Orbital-Free Density Functional Theory: Kinetic Potentials and Ab-Initio Local Pseudopotentials

In the density functional (DF) theory of Kohn and Sham, the kinetic energy of the ground state of a system of noninteracting electrons in a general external field is calculated using a set of orbitals. Orbital free methods attempt to calculate this directly from the electron density by approximating the universal but unknown kinetic energy density functional. However simple local approximations are inaccurate and it has proved very difficult to devise generally accurate nonlocal approximations. We focus instead on the kinetic potential, the functional derivative of the kinetic energy DF, which appears in the Euler equation for the electron density. We argue that the kinetic potential is more local and more amenable to simple physically motivated approximations in many relevant cases, and describe two pathways by which the value of the kinetic energy can be efficiently calculated. We propose two nonlocal orbital free kinetic potentials that reduce to known exact forms for both slowly varying and rapidly varying perturbations and also reproduce exact results for the linear response of the density of the homogeneous system to small perturbations. A simple and systematic approach for generating accurate and weak ab-initio local pseudopotentials which produce a smooth slowly varying valence component of the electron density is proposed for use in orbital free DF calculations of molecules and solids. The use of these local pseudopotentials further minimizes the possible errors from the kinetic potentials. Our theory yields results for the total energies and ionization energies of atoms, and for the shell structure in the atomic radial density profiles that are in very good agreement with calculations using the full Kohn-Sham theory.Comment: To be published in Phys. Rev.

Modeling of Two-Phase Flow with Deposition in Vertical Pipes

Deposition is found in many engineering processes, such as the asphaltene deposition in oil pipelines/wellbores, and biological and chemical foulings in pipes or heat exchangers. These deposition processes usually occur in a two-phase flow environment. This study develops a model for two-phase flow with deposition in vertical pipes. The model consists of three modules: Fluid Transport, Particle Transport, and Particle Deposition. The Fluid Transport module predicts the fluids’ velocities and pressure. The Particle Transport module calculates the particle distribution. The Particle Deposition module models the actual attachment of particles onto the wall. The model is verified against a few limiting cases with analytical solutions. Then, it is validated against experimental data for two-phase flow without deposition. Demonstration of the model for bubbly flow with deposition is performe

Three Dimensional Measurements of Asphaltene Deposition in a Transparent Micro-Channel

This study describes a novel experimental approach to directly measure the thicknesses of asphaltene deposits in micro-channels. The thickness of the asphaltene deposit is estimated using a visualization technique based on 3D digital microscopy. The working fluid is a mixture of n-heptane and dead oil. Induced by the addition of n-heptane, the asphaltenes present in crude oil phase separate at ambient temperature to form aggregates of asphaltene-rich phase. Part of the asphaltene aggregates deposit on the walls of the transparent micro-channel. A two-dimensional profile of the deposit across the channel at selected axial sections is measured. The influences of injection mixture volume on the growth of the thickness of deposited asphaltenes is investigated using two experimental conditions, (i) varying elapsed time at constant flow rate and (ii) increasing the flow rate at a constant elapsed time. In both cases the deposit thickness of asphaltene (δ) increases with the total injection volume (V). The experimental results obtained in this work provide new insights into the deposition process at the micro-scale level, which can be used to facilitate the development of more accurate numerical model for this applicatio

Integrated One-Dimensional Modeling of Asphaltene Deposition in Wellbores/Pipelines

—Asphaltene deposition in wellbores/pipelines causes serious production losses in the oil and gas industry. This work presents a numerical model to predict asphaltene deposition in wellbores/pipelines. This model consists of two modules: a Thermodynamic Module and a Transport Module. The Thermodynamic Module models asphaltene precipitation using the Peng-Robinson Equation of State with Peneloux volume translation (PR-Peneloux EOS). The Transport Module covers the modeling of fluid transport, asphaltene particle transport and asphaltene deposition. These modules are combined via a thermodynamic properties lookup-table generated by the Thermodynamic Module prior to simulation. In this work, the Transport Module and the Thermodynamic Module are first verified and validated separately. Then, the integrated model is applied to an oilfield case with asphaltene deposition problem where a reasonably accurate prediction of asphaltene deposit profile is achieve

Conjugate Heat Transfer in Stratified Two-Fluid Flows with a Growing Deposit Layer

The article presents a numerical model for moving boundary conjugate heat transfer in stratified two-fluid flows with a growing deposit layer. The model is applicable to other general moving boundary conjugate heat transfer problem in a two-fluid flow environment with deposition occurring simultaneously. The level-set method is adopted to capture the fluid-fluid interface and fluid-deposit interface. The governing equations are solved using a finite volume method. Upon verification of the model, the effects of inlet velocity ratio, Damköhler number and thermal conductivity ratio on the flow, deposition as well as heat transfer are investigated. Generally, Nusselt number on the lower wall (with a growing deposit layer), Nulx and upper wall, Nuux show distinct features with the change of these parameters. Nuux increases with the increase of lower fluid layer (fluid 1) inlet velocity and the thermal conductivity of deposit layer while it decreases with the increase of Damkholer number. Nulx varies differently in the upstream and the downstream of the channel. A higher lower fluid layer (fluid 1) velocity and a higher thermal conductivity of deposit layer result in a higher Nulx upstream but a lower Nulx downstream. However, a higher Damkholer number results in a lower Nulx upstream and a higher Nulx downstream

The Role of Sialyl Glycan Recognition in Host Tissue Tropism of the Avian Parasite Eimeria tenella

Eimeria spp. are a highly successful group of intracellular protozoan parasites that develop within intestinal epithelial cells of poultry, causing coccidiosis. As a result of resistance against anticoccidial drugs and the expense of manufacturing live vaccines, it is necessary to understand the relationship between Eimeria and its host more deeply, with a view to developing recombinant vaccines. Eimeria possesses a family of microneme lectins (MICs) that contain microneme adhesive repeat regions (MARR). We show that the major MARR protein from Eimeria tenella, EtMIC3, is deployed at the parasite-host interface during the early stages of invasion. EtMIC3 consists of seven tandem MAR1-type domains, which possess a high specificity for sialylated glycans as shown by cell-based assays and carbohydrate microarray analyses. The restricted tissue staining pattern observed for EtMIC3 in the chicken caecal epithelium indicates that EtMIC3 contributes to guiding the parasite to the site of invasion in the chicken gut. The microarray analyses also reveal a lack of recognition of glycan sequences terminating in the N-glycolyl form of sialic acid by EtMIC3. Thus the parasite is well adapted to the avian host which lacks N-glycolyl neuraminic acid. We provide new structural insight into the MAR1 family of domains and reveal the atomic resolution basis for the sialic acid-based carbohydrate recognition. Finally, a preliminary chicken immunization trial provides evidence that recombinant EtMIC3 protein and EtMIC3 DNA are effective vaccine candidates

Measurement of the quasi-elastic axial vector mass in neutrino-oxygen interactions

The weak nucleon axial-vector form factor for quasi-elastic interactions is determined using neutrino interaction data from the K2K Scintillating Fiber detector in the neutrino beam at KEK. More than 12,000 events are analyzed, of which half are charged-current quasi-elastic interactions nu-mu n to mu- p occurring primarily in oxygen nuclei. We use a relativistic Fermi gas model for oxygen and assume the form factor is approximately a dipole with one parameter, the axial vector mass M_A, and fit to the shape of the distribution of the square of the momentum transfer from the nucleon to the nucleus. Our best fit result for M_A = 1.20 \pm 0.12 GeV. Furthermore, this analysis includes updated vector form factors from recent electron scattering experiments and a discussion of the effects of the nucleon momentum on the shape of the fitted distributions.Comment: 14 pages, 10 figures, 6 table

Search for the W-exchange decays B0 --> Ds(*)- Ds(*)+

We report a search for the decays $B^{0} \to D_{s}^{-} D_{s}^{+}$, $B^{0} \to D_{s}^{*-} D_{s}^{+}$, $B^{0} \to D_{s}^{*-} D_{s}^{*+}$ in a sample of 232 million $\Upsilon(4S)$ decays to \BBb ~pairs collected with the \babar detector at the PEP-II asymmetric-energy $e^+ e^-$ storage ring. We find no significant signal and set upper bounds for the branching fractions: ${\cal B}(B^{0} \to D_{s}^{-} D_{s}^{+}) < 1.0 \times 10^{-4}, {\cal B}(B^{0} \to D_{s}^{*-} D_{s}^{+}) < 1.3 \times 10^{-4}$ and ${\cal B}(B^{0} \to D_{s}^{*-} D_{s}^{*+}) < 2.4 \times 10^{-4}$ at 90% confidence level.Comment: 8 pages, 2 figures, submitted to PRD-R

Stem Cell Factor SALL4 Represses the Transcriptions of PTEN and SALL1 through an Epigenetic Repressor Complex

Background The embryonic stem cell (ESC) factor, SALL4, plays an essential role in both development and leukemogenesis. It is a unique gene that is involved in self-renewal in ESC and leukemic stem cell (LSC).Methodology/Principal Findings To understand the mechanism(s) of SALL4 function(s), we sought to identify SALL4-associated proteins by tandem mass spectrometry. Components of a transcription repressor Mi-2/Nucleosome Remodeling and Deacetylase (NuRD) complex were found in the SALL4-immunocomplexes with histone deacetylase (HDAC) activity in ESCs with endogenous SALL4 expression and 293T cells overexpressing SALL4. The SALL4-mediated transcriptional regulation was tested on two potential target genes: PTEN and SALL1. Both genes were confirmed as SALL4 downstream targets by chromatin-immunoprecipitation, and their expression levels, when tested by quantitative reverse transcription polymerase chain reaction (qRT-PCR), were decreased in 293T cells overexpressing SALL4. Moreover, SALL4 binding sites at the promoter regions of PTEN and SALL1 were co-occupied by NuRD components, suggesting that SALL4 represses the transcriptions of PTEN and SALL1 through its interactions with the Mi-2/NuRD complex. The in vivo repressive effect(s) of SALL4 were evaluated in SALL4 transgenic mice, where decreased expressions of PTEN and SALL1 were associated with myeloid leukemia and cystic kidneys, respectively.Conclusions/Significance In summary, we are the first to demonstrate that stem cell protein SALL4 represses its target genes, PTEN and SALL1, through the epigenetic repressor Mi-2/NuRD complex. Our novel finding provides insight into the mechanism(s) of SALL4 functions in kidney development and leukemogenesis

Search for rare quark-annihilation decays, B --> Ds(*) Phi

We report on searches for B- --> Ds- Phi and B- --> Ds*- Phi. In the context of the Standard Model, these decays are expected to be highly suppressed since they proceed through annihilation of the b and u-bar quarks in the B- meson. Our results are based on 234 million Upsilon(4S) --> B Bbar decays collected with the BABAR detector at SLAC. We find no evidence for these decays, and we set Bayesian 90% confidence level upper limits on the branching fractions BF(B- --> Ds- Phi) Ds*- Phi)<1.2x10^(-5). These results are consistent with Standard Model expectations.Comment: 8 pages, 3 postscript figues, submitted to Phys. Rev. D (Rapid Communications