range. If a hard-backed porous layer contains periodical arrangements of rigid partitions that are coordinated parallel and perpendicular to the direction of incoming sound waves, the lower bound of the effective sound absorption can be lowered much more and the overall absorption performance enhanced. The consequence of rigid partitioning in a porous layer is to make the first thickness resonance mode in the layer appear at much lower frequencies compared to that in the original homogeneous porous layer with the same thickness. Moreover, appropriate partitioning yields multiple thickness resonances with higher absorption peaks through impedance matching. The physics of the partitioned porous layer, or the metaporous layer, is theoretically investigated in this study.
ARSENIC SOLID-PHASE PARTITIONING IN REDUCING SEDIMENTS OF CONTAMINATED WETLAND
The geochemical partitioning of arsenic in organic-rich sediments from a contaminated wetland is examined using X-ray absorption spectroscopy and selective chemical extraction procedures, and evaluated in context to the anoxic diagenesis of iron and sulfur. The interaction betwe...
Size-dependent forced PEG partitioning into channels: VDAC, OmpC, and α-hemolysin
Aksoyoglu, M. Alphan; Podgornik, Rudolf; Bezrukov, Sergey M.; Gurnev, Philip A.; Muthukumar, Murugappan; Parsegian, V. Adrian
2016-01-01
Nonideal polymer mixtures of PEGs of different molecular weights partition differently into nanosize protein channels. Here, we assess the validity of the recently proposed theoretical approach of forced partitioning for three structurally different β-barrel channels: voltage-dependent anion channel from outer mitochondrial membrane VDAC, bacterial porin OmpC (outer membrane protein C), and bacterial channel-forming toxin α-hemolysin. Our interpretation is based on the idea that relatively less-penetrating polymers push the more easily penetrating ones into nanosize channels in excess of their bath concentration. Comparison of the theory with experiments is excellent for VDAC. Polymer partitioning data for the other two channels are consistent with theory if additional assumptions regarding the energy penalty of pore penetration are included. The obtained results demonstrate that the general concept of “polymers pushing polymers” is helpful in understanding and quantification of concrete examples of size-dependent forced partitioning of polymers into protein nanopores. PMID:27466408
Size-dependent forced PEG partitioning into channels: VDAC, OmpC, and α-hemolysin.
Aksoyoglu, M Alphan; Podgornik, Rudolf; Bezrukov, Sergey M; Gurnev, Philip A; Muthukumar, Murugappan; Parsegian, V Adrian
2016-08-01
Nonideal polymer mixtures of PEGs of different molecular weights partition differently into nanosize protein channels. Here, we assess the validity of the recently proposed theoretical approach of forced partitioning for three structurally different β-barrel channels: voltage-dependent anion channel from outer mitochondrial membrane VDAC, bacterial porin OmpC (outer membrane protein C), and bacterial channel-forming toxin α-hemolysin. Our interpretation is based on the idea that relatively less-penetrating polymers push the more easily penetrating ones into nanosize channels in excess of their bath concentration. Comparison of the theory with experiments is excellent for VDAC. Polymer partitioning data for the other two channels are consistent with theory if additional assumptions regarding the energy penalty of pore penetration are included. The obtained results demonstrate that the general concept of "polymers pushing polymers" is helpful in understanding and quantification of concrete examples of size-dependent forced partitioning of polymers into protein nanopores. PMID:27466408
NASA Technical Reports Server (NTRS)
Butler, Carolyn; Spencer, Randall
1988-01-01
The improvement of computer hardware and software of the NASA Multipurpose Differential Absorption Lidar (DIAL) system is documented. The NASA DIAL system has undergone development and experimental deployment at NASA/Langley Res. Center for the remote measurement of atmospheric trace gas concentrations from ground and aircraft platforms. A viable DIAL system was developed capable of remotely measuring O3 and H2O concentrations from an aircraft platform. The DIAL Data Acquisition System (DAS) has undergone a number of improvements also. Due to the participation of the DIAL in the Global Tropospheric Experiment, modifications and improvements of the system were tested and used both in the lab and in air. Therefore, this is an operational manual for the DIAL DAS.
Petit, Andrew S.; Subotnik, Joseph E.
2014-07-07
In this paper, we develop a surface hopping approach for calculating linear absorption spectra using ensembles of classical trajectories propagated on both the ground and excited potential energy surfaces. We demonstrate that our method allows the dipole-dipole correlation function to be determined exactly for the model problem of two shifted, uncoupled harmonic potentials with the same harmonic frequency. For systems where nonadiabatic dynamics and electronic relaxation are present, preliminary results show that our method produces spectra in better agreement with the results of exact quantum dynamics calculations than spectra obtained using the standard ground-state Kubo formalism. As such, our proposed surface hopping approach should find immediate use for modeling condensed phase spectra, especially for expensive calculations using ab initio potential energy surfaces.
NASA Astrophysics Data System (ADS)
Nakazawa, M.; Fukui, K.; Kotani, A.
2003-02-01
We have made precise theoretical calculations for both 2 p3/2→4 f X-ray absorption spectroscopy (XAS) and 4 d→2 p3/2 resonant X-ray emission spectroscopy (RXES) by electric quadrupole excitations at the L3 edge of light rare-earth elements, by means of atomic model with full multiplet effects. The calculation is based on the second-order optical formula, and the effect of the incident photon polarization is taken into account. It is shown that the 4 d-4 f interaction plays a more important role in 4 d→2 p3/2 RXES than the 4 f-4 f interaction does. Moreover, the calculated results of 4 d→2 p3/2 RXES show the strong polarization dependence, and it is originated from the spin multiplicity, which is derived from the 4 d-4 f interaction, of the RXES final states.
Equilibrium partitioning of Ficoll in composite hydrogels.
Kosto, Kimberly B; Panuganti, Swapna; Deen, William M
2004-09-15
Equilibrium partition coefficients (phi, the concentration in the gel divided by that in free solution) of fluorescein-labeled Ficolls in pure agarose and agarose-dextran composite gels were measured as a function of gel composition and Ficoll size. The four narrow fractions of Ficoll, a spherical polysaccharide, had Stokes-Einstein radii ranging from 2.7 to 5.9 nm. Gels with agarose volume fractions of 0.040 and 0.080 were studied, with dextran volume fractions (calculated as if the chain were a long fiber) up to 0.011. As expected, phi generally decreased as the Ficoll size increased (for a given gel composition) or as the amount of dextran incorporated into the gel increased (for a given agarose concentration and Ficoll size). The decrease in phi that accompanied dextran addition was predicted well by an excluded volume theory in which agarose and dextran were both treated as rigid, straight, randomly positioned and oriented fibers. Modeling dextran as a spherical coil within a fibrous agarose gel produced much less accurate predictions. The diffusional permeabilities of these gels were assessed by combining the current partitioning data with relative diffusivities (Kd, the diffusivity in the gel divided by that in free solution) reported previously. The values of phi Kd for a synthetic gel with 8.0% agarose and 1.1% dextran (by volume) were found to be very similar to those for the glomerular basement membrane, a physiologically important material which also has a total solids content of approximately 10%. PMID:15341852
Mbah, C J
2007-01-01
Sunscreen products are widely used to protect the skin from sun-related deleterious effects. The objective of the study was to investigate the potential effect of glycerol, propylene glycol and polyethylene glycol 400 on dermal absorption of oxybenzone by studying their effects on its partition coefficient. The partition coefficient was evaluated in a chloroform-water system at room temperature. It was found that glycerol and propylene glycol decreased the partition coefficient of oxybenzone, while an increase in partition coefficient was observed with polyethylene glycol 400. The findings suggest that polyethylene glycol 400 in contrast to glycerol and propylene glycol has the potential of increasing the vehicle-skin partition coefficient of oxybenzone when cosmetic products containing such an UV absorber are topically applied to the skin. PMID:17294811
Optical Absorption in Liquid Semiconductors
NASA Astrophysics Data System (ADS)
Bell, Florian Gene
An infrared absorption cell has been developed which is suitable for high temperature liquids which have absorptions in the range .1-10('3) cm('-1). The cell is constructed by clamping a gasket between two flat optical windows. This unique design allows the use of any optical windows chemically compatible with the liquid. The long -wavelength limit of the measurements is therefore limited only by the choice of the optical windows. The thickness of the cell can easily be set during assembly, and can be varied from 50 (mu)m to .5 cm. Measurements of the optical absorption edge were performed on the liquid alloy Se(,1-x)Tl(,x) for x = 0, .001, .002, .003, .005, .007, and .009, from the melting point up to 475(DEGREES)C. The absorption was found to be exponential in the photon energy over the experimental range from 0.3 eV to 1.2 eV. The absorption increased linearly with concentration according to the empirical relation (alpha)(,T)(h(nu)) = (alpha)(,1) + (alpha)(,2)x, and the absorption (alpha)(,1) was interpreted as the absorption in the absence of T1. (alpha)(,1) also agreed with the measured absorption in 100% Se at corresponding temperatures and energies. The excess absorption defined by (DELTA)(alpha) = (alpha)(,T)(h(nu))-(alpha)(,1) was interpreted as the absorption associated with Tl and was found to be thermally activated with an activation energy E(,t) = 0.5 eV. The exponential edge is explained as absorption on atoms immersed in strong electric fields surrounding ions. The strong fields give rise to an absorption tail similar to the Franz-Keldysh effect. A simple calculation is performed which is based on the Dow-Redfield theory of absorption in an electric field with excitonic effects included. The excess absorption at low photon energies is proportional to the square of the concentration of ions, which are proposed to exist in the liquid according to the relation C(,i) (PROPORTIONAL) x(' 1/2)(.)e('-E)t('/kT), which is the origin of the thermal activation
Reuter, Matthew G.; Harrison, Robert J.
2014-05-07
The thesis of Brandbyge's comment [J. Chem. Phys. 140, 177103 (2014)] is that our operator decoupling condition is immaterial to transport theories, and it appeals to discussions of nonorthogonal basis sets in transport calculations in its arguments. We maintain that the operator condition is to be preferred over the usual matrix conditions and subsequently detail problems in the existing approaches. From this operator perspective, we conclude that nonorthogonal projectors cannot be used and that the projectors must be selected to satisfy the operator decoupling condition. Because these conclusions pertain to operators, the choice of basis set is not germane.
Scattering with absorptive interaction
NASA Astrophysics Data System (ADS)
Cassing, W.; Stingl, M.; Weiguny, A.
1982-07-01
The S matrix for a wide class of complex and nonlocal potentials is studied, with special attention given to the motion of singularities in the complex k plane as a function of the imaginary coupling strength. Modifications of Levinson's theorem are obtained and discussed. Analytic approximations to the S matrix in the vicinity of narrow resonances are exhibited and compared to numerical results of resonating-group calculations. The problem of defining resonances in the case of complex interactions is discussed, making contact with the usual analysis of scattering in terms of Argand diagrams. NUCLEAR REACTIONS Scattering theory, S matrix for absorptive potentials.
About Thinning Invariant Partition Structures
NASA Astrophysics Data System (ADS)
Starr, Shannon; Vermesi, Brigitta; Wei, Ang
2012-08-01
Bernoulli- p thinning has been well-studied for point processes. Here we consider three other cases: (1) sequences ( X 1, X 2,…); (2) gaps of such sequences ( X n+1- X 1) n∈ℕ; (3) partition structures. For the first case we characterize the distributions which are simultaneously invariant under Bernoulli- p thinning for all p∈(0,1]. Based on this, we make conjectures for the latter two cases, and provide a potential approach for proof. We explain the relation to spin glasses, which is complementary to important previous work of Aizenman and Ruzmaikina, Arguin, and Shkolnikov.
Fransson, Thomas; Burdakova, Daria; Norman, Patrick
2016-05-21
X-ray absorption spectra of carbon, silicon, germanium, and sulfur compounds have been investigated by means of damped four-component density functional response theory. It is demonstrated that a reliable description of relativistic effects is obtained at both K- and L-edges. Notably, an excellent agreement with experimental results is obtained for L2,3-spectra-with spin-orbit effects well accounted for-also in cases when the experimental intensity ratio deviates from the statistical one of 2 : 1. The theoretical results are consistent with calculations using standard response theory as well as recently reported real-time propagation methods in time-dependent density functional theory, and the virtues of different approaches are discussed. As compared to silane and silicon tetrachloride, an anomalous error in the absolute energy is reported for the L2,3-spectrum of silicon tetrafluoride, amounting to an additional spectral shift of ∼1 eV. This anomaly is also observed for other exchange-correlation functionals, but it is seen neither at other silicon edges nor at the carbon K-edge of fluorine derivatives of ethene. Considering the series of molecules SiH4-XFX with X = 1, 2, 3, 4, a gradual divergence from interpolated experimental ionization potentials is observed at the level of Kohn-Sham density functional theory (DFT), and to a smaller extent with the use of Hartree-Fock. This anomalous error is thus attributed partly to difficulties in correctly emulating the electronic structure effects imposed by the very electronegative fluorines, and partly due to inconsistencies in the spurious electron self-repulsion in DFT. Substitution with one, or possibly two, fluorine atoms is estimated to yield small enough errors to allow for reliable interpretations and predictions of L2,3-spectra of more complex and extended silicon-based systems. PMID:27136720
Brooksbank, W.A. Jr.; Leddicotte, G.W.; Strain, J.E.; Hendon, H.H. Jr.
1961-11-14
A means was developed for continuously computing and indicating the isotopic assay of a process solution and for automatically controlling the process output of isotope separation equipment to provide a continuous output of the desired isotopic ratio. A counter tube is surrounded with a sample to be analyzed so that the tube is exactly in the center of the sample. A source of fast neutrons is provided and is spaced from the sample. The neutrons from the source are thermalized by causing them to pass through a neutron moderator, and the neutrons are allowed to diffuse radially through the sample to actuate the counter. A reference counter in a known sample of pure solvent is also actuated by the thermal neutrons from the neutron source. The number of neutrons which actuate the detectors is a function of a concentration of the elements in solution and their neutron absorption cross sections. The pulses produced by the detectors responsive to each neu tron passing therethrough are amplified and counted. The respective times required to accumulate a selected number of counts are measured by associated timing devices. The concentration of a particular element in solution may be determined by utilizing the following relation: T2/Ti = BCR, where B is a constant proportional to the absorption cross sections, T2 is the time of count collection for the unknown solution, Ti is the time of count collection for the pure solvent, R is the isotopic ratlo, and C is the molar concentration of the element to be determined. Knowing the slope constant B for any element and when the chemical concentration is known, the isotopic concentration may be readily determined, and conversely when the isotopic ratio is known, the chemical concentrations may be determined. (AEC)
On some trees having partition dimension four
NASA Astrophysics Data System (ADS)
Ida Bagus Kade Puja Arimbawa, K.; Baskoro, Edy Tri
2016-02-01
In 1998, G. Chartrand, E. Salehi and P. Zhang introduced the notion of partition dimension of a graph. Since then, the study of this graph parameter has received much attention. A number of results have been obtained to know the values of partition dimensions of various classes of graphs. However, for some particular classes of graphs, finding of their partition dimensions is still not completely solved, for instances a class of general tree. In this paper, we study the properties of trees having partition dimension 4. In particular, we show that, for olive trees O(n), its partition dimension is equal to 4 if and only if 8 ≤ n ≤ 17. We also characterize all centipede trees having partition dimension 4.
Chemical amplification based on fluid partitioning in an immiscible liquid
Anderson, Brian L.; Colston, Bill W.; Elkin, Christopher J.
2010-09-28
A system for nucleic acid amplification of a sample comprises partitioning the sample into partitioned sections and performing PCR on the partitioned sections of the sample. Another embodiment of the invention provides a system for nucleic acid amplification and detection of a sample comprising partitioning the sample into partitioned sections, performing PCR on the partitioned sections of the sample, and detecting and analyzing the partitioned sections of the sample.
NASA Astrophysics Data System (ADS)
Nakajima, Tetsuo
2008-11-01
The recursion formulas for the photon paths in the Borrmann triangle, which satisfy a new modified Pascal triangle can be derived from the binomial theorem by regarding the permutation of the stochastic variables of the diffracted and transmitted X-ray photons. The Borrmann triangle for the n-multiple X-ray reflections expanded by the n-degree binomial distribution consists of the two sub-triangles given by the ( n-1)-degree binomial distribution of the diffracted and transmitted photons. The former sub-triangle shows perfectly flawless symmetry but the latter one shows inevitable asymmetry. A reasonable understanding of both the high intense and very weak photon flows in the Borrmann triangle, which are popularly known as the anomalous transmission and absorption, respectively, are derived from the binomial theorem. Incident photons irradiated at a point O that forms the vertex of the Borrmann triangle propagate through the bypasses parallel to only the complementary half of the integral whole median with the high probabilities from the binomial theorem and emanate them from a short width slit of overline{O'O''} on the base of the high intense photon flow Borrmann triangle ▵ OO' O″, which can be defined by the standard deviation of the normal distribution. The parallel paths to the whole median also pass the very weak photon flows from the high power exponent of d multinomials through the triangle ▵ OO' O″. Both the above contrastive photon flows could coexist in ▵ OO' O″ based upon the complementary rivalry duality from the binomial theorem of ( d+ t) n =1, including the very weak photon flows from the high power exponent of t multinomials near both sides of the Borrmann triangle.
Dumas, Thomas; Guillaumont, Dominique; Fillaux, Clara; Scheinost, Andreas; Moisy, Philippe; Petit, Sébastien; Shuh, David K; Tyliszczak, Tolek; Den Auwer, Christophe
2016-01-28
The electronic properties of actinide cations are of fundamental interest to describe intramolecular interactions and chemical bonding in the context of nuclear waste reprocessing or direct storage. The 5f and 6d orbitals are the first partially or totally vacant states in these elements, and the nature of the actinide ligand bonds is related to their ability to overlap with ligand orbitals. Because of its chemical and orbital selectivities, X-ray absorption spectroscopy (XAS) is an effective probe of actinide species frontier orbitals and for understanding actinide cation reactivity toward chelating ligands. The soft X-ray probes of the light elements provide better resolution than actinide L3-edges to obtain electronic information from the ligand. Thus coupling simulations to experimental soft X-ray spectral measurements and complementary quantum chemical calculations yields quantitative information on chemical bonding. In this study, soft X-ray XAS at the K-edges of C and N, and the L2,3-edges of Fe was used to investigate the electronic structures of the well-known ferrocyanide complexes K4Fe(II)(CN)6, thorium hexacyanoferrate Th(IV)Fe(II)(CN)6, and neodymium hexacyanoferrate KNd(III)Fe(II)(CN)6. The soft X-ray spectra were simulated based on quantum chemical calculations. Our results highlight the orbital overlapping effects and atomic effective charges in the Fe(II)(CN)6 building block. In addition to providing a detailed description of the electronic structure of the ferrocyanide complex (K4Fe(II)(CN)6), the results strongly contribute to confirming the actinide 5f and 6d orbital oddity in comparison to lanthanide 4f and 5d. PMID:26733312
Displaying multimedia environmental partitioning by triangular diagrams
Lee, S.C.; Mackay, D.
1995-11-01
It is suggested that equilateral triangular diagrams are a useful method of depicting the equilibrium partitioning of organic chemicals among the three primary environmental media of the atmosphere, the hydrosphere, and the organosphere (natural organic matter and biotic lipids and waxes). The technique is useful for grouping chemicals into classes according to their partitioning tendencies, for depicting the incremental effects of substituents such as alkyl groups and chlorine, and for showing how partitioning changes in response to changes in temperature.
Thermodynamics of sodium dodecyl sulfate partitioning into lipid membranes.
Tan, Anmin; Ziegler, André; Steinbauer, Bernhard; Seelig, Joachim
2002-09-01
The partition equilibria of sodium dodecyl sulfate (SDS) and lithium dodecyl sulfate between water and bilayer membranes were investigated with isothermal titration calorimetry and spectroscopic methods (light scattering, (31)P-nuclear magnetic resonance) in the temperature range of 28 degrees C to 56 degrees C. The partitioning of the dodecyl sulfate anion (DS(-)) into the bilayer membrane is energetically favored by an exothermic partition enthalpy of Delta H(O)(D) = -6.0 kcal/mol at 28 degrees C. This is in contrast to nonionic detergents where Delta H(O)(D) is usually positive. The partition enthalpy decreases linearly with increasing temperature and the molar heat capacity is Delta C(O)(P) = -50 +/- 3 cal mol(-1) K(-1). The partition isotherm is nonlinear if the bound detergent is plotted versus the free detergent concentration in bulk solution. This is caused by the electrostatic repulsion between the DS(-) ions inserted into the membrane and those free in solution near the membrane surface. The surface concentration of DS(-) immediately above the plane of binding was hence calculated with the Gouy-Chapman theory, and a strictly linear relationship was obtained between the surface concentration and the extent of DS(-) partitioning. The surface partition constant K describes the chemical equilibrium in the absence of electrostatic effects. For the SDS-membrane equilibrium K was found to be 1.2 x 10(4) M(-1) to 6 x 10(4) M(-1) for the various systems and conditions investigated, very similar to data available for nonionic detergents of the same chain length. The membrane-micelle phase diagram was also studied. Complete membrane solubilization requires a ratio of 2.2 mol SDS bound per mole of total lipid at 56 degrees C. The corresponding equilibrium concentration of SDS free in solution is C (sat)(D,F) approximately 1.7 mM and is slightly below the critical micelles concentration (CMC) = 2.1 mM (at 56 degrees C and 0.11 M buffer). Membrane saturation occurs at
Mass partitioning effects in diffusion transport.
Kojic, Milos; Milosevic, Miljan; Wu, Suhong; Blanco, Elvin; Ferrari, Mauro; Ziemys, Arturas
2015-08-28
Frequent mass exchange takes place in a heterogeneous environment among several phases, where mass partitioning may occur at the interface of phases. Analytical and computational methods for diffusion do not usually incorporate molecule partitioning masking the true picture of mass transport. Here we present a computational finite element methodology to calculate diffusion mass transport with a partitioning phenomenon included and the analysis of the effects of partitioning. Our numerical results showed that partitioning controls equilibrated mass distribution as expected from analytical solutions. The experimental validation of mass release from drug-loaded nanoparticles showed that partitioning might even dominate in some cases with respect to diffusion itself. The analysis of diffusion kinetics in the parameter space of partitioning and diffusivity showed that partitioning is an extremely important parameter in systems, where mass diffusivity is fast and that the concentration of nanoparticles can control payload retention inside nanoparticles. The computational and experimental results suggest that partitioning and physiochemical properties of phases play an important, if not crucial, role in diffusion transport and should be included in the studies of mass transport processes. PMID:26204522
Xia, Huan; Gomez-Eyles, Jose L; Ghosh, Upal
2016-04-01
The bioavailability of polycyclic aromatic hydrocarbons (PAHs) in soils can be influenced by the source material they are emitted within, the properties of the receiving soil, weathering processes, and the concentration of PAHs. In this study 30 contaminated soils were constructed with common PAH sources (fuel oil, soot, coal tar based skeet particles) and direct spike with a solvent added to different types and contents of soil organic matter and minerals to achieve PAH concentrations spanning 4 orders of magnitude. Source material had the greatest impact on PAH partitioning. Soils containing skeet generally exhibited the highest KD values, followed by soot, fuel oil, and solvent spiked soils. Among all soil compositions, the presence of 2% charcoal had the largest enhancement of KD. Partitioning behavior could not be predicted by an organic carbon and black carbon partitioning model. Including independently measured partitioning behavior of the soil components and PAH sources allowed better prediction but still suffered from issues of interaction (oil sorption in peat) and highly nonlinear partitioning with depletion (for skeet). Dermal absorption of PAHs measured using pig skin was directly related to the freely dissolved aqueous concentration in soil and not the total concentration in the soil. Overall, we show that PAH source materials have a dominating influence on partitioning, highlighting the importance of using native field soils in bioavailability and risk assessments. PMID:26964018
Nanda, Kaushik D.; Krylov, Anna I.
2015-02-14
The equation-of-motion coupled-cluster (EOM-CC) methods provide a robust description of electronically excited states and their properties. Here, we present a formalism for two-photon absorption (2PA) cross sections for the equation-of-motion for excitation energies CC with single and double substitutions (EOM-CC for electronically excited states with single and double substitutions) wave functions. Rather than the response theory formulation, we employ the expectation-value approach which is commonly used within EOM-CC, configuration interaction, and algebraic diagrammatic construction frameworks. In addition to canonical implementation, we also exploit resolution-of-the-identity (RI) and Cholesky decomposition (CD) for the electron-repulsion integrals to reduce memory requirements and to increase parallel efficiency. The new methods are benchmarked against the CCSD and CC3 response theories for several small molecules. We found that the expectation-value 2PA cross sections are within 5% from the quadratic response CCSD values. The RI and CD approximations lead to small errors relative to the canonical implementation (less than 4%) while affording computational savings. RI/CD successfully address the well-known issue of large basis set requirements for 2PA cross sections calculations. The capabilities of the new code are illustrated by calculations of the 2PA cross sections for model chromophores of the photoactive yellow and green fluorescent proteins.
NASA Astrophysics Data System (ADS)
Nanda, Kaushik D.; Krylov, Anna I.
2015-02-01
The equation-of-motion coupled-cluster (EOM-CC) methods provide a robust description of electronically excited states and their properties. Here, we present a formalism for two-photon absorption (2PA) cross sections for the equation-of-motion for excitation energies CC with single and double substitutions (EOM-CC for electronically excited states with single and double substitutions) wave functions. Rather than the response theory formulation, we employ the expectation-value approach which is commonly used within EOM-CC, configuration interaction, and algebraic diagrammatic construction frameworks. In addition to canonical implementation, we also exploit resolution-of-the-identity (RI) and Cholesky decomposition (CD) for the electron-repulsion integrals to reduce memory requirements and to increase parallel efficiency. The new methods are benchmarked against the CCSD and CC3 response theories for several small molecules. We found that the expectation-value 2PA cross sections are within 5% from the quadratic response CCSD values. The RI and CD approximations lead to small errors relative to the canonical implementation (less than 4%) while affording computational savings. RI/CD successfully address the well-known issue of large basis set requirements for 2PA cross sections calculations. The capabilities of the new code are illustrated by calculations of the 2PA cross sections for model chromophores of the photoactive yellow and green fluorescent proteins.
Dey, A.; Jenney, F.E.; Jr.; Adams, M.W.W.; Johnson, M.K.; Hodgson, K.O.; Hedman, B.; Solomon, E.I.
2009-06-02
Superoxide reductase (SOR) is a non-heme iron enzyme that reduces superoxide to peroxide at a diffusion-controlled rate. Sulfur K-edge X-ray absorption spectroscopy (XAS) is used to investigate the ground-state electronic structure of the resting high-spin and CN- bound low-spin FeIII forms of the 1Fe SOR from Pyrococcus furiosus. A computational model with constrained imidazole rings (necessary for reproducing spin states), H-bonding interaction to the thiolate (necessary for reproducing Fe-S bond covalency of the high-spin and low-spin forms), and H-bonding to the exchangeable axial ligand (necessary to reproduce the ground state of the low-spin form) was developed and then used to investigate the enzymatic reaction mechanism. Reaction of the resting ferrous site with superoxide and protonation leading to a high-spin FeIII-OOH species and its subsequent protonation resulting in H2O2 release is calculated to be the most energetically favorable reaction pathway. Our results suggest that the thiolate acts as a covalent anionic ligand. Replacing the thiolate with a neutral noncovalent ligand makes protonation very endothermic and greatly raises the reduction potential. The covalent nature of the thiolate weakens the FeIII bond to the proximal oxygen of this hydroperoxo species, which raises its pKa by an additional 5 log units relative to the pKa of a primarily anionic ligand, facilitating its protonation. A comparison with cytochrome P450 indicates that the stronger equatorial ligand field from the porphyrin results in a low-spin FeIII-OOH species that would not be capable of efficient H2O2 release due to a spin-crossing barrier associated with formation of a high-spin 5C FeIII product. Additionally, the presence of the dianionic porphyrin pi ring in cytochrome P450 allows O-O heterolysis, forming an FeIV-oxo porphyrin radical species, which is calculated to be extremely unfavorable for the non-heme SOR ligand environment. Finally, the 5C FeIII site that results
Xie, Mingjie; Hannigan, Michael P; Barsanti, Kelley C
2014-08-19
To quantify and minimize the influence of gas/particle (G/P) partitioning on receptor-based source apportionment using particle-phase semivolatile organic compound (SVOC) data, positive matrix factorization (PMF) coupled with a bootstrap technique was applied to three data sets mainly composed of "measured-total" (measured particle- + gas-phase), "particle-only" (measured particle-phase) and "predicted-total" (measured particle-phase + predicted gas-phase) SVOCs to apportion carbonaceous aerosols. Particle- (PM2.5) and gas-phase SVOCs were collected using quartz fiber filters followed by PUF/XAD-4/PUF adsorbents and measured using gas chromatography-mass spectrometry (GC-MS). Concentrations of gas-phase SVOCs were also predicted from their particle-phase concentrations using absorptive partitioning theory. Five factors were resolved for each data set, and the factor profiles were generally consistent across the three PMF solutions. Using a previous source apportionment study at the same receptor site, those five factors were linked to summertime biogenic emissions (odd n-alkane factor), unburned fossil fuels (light SVOC factor), road dust and/or cooking (n-alkane factor), motor vehicle emissions (PAH factor), and lubricating oil combustion (sterane factor). The "measured-total" solution was least influenced by G/P partitioning and used as reference. Two out of the five factors (odd n-alkane and PAH factors) exhibited consistent contributions for "particle-only" vs "measured-total" and "predicted-total" vs "measured-total" solutions. Factor contributions of light SVOC and n-alkane factors were more consistent for "predicted-total" vs "measured-total" than "particle-only" vs "measured-total" solutions. The remaining factor (sterane factor) underestimated the contribution by around 50% from both "particle-only" and "predicted-total" solutions. The results of this study confirm that when measured gas-phase SVOCs are not available, "predicted-total" SVOCs should be used
NASA Astrophysics Data System (ADS)
Verma, Prakash; Bartlett, Rodney J.
2016-07-01
Core excitation energies are computed with time-dependent density functional theory (TD-DFT) using the ionization energy corrected exchange and correlation potential QTP(0,0). QTP(0,0) provides C, N, and O K-edge spectra to about an electron volt. A mean absolute error (MAE) of 0.77 and a maximum error of 2.6 eV is observed for QTP(0,0) for many small molecules. TD-DFT based on QTP (0,0) is then used to describe the core-excitation spectra of the 22 amino acids. TD-DFT with conventional functionals greatly underestimates core excitation energies, largely due to the significant error in the Kohn-Sham occupied eigenvalues. To the contrary, the ionization energy corrected potential, QTP(0,0), provides excellent approximations (MAE of 0.53 eV) for core ionization energies as eigenvalues of the Kohn-Sham equations. As a consequence, core excitation energies are accurately described with QTP(0,0), as are the core ionization energies important in X-ray photoionization spectra or electron spectroscopy for chemical analysis.
Verma, Prakash; Bartlett, Rodney J
2016-07-21
Core excitation energies are computed with time-dependent density functional theory (TD-DFT) using the ionization energy corrected exchange and correlation potential QTP(0,0). QTP(0,0) provides C, N, and O K-edge spectra to about an electron volt. A mean absolute error (MAE) of 0.77 and a maximum error of 2.6 eV is observed for QTP(0,0) for many small molecules. TD-DFT based on QTP (0,0) is then used to describe the core-excitation spectra of the 22 amino acids. TD-DFT with conventional functionals greatly underestimates core excitation energies, largely due to the significant error in the Kohn-Sham occupied eigenvalues. To the contrary, the ionization energy corrected potential, QTP(0,0), provides excellent approximations (MAE of 0.53 eV) for core ionization energies as eigenvalues of the Kohn-Sham equations. As a consequence, core excitation energies are accurately described with QTP(0,0), as are the core ionization energies important in X-ray photoionization spectra or electron spectroscopy for chemical analysis. PMID:27448875
Dey, A.; Jenney, F.E., Jr.; Adams, M.W.; Johnson, M.K.; Hodgson, K.O.; Hedman, B.; Solomon, E.I.; /Stanford U., Chem. Dept. /Athens U. /SLAC, SSRL
2007-10-26
Superoxide reductase (SOR) is a non-heme iron enzyme that reduces superoxide to peroxide at a diffusion-controlled rate. Sulfur K-edge X-ray absorption spectroscopy (XAS) is used to investigate the ground-state electronic structure of the resting high-spin and CN{sup -} bound low-spin Fe{sup III} forms of the 1Fe SOR from Pyrococcus furiosus. A computational model with constrained imidazole rings (necessary for reproducing spin states), H-bonding interaction to the thiolate (necessary for reproducing Fe-S bond covalency of the high-spin and low-spin forms), and H-bonding to the exchangeable axial ligand (necessary to reproduce the ground state of the low-spin form) was developed and then used to investigate the enzymatic reaction mechanism. Reaction of the resting ferrous site with superoxide and protonation leading to a high-spin Fe{sup III}-OOH species and its subsequent protonation resulting in H2O2 release is calculated to be the most energetically favorable reaction pathway. Our results suggest that the thiolate acts as a covalent anionic ligand. Replacing the thiolate with a neutral noncovalent ligand makes protonation very endothermic and greatly raises the reduction potential. The covalent nature of the thiolate weakens the Fe{sup III} bond to the proximal oxygen of this hydroperoxo species, which raises its pKa by an additional 5 log units relative to the pK{sub a} of a primarily anionic ligand, facilitating its protonation. A comparison with cytochrome P450 indicates that the stronger equatorial ligand field from the porphyrin results in a low-spin Fe{sup III}-OOH species that would not be capable of efficient H2O2 release due to a spin-crossing barrier associated with formation of a high-spin 5C Fe{sup III} product. Additionally, the presence of the dianionic porphyrin {pi} ring in cytochrome P450 allows O-O heterolysis, forming an Fe{sup IV}-oxo porphyrin radical species, which is calculated to be extremely unfavorable for the non-heme SOR ligand
Kinetic partitioning mechanism of HDV ribozyme folding
NASA Astrophysics Data System (ADS)
Chen, Jiawen; Gong, Sha; Wang, Yujie; Zhang, Wenbing
2014-01-01
RNA folding kinetics is directly tied to RNA biological functions. We introduce here a new approach for predicting the folding kinetics of RNA secondary structure with pseudoknots. This approach is based on our previous established helix-based method for predicting the folding kinetics of RNA secondary structure. In this approach, the transition rates for an elementary step: (1) formation, (2) disruption of a helix stem, and (3) helix formation with concomitant partial melting of an incompatible helix, are calculated with the free energy landscape. The folding kinetics of the Hepatitis delta virus (HDV) ribozyme and the mutated sequences are studied with this method. The folding pathways are identified by recursive searching the states with high net flux-in(out) population starting from the native state. The theory results are in good agreement with that of the experiments. The results indicate that the bi-phasic folding kinetics for the wt HDV sequence is ascribed to the kinetic partitioning mechanism: Part of the population will quickly fold to the native state along the fast pathway, while another part of the population will fold along the slow pathway, in which the population is trapped in a non-native state. Single mutation not only changes the folding rate but also the folding pathway.
Kinetic partitioning mechanism of HDV ribozyme folding
Chen, Jiawen; Gong, Sha; Wang, Yujie; Zhang, Wenbing
2014-01-14
RNA folding kinetics is directly tied to RNA biological functions. We introduce here a new approach for predicting the folding kinetics of RNA secondary structure with pseudoknots. This approach is based on our previous established helix-based method for predicting the folding kinetics of RNA secondary structure. In this approach, the transition rates for an elementary step: (1) formation, (2) disruption of a helix stem, and (3) helix formation with concomitant partial melting of an incompatible helix, are calculated with the free energy landscape. The folding kinetics of the Hepatitis delta virus (HDV) ribozyme and the mutated sequences are studied with this method. The folding pathways are identified by recursive searching the states with high net flux-in(out) population starting from the native state. The theory results are in good agreement with that of the experiments. The results indicate that the bi-phasic folding kinetics for the wt HDV sequence is ascribed to the kinetic partitioning mechanism: Part of the population will quickly fold to the native state along the fast pathway, while another part of the population will fold along the slow pathway, in which the population is trapped in a non-native state. Single mutation not only changes the folding rate but also the folding pathway.
NASA Astrophysics Data System (ADS)
Simoniello, R.; Finsterle, W.; García, R. A.; Salabert, D.; Jiménez, A.; Elsworth, Y.; Schunker, H.
2010-06-01
We used long duration, high quality, unresolved (Sun-as-a star) observations collected by the ground based network BiSON and by the instruments GOLF and VIRGO on board the ESA/NASA SOHO satellite to search for solar-cycle-related changes in mode characteristics in velocity and continuum intensity for the frequency range between 2.5 mHz <ν< 6.8 mHz. Over the ascending phase of solar cycle 23 we found a suppression in the p-mode amplitudes both in the velocity and intensity data between 2.5 mHz <ν< 4.5 mHz with a maximum suppression for frequencies in the range between 2.5 mHz <ν< 3.5 mHz. The size of the amplitude suppression is 13 ± 2 per cent for the velocity and 9 ± 2 per cent for the intensity observations. Over the range of 4.5 mHz <ν< 5.5 mHz the findings hint within the errors to a null change both in the velocity and intensity amplitudes. At still higher frequencies, in the so called High-frequency Interference Peaks (HIPs) between 5.8 mHz <ν< 6.8 mHz, we found an enhancement in the velocity amplitudes with the maximum 36 ± 7 per cent occurring for 6.3 mHz <ν< 6.8 mHz. However, in intensity observations we found a rather smaller enhancement of about 5 ± 2 per cent in the same interval. There is evidence that the frequency dependence of solar-cycle velocity amplitude changes is consistent with the theory behind the mode conversion of acoustic waves in a non-vertical magnetic field, but there are some problems with the intensity data, which may be due to the height in the solar atmosphere at which the VIRGO data are taken.
A general approach to association using cluster partition functions
NASA Astrophysics Data System (ADS)
Hendriks, E. M.; Walsh, J.; van Bergen, A. R. D.
1997-06-01
A systematic and fundamental approach to associating mixtures is presented. It is shown how the thermodynamic functions may be computed starting from a partition function based on the cluster concept such as occurs in chemical theory. The theory provides a basis for and an extension of the existing chemical theory of (continuous) association. It is applicable to arbitrary association schemes. Analysis of separate cases is not necessary. The assumptions that were made to allow the development were chosen such as to make the principle of reactivity valid. It is this same principle that links various theories: the chemical theory of continuous association, the lattice fluid hydrogen bonding model, and first-order perturbation theory. The equivalence between these theories in appropriate limits is shown in a general and rigorous way. The theory is believed to provide a practical framework for engineering modeling work. Binary interaction parameters can be incorporated. The association scheme is accounted for by a set of generic equations, which should facilitate robust implementation in computer programs.
Assimilate partitioning during reproductive growth
Finazzo, S.F.; Davenport, T.L.
1987-04-01
Leaves having various phyllotactic relationships to fruitlets were labeled for 1 hour with 10/sub r/Ci of /sup 14/CO/sub 2/. Fruitlets were also labeled. Fruitlets did fix /sup 14/CO/sub 2/. Translocation of radioactivity from the peel into the fruit occurred slowly and to a limited extent. No evidence of translocation out of the fruitlets was observed. Assimilate partitioning in avocado was strongly influenced by phyllotaxy. If a fruit and the labeled leaf had the same phyllotaxy then greater than 95% of the radiolabel was present in this fruit. When the fruit did not have the same phyllotaxy as the labeled leaf, the radiolabel distribution was skewed with 70% of the label going to a single adjacent position. Avocado fruitlets exhibit uniform labeling throughout a particular tissue. In avocado, assimilates preferentially move from leaves to fruits with the same phyllotaxy.
Building Ecology and Partition Design. Technical Bulletin.
ERIC Educational Resources Information Center
Maryland State Dept. of Education, Baltimore.
This bulletin is intended as a resource for school system facility planners and architects who design schools. Ways in which decision makers can incorporate environmental concerns in the design of school buildings are detailed. Focus is on the design of interior partition systems. Partition systems in schools serve several purposes; they define…
A Partitioning Technique for Defining Instructional Groups.
ERIC Educational Resources Information Center
Baker, Frank B.; Hubert, Lawrence J.
1979-01-01
A technique is presented for partitioning N students into K groups of fixed sizes using a given measure of proximity for all student pairs. The measure of proximity is typically calculated from a set of variables and constitutes the data needed for a criterion of partition "fit." (Author)
Purification of biomaterials by phase partitioning
NASA Technical Reports Server (NTRS)
Harris, J. M.
1984-01-01
A technique which is particularly suited to microgravity environments and which is potentially more powerful than electrophoresis is phase partitioning. Phase partitioning is purification by partitioning between the two immiscible aqueous layers formed by solution of the polymers poly(ethylene glycol) and dextran in water. This technique proved to be very useful for separations in one-g but is limited for cells because the cells are more dense than the phase solutions thus tend to sediment to the bottom of the container before reaching equilibrium with the preferred phase. There are three phases to work in this area: synthesis of new polymers for affinity phase partitioning; development of automated apparatus for ground-based separations; and design of apparatus for performing simple phase partitioning space experiments, including examination of mechanisms for separating phases in the absence of gravity.
Bicriterion methods for partitioning dissimilarity matrices.
Brusco, Michael J; Cradit, J Dennis
2005-11-01
Partitioning indices associated with the within-cluster sums of pairwise dissimilarities often exhibit a systematic bias towards clusters of a particular size, whereas minimization of the partition diameter (i.e. the maximum dissimilarity element across all pairs of objects within the same cluster) does not typically have this problem. However, when the partition-diameter criterion is used, there is often a myriad of alternative optimal solutions that can vary significantly with respect to their substantive interpretation. We propose a bicriterion partitioning approach that considers both diameter and within-cluster sums in the optimization problem and facilitates selection from among the alternative optima. We developed several MATLAB-based exchange algorithms that rapidly provide excellent solutions to bicriterion partitioning problems. These algorithms were evaluated using synthetic data sets, as well as an empirical dissimilarity matrix. PMID:16293203
Cell partition in two phase polymer systems
NASA Technical Reports Server (NTRS)
Brooks, D. E.
1979-01-01
Aqueous phase-separated polymer solutions can be used as support media for the partition of biological macromolecules, organelles and cells. Cell separations using the technique have proven to be extremely sensitive to cell surface properties but application of the systems are limited to cells or aggregates which do not significantly while the phases are settling. Partition in zero g in principle removes this limitation but an external driving force must be applied to induce the phases to separate since their density difference disappears. We have recently shown that an applied electric field can supply the necessary driving force. We are proposing to utilize the NASA FES to study field-driven phase separation and cell partition on the ground and in zero g to help define the separation/partition process, with the ultimate goal being to develop partition as a zero g cell separation technique.
IRON DISSOCIATES FROM THE NAFEEDTA COMPLEX PRIOR TO OR DURING INTESTINAL ABSORPTION IN RATS
Technology Transfer Automated Retrieval System (TEKTRAN)
Sodium Iron EDTA (NaFeEDTA) has superior iron bioavailability especially in foods containing iron absorption inhibitors. However, mechanisms involved in the absorption and subsequent partitioning of iron complexed with EDTA are poorly understood. Our objectives were to compare retention and tissue...
Partition function of N={2}^{ast } SYM on a large four-sphere
NASA Astrophysics Data System (ADS)
Hollowood, Timothy J.; Kumar, S. Prem
2015-12-01
We examine the partition function of N={2}^{ast } supersymmetric SU( N) Yang-Mills theory on the four-sphere in the large radius limit. We point out that the large radius partition function, at fixed N, is computed by saddle-points lying on walls of marginal stability on the Coulomb branch of the theory on {R}^4 . For N an even (odd) integer and θ YM = 0( π), these include a point of maximal degeneration of the Donagi-Witten curve to a torus where BPS dyons with electric charge [N/2] become massless. We argue that the dyon singularity is the lone saddle-point in the SU(2) theory, while for SU( N) with N > 2, we characterize potentially competing saddle-points by obtaining the relations between the Seiberg-Witten periods at such points. Using Nekrasov's instanton partition function, we solve for the maximally degenerate saddle-point and obtain its free energy as a function of g YM and N, and show that the results are "large- N exact". In the large- N theory our results provide analytical expressions for the periods/eigenvalues at the maximally degenerate saddle-point, precisely matching previously known formulae following from the correspondence between N={2}^{ast } theory and the elliptic Calogero-Moser integrable model. The maximally singular point ceases to be a saddle-point of the partition function above a critical value of the coupling, in agreement with the recent findings of Russo and Zarembo.
Do Psychological Sex Differences Reflect Evolutionary Bisexual Partitioning?
Trofimova, Irina
2015-01-01
This article analyzes sex differences in communicative and exploratory abilities and mental disabilities from the rarely discussed perspective of sex differences in the shape of phenotypic distributions. The article reviews the most consistent findings related to such differences and compares them with the evolutionary theory of sex (ETS). The ETS considers sexual dimorphism as a functional specialization of a species into 2 partitions: variational and conservational. The analysis suggests that male superiority in risk and sensation seeking and physical abilities; higher rates of psychopathy, dyslexia, and autism; and higher birth and accidental death rates reflects the systemic variational function of the male sex. Female superiority in verbal abilities, lawfulness, socialization, empathy, and agreeableness is presented as a reflection of the systemic conservational function of the female sex. From this perspective psychological sex differences in communicative and exploratory abilities might not just be an accidental result of sexual selection or labor distribution in early humans. It might reflect a global functional differentiation tendency within a species to expand its phenotypic diversity and at the same time to conserve beneficial features in the species' behavior. The article also offers an addition to the ETS by suggesting that the male sex (variable partition) plays an evolutionary role in pruning of the redundant excesses in a species' bank of beneficial characteristics despite resistance from the conservational partition. PMID:26721176
Automorphic instanton partition functions on Calabi-Yau threefolds
NASA Astrophysics Data System (ADS)
Persson, Daniel
2012-02-01
We survey recent results on quantum corrections to the hypermultiplet moduli space Script M in type IIA/B string theory on a compact Calabi-Yau threefold X, or, equivalently, the vector multiplet moduli space in type IIB/A on X × S1. Our main focus lies on the problem of resumming the infinite series of D-brane and NS5-brane instantons, using the mathematical machinery of automorphic forms. We review the proposal that when the theory in three dimensions exhibits an arithmetic "U-duality" symmetry G(Bbb Z) the total instanton partition function arises from a certain unitary automorphic representation of G, whose Fourier coefficients reproduce the BPS-degeneracies. In the case of four-dimensional Script N = 2 theories on Bbb R × S1 we argue that the relevant automorphic representation falls in the quaternionic discrete series of G, and that the partition function is a holomorphic section on the twistor space over Script M.
Kamei, Daniel T; King, Jonathan A; Wang, Daniel I C; Blankschtein, Daniel
2002-04-20
Unlike the partitioning behavior of hydrophilic, water-soluble proteins, the partitioning behavior of viruses in the two-phase aqueous nonionic n-decyl tetra(ethylene oxide) (C10E4) micellar system cannot be fully explained using the excluded-volume theory developed recently by our group. A central assumption underlying the excluded-volume theory--that macroscopic phase separation equilibrium is attained--was therefore challenged experimentally and theoretically. Photographs of the two-phase aqueous C10E4 micellar system were taken for different volume ratios to demonstrate that the entrainment of micelle-poor (virus-rich) domains in the macroscopic, top, micelle-rich phase decreases with a decrease in the volume ratio. Partitioning experiments were then conducted with the model virus bacteriophage P22 and the model protein cytochrome c at different operating temperatures for different volume ratios. For bacteriophage P22, the measured viral partition coefficient at each temperature decreased by about an order of magnitude when the volume ratio was decreased from 10 to 0.1, which clearly indicated that entrainment is an important factor influencing viral partitioning. For cytochrome c, the measured protein partition coefficient did not change, which demonstrated that this entrainment effect negligibly influences protein partitioning. A new theoretical description of partitioning was also developed that combines the excluded-volume theory with this entrainment effect. In this theory, one fitted parameter--the volume fraction of entrained micelle-poor domains in the macroscopic, top, micelle-rich phase--is used to account for the entrainment. To fit this parameter, only a single partitioning experiment is required for a given volume ratio, irrespectively of the partitioning solute. The new theoretical description of partitioning yielded very good quantitative predictions of the viral partition coefficients. Accordingly, it can be concluded that the primary mechanisms
Stress partition and microstructure in size-segregating granular flows.
Staron, L; Phillips, J C
2015-08-01
When a granular mixture involving grains of different sizes is shaken, sheared, mixed, or left to flow, grains tend to separate by sizes in a process known as size segregation. In this study, we explore the size segregation mechanism in granular chute flows in terms of the pressure distribution and granular microstructure. Therefore, two-dimensional discrete numerical simulations of bidisperse granular chute flows are systematically analyzed. Based on the theoretical models of J. M. N. T. Gray and A. R. Thornton [Proc. R. Soc. A 461, 1447] and K. M. Hill and D. S. Tan [J. Fluid Mech. 756, 54 (2014)], we explore the stress partition in the phases of small and large grains, discriminating between contact stresses and kinetic stresses. Our results support both gravity-induced and shear-gradient-induced segregation mechanisms. However, we show that the contact stress partition is extremely sensitive to the definition of the partial stress tensors and, more specifically, to the way mixed contacts (i.e., involving a small grain and a large grain) are handled, making conclusions on gravity-induced segregation uncertain. By contrast, the computation of the partial kinetic stress tensors is robust. The kinetic pressure partition exhibits a deviation from continuum mixture theory of a significantly higher amplitude than the contact pressure and displays a clear dependence on the flow dynamics. Finally, using a simple approximation for the contact partial stress tensors, we investigate how the contact stress partition relates to the flow microstructure and suggest that the latter may provide an interesting proxy for studying gravity-induced segregation. PMID:26382397
Stress partition and microstructure in size-segregating granular flows
NASA Astrophysics Data System (ADS)
Staron, L.; Phillips, J. C.
2015-08-01
When a granular mixture involving grains of different sizes is shaken, sheared, mixed, or left to flow, grains tend to separate by sizes in a process known as size segregation. In this study, we explore the size segregation mechanism in granular chute flows in terms of the pressure distribution and granular microstructure. Therefore, two-dimensional discrete numerical simulations of bidisperse granular chute flows are systematically analyzed. Based on the theoretical models of J. M. N. T. Gray and A. R. Thornton [Proc. R. Soc. A 461, 1447 (2005), 10.1098/rspa.2004.1420] and K. M. Hill and D. S. Tan [J. Fluid Mech. 756, 54 (2014), 10.1017/jfm.2014.271], we explore the stress partition in the phases of small and large grains, discriminating between contact stresses and kinetic stresses. Our results support both gravity-induced and shear-gradient-induced segregation mechanisms. However, we show that the contact stress partition is extremely sensitive to the definition of the partial stress tensors and, more specifically, to the way mixed contacts (i.e., involving a small grain and a large grain) are handled, making conclusions on gravity-induced segregation uncertain. By contrast, the computation of the partial kinetic stress tensors is robust. The kinetic pressure partition exhibits a deviation from continuum mixture theory of a significantly higher amplitude than the contact pressure and displays a clear dependence on the flow dynamics. Finally, using a simple approximation for the contact partial stress tensors, we investigate how the contact stress partition relates to the flow microstructure and suggest that the latter may provide an interesting proxy for studying gravity-induced segregation.
Selecting optimal partitioning schemes for phylogenomic datasets
2014-01-01
Background Partitioning involves estimating independent models of molecular evolution for different subsets of sites in a sequence alignment, and has been shown to improve phylogenetic inference. Current methods for estimating best-fit partitioning schemes, however, are only computationally feasible with datasets of fewer than 100 loci. This is a problem because datasets with thousands of loci are increasingly common in phylogenetics. Methods We develop two novel methods for estimating best-fit partitioning schemes on large phylogenomic datasets: strict and relaxed hierarchical clustering. These methods use information from the underlying data to cluster together similar subsets of sites in an alignment, and build on clustering approaches that have been proposed elsewhere. Results We compare the performance of our methods to each other, and to existing methods for selecting partitioning schemes. We demonstrate that while strict hierarchical clustering has the best computational efficiency on very large datasets, relaxed hierarchical clustering provides scalable efficiency and returns dramatically better partitioning schemes as assessed by common criteria such as AICc and BIC scores. Conclusions These two methods provide the best current approaches to inferring partitioning schemes for very large datasets. We provide free open-source implementations of the methods in the PartitionFinder software. We hope that the use of these methods will help to improve the inferences made from large phylogenomic datasets. PMID:24742000
Younker, Jarod M.; Krest, Courtney M.; Jiang, Wei; Krebs, Carsten; Bollinger, J. Martin; Green, Michael T.
2009-01-01
The class Ic ribonucleotide reductase from Chlamydia trachomatis (Ct) uses a stable Mn(IV)/Fe(III) cofactor to initiate nucleotide reduction by a free-radical mechanism. Extended X-ray absorption fine structure (EXAFS) spectroscopy and density functional theory (DFT) calculations are used to postulate a structure for this cofactor. Fe and Mn K-edge EXAFS data yield an intermetallic distance of ~2.92 Å. The Mn data also suggest the presence of a short 1.74 Å Mn—O bond. These metrics are compared to the results of DFT calculations on 12 cofactor models derived from the crystal structure of the inactive Fe2(III/III) form of the protein. Models are differentiated by the protonation states of their bridging and terminal OHX ligands as well as the location of the Mn(IV) ion (site 1 or 2). The models that agree best with experimental observation feature a µ-1,3-carboxylate bridge (E120), terminal solvent (H2O/OH) to site 1, one µ-O bridge, and one µ-OH bridge. The site-placement of the metal ions cannot be discerned from the available data. PMID:18937466
Younker, J.M.; Krest, C.M.; Jiang, W.; Krebs, C.; Bollinger, J.M.Jr.; Green, M.T.
2009-05-28
The class Ic ribonucleotide reductase from Chlamydia trachomatis (C{bar A}) uses a stable Mn(lV)/ Fe(lll) cofactor to initiate nucleotide reduction by a free-radical mechanism. Extended X-ray absorption fine structure (EXAFS) spectroscopy and density functional theory (DFT) calculations are used to postulate a structure for this cofactor. Fe and Mn K-edge EXAFS data yield an intermetallic distance of -2.92 {angstrom}. The Mn data also suggest the presence of a short 1.74 {angstrom} Mn-O bond. These metrics are compared to the results of DFT calculations on 12 cofactor models derived from the crystal structure of the inactive Fe2(lll/ III) form of the protein. Models are differentiated by the protonation states of their bridging and terminal OH{sub x} ligands as well as the location of the Mn(lV) ion (site 1 or 2). The models that agree best with experimental observation feature a{mu}-1, 3-carboxylate bridge (E120), terminal solvent (H{sub 2}O/OH) to site 1, one {mu}-O bridge, and one {mu}-OH bridge. The site-placement of the metal ions cannot be discerned from the available data.
Partitioning of regular computation on multiprocessor systems
NASA Technical Reports Server (NTRS)
Lee, Fung Fung
1988-01-01
Problem partitioning of regular computation over two dimensional meshes on multiprocessor systems is examined. The regular computation model considered involves repetitive evaluation of values at each mesh point with local communication. The computational workload and the communication pattern are the same at each mesh point. The regular computation model arises in numerical solutions of partial differential equations and simulations of cellular automata. Given a communication pattern, a systematic way to generate a family of partitions is presented. The influence of various partitioning schemes on performance is compared on the basis of computation to communication ratio.
Convex Regression with Interpretable Sharp Partitions
Petersen, Ashley; Simon, Noah; Witten, Daniela
2016-01-01
We consider the problem of predicting an outcome variable on the basis of a small number of covariates, using an interpretable yet non-additive model. We propose convex regression with interpretable sharp partitions (CRISP) for this task. CRISP partitions the covariate space into blocks in a data-adaptive way, and fits a mean model within each block. Unlike other partitioning methods, CRISP is fit using a non-greedy approach by solving a convex optimization problem, resulting in low-variance fits. We explore the properties of CRISP, and evaluate its performance in a simulation study and on a housing price data set.
Quantum Dilogarithms and Partition q-Series
NASA Astrophysics Data System (ADS)
Kato, Akishi; Terashima, Yuji
2015-08-01
In our previous work (Kato and Terashima, Commun Math Phys. arXiv:1403.6569, 2014), we introduced the partition q-series for mutation loop γ—a loop in exchange quiver. In this paper, we show that for a certain class of mutation sequences, called reddening sequences, the graded version of partition q-series essentially coincides with the ordered product of quantum dilogarithm associated with each mutation; the partition q-series provides a state-sum description of combinatorial Donaldson-Thomas invariants introduced by Keller.
How pervasive is the Hirshfeld partitioning?
Heidar-Zadeh, Farnaz; Ayers, Paul W.
2015-01-28
One can partition the molecular density into its atomic contributions by minimizing the divergence of the atom-in-molecule densities from their corresponding reference pro-atomic densities, subject to the constraint that the sum of the atom-in-molecule densities is the total molecular density. We expose conditions on the divergence measure that are necessary, and sufficient, to recover the popular Hirshfeld partitioning. Specifically, among all local measures of the divergence between two probability distribution functions, the Hirshfeld partitioning is obtained only for f-divergences.
Lipid partitioning during cardiac stress.
Kolwicz, Stephen C
2016-10-01
It is well documented that fatty acids serve as the primary fuel substrate for the contracting myocardium. However, extensive research has identified significant changes in the myocardial oxidation of fatty acids during acute or chronic cardiac stress. As a result, the redistribution or partitioning of fatty acids due to metabolic derangements could have biological implications. Fatty acids can be stored as triacylglycerols, serve as critical components for biosynthesis of phospholipid membranes, and form the potent signaling molecules, diacylglycerol and ceramides. Therefore, the contribution of lipid metabolism to health and disease is more intricate than a balance of uptake and oxidation. In this review, the available data regarding alterations that occur in endogenous cardiac lipid pathways during the pathological stressors of ischemia-reperfusion and pathological hypertrophy/heart failure are highlighted. In addition, changes in endogenous lipids observed in exercise training models are presented for comparison. This article is part of a Special Issue entitled: Heart Lipid Metabolism edited by G.D. Lopaschuk. PMID:27040509
HPAM: Hirshfeld Partitioned Atomic Multipoles
Elking, Dennis M.; Perera, Lalith; Pedersen, Lee G.
2011-01-01
An implementation of the Hirshfeld (HD) and Hirshfeld-Iterated (HD-I) atomic charge density partitioning schemes is described. Atomic charges and atomic multipoles are calculated from the HD and HD-I atomic charge densities for arbitrary atomic multipole rank lmax on molecules of arbitrary shape and size. The HD and HD-I atomic charges/multipoles are tested by comparing molecular multipole moments and the electrostatic potential (ESP) surrounding a molecule with their reference ab initio values. In general, the HD-I atomic charges/multipoles are found to better reproduce ab initio electrostatic properties over HD atomic charges/multipoles. A systematic increase in precision for reproducing ab initio electrostatic properties is demonstrated by increasing the atomic multipole rank from lmax = 0 (atomic charges) to lmax = 4 (atomic hexadecapoles). Both HD and HD-I atomic multipoles up to rank lmax are shown to exactly reproduce ab initio molecular multipole moments of rank L for L ≤ lmax. In addition, molecular dipole moments calculated by HD, HD-I, and ChelpG atomic charges only (lmax = 0) are compared with reference ab initio values. Significant errors in reproducing ab initio molecular dipole moments are found if only HD or HD-I atomic charges used. PMID:22140274
REE Partitioning in Lunar Minerals
NASA Technical Reports Server (NTRS)
Rapp, J. F.; Lapen, T. J.; Draper, D. S.
2015-01-01
Rare earth elements (REE) are an extremely useful tool in modeling lunar magmatic processes. Here we present the first experimentally derived plagioclase/melt partition coefficients in lunar compositions covering the entire suite of REE. Positive europium anomalies are ubiquitous in the plagioclase-rich rocks of the lunar highlands, and complementary negative Eu anomalies are found in most lunar basalts. These features are taken as evidence of a large-scale differentiation event, with crystallization of a global-scale lunar magma ocean (LMO) resulting in a plagioclase flotation crust and a mafic lunar interior from which mare basalts were subsequently derived. However, the extent of the Eu anomaly in lunar rocks is variable. Fagan and Neal [1] reported highly anorthitic plagioclase grains in lunar impact melt rock 60635,19 that displayed negative Eu anomalies as well as the more usual positive anomalies. Indeed some grains in the sample are reported to display both positive and negative anomalies. Judging from cathodoluminescence images, these anomalies do not appear to be associated with crystal overgrowths or zones.
Energy partitioning schemes: a dilemma.
Mayer, I
2007-01-01
Two closely related energy partitioning schemes, in which the total energy is presented as a sum of atomic and diatomic contributions by using the "atomic decomposition of identity", are compared on the example of N,N-dimethylformamide, a simple but chemically rich molecule. Both schemes account for different intramolecular interactions, for instance they identify the weak C-H...O intramolecular interactions, but give completely different numbers. (The energy decomposition scheme based on the virial theorem is also considered.) The comparison of the two schemes resulted in a dilemma which is especially striking when these schemes are applied for molecules distorted from their equilibrium structures: one either gets numbers which are "on the chemical scale" and have quite appealing values at the equilibrium molecular geometries, but exhibiting a counter-intuitive distance dependence (the two-center energy components increase in absolute value with the increase of the interatomic distances)--or numbers with too large absolute values but "correct" distance behaviour. The problem is connected with the quick decay of the diatomic kinetic energy components. PMID:17328441
NASA Astrophysics Data System (ADS)
Galarneau, Elisabeth; Bidleman, Terry F.; Blanchard, Pierrette
This study presents partitioning data from eight locations in the Laurentian Great Lakes region collected by the Integrated Atmospheric Deposition Network (IADN) over periods ranging from 1 to 6 years. Particle/gas partitioning varies sufficiently between sites in the Great Lakes region to preclude the use of a uniform temperature dependence for its description. Site-specific parameters for describing partitioning as a function of inverse temperature are presented. Relationships between partitioning of appreciably semivolatile PAHs and saturated vapour pressure at Chicago (IIT) and Sturgeon Point (STP) demonstrate that anthracene, benz[a]anthracene and retene behave differently than phenanthrene, fluoranthene, pyrene and chrysene+triphenylene. Possible reasons for these differences include interspecies variations in the fraction of atmospherically non-exchangeable, though analytically extractable, PAHs on particles and differences in soot-air partition coefficients as they relate to saturated vapour pressure. The observed interspecies differences are not consistent with sampling artefacts such as filter adsorption or sorbent breakthrough. At IIT, but not at STP, values of the slope of the relationship between the log partition coefficient and log vapour pressure vary in a manner opposing the annual temperature cycle. A comparison of partitioning calculated by a combined absorption/adsorption model shows good predictability at Chicago but underestimates values at a rural site (Eagle Harbor, EGH) by an order of magnitude.