Development of a Multicenter Density Functional Tight Binding Model for Plutonium Surface Hydriding.

PubMed

Goldman, Nir; Aradi, Bálint; Lindsey, Rebecca K; Fried, Laurence E

2018-05-08

We detail the creation of a multicenter density functional tight binding (DFTB) model for hydrogen on δ-plutonium, using a framework of new Slater-Koster interaction parameters and a repulsive energy based on the Chebyshev Interaction Model for Efficient Simulation (ChIMES), where two- and three-center atomic interactions are represented by linear combinations of Chebyshev polynomials. We find that our DFTB/ChIMES model yields a total electron density of states for bulk δ-Pu that compares well to that from Density Functional Theory, as well as to a grid of energy calculations representing approximate H 2 dissociation paths on the δ-Pu (100) surface. We then perform molecular dynamics simulations and minimum energy pathway calculations to determine the energetics of surface dissociation and subsurface diffusion on the (100) and (111) surfaces. Our approach allows for the efficient creation of multicenter repulsive energies with a relatively small investment in initial DFT calculations. Our efforts are particularly pertinent to studies that rely on quantum calculations for interpretation and validation, such as experimental determination of chemical reactivity both on surfaces and in condensed phases.

Adaptive frozen orbital treatment for the fragment molecular orbital method combined with density-functional tight-binding

NASA Astrophysics Data System (ADS)

Nishimoto, Yoshio; Fedorov, Dmitri G.

2018-02-01

The exactly analytic gradient is derived and implemented for the fragment molecular orbital (FMO) method combined with density-functional tight-binding (DFTB) using adaptive frozen orbitals. The response contributions which arise from freezing detached molecular orbitals on the border between fragments are computed by solving Z-vector equations. The accuracy of the energy, its gradient, and optimized structures is verified on a set of representative inorganic materials and polypeptides. FMO-DFTB is applied to optimize the structure of a silicon nano-wire, and the results are compared to those of density functional theory and experiment. FMO accelerates the DFTB calculation of a boron nitride nano-ring with 7872 atoms by a factor of 406. Molecular dynamics simulations using FMO-DFTB applied to a 10.7 μm chain of boron nitride nano-rings, consisting of about 1.2 × 106 atoms, reveal the rippling and twisting of nano-rings at room temperature.

Self-Consistent Optimization of Excited States within Density-Functional Tight-Binding.

PubMed

Kowalczyk, Tim; Le, Khoa; Irle, Stephan

2016-01-12

We present an implementation of energies and gradients for the ΔDFTB method, an analogue of Δ-self-consistent-field density functional theory (ΔSCF) within density-functional tight-binding, for the lowest singlet excited state of closed-shell molecules. Benchmarks of ΔDFTB excitation energies, optimized geometries, Stokes shifts, and vibrational frequencies reveal that ΔDFTB provides a qualitatively correct description of changes in molecular geometries and vibrational frequencies due to excited-state relaxation. The accuracy of ΔDFTB Stokes shifts is comparable to that of ΔSCF-DFT, and ΔDFTB performs similarly to ΔSCF with the PBE functional for vertical excitation energies of larger chromophores where the need for efficient excited-state methods is most urgent. We provide some justification for the use of an excited-state reference density in the DFTB expansion of the electronic energy and demonstrate that ΔDFTB preserves many of the properties of its parent ΔSCF approach. This implementation fills an important gap in the extended framework of DFTB, where access to excited states has been limited to the time-dependent linear-response approach, and affords access to rapid exploration of a valuable class of excited-state potential energy surfaces.

Numerical Optimization of Density Functional Tight Binding Models: Application to Molecules Containing Carbon, Hydrogen, Nitrogen, and Oxygen

DOE Office of Scientific and Technical Information (OSTI.GOV)

Krishnapriyan, A.; Yang, P.; Niklasson, A. M. N.

New parametrizations for semiempirical density functional tight binding (DFTB) theory have been developed by the numerical optimization of adjustable parameters to minimize errors in the atomization energy and interatomic forces with respect to ab initio calculated data. Initial guesses for the radial dependences of the Slater- Koster bond integrals and overlap integrals were obtained from minimum basis density functional theory calculations. The radial dependences of the pair potentials and the bond and overlap integrals were represented by simple analytic functions. The adjustable parameters in these functions were optimized by simulated annealing and steepest descent algorithms to minimize the value ofmore » an objective function that quantifies the error between the DFTB model and ab initio calculated data. The accuracy and transferability of the resulting DFTB models for the C, H, N, and O system were assessed by comparing the predicted atomization energies and equilibrium molecular geometries of small molecules that were not included in the training data from DFTB to ab initio data. The DFTB models provide accurate predictions of the properties of hydrocarbons and more complex molecules containing C, H, N, and O.« less

Numerical Optimization of Density Functional Tight Binding Models: Application to Molecules Containing Carbon, Hydrogen, Nitrogen, and Oxygen

DOE PAGES

Krishnapriyan, A.; Yang, P.; Niklasson, A. M. N.; ...

2017-10-17

New parametrizations for semiempirical density functional tight binding (DFTB) theory have been developed by the numerical optimization of adjustable parameters to minimize errors in the atomization energy and interatomic forces with respect to ab initio calculated data. Initial guesses for the radial dependences of the Slater- Koster bond integrals and overlap integrals were obtained from minimum basis density functional theory calculations. The radial dependences of the pair potentials and the bond and overlap integrals were represented by simple analytic functions. The adjustable parameters in these functions were optimized by simulated annealing and steepest descent algorithms to minimize the value ofmore » an objective function that quantifies the error between the DFTB model and ab initio calculated data. The accuracy and transferability of the resulting DFTB models for the C, H, N, and O system were assessed by comparing the predicted atomization energies and equilibrium molecular geometries of small molecules that were not included in the training data from DFTB to ab initio data. The DFTB models provide accurate predictions of the properties of hydrocarbons and more complex molecules containing C, H, N, and O.« less

A Sparse Self-Consistent Field Algorithm and Its Parallel Implementation: Application to Density-Functional-Based Tight Binding.

PubMed

Scemama, Anthony; Renon, Nicolas; Rapacioli, Mathias

2014-06-10

We present an algorithm and its parallel implementation for solving a self-consistent problem as encountered in Hartree-Fock or density functional theory. The algorithm takes advantage of the sparsity of matrices through the use of local molecular orbitals. The implementation allows one to exploit efficiently modern symmetric multiprocessing (SMP) computer architectures. As a first application, the algorithm is used within the density-functional-based tight binding method, for which most of the computational time is spent in the linear algebra routines (diagonalization of the Fock/Kohn-Sham matrix). We show that with this algorithm (i) single point calculations on very large systems (millions of atoms) can be performed on large SMP machines, (ii) calculations involving intermediate size systems (1000-100 000 atoms) are also strongly accelerated and can run efficiently on standard servers, and (iii) the error on the total energy due to the use of a cutoff in the molecular orbital coefficients can be controlled such that it remains smaller than the SCF convergence criterion.

Analytical excited state forces for the time-dependent density-functional tight-binding method.

PubMed

Heringer, D; Niehaus, T A; Wanko, M; Frauenheim, Th

2007-12-01

An analytical formulation for the geometrical derivatives of excitation energies within the time-dependent density-functional tight-binding (TD-DFTB) method is presented. The derivation is based on the auxiliary functional approach proposed in [Furche and Ahlrichs, J Chem Phys 2002, 117, 7433]. To validate the quality of the potential energy surfaces provided by the method, adiabatic excitation energies, excited state geometries, and harmonic vibrational frequencies were calculated for a test set of molecules in excited states of different symmetry and multiplicity. According to the results, the TD-DFTB scheme surpasses the performance of configuration interaction singles and the random phase approximation but has a lower quality than ab initio time-dependent density-functional theory. As a consequence of the special form of the approximations made in TD-DFTB, the scaling exponent of the method can be reduced to three, similar to the ground state. The low scaling prefactor and the satisfactory accuracy of the method makes TD-DFTB especially suitable for molecular dynamics simulations of dozens of atoms as well as for the computation of luminescence spectra of systems containing hundreds of atoms. (c) 2007 Wiley Periodicals, Inc.

Shift-and-invert parallel spectral transformation eigensolver: Massively parallel performance for density-functional based tight-binding

DOE PAGES

Zhang, Hong; Zapol, Peter; Dixon, David A.; ...

2015-11-17

The Shift-and-invert parallel spectral transformations (SIPs), a computational approach to solve sparse eigenvalue problems, is developed for massively parallel architectures with exceptional parallel scalability and robustness. The capabilities of SIPs are demonstrated by diagonalization of density-functional based tight-binding (DFTB) Hamiltonian and overlap matrices for single-wall metallic carbon nanotubes, diamond nanowires, and bulk diamond crystals. The largest (smallest) example studied is a 128,000 (2000) atom nanotube for which ~330,000 (~5600) eigenvalues and eigenfunctions are obtained in ~190 (~5) seconds when parallelized over 266,144 (16,384) Blue Gene/Q cores. Weak scaling and strong scaling of SIPs are analyzed and the performance of SIPsmore » is compared with other novel methods. Different matrix ordering methods are investigated to reduce the cost of the factorization step, which dominates the time-to-solution at the strong scaling limit. As a result, a parallel implementation of assembling the density matrix from the distributed eigenvectors is demonstrated.« less

Shift-and-invert parallel spectral transformation eigensolver: Massively parallel performance for density-functional based tight-binding

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Hong; Zapol, Peter; Dixon, David A.

The Shift-and-invert parallel spectral transformations (SIPs), a computational approach to solve sparse eigenvalue problems, is developed for massively parallel architectures with exceptional parallel scalability and robustness. The capabilities of SIPs are demonstrated by diagonalization of density-functional based tight-binding (DFTB) Hamiltonian and overlap matrices for single-wall metallic carbon nanotubes, diamond nanowires, and bulk diamond crystals. The largest (smallest) example studied is a 128,000 (2000) atom nanotube for which ~330,000 (~5600) eigenvalues and eigenfunctions are obtained in ~190 (~5) seconds when parallelized over 266,144 (16,384) Blue Gene/Q cores. Weak scaling and strong scaling of SIPs are analyzed and the performance of SIPsmore » is compared with other novel methods. Different matrix ordering methods are investigated to reduce the cost of the factorization step, which dominates the time-to-solution at the strong scaling limit. As a result, a parallel implementation of assembling the density matrix from the distributed eigenvectors is demonstrated.« less

Effect of impurity doping on tunneling conductance in AB-stacked bi-layer graphene: A tight-binding study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rout, G. C., E-mail: siva1987@iopb.res.in, E-mail: skp@iopb.res.in, E-mail: gcr@iopb.res.in; Sahu, Sivabrata; Panda, S. K.

2016-04-13

We report here a microscopic tight-binding model calculation for AB-stacked bilayer graphene in presence of biasing potential between the two layers and the impurity effects to study the evolution of the total density of states with special emphasis on opening of band gap near Dirac point. We have calculated the electron Green’s functions for both the A and B sub-lattices by Zubarev technique. The imaginary part of the Green’s function gives the partial and total density of states of electrons. The density of states are computed numerically for 1000 × 1000 grid points of the electron momentum. The evolution ofmore » the opening of band gap near van-Hove singularities as well as near Dirac point is investigated by varying the different interlayer hoppings and the biasing potentials. The inter layer hopping splits the density of states at van-Hove singularities and produces a V-shaped gap near Dirac point. Further the biasing potential introduces a U shaped gap near Dirac point with a density minimum at the applied potential(i.e. at V/2).« less

Molecular dynamics simulations of dense plasmas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Collins, L.A.; Kress, J.D.; Kwon, I.

1993-12-31

We have performed quantum molecular dynamics simulations of hot, dense plasmas of hydrogen over a range of temperatures(0.1-5eV) and densities(0.0625-5g/cc). We determine the forces quantum mechanically from density functional, extended Huckel, and tight binding techniques and move the nuclei according to the classical equations of motion. We determine pair-correlation functions, diffusion coefficients, and electrical conductivities. We find that many-body effects predominate in this regime. We begin to obtain agreement with the OCP and Thomas-Fermi models only at the higher temperatures and densities.

A tight binding model study of tunneling conductance spectra of spin and orbitally ordered CMR manganites

NASA Astrophysics Data System (ADS)

Panda, Saswati; Sahoo, D. D.; Rout, G. C.

2018-04-01

We report here a tight binding model for colossal magnetoresistive (CMR) manganites to study the pseudo gap (PG) behavior near Fermi level. In the Kubo-Ohata type DE model, we consider first and second nearest neighbor interactions for transverse spin fluctuations in core band and hopping integrals in conduction band, in the presence of static band Jahn-Teller distortion. The model Hamiltonian is solved using Zubarev's Green's function technique. The electron density of states (DOS) is found out from the Green's functions. We observe clear PG near Fermi level in the electron DOS.

Three pillars for achieving quantum mechanical molecular dynamics simulations of huge systems: Divide-and-conquer, density-functional tight-binding, and massively parallel computation.

PubMed

Nishizawa, Hiroaki; Nishimura, Yoshifumi; Kobayashi, Masato; Irle, Stephan; Nakai, Hiromi

2016-08-05

The linear-scaling divide-and-conquer (DC) quantum chemical methodology is applied to the density-functional tight-binding (DFTB) theory to develop a massively parallel program that achieves on-the-fly molecular reaction dynamics simulations of huge systems from scratch. The functions to perform large scale geometry optimization and molecular dynamics with DC-DFTB potential energy surface are implemented to the program called DC-DFTB-K. A novel interpolation-based algorithm is developed for parallelizing the determination of the Fermi level in the DC method. The performance of the DC-DFTB-K program is assessed using a laboratory computer and the K computer. Numerical tests show the high efficiency of the DC-DFTB-K program, a single-point energy gradient calculation of a one-million-atom system is completed within 60 s using 7290 nodes of the K computer. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Accurate modeling of defects in graphene transport calculations

NASA Astrophysics Data System (ADS)

Linhart, Lukas; Burgdörfer, Joachim; Libisch, Florian

2018-01-01

We present an approach for embedding defect structures modeled by density functional theory into large-scale tight-binding simulations. We extract local tight-binding parameters for the vicinity of the defect site using Wannier functions. In the transition region between the bulk lattice and the defect the tight-binding parameters are continuously adjusted to approach the bulk limit far away from the defect. This embedding approach allows for an accurate high-level treatment of the defect orbitals using as many as ten nearest neighbors while keeping a small number of nearest neighbors in the bulk to render the overall computational cost reasonable. As an example of our approach, we consider an extended graphene lattice decorated with Stone-Wales defects, flower defects, double vacancies, or silicon substitutes. We predict distinct scattering patterns mirroring the defect symmetries and magnitude that should be experimentally accessible.

Density functional tight-binding and infrequent metadynamics can capture entropic effects in intramolecular hydrogen transfer reactions

NASA Astrophysics Data System (ADS)

Oliveira, Luiz F. L.; Fu, Christopher D.; Pfaendtner, Jim

2018-04-01

Infrequent metadynamics uses biased simulations to estimate the unbiased kinetics of a system, facilitating the calculation of rates and barriers. Here the method is applied to study intramolecular hydrogen transfer reactions involving peroxy radicals, a class of reactions that is challenging to model due to the entropic contributions of the formation of ring structures in the transition state. Using the self-consistent charge density-functional based tight-binding (DFTB) method, we applied infrequent metadynamics to the study of four intramolecular H-transfer reactions, demonstrating that the method can qualitatively reproduce these high entropic contributions, as observed in experiments and those predicted by transition state theory modeled by higher levels of theory. We also show that infrequent metadynamics and DFTB are successful in describing the relationship between transition state ring size and kinetic coefficients (e.g., activation energies and the pre-exponential factors).

Development of tight-binding based GW algorithm and its computational implementation for graphene

DOE Office of Scientific and Technical Information (OSTI.GOV)

Majidi, Muhammad Aziz; NUSNNI-NanoCore, Department of Physics, National University of Singapore; Singapore Synchrotron Light Source

Graphene has been a hot subject of research in the last decade as it holds a promise for various applications. One interesting issue is whether or not graphene should be classified into a strongly or weakly correlated system, as the optical properties may change upon several factors, such as the substrate, voltage bias, adatoms, etc. As the Coulomb repulsive interactions among electrons can generate the correlation effects that may modify the single-particle spectra (density of states) and the two-particle spectra (optical conductivity) of graphene, we aim to explore such interactions in this study. The understanding of such correlation effects ismore » important because eventually they play an important role in inducing the effective attractive interactions between electrons and holes that bind them into excitons. We do this study theoretically by developing a GW method implemented on the basis of the tight-binding (TB) model Hamiltonian. Unlike the well-known GW method developed within density functional theory (DFT) framework, our TB-based GW implementation may serve as an alternative technique suitable for systems which Hamiltonian is to be constructed through a tight-binding based or similar models. This study includes theoretical formulation of the Green’s function G, the renormalized interaction function W from random phase approximation (RPA), and the corresponding self energy derived from Feynman diagrams, as well as the development of the algorithm to compute those quantities. As an evaluation of the method, we perform calculations of the density of states and the optical conductivity of graphene, and analyze the results.« less

Communication: Charge-population based dispersion interactions for molecules and materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stöhr, Martin; Department Chemie, Technische Universität München, Lichtenbergstr. 4, D-85748 Garching; Michelitsch, Georg S.

2016-04-21

We introduce a system-independent method to derive effective atomic C{sub 6} coefficients and polarizabilities in molecules and materials purely from charge population analysis. This enables the use of dispersion-correction schemes in electronic structure calculations without recourse to electron-density partitioning schemes and expands their applicability to semi-empirical methods and tight-binding Hamiltonians. We show that the accuracy of our method is en par with established electron-density partitioning based approaches in describing intermolecular C{sub 6} coefficients as well as dispersion energies of weakly bound molecular dimers, organic crystals, and supramolecular complexes. We showcase the utility of our approach by incorporation of the recentlymore » developed many-body dispersion method [Tkatchenko et al., Phys. Rev. Lett. 108, 236402 (2012)] into the semi-empirical density functional tight-binding method and propose the latter as a viable technique to study hybrid organic-inorganic interfaces.« less

Density function theory study of the adsorption and dissociation of carbon monoxide on tungsten nanoparticles.

PubMed

Weng, Meng-Hsiung; Ju, Shin-Pon; Chen, Hsin-Tsung; Chen, Hui-Lung; Lu, Jian-Ming; Lin, Ken-Huang; Lin, Jenn-Sen; Hsieh, Jin-Yuan; Yang, Hsi-Wen

2013-02-01

The adsorption and dissociation properties of carbon monoxide (CO) molecule on tungsten W(n) (n = 10-15) nanoparticles have been investigated by density-functional theory (DFT) calculations. The lowest-energy structures for W(n) (n = 10-15) nanoparticles are found by the basin-hopping method and big-bang method with the modified tight-binding many-body potential. We calculated the corresponding adsorption energies, C-O bond lengths and dissociation barriers for adsorption of CO on nanoparticles. The electronic properties of CO on nanoparticles are studied by the analysis of density of state and charge density. The characteristic of CO on W(n) nanoparticles are also compared with that of W bulk.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sahu, Sivabrata, E-mail: siva1987@iopb.res.in; Parashar, S. K. S., E-mail: sksparashar@yahoo.com; Rout, G. C., E-mail: gcr@iopb.res.in

We address here a tight-binding theoretical model calculation for AA-stacked bi-layer graphene taking into account of a biased potential between two layers to study the density of states and the band dispersion within the total Brillouin zone. We have calculated the electronic Green’s function for electron operator corresponding to A and B sub lattices by Zubarev’s Green’s function technique from which the electronic density of states and the electron band energy dispersion are calculated. The numerically computed density of states and band energy dispersions are investigated by tuning the biased potential to exhibit the band gap by varying the differentmore » physical parameters.« less

Density-functional expansion methods: Grand challenges.

PubMed

Giese, Timothy J; York, Darrin M

2012-03-01

We discuss the source of errors in semiempirical density functional expansion (VE) methods. In particular, we show that VE methods are capable of well-reproducing their standard Kohn-Sham density functional method counterparts, but suffer from large errors upon using one or more of these approximations: the limited size of the atomic orbital basis, the Slater monopole auxiliary basis description of the response density, and the one- and two-body treatment of the core-Hamiltonian matrix elements. In the process of discussing these approximations and highlighting their symptoms, we introduce a new model that supplements the second-order density-functional tight-binding model with a self-consistent charge-dependent chemical potential equalization correction; we review our recently reported method for generalizing the auxiliary basis description of the atomic orbital response density; and we decompose the first-order potential into a summation of additive atomic components and many-body corrections, and from this examination, we provide new insights and preliminary results that motivate and inspire new approximate treatments of the core-Hamiltonian.

Structure and Stability of Molecular Crystals with Many-Body Dispersion-Inclusive Density Functional Tight Binding.

PubMed

Mortazavi, Majid; Brandenburg, Jan Gerit; Maurer, Reinhard J; Tkatchenko, Alexandre

2018-01-18

Accurate prediction of structure and stability of molecular crystals is crucial in materials science and requires reliable modeling of long-range dispersion interactions. Semiempirical electronic structure methods are computationally more efficient than their ab initio counterparts, allowing structure sampling with significant speedups. We combine the Tkatchenko-Scheffler van der Waals method (TS) and the many-body dispersion method (MBD) with third-order density functional tight-binding (DFTB3) via a charge population-based method. We find an overall good performance for the X23 benchmark database of molecular crystals, despite an underestimation of crystal volume that can be traced to the DFTB parametrization. We achieve accurate lattice energy predictions with DFT+MBD energetics on top of vdW-inclusive DFTB3 structures, resulting in a speedup of up to 3000 times compared with a full DFT treatment. This suggests that vdW-inclusive DFTB3 can serve as a viable structural prescreening tool in crystal structure prediction.

Density-functional expansion methods: evaluation of LDA, GGA, and meta-GGA functionals and different integral approximations.

PubMed

Giese, Timothy J; York, Darrin M

2010-12-28

We extend the Kohn-Sham potential energy expansion (VE) to include variations of the kinetic energy density and use the VE formulation with a 6-31G* basis to perform a "Jacob's ladder" comparison of small molecule properties using density functionals classified as being either LDA, GGA, or meta-GGA. We show that the VE reproduces standard Kohn-Sham DFT results well if all integrals are performed without further approximation, and there is no substantial improvement in using meta-GGA functionals relative to GGA functionals. The advantages of using GGA versus LDA functionals becomes apparent when modeling hydrogen bonds. We furthermore examine the effect of using integral approximations to compute the zeroth-order energy and first-order matrix elements, and the results suggest that the origin of the short-range repulsive potential within self-consistent charge density-functional tight-binding methods mainly arises from the approximations made to the first-order matrix elements.

Subacute stress and chronic stress interact to decrease intestinal barrier function in rats.

PubMed

Lauffer, Adriana; Vanuytsel, Tim; Vanormelingen, Christophe; Vanheel, Hanne; Salim Rasoel, Shadea; Tóth, Joran; Tack, Jan; Fornari, Fernando; Farré, Ricard

2016-01-01

Psychological stress increases intestinal permeability, potentially leading to low-grade inflammation and symptoms in functional gastrointestinal disorders. We assessed the effect of subacute, chronic and combined stress on intestinal barrier function and mast cell density. Male Wistar rats were allocated to four experimental groups (n = 8/group): 1/sham; 2/subacute stress (isolation and limited movement for 24 h); 3/chronic crowding stress for 14 days and 4/combined subacute and chronic stress. Jejunum and colon were collected to measure: transepithelial electrical resistance (TEER; a measure of epithelial barrier function); gene expression of tight junction molecules; mast cell density. Plasma corticosterone concentration was increased in all three stress conditions versus sham, with highest concentrations in the combined stress condition. TEER in the jejunum was decreased in all stress conditions, but was significantly lower in the combined stress condition than in the other groups. TEER in the jejunum correlated negatively with corticosterone concentration. Increased expression of claudin 1, 5 and 8, occludin and zonula occludens 1 mRNAs was detected after subacute stress in the jejunum. In contrast, colonic TEER was decreased only after combined stress, and the expression of tight junction molecules was unaltered. Increased mast cell density was observed in the chronic and combined stress condition in the colon only. In conclusion, our data show that chronic stress sensitizes the gastrointestinal tract to the effects of subacute stress on intestinal barrier function; different underlying cellular and molecular alterations are indicated in the small intestine versus the colon.

Effects of Cultural Tightness-Looseness and Social Network Density on Expression of Positive and Negative Emotions: A Large-Scale Study of Impression Management by Facebook Users.

PubMed

Liu, Pan; Chan, David; Qiu, Lin; Tov, William; Tong, Victor Joo Chuan

2018-05-01

Using data from 13,789 Facebook users across U.S. states, this study examined the main effects of societal-level cultural tightness-looseness and its interaction effects with individuals' social network density on impression management (IM) in terms of online emotional expression. Results showed that individuals from culturally tight (vs. loose) states were more likely to express positive emotions and less likely to express negative emotions. Meanwhile, for positive emotional expression, there was a tightness-looseness by social network density interaction effect. In culturally tight states, individuals with dense (vs. sparse) networks were more likely to express positive emotions, while in culturally loose states this pattern was reversed. For negative emotional expression, however, no such interaction was observed. Our findings highlight the influence of cultural norms and social network structure on emotional expressions as IM strategies.

Plato: A localised orbital based density functional theory code

NASA Astrophysics Data System (ADS)

Kenny, S. D.; Horsfield, A. P.

2009-12-01

The Plato package allows both orthogonal and non-orthogonal tight-binding as well as density functional theory (DFT) calculations to be performed within a single framework. The package also provides extensive tools for analysing the results of simulations as well as a number of tools for creating input files. The code is based upon the ideas first discussed in Sankey and Niklewski (1989) [1] with extensions to allow high-quality DFT calculations to be performed. DFT calculations can utilise either the local density approximation or the generalised gradient approximation. Basis sets from minimal basis through to ones containing multiple radial functions per angular momenta and polarisation functions can be used. Illustrations of how the package has been employed are given along with instructions for its utilisation. Program summaryProgram title: Plato Catalogue identifier: AEFC_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFC_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 219 974 No. of bytes in distributed program, including test data, etc.: 1 821 493 Distribution format: tar.gz Programming language: C/MPI and PERL Computer: Apple Macintosh, PC, Unix machines Operating system: Unix, Linux and Mac OS X Has the code been vectorised or parallelised?: Yes, up to 256 processors tested RAM: Up to 2 Gbytes per processor Classification: 7.3 External routines: LAPACK, BLAS and optionally ScaLAPACK, BLACS, PBLAS, FFTW Nature of problem: Density functional theory study of electronic structure and total energies of molecules, crystals and surfaces. Solution method: Localised orbital based density functional theory. Restrictions: Tight-binding and density functional theory only, no exact exchange. Unusual features: Both atom centred and uniform meshes available. Can deal with arbitrary angular momenta for orbitals, whilst still retaining Slater-Koster tables for accuracy. Running time: Test cases will run in a few minutes, large calculations may run for several days.

DFTB+ and lanthanides

NASA Astrophysics Data System (ADS)

Hourahine, B.; Aradi, B.; Frauenheim, T.

2010-07-01

DFTB+ is a recent general purpose implementation of density-functional based tight binding. One of the early motivators to develop this code was to investigate lanthanide impurities in nitride semiconductors, leading to a series of successful studies into structure and electrical properties of these systems. Here we describe our general framework to treat the physical effects needed for these problematic impurities within a tight-binding formalism, additionally discussing forces and stresses in DFTB. We also present an approach to evaluate the general case of Slater-Koster transforms and all of their derivatives in Cartesian coordinates. These developments are illustrated by simulating isolated Gd impurities in GaN.

Phosphorene quantum dot-fullerene nanocomposites for solar energy conversion: An unexplored inorganic-organic nanohybrid with novel photovoltaic properties

NASA Astrophysics Data System (ADS)

Rajbanshi, Biplab; Kar, Moumita; Sarkar, Pallavi; Sarkar, Pranab

2017-10-01

Using the self-consistent charge density-functional based tight-binding (SCC-DFTB) method, coupled with time-dependent density functional theory (TDDFT) calculations, for the first time we explore the possibility of use of phosphorene quantum dots in solar energy harvesting devices. The phosphorene quantum dots-fullerene (PQDs-PCBA) nanocomposites show type-II band alignment indicating spatial separation of charge carriers. The TDDFT calculations also show that the PQD-fullerene nanocomposites seem to be exciting material for future generation solar energy harvester, with extremely fast charge transfer and very poor recombination rate.

Benchmarking density functional tight binding models for barrier heights and reaction energetics of organic molecules.

PubMed

Gruden, Maja; Andjeklović, Ljubica; Jissy, Akkarapattiakal Kuriappan; Stepanović, Stepan; Zlatar, Matija; Cui, Qiang; Elstner, Marcus

2017-09-30

Density Functional Tight Binding (DFTB) models are two to three orders of magnitude faster than ab initio and Density Functional Theory (DFT) methods and therefore are particularly attractive in applications to large molecules and condensed phase systems. To establish the applicability of DFTB models to general chemical reactions, we conduct benchmark calculations for barrier heights and reaction energetics of organic molecules using existing databases and several new ones compiled in this study. Structures for the transition states and stable species have been fully optimized at the DFTB level, making it possible to characterize the reliability of DFTB models in a more thorough fashion compared to conducting single point energy calculations as done in previous benchmark studies. The encouraging results for the diverse sets of reactions studied here suggest that DFTB models, especially the most recent third-order version (DFTB3/3OB augmented with dispersion correction), in most cases provide satisfactory description of organic chemical reactions with accuracy almost comparable to popular DFT methods with large basis sets, although larger errors are also seen for certain cases. Therefore, DFTB models can be effective for mechanistic analysis (e.g., transition state search) of large (bio)molecules, especially when coupled with single point energy calculations at higher levels of theory. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Improving Density Functional Tight Binding Predictions of Free Energy Surfaces for Slow Chemical Reactions in Solution

NASA Astrophysics Data System (ADS)

Kroonblawd, Matthew; Goldman, Nir

2017-06-01

First principles molecular dynamics using highly accurate density functional theory (DFT) is a common tool for predicting chemistry, but the accessible time and space scales are often orders of magnitude beyond the resolution of experiments. Semi-empirical methods such as density functional tight binding (DFTB) offer up to a thousand-fold reduction in required CPU hours and can approach experimental scales. However, standard DFTB parameter sets lack good transferability and calibration for a particular system is usually necessary. Force matching the pairwise repulsive energy term in DFTB to short DFT trajectories can improve the former's accuracy for reactions that are fast relative to DFT simulation times (<10 ps), but the effects on slow reactions and the free energy surface are not well-known. We present a force matching approach to improve the chemical accuracy of DFTB. Accelerated sampling techniques are combined with path collective variables to generate the reference DFT data set and validate fitted DFTB potentials. Accuracy of force-matched DFTB free energy surfaces is assessed for slow peptide-forming reactions by direct comparison to DFT for particular paths. Extensions to model prebiotic chemistry under shock conditions are discussed. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

Improving density functional tight binding predictions of free energy surfaces for peptide condensation reactions in solution

NASA Astrophysics Data System (ADS)

Kroonblawd, Matthew; Goldman, Nir

First principles molecular dynamics using highly accurate density functional theory (DFT) is a common tool for predicting chemistry, but the accessible time and space scales are often orders of magnitude beyond the resolution of experiments. Semi-empirical methods such as density functional tight binding (DFTB) offer up to a thousand-fold reduction in required CPU hours and can approach experimental scales. However, standard DFTB parameter sets lack good transferability and calibration for a particular system is usually necessary. Force matching the pairwise repulsive energy term in DFTB to short DFT trajectories can improve the former's accuracy for chemistry that is fast relative to DFT simulation times (<10 ps), but the effects on slow chemistry and the free energy surface are not well-known. We present a force matching approach to increase the accuracy of DFTB predictions for free energy surfaces. Accelerated sampling techniques are combined with path collective variables to generate the reference DFT data set and validate fitted DFTB potentials without a priori knowledge of transition states. Accuracy of force-matched DFTB free energy surfaces is assessed for slow peptide-forming reactions by direct comparison to DFT results for particular paths. Extensions to model prebiotic chemistry under shock conditions are discussed. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

Local representation of the electronic dielectric response function

DOE PAGES

Lu, Deyu; Ge, Xiaochuan

2015-12-11

We present a local representation of the electronic dielectric response function, based on a spatial partition of the dielectric response into contributions from each occupied Wannier orbital using a generalized density functional perturbation theory. This procedure is fully ab initio, and therefore allows us to rigorously define local metrics, such as “bond polarizability,” on Wannier centers. We show that the locality of the bare response function is determined by the locality of three quantities: Wannier functions of the occupied manifold, the density matrix, and the Hamiltonian matrix. Furthermore, in systems with a gap, the bare dielectric response is exponentially localized,more » which supports the physical picture of the dielectric response function as a collection of interacting local responses that can be captured by a tight-binding model.« less

Molecular dynamics simulations of the amino acid-ZnO (10-10) interface: a comparison between density functional theory and density functional tight binding results.

PubMed

grosse Holthaus, Svea; Köppen, Susan; Frauenheim, Thomas; Ciacchi, Lucio Colombi

2014-06-21

We investigate the adsorption behavior of four different amino acids (glutamine, glutamate, serine, cysteine) on the zinc oxide (101̄0) surface, comparing the geometry and energy associated with a number of different adsorption configurations. In doing this, we highlight the benefits and limits of using density-functional tight-binding (DFTB) with respect to standard density functional theory (DFT). The DFTB method is found to reliably reproduce the DFT adsorption geometries. Analysis of the adsorption configurations emphasizes the fundamental role of the first hydration layer in mediating the interactions between the amino acids and the surface. Direct surface-molecule bonds are found to form predominantly via the carboxylate groups of the studied amino acids. No surface-mediated chemical reactions are observed, with the notable exception of a proton transfer from the thiol group of cysteine to a hydroxyl group of the surface hydration layer. The adsorption energies are found to be dominated both by the formation of direct or indirect surface-molecule hydrogen bonds, but also by the rearrangement of the hydrogen-bond network in surface proximity in a non-intuitive way. Energetic comparisons between DFTB and DFT are made difficult on one side by the long time necessary to achieve convergence of potential energy values in MD simulations and on the other side by the necessity of including higher-order corrections to DFTB to obtain a good description of the hydrogen bond energetics. Overall, our results suggest that DFTB is a good reference method to set the correct chemical states and the initial geometries of hybrid biomolecule/ZnO systems to be simulated with non-reactive force fields.

Molecular dynamics simulations of the amino acid-ZnO (10-10) interface: A comparison between density functional theory and density functional tight binding results

DOE Office of Scientific and Technical Information (OSTI.GOV)

Holthaus, Svea große; Köppen, Susan, E-mail: koeppen@hmi.uni-bremen.de; Frauenheim, Thomas

2014-06-21

We investigate the adsorption behavior of four different amino acids (glutamine, glutamate, serine, cysteine) on the zinc oxide (101{sup ¯}0) surface, comparing the geometry and energy associated with a number of different adsorption configurations. In doing this, we highlight the benefits and limits of using density-functional tight-binding (DFTB) with respect to standard density functional theory (DFT). The DFTB method is found to reliably reproduce the DFT adsorption geometries. Analysis of the adsorption configurations emphasizes the fundamental role of the first hydration layer in mediating the interactions between the amino acids and the surface. Direct surface-molecule bonds are found to formmore » predominantly via the carboxylate groups of the studied amino acids. No surface-mediated chemical reactions are observed, with the notable exception of a proton transfer from the thiol group of cysteine to a hydroxyl group of the surface hydration layer. The adsorption energies are found to be dominated both by the formation of direct or indirect surface-molecule hydrogen bonds, but also by the rearrangement of the hydrogen-bond network in surface proximity in a non-intuitive way. Energetic comparisons between DFTB and DFT are made difficult on one side by the long time necessary to achieve convergence of potential energy values in MD simulations and on the other side by the necessity of including higher-order corrections to DFTB to obtain a good description of the hydrogen bond energetics. Overall, our results suggest that DFTB is a good reference method to set the correct chemical states and the initial geometries of hybrid biomolecule/ZnO systems to be simulated with non-reactive force fields.« less

Grain boundaries in bcc-Fe: a density-functional theory and tight-binding study

NASA Astrophysics Data System (ADS)

Wang, Jingliang; Madsen, Georg K. H.; Drautz, Ralf

2018-02-01

Grain boundaries (GBs) have a significant influence on material properties. In the present paper, we calculate the energies of eleven low-Σ ({{Σ }}≤slant 13) symmetrical tilt GBs and two twist GBs in ferromagnetic bcc iron using first-principles density functional theory (DFT) calculations. The results demonstrate the importance of a sufficient sampling of initial rigid body translations in all three directions. We show that the relative GB energies can be explained by the miscoordination of atoms at the GB region. While the main features of the studied GB structures were captured by previous empirical interatomic potential calculations, it is shown that the absolute values of GB energies calculated were substantially underestimated. Based on DFT-calculated GB structures and energies, we construct a new d-band orthogonal tight-binding (TB) model for bcc iron. The TB model is validated by its predictive power on all the studied GBs. We apply the TB model to block boundaries in lath martensite and demonstrate that the experimentally observed GB character distribution can be explained from the viewpoint of interface energy.

Self-Consistent Charge Density Functional Tight-Binding Study of Poly(3,4-ethylenedioxythiophene): Poly(styrenesulfonate) Ammonia Gas Sensor.

PubMed

Marutaphan, Ampaiwan; Seekaew, Yotsarayuth; Wongchoosuk, Chatchawal

2017-12-01

Geometric and electronic properties of 3,4-ethylenedioxythiophene (EDOT), styrene sulfonate (SS), and EDOT: SS oligomers up to 10 repeating units were studied by the self-consistent charge density functional tight-binding (SCC-DFTB) method. An application of PEDOT:PSS for ammonia (NH 3 ) detection was highlighted and investigated both experimentally and theoretically. The results showed an important role of H-bonds in EDOT:SS oligomers complex conformation. Electrical conductivity of EDOT increased with increasing oligomers and doping SS due to enhancement of π conjugation. Printed PEDOT:PSS gas sensor exhibited relatively high response and selectivity to NH 3 . The SCC-DFTB calculation suggested domination of direct charge transfer process in changing of PEDOT:PSS conductivity upon NH 3 exposure at room temperature. The NH 3 molecules preferred to bind with PEDOT:PSS via physisorption. The most favorable adsorption site for PEDOT:PSS-NH 3 interaction was found to be at the nitrogen atom of NH 3 and hydrogen atoms of SS with an average optimal binding distance of 2.00 Å.

Evaluation of the grand-canonical partition function using expanded Wang-Landau simulations. IV. Performance of many-body force fields and tight-binding schemes for the fluid phases of silicon

DOE Office of Scientific and Technical Information (OSTI.GOV)

Desgranges, Caroline; Delhommelle, Jerome

We extend Expanded Wang-Landau (EWL) simulations beyond classical systems and develop the EWL method for systems modeled with a tight-binding Hamiltonian. We then apply the method to determine the partition function and thus all thermodynamic properties, including the Gibbs free energy and entropy, of the fluid phases of Si. We compare the results from quantum many-body (QMB) tight binding models, which explicitly calculate the overlap between the atomic orbitals of neighboring atoms, to those obtained with classical many-body (CMB) force fields, which allow to recover the tetrahedral organization in condensed phases of Si through, e.g., a repulsive 3-body term thatmore » favors the ideal tetrahedral angle. Along the vapor-liquid coexistence, between 3000 K and 6000 K, the densities for the two coexisting phases are found to vary significantly (by 5 orders of magnitude for the vapor and by up to 25% for the liquid) and to provide a stringent test of the models. Transitions from vapor to liquid are predicted to occur for chemical potentials that are 10%–15% higher for CMB models than for QMB models, and a ranking of the force fields is provided by comparing the predictions for the vapor pressure to the experimental data. QMB models also reveal the formation of a gap in the electronic density of states of the coexisting liquid at high temperatures. Subjecting Si to a nanoscopic confinement has a dramatic effect on the phase diagram with, e.g. at 6000 K, a decrease in liquid densities by about 50% for both CMB and QMB models and an increase in vapor densities between 90% (CMB) and 170% (QMB). The results presented here provide a full picture of the impact of the strategy (CMB or QMB) chosen to model many-body effects on the thermodynamic properties of the fluid phases of Si.« less

Hybrid k .p tight-binding model for intersubband optics in atomically thin InSe films

NASA Astrophysics Data System (ADS)

Magorrian, S. J.; Ceferino, A.; Zólyomi, V.; Fal'ko, V. I.

2018-04-01

We propose atomic films of n -doped γ -InSe as a platform for intersubband optics in the infrared and far-infrared range, coupled to out-of-plane polarized light. Depending on the film thickness (number of layers) and the amount of n -doping of the InSe film, these transitions span from ˜0.7 eV for bilayer to ˜0.05 eV for 15-layer InSe. We use a hybrid k .p theory and tight-binding model, fully parametrized using density-functional theory, to predict their oscillator strengths and thermal linewidths at room temperature.

The tight binding model study of the role of anisotropic AFM spin ordering in the charge ordered CMR manganites

NASA Astrophysics Data System (ADS)

Kar, J. K.; Panda, Saswati; Rout, G. C.

2017-05-01

We propose here a tight binding model study of the interplay between charge and spin orderings in the CMR manganites taking anisotropic effect due to electron hoppings and spin exchanges. The Hamiltonian consists of the kinetic energies of eg and t2g electrons of manganese ion. It further includes double exchange and Heisenberg interactions. The charge density wave interaction (CDW) describes an extra mechanism for the insulating character of the system. The CDW gap and spin parameters are calculated using Zubarev's Green's function technique and computed self-consistently. The results are reported in this communication.

Computational predictions of zinc oxide hollow structures

NASA Astrophysics Data System (ADS)

Tuoc, Vu Ngoc; Huan, Tran Doan; Thao, Nguyen Thi

2018-03-01

Nanoporous materials are emerging as potential candidates for a wide range of technological applications in environment, electronic, and optoelectronics, to name just a few. Within this active research area, experimental works are predominant while theoretical/computational prediction and study of these materials face some intrinsic challenges, one of them is how to predict porous structures. We propose a computationally and technically feasible approach for predicting zinc oxide structures with hollows at the nano scale. The designed zinc oxide hollow structures are studied with computations using the density functional tight binding and conventional density functional theory methods, revealing a variety of promising mechanical and electronic properties, which can potentially find future realistic applications.

Understanding the effects of packing and chemical terminations on the optical excitations of azobenzene-functionalized self-assembled monolayers

NASA Astrophysics Data System (ADS)

Cocchi, Caterina; Draxl, Claudia

2017-10-01

In a first-principles study based on many-body perturbation theory, we analyze the optical excitations of azobenzene-functionalized self-assembled monolayers (SAMs) with increasing packing density and different terminations, considering for comparison the corresponding gas-phase molecules and dimers. Intermolecular coupling increases with the density of the chromophores independently of the functional groups. The intense π → π* resonance that triggers photo-isomerization is present in the spectra of isolated dimers and diluted SAMs, but it is almost completely washed out in tightly packed architectures. Intermolecular coupling is partially inhibited by mixing differently functionalized azobenzene derivatives, in particular when large groups are involved. In this way, the excitation band inducing the photo-isomerization process is partially preserved and the effects of dense packing partly counterbalanced. Our results suggest that a tailored design of azobenzene-functionalized SAMs which optimizes the interplay between the packing density of the chromophores and their termination can lead to significant improvements in the photo-switching efficiency of these systems.

Proton transfer along water bridges in biological systems with density-functional tight-binding

NASA Astrophysics Data System (ADS)

Reiss, Krystle; Wise, Abigail; Mazzuca, James

2015-03-01

When examining the dynamics of charge transfer in high dimensional enzymatic systems, the cost of quantum mechanical treatment of electrons increases exponentially with the size of the system. As a semi-empirical method, density-functional tight-binding aids in shortening these calculation times, but can be inaccurate in the regime where bonds are being formed and broken. To address these inaccuracies with respect to proton transfer in an enzymatic system, DFTB is being used to calculate small model systems containing only a single amino acid residue donor, represented by an imidazole molecule, and a water acceptor. When DFTB calculations are compared to B3LYP geometry calculations of the donor molecule, we observe a bond angle error on the order of 1.2 degrees and a bond length error on the order of 0.011 Å. As we move forward with small donor-acceptor systems, comparisons between DFTB and B3LYP energy profiles will provide a better clue as to what extent improvements need to be made. To improve the accuracy of the DFTB calculations, the internuclear repulsion term may be altered. This would result in energy profiles that closely resemble those produced by higher-level theory. Alma College Provost's Office.

Mask patterning process using the negative tone chemically amplified resist TOK OEBR-CAN024

NASA Astrophysics Data System (ADS)

Irmscher, Mathias; Beyer, Dirk; Butschke, Joerg; Hudek, Peter; Koepernik, Corinna; Plumhoff, Jason; Rausa, Emmanuel; Sato, Mitsuru; Voehringer, Peter

2004-08-01

Optimized process parameters using the TOK OEBR-CAN024 resist for high chrome load patterning have been determined. A tight linearity tolerance for opaque and clear features, independent on the local pattern density, was the goal of our process integration work. For this purpose we evaluated a new correction method taking into account electron scattering and process influences. The method is based on matching of measured pattern geometry by iterative back-simulation using multiple Gauss and/or exponential functions. The obtained control function acts as input for the proximity correction software PROXECCO. Approaches with different pattern oversize and two Cr thicknesses were accomplished and the results have been reported. Isolated opaque and clear lines could be realized in a very tight linearity range. The increasing line width of small dense lines, induced by the etching process, could be corrected only partially.

Spectral densities for Frenkel exciton dynamics in molecular crystals: A TD-DFTB approach

NASA Astrophysics Data System (ADS)

Plötz, Per-Arno; Megow, Jörg; Niehaus, Thomas; Kühn, Oliver

2017-02-01

Effects of thermal fluctuations on the electronic excitation energies and intermonomeric Coulomb couplings are investigated for a perylene-tetracarboxylic-diimide crystal. To this end, time dependent density functional theory based tight binding (TD-DFTB) in the linear response formulation is used in combination with electronic ground state classical molecular dynamics. As a result, a parametrized Frenkel exciton Hamiltonian is obtained, with the effect of exciton-vibrational coupling being described by spectral densities. Employing dynamically defined normal modes, these spectral densities are analyzed in great detail, thus providing insight into the effect of specific intramolecular motions on excitation energies and Coulomb couplings. This distinguishes the present method from approaches using fixed transition densities. The efficiency by which intramolecular contributions to the spectral density can be calculated is a clear advantage of this method as compared with standard TD-DFT.

Tight junctions and human diseases.

PubMed

Sawada, Norimasa; Murata, Masaki; Kikuchi, Keisuke; Osanai, Makoto; Tobioka, Hirotoshi; Kojima, Takashi; Chiba, Hideki

2003-09-01

Tight junctions are intercellular junctions adjacent to the apical end of the lateral membrane surface. They have two functions, the barrier (or gate) function and the fence function. The barrier function of tight junctions regulates the passage of ions, water, and various macromolecules, even of cancer cells, through paracellular spaces. The barrier function is thus relevant to edema, jaundice, diarrhea, and blood-borne metastasis. On the other hand, the fence function maintains cell polarity. In other words, tight junctions work as a fence to prevent intermixing of molecules in the apical membrane with those in the lateral membrane. This function is deeply involved in cancer cell biology, in terms of loss of cell polarity. Of the proteins comprising tight junctions, integral membrane proteins occludin, claudins, and JAMs have been recently discovered. Of these molecules, claudins are exclusively responsible for the formation of tight-junction strands and are connected with the actin cytoskeleton mediated by ZO-1. Thus, both functions of tight junctions are dependent on the integrity of the actin cytoskeleton as well as ATP. Mutations in the claudin14 and the claudin16 genes result in hereditary deafness and hereditary hypomagnesemia, respectively. Some pathogenic bacteria and viruses target and affect the tight-junction function, leading to diseases. In this review, the relationship between tight junctions and human diseases is summarized.

An efficient method for quantum transport simulations in the time domain

NASA Astrophysics Data System (ADS)

Wang, Y.; Yam, C.-Y.; Frauenheim, Th.; Chen, G. H.; Niehaus, T. A.

2011-11-01

An approximate method based on adiabatic time dependent density functional theory (TDDFT) is presented, that allows for the description of the electron dynamics in nanoscale junctions under arbitrary time dependent external potentials. The density matrix of the device region is propagated according to the Liouville-von Neumann equation. The semi-infinite leads give rise to dissipative terms in the equation of motion which are calculated from first principles in the wide band limit. In contrast to earlier ab initio implementations of this formalism, the Hamiltonian is here approximated in the spirit of the density functional based tight-binding (DFTB) method. Results are presented for two prototypical molecular devices and compared to full TDDFT calculations. The temporal profile of the current traces is qualitatively well captured by the DFTB scheme. Steady state currents show considerable variations, both in comparison of approximate and full TDDFT, but also among TDDFT calculations with different basis sets.

Field effect transistors based on phosphorene nanoribbon with selective edge-adsorption: A first-principles study

NASA Astrophysics Data System (ADS)

Hu, Mengli; Yang, Zhixiong; Zhou, Wenzhe; Li, Aolin; Pan, Jiangling; Ouyang, Fangping

2018-04-01

By using density functional theory (DFT) and nonequilibrium Green's function (NEGF), field effect transistor (FET) based on zigzag shaped phosphorene nanoribbons (ZPNR) are investigated. The FETs are constructed with bare-edged ZPNRs as electrodes and H, Cl or OH adsorbed ZPNRs as channel. It is found FETs with the three kinds of channel show similar transport properties. The FET is p-type with a maximum current on/off ratio of 104 and a minimum off-current of 1 nA. The working mode of FETs is dependent on the parity of channel length. It can be either enhancement mode or depletion mode and the off-state current shows an even-odd oscillation. The current oscillations are interpreted with density of states (DOS) analysis and methods of evolution operator and tight-binding Hamiltonian. Operating mechanism of the designed FETs is also presented with projected local density of states and band diagrams.

A marked correlation function for constraining modified gravity models

NASA Astrophysics Data System (ADS)

White, Martin

2016-11-01

Future large scale structure surveys will provide increasingly tight constraints on our cosmological model. These surveys will report results on the distance scale and growth rate of perturbations through measurements of Baryon Acoustic Oscillations and Redshift-Space Distortions. It is interesting to ask: what further analyses should become routine, so as to test as-yet-unknown models of cosmic acceleration? Models which aim to explain the accelerated expansion rate of the Universe by modifications to General Relativity often invoke screening mechanisms which can imprint a non-standard density dependence on their predictions. This suggests density-dependent clustering as a `generic' constraint. This paper argues that a density-marked correlation function provides a density-dependent statistic which is easy to compute and report and requires minimal additional infrastructure beyond what is routinely available to such survey analyses. We give one realization of this idea and study it using low order perturbation theory. We encourage groups developing modified gravity theories to see whether such statistics provide discriminatory power for their models.

Studying the varied shapes of gold clusters by an elegant optimization algorithm that hybridizes the density functional tight-binding theory and the density functional theory

NASA Astrophysics Data System (ADS)

Yen, Tsung-Wen; Lim, Thong-Leng; Yoon, Tiem-Leong; Lai, S. K.

2017-11-01

We combined a new parametrized density functional tight-binding (DFTB) theory (Fihey et al. 2015) with an unbiased modified basin hopping (MBH) optimization algorithm (Yen and Lai 2015) and applied it to calculate the lowest energy structures of Au clusters. From the calculated topologies and their conformational changes, we find that this DFTB/MBH method is a necessary procedure for a systematic study of the structural development of Au clusters but is somewhat insufficient for a quantitative study. As a result, we propose an extended hybridized algorithm. This improved algorithm proceeds in two steps. In the first step, the DFTB theory is employed to calculate the total energy of the cluster and this step (through running DFTB/MBH optimization for given Monte-Carlo steps) is meant to efficiently bring the Au cluster near to the region of the lowest energy minimum since the cluster as a whole has explicitly considered the interactions of valence electrons with ions, albeit semi-quantitatively. Then, in the second succeeding step, the energy-minimum searching process will continue with a skilledly replacement of the energy function calculated by the DFTB theory in the first step by one calculated in the full density functional theory (DFT). In these subsequent calculations, we couple the DFT energy also with the MBH strategy and proceed with the DFT/MBH optimization until the lowest energy value is found. We checked that this extended hybridized algorithm successfully predicts the twisted pyramidal structure for the Au40 cluster and correctly confirms also the linear shape of C8 which our previous DFTB/MBH method failed to do so. Perhaps more remarkable is the topological growth of Aun: it changes from a planar (n =3-11) → an oblate-like cage (n =12-15) → a hollow-shape cage (n =16-18) and finally a pyramidal-like cage (n =19, 20). These varied forms of the cluster's shapes are consistent with those reported in the literature.

Effects of Structural Deformation and Tube Chirality on Electronic Conductance of Carbon Nanotubes

NASA Technical Reports Server (NTRS)

Svizhenko, Alexei; Maiti, Amitesh; Anantram, M. P.; Biegel, Bryan A. (Technical Monitor)

2002-01-01

A combination of large scale classical force-field (UFF), density functional theory (DFT), and tight-binding Green's function transport calculations is used to study the electronic properties of carbon nanotubes under the twist, bending, and atomic force microscope (AFM)-tip deformation. We found that in agreement with experiment a significant change in electronic conductance can be induced by AFM-tip deformation of metallic zigzag tubes and by twist deformation of armchair tubes. The effect is explained in terms of bandstructure change under deformation.

Density-functional tight-binding investigation of the structure, stability and material properties of nickel hydroxide nanotubes

NASA Astrophysics Data System (ADS)

Jahangiri, Soran; Mosey, Nicholas J.

2018-01-01

Nickel hydroxide is a material composed of two-dimensional layers that can be rolled up to form cylindrical nanotubes belonging to a class of inorganic metal hydroxide nanotubes that are candidates for applications in catalysis, energy storage, and microelectronics. The stabilities and other properties of this class of inorganic nanotubes have not yet been investigated in detail. The present study uses self-consistent-charge density-functional tight-binding calculations to examine the stabilities, mechanical properties, and electronic properties of nickel hydroxide nanotubes along with the energetics associated with the adsorption of water by these systems. The tight-binding model was parametrized for this system based on the results of first-principles calculations. The stabilities of the nanotubes were examined by calculating strain energies and performing molecular dynamics simulations. The results indicate that single-walled nickel hydroxide nanotubes are stable at room temperature, which is consistent with experimental investigations. The nanotubes possess size-dependent mechanical properties that are similar in magnitude to those of other inorganic nanotubes. The electronic properties of the nanotubes were also found to be size-dependent and small nickel oxyhydroxide nanotubes are predicted to be semiconductors. Despite this size-dependence, both the mechanical and electronic properties were found to be almost independent of the helical structure of the nanotubes. The calculations also show that water molecules have higher adsorption energies when binding to the interior of the nickel hydroxide nanotubes when compared to adsorption in nanotubes formed from other two-dimensional materials such as graphene. The increased adsorption energy is due to the hydrophilic nature of nickel hydroxide. Due to the broad applications of nickel hydroxide, the nanotubes investigated here are also expected to be used in catalysis, electronics, and clean energy production.

Ultra-fast computation of electronic spectra for large systems by tight-binding based simplified Tamm-Dancoff approximation (sTDA-xTB)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grimme, Stefan, E-mail: grimme@thch.uni-bonn.de; Bannwarth, Christoph

2016-08-07

The computational bottleneck of the extremely fast simplified Tamm-Dancoff approximated (sTDA) time-dependent density functional theory procedure [S. Grimme, J. Chem. Phys. 138, 244104 (2013)] for the computation of electronic spectra for large systems is the determination of the ground state Kohn-Sham orbitals and eigenvalues. This limits such treatments to single structures with a few hundred atoms and hence, e.g., sampling along molecular dynamics trajectories for flexible systems or the calculation of chromophore aggregates is often not possible. The aim of this work is to solve this problem by a specifically designed semi-empirical tight binding (TB) procedure similar to the wellmore » established self-consistent-charge density functional TB scheme. The new special purpose method provides orbitals and orbital energies of hybrid density functional character for a subsequent and basically unmodified sTDA procedure. Compared to many previous semi-empirical excited state methods, an advantage of the ansatz is that a general eigenvalue problem in a non-orthogonal, extended atomic orbital basis is solved and therefore correct occupied/virtual orbital energy splittings as well as Rydberg levels are obtained. A key idea for the success of the new model is that the determination of atomic charges (describing an effective electron-electron interaction) and the one-particle spectrum is decoupled and treated by two differently parametrized Hamiltonians/basis sets. The three-diagonalization-step composite procedure can routinely compute broad range electronic spectra (0-8 eV) within minutes of computation time for systems composed of 500-1000 atoms with an accuracy typical of standard time-dependent density functional theory (0.3-0.5 eV average error). An easily extendable parametrization based on coupled-cluster and density functional computed reference data for the elements H–Zn including transition metals is described. The accuracy of the method termed sTDA-xTB is first benchmarked for vertical excitation energies of open- and closed-shell systems in comparison to other semi-empirical methods and applied to exemplary problems in electronic spectroscopy. As side products of the development, a robust and efficient valence electron TB method for the accurate determination of atomic charges as well as a more accurate calculation scheme of dipole rotatory strengths within the Tamm-Dancoff approximation is proposed.« less

GABAB receptor cell surface export is controlled by an endoplasmic reticulum gatekeeper

PubMed Central

Doly, Stéphane; Shirvani, Hamasseh; Gäta, Gabriel; Meye, Frank; Emerit, Michel-Boris; Enslen, Hervé; Achour, Lamia; Pardo-Lopez, Liliana; Kwon, Yang Seung; Armand, Vincent; Gardette, Robert; Giros, Bruno; Gassmann, Martin; Bettler, Bernhard; Mameli, Manuel; Darmon, Michèle; Marullo, Stefano

2016-01-01

Summary Endoplasmic reticulum (ER) release and cell surface export of many G protein-coupled receptors (GPCRs), are tightly regulated. For GABAB receptors of GABA, the major mammalian inhibitory neurotransmitter, the ligand-binding GB1 subunit is maintained in the ER by unknown mechanisms in the absence of hetero-dimerization with the GB2 subunit. We report that GB1 retention is regulated by a specific gatekeeper, PRAF2. This ER resident transmembrane protein binds to GB1, preventing its progression in the biosynthetic pathway. GB1 release occurs upon competitive displacement from PRAF2 by GB2. PRAF2 concentration, relative to that of GB1 and GB2, tightly controls cell surface receptor density and controls GABAB function in neurons. Experimental perturbation of PRAF2 levels in vivo caused marked hyperactivity disorders in mice. These data reveal an unanticipated major impact of specific ER gate-keepers on GPCR function and identify PRAF2 as a new molecular target with therapeutic potential for psychiatric and neurological diseases involving GABAB function. PMID:26033241

Descriptions of carbon isotopes within the energy density functional theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ismail, Atef; Cheong, Lee Yen; Yahya, Noorhana

2014-10-24

Within the energy density functional (EDF) theory, the structure properties of Carbon isotopes are systematically studied. The shell model calculations are done for both even-A and odd-A nuclei, to study the structure of rich-neutron Carbon isotopes. The EDF theory indicates the single-neutron halo structures in {sup 15}C, {sup 17}C and {sup 19}C, and the two-neutron halo structures in {sup 16}C and {sup 22}C nuclei. It is also found that close to the neutron drip-line, there exist amazing increase in the neutron radii and decrease on the binding energies BE, which are tightly related with the blocking effect and correspondingly themore » blocking effect plays a significant role in the shell model configurations.« less

Improved Density Functional Tight Binding Potentials for Metalloid Aluminum Clusters

DTIC Science & Technology

2016-06-01

simulations of the oxidation of Al4Cp * 4 show reasonable comparison with a DFT-based Car -Parrinello method, including correct prediction of hydride transfers...comparison with a DFT-based Car -Parrinello method, including correct prediction of hydride transfers from Cp* to the metal centers during the...initio molecular dynamics of the oxidation of Al4Cp * 4 using a DFT-based Car -Parrinello method. This simulation, which 43 several months on the

Studying the hopping parameters of half-Heusler NaAuS using maximally localized Wannier function

NASA Astrophysics Data System (ADS)

Sihi, Antik; Lal, Sohan; Pandey, Sudhir K.

2018-04-01

Here, the electronic behavior of half-Heusler NaAuS is studied using PBEsol exchange correlation functional by plotting the band structure curve. These bands are reproduced using maximally localized Wannier function using WANNIER90. Tight-binding bands are nicely matched with density functional theory bands. By fitting the tight-binding model, hopping parameter for NaAuS is obtained by including Na 2s, 2p, Au 6s, 5p, 5d and S 3s, 3p orbitals within the energy interval of -5 to 16 eV around the Fermi level. In present study, hopping integrals for NaAuS are computed for the first primitive unit cell atoms as well as the first nearest neighbor primitive unit cell. The most dominating hopping integrals are found for Na (3s) - S (3s), Na (2px) - S (2px), Au (6s) - S (3px), Au (6s) - S (3py) and Au (6s) - S (3pz) orbitals. The hopping integrals for the first nearest neighbor primitive unit cell are also discussed in this manuscript. In future, these hopping integrals are very important to find the topological invariant for NaAuS compound.

Possible Involvement of Tight Junctions, Extracellular Matrix and Nuclear Receptors in Epithelial Differentiation

PubMed Central

Ichikawa-Tomikawa, Naoki; Sugimoto, Kotaro; Satohisa, Seiro; Nishiura, Keisuke; Chiba, Hideki

2011-01-01

Tight junctions are intercellular junctions localized at the most apical end of the lateral plasma membrane. They consist of four kinds of transmembrane proteins (occludin, claudins, junctional adhesion molecules, and tricellulin) and huge numbers of scaffolding proteins and contribute to the paracellular barrier and fence function. The mutation and deletion of these proteins impair the functions of tight junctions and cause various human diseases. In this paper, we provide an overview of recent studies on transmembrane proteins of tight junctions and highlight the functional significance of tight junctions, extracellular matrix, and nuclear receptors in epithelial differentiation. PMID:22162632

Universal tight binding model for chemical reactions in solution and at surfaces. II. Water.

PubMed

Lozovoi, A Y; Sheppard, T J; Pashov, D L; Kohanoff, J J; Paxton, A T

2014-07-28

A revised water model intended for use in condensed phase simulations in the framework of the self consistent polarizable ion tight binding theory is constructed. The model is applied to water monomer, dimer, hexamers, ice, and liquid, where it demonstrates good agreement with theoretical results obtained by more accurate methods, such as DFT and CCSD(T), and with experiment. In particular, the temperature dependence of the self diffusion coefficient in liquid water predicted by the model, closely reproduces experimental curves in the temperature interval between 230 K and 350 K. In addition, and in contrast to standard DFT, the model properly orders the relative densities of liquid water and ice. A notable, but inevitable, shortcoming of the model is underestimation of the static dielectric constant by a factor of two. We demonstrate that the description of inter and intramolecular forces embodied in the tight binding approximation in quantum mechanics leads to a number of valuable insights which can be missing from ab initio quantum chemistry and classical force fields. These include a discussion of the origin of the enhanced molecular electric dipole moment in the condensed phases, and a detailed explanation for the increase of coordination number in liquid water as a function of temperature and compared with ice--leading to insights into the anomalous expansion on freezing. The theory holds out the prospect of an understanding of the currently unexplained density maximum of water near the freezing point.

Communication: Photoinduced carbon dioxide binding with surface-functionalized silicon quantum dots.

PubMed

Douglas-Gallardo, Oscar A; Sánchez, Cristián Gabriel; Vöhringer-Martinez, Esteban

2018-04-14

Nowadays, the search for efficient methods able to reduce the high atmospheric carbon dioxide concentration has turned into a very dynamic research area. Several environmental problems have been closely associated with the high atmospheric level of this greenhouse gas. Here, a novel system based on the use of surface-functionalized silicon quantum dots (sf-SiQDs) is theoretically proposed as a versatile device to bind carbon dioxide. Within this approach, carbon dioxide trapping is modulated by a photoinduced charge redistribution between the capping molecule and the silicon quantum dots (SiQDs). The chemical and electronic properties of the proposed SiQDs have been studied with a Density Functional Theory and Density Functional Tight-Binding (DFTB) approach along with a time-dependent model based on the DFTB framework. To the best of our knowledge, this is the first report that proposes and explores the potential application of a versatile and friendly device based on the use of sf-SiQDs for photochemically activated carbon dioxide fixation.

Communication: Photoinduced carbon dioxide binding with surface-functionalized silicon quantum dots

NASA Astrophysics Data System (ADS)

Douglas-Gallardo, Oscar A.; Sánchez, Cristián Gabriel; Vöhringer-Martinez, Esteban

2018-04-01

Nowadays, the search for efficient methods able to reduce the high atmospheric carbon dioxide concentration has turned into a very dynamic research area. Several environmental problems have been closely associated with the high atmospheric level of this greenhouse gas. Here, a novel system based on the use of surface-functionalized silicon quantum dots (sf-SiQDs) is theoretically proposed as a versatile device to bind carbon dioxide. Within this approach, carbon dioxide trapping is modulated by a photoinduced charge redistribution between the capping molecule and the silicon quantum dots (SiQDs). The chemical and electronic properties of the proposed SiQDs have been studied with a Density Functional Theory and Density Functional Tight-Binding (DFTB) approach along with a time-dependent model based on the DFTB framework. To the best of our knowledge, this is the first report that proposes and explores the potential application of a versatile and friendly device based on the use of sf-SiQDs for photochemically activated carbon dioxide fixation.

Effect of disorder on the optical properties of short period superlattices

NASA Technical Reports Server (NTRS)

Strozier, J. A.; Zhang, Y. A.; Horton, C.; Ignatiev, A.; Shih, H. D.

1993-01-01

The optical properties of disordered short period superlattices are studied using a one-dimensional tight-binding model. A difference vector and disorder structure factor are proposed to characterize the disordered superlattice. The density of states, participation number, and optical absorption coefficients for both ordered and disordered superlattices are calculated as a function of energy. The results show that introduction of disorder into an indirect band gap material enhances the optical transition near the indirect band edge.

Intense conductivity suppression by edge defects in zigzag MoS2 and WSe2 nanoribbons: a density functional based tight-binding study.

PubMed

Silva, F W N; Costa, A L M T; Liu, Lei; Barros, E B

2016-11-04

The effects of edge vacancies on the electron transport properties of zigzag MoS2/WSe2 nanoribbons are studied using a density functional theory (DFT)-based tight-binding model with a sp(3)d(5) basis set for the electronic structure calculation and applying the Landauer-Büttiker approach for the electronic transport. Our results show that the presence of a single edge vacancy, with a missing MoS2/WSe2 triplet, is enough to suppress the conductance of the system by almost one half for most energies around the Fermi level. Furthermore, the presence of other single defects along the same edge has little effect on the overall conductance, indicating that the conductance of that particular edge has been strongly suppressed by the first defect. The presence of another defect on the opposite edge further suppresses the quantum conductance, independently of the relative position between the two defects in opposite edges. The introduction of other defects cause the suppression to be energy dependent, leading to conductance peaks which depend on the geometry of the edges. The strong conductance dependence on the presence of edge defects is corroborated by DFT calculations using SIESTA, which show that the electronic bands near the Fermi energy are strongly localized at the edge.

Conductance of three-terminal molecular bridge based on tight-binding theory

NASA Astrophysics Data System (ADS)

Wang, Li-Guang; Li, Yong; Yu, Ding-Wen; Katsunori, Tagami; Masaru, Tsukada

2005-05-01

The quantum transmission characteristic of three-benzene ring nano-molecular bridge is investigated theoretically by using Green's function approach based on tight-binding theory with only a π orbital per carbon atom at the site. The transmission probabilities that electrons transport through the molecular bridge from one terminal to the other two terminals are obtained. The electronic current distributions inside the molecular bridge are calculated and shown in graphical analogy by the current density method based on Fisher-Lee formula at the energy points E = ±0.42, ±1.06 and ±1.5, respectively, where the transmission spectra appear peaks. We find that the transmission spectra are related to the incident electronic energy and the molecular levels strongly and the current distributions agree well with Kirchhoff quantum current momentum conservation law.

Investigation of Structure and Reactivity Relationship in M-N-C Type Catalysts using Density Functional Tight Binding

DOE Office of Scientific and Technical Information (OSTI.GOV)

Negre, Christian Francisco Andres; Gonzales, Ivana

Catalysts inhibition studies were performed to indisputably confirm the role of various metal, carbon, and nitrogen moieties in the individual steps of oxygen reduction reaction (ORR) on M-N-C catalysts. ORR activity was studied at University of New Mexico by rotating ring disk electrode method in the acidic electrolyte with the addition of Tris (tris(hydroxymethyl)-aminomethane) as inhibiting agent. To understand the interaction of Tris with different defects that exist in Fe-N-C materials and provide the support for the experimental data, we used density functional theory (DFT) and modeled the interaction of protonated Tris (TrisH) with Fe containingcenters (Fe-N 4 and Fe-Nmore » 2C 2), pyridinic nitrogen, graphitic nitrogen, and pyrrolic nitrogen both as in plane and edge defects.« less

The Role of Cytosine Methylation on Charge Transport through a DNA Strand

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qi, Jianqing; Govind, Niranjan; Anantram, M. P.

Cytosine methylation has been found to play a crucial role in various biological processes, including a number of human diseases. The detection of this small modifi-cation remains challenging. In this work, we computationally explore the possibility of detecting methylated DNA strands through direct electrical conductance measurements. Using density functional theory and the Landauer-Buttiker method, we study the electronic properties and charge transport through an eight base-pair methylated DNA strand and its native counterpart. Specifically, we compare the results generated with the widely used B3LYP exchange-correlation (XC) functional and CAM-B3LYP based tuned range-separated hybrid density functional. We first analyze the effectmore » of cytosine methylation on the tight-binding parameters of two DNA strands and then model the transmission of the electrons and conductance through the strands both with and without decoherence. We find that with both functionals, the main difference of the tight-binding parameters between the native DNA and the methylated DNA lies in the on-site energies of (methylated) cytosine bases. The intra- and interstrand hopping integrals between two nearest neighboring guanine base and (methylated) cytosine base also change with the addition of the methyl groups. Our calculations show that in the phase-coherent limit, the transmission of the methylated strand is close to the native strand when the energy is nearby the highest occupied molecular orbital (HOMO) level and larger than the native strand by 5 times in the bandgap. The trend in transmission also holds in the presence of the decoherence with both functionals. We also study the effect of contact coupling by choosing coupling strengths ranging from weak to strong coupling limit. Our results suggest that the effect of the two different functionals is to alter the on-site energies of the DNA bases at the HOMO level, while the transport properties don't depend much on the two functionals.« less

Thermodynamically accessible titanium clusters TiN, N = 2-32.

PubMed

Lazauskas, Tomas; Sokol, Alexey A; Buckeridge, John; Catlow, C Richard A; Escher, Susanne G E T; Farrow, Matthew R; Mora-Fonz, David; Blum, Volker W; Phaahla, Tshegofatso M; Chauke, Hasani R; Ngoepe, Phuti E; Woodley, Scott M

2018-05-10

We have performed a genetic algorithm search on the tight-binding interatomic potential energy surface (PES) for small TiN (N = 2-32) clusters. The low energy candidate clusters were further refined using density functional theory (DFT) calculations with the PBEsol exchange-correlation functional and evaluated with the PBEsol0 hybrid functional. The resulting clusters were analysed in terms of their structural features, growth mechanism and surface area. The results suggest a growth mechanism that is based on forming coordination centres by interpenetrating icosahedra, icositetrahedra and Frank-Kasper polyhedra. We identify centres of coordination, which act as centres of bulk nucleation in medium sized clusters and determine the morphological features of the cluster.

Butadiene-Isoprene Block Copolymers and Their Hydrogenated Derivatives.

DTIC Science & Technology

1981-04-01

polyethylene, LDPE. The crystallinity, density and AHf for all of the block copolymers were found to be linearly de - pendent on HB content indicating...etc. It is known for example, that carbanions can exist in "tight", "loose", or even "free" structures as a function of counterion and solvent. (5,6...is then observed for the styrene segment. Thus in these systems , there is an apparent "reversal of reactivity" of styrene and the diene, since for the

III-Nitride, SiC and Diamond Materials for Electronic Devices. Symposium Held April 8-12 1996, San Francisco, California, U.S.A. Volume 423.

DTIC Science & Technology

1996-12-01

gallium, nitrogen and gallium nitride structures. Thus it can be shown to be transferable and efficient for predictive molecular -dynamic simulations on...potentials and forces for the molecular dynamics simulations are derived by means of a density-functional based nonorthogonal tight-binding (DF-TB) scheme...LDA). Molecular -dynamics simulations for determining the different reconstructions of the SiC surface use the slab method (two-dimensional periodic

An environment-dependent semi-empirical tight binding model suitable for electron transport in bulk metals, metal alloys, metallic interfaces, and metallic nanostructures. I. Model and validation

NASA Astrophysics Data System (ADS)

Hegde, Ganesh; Povolotskyi, Michael; Kubis, Tillmann; Boykin, Timothy; Klimeck, Gerhard

2014-03-01

Semi-empirical Tight Binding (TB) is known to be a scalable and accurate atomistic representation for electron transport for realistically extended nano-scaled semiconductor devices that might contain millions of atoms. In this paper, an environment-aware and transferable TB model suitable for electronic structure and transport simulations in technologically relevant metals, metallic alloys, metal nanostructures, and metallic interface systems are described. Part I of this paper describes the development and validation of the new TB model. The new model incorporates intra-atomic diagonal and off-diagonal elements for implicit self-consistency and greater transferability across bonding environments. The dependence of the on-site energies on strain has been obtained by appealing to the Moments Theorem that links closed electron paths in the system to energy moments of angular momentum resolved local density of states obtained ab initio. The model matches self-consistent density functional theory electronic structure results for bulk face centered cubic metals with and without strain, metallic alloys, metallic interfaces, and metallic nanostructures with high accuracy and can be used in predictive electronic structure and transport problems in metallic systems at realistically extended length scales.

Electronic Structure and Properties of Deformed Carbon Nanotubes

NASA Technical Reports Server (NTRS)

Yang, Liu; Arnold, Jim (Technical Monitor)

2001-01-01

A theoretical framework based on Huckel tight-binding model has been formulated to analyze the electronic structure of carbon nanotubes under uniform deformation. The model successfully quantifies the dispersion relation, density of states and bandgap change of nanotubes under uniform stretching, compression, torsion and bending. Our analysis shows that the shifting of the Fermi point away from the Brillouin zone vertices is the key reason for these changes. As a result of this shifting, the electronic structure of deformed carbon nanotubes varies dramatically depending on their chirality and deformation mode. Treating the Fermi point as a function of strain and tube chirality, the analytical solution preserves the concise form of undeformed carbon nanotubes. It predicts the shifting, merging and splitting of the Van Hove singularities in the density of states and the zigzag pattern of bandgap change under strains. Four orbital tight-binding simulations of carbon nanotubes under uniform stretching, compression, torsion and bending have been performed to verify the analytical solution. Extension to more complex systems are being performed to relate this analytical solution to the spectroscopic characterization, device performance and proposed quantum structures induced by the deformation. The limitations of this model will also be discussed.

Overcritical plasma ignition and diagnostics from oncoming interaction of two color low energy tightly focused femtosecond laser pulses inside fused silica

NASA Astrophysics Data System (ADS)

Potemkin, F. V.; Bravy, B. G.; Bezsudnova, Yu I.; Mareev, E. I.; Starostin, V. M.; Platonenko, V. T.; Gordienko, V. M.

2016-04-01

We report overcritical (3.3  ×  1021 cm-3) microplasma produced by low energy colliding IR (infrared) (1.24 μm) and visible (0.62 μm) femtosecond pulses tightly focused (NA  =  0.5) into the bulk of fused silica with on-line monitoring based on third harmonic generated by the IR beam. It was established that the absorbed energy density is the key parameter that determines the micromodification formation threshold and in our experimental conditions it is close to 4.5 kJ cm-3. Non-monotonic behavior of the third harmonic signal as a function of time delay between visible (0.62 μm) and IR (1.24 μm) femtosecond pulses demonstrates the qualitative differences about the two phenomena: one is the seed electrons generation by the visible pulse via multiphoton ionization and second is the avalanche ionization by the IR pulse. We predict that the tandem two-color excitation of wide-bandgap dielectric in comparison with single-color pulse interaction regime allows providing a much higher absorbed energy density and overcritical plasma.

Maximally localized Wannier functions in LaMnO3 within PBE + U, hybrid functionals and partially self-consistent GW: an efficient route to construct ab initio tight-binding parameters for eg perovskites.

PubMed

Franchini, C; Kováčik, R; Marsman, M; Murthy, S Sathyanarayana; He, J; Ederer, C; Kresse, G

2012-06-13

Using the newly developed VASP2WANNIER90 interface we have constructed maximally localized Wannier functions (MLWFs) for the e(g) states of the prototypical Jahn-Teller magnetic perovskite LaMnO(3) at different levels of approximation for the exchange-correlation kernel. These include conventional density functional theory (DFT) with and without the additional on-site Hubbard U term, hybrid DFT and partially self-consistent GW. By suitably mapping the MLWFs onto an effective e(g) tight-binding (TB) Hamiltonian we have computed a complete set of TB parameters which should serve as guidance for more elaborate treatments of correlation effects in effective Hamiltonian-based approaches. The method-dependent changes of the calculated TB parameters and their interplay with the electron-electron (el-el) interaction term are discussed and interpreted. We discuss two alternative model parameterizations: one in which the effects of the el-el interaction are implicitly incorporated in the otherwise 'noninteracting' TB parameters and a second where we include an explicit mean-field el-el interaction term in the TB Hamiltonian. Both models yield a set of tabulated TB parameters which provide the band dispersion in excellent agreement with the underlying ab initio and MLWF bands.

Impact of Many-Body Effects on Landau Levels in Graphene

NASA Astrophysics Data System (ADS)

Sonntag, J.; Reichardt, S.; Wirtz, L.; Beschoten, B.; Katsnelson, M. I.; Libisch, F.; Stampfer, C.

2018-05-01

We present magneto-Raman spectroscopy measurements on suspended graphene to investigate the charge carrier density-dependent electron-electron interaction in the presence of Landau levels. Utilizing gate-tunable magnetophonon resonances, we extract the charge carrier density dependence of the Landau level transition energies and the associated effective Fermi velocity vF. In contrast to the logarithmic divergence of vF at zero magnetic field, we find a piecewise linear scaling of vF as a function of the charge carrier density, due to a magnetic-field-induced suppression of the long-range Coulomb interaction. We quantitatively confirm our experimental findings by performing tight-binding calculations on the level of the Hartree-Fock approximation, which also allow us to estimate an excitonic binding energy of ≈6 meV contained in the experimentally extracted Landau level transitions energies.

Large deviation function for a driven underdamped particle in a periodic potential

NASA Astrophysics Data System (ADS)

Fischer, Lukas P.; Pietzonka, Patrick; Seifert, Udo

2018-02-01

Employing large deviation theory, we explore current fluctuations of underdamped Brownian motion for the paradigmatic example of a single particle in a one-dimensional periodic potential. Two different approaches to the large deviation function of the particle current are presented. First, we derive an explicit expression for the large deviation functional of the empirical phase space density, which replaces the level 2.5 functional used for overdamped dynamics. Using this approach, we obtain several bounds on the large deviation function of the particle current. We compare these to bounds for overdamped dynamics that have recently been derived, motivated by the thermodynamic uncertainty relation. Second, we provide a method to calculate the large deviation function via the cumulant generating function. We use this method to assess the tightness of the bounds in a numerical case study for a cosine potential.

Charge Transport Properties of Durene Crystals from First-Principles.

PubMed

Motta, Carlo; Sanvito, Stefano

2014-10-14

We establish a rigorous computational scheme for constructing an effective Hamiltonian to be used for the determination of the charge carrier mobility of pure organic crystals at finite temperature, which accounts for van der Waals interactions, and it includes vibrational contributions from the entire phonon spectrum of the crystal. Such an approach is based on the ab initio framework provided by density functional theory and the construction of a tight-binding effective model via Wannier transformation. The final Hamiltonian includes coupling of the electrons to the crystals phonons, which are also calculated from density functional theory. We apply this methodology to the case of durene, a small π-conjugated molecule, which forms a high-mobility herringbone-stacked crystal. We show that accounting correctly for dispersive forces is fundamental for obtaining a high-quality phonon spectrum, in agreement with experiments. Then, the mobility as a function of temperature is calculated along different crystallographic directions and the phonons most responsible for the scattering are identified.

Performance of the DFTB method in comparison to DFT and semiempirical methods for geometries and energies of C20-C86fullerene isomers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zheng, Guishan; Irle, Stephan; Morokuma, Keiji

2005-07-20

The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. The performance of both non-iterative (NCC) and self-consistent charge (SCC) versions of the density functional tight binding (DFTB) method, as well as AM1 and PM3 methods, has been compared with the B3LYP method, a hybrid density functional theory (DFT) method, for equilibrium geometries and relative energies of various isomers of C20–C86 fullerenes. Both NCC- and SCCDFTB methods compare very favorablymore » with B3LYP both in geometries and isomer relative energies, while AM1 and PM3 do noticeably worse.« less

A new efficient method for calculation of Frenkel exciton parameters in molecular aggregates

NASA Astrophysics Data System (ADS)

Plötz, Per-Arno; Niehaus, Thomas; Kühn, Oliver

2014-05-01

The Frenkel exciton Hamiltonian is at the heart of many simulations of excitation energy transfer in molecular aggregates. It separates the aggregate into Coulomb-coupled monomers. Here it is shown that the respective parameters, i.e., monomeric excitation energies and Coulomb couplings between transition densities can be efficiently calculated using time-dependent tight-binding-based density functional theory (TD-DFTB). Specifically, Coulomb couplings are expressed in terms of self-consistently determined Mulliken transition charges. The approach is applied to two dimer systems. First, formaldehyde oxime for which a detailed comparison with standard DFT using the B3LYP and the PBE functionals as well as with SCS-CC2 is provided. Second, the Coulomb coupling is explored in dependence on the intermolecular coordinates for a perylene bisimide dimer. This provides structural evidence for the previously observed biphasic aggregation behavior of this dye.

Computational predictions of the new Gallium nitride nanoporous structures

NASA Astrophysics Data System (ADS)

Lien, Le Thi Hong; Tuoc, Vu Ngoc; Duong, Do Thi; Thu Huyen, Nguyen

2018-05-01

Nanoporous structural prediction is emerging area of research because of their advantages for a wide range of materials science and technology applications in opto-electronics, environment, sensors, shape-selective and bio-catalysis, to name just a few. We propose a computationally and technically feasible approach for predicting Gallium nitride nanoporous structures with hollows at the nano scale. The designed porous structures are studied with computations using the density functional tight binding (DFTB) and conventional density functional theory methods, revealing a variety of promising mechanical and electronic properties, which can potentially find future realistic applications. Their stability is discussed by means of the free energy computed within the lattice-dynamics approach. Our calculations also indicate that all the reported hollow structures are wide band gap semiconductors in the same fashion with their parent’s bulk stable phase. The electronic band structures of these nanoporous structures are finally examined in detail.

Tight junction-associated MARVEL proteins marveld3, tricellulin, and occludin have distinct but overlapping functions.

PubMed

Raleigh, David R; Marchiando, Amanda M; Zhang, Yong; Shen, Le; Sasaki, Hiroyuki; Wang, Yingmin; Long, Manyuan; Turner, Jerrold R

2010-04-01

In vitro studies have demonstrated that occludin and tricellulin are important for tight junction barrier function, but in vivo data suggest that loss of these proteins can be overcome. The presence of a heretofore unknown, yet related, protein could explain these observations. Here, we report marvelD3, a novel tight junction protein that, like occludin and tricellulin, contains a conserved four-transmembrane MARVEL (MAL and related proteins for vesicle trafficking and membrane link) domain. Phylogenetic tree reconstruction; analysis of RNA and protein tissue distribution; immunofluorescent and electron microscopic examination of subcellular localization; characterization of intracellular trafficking, protein interactions, dynamic behavior, and siRNA knockdown effects; and description of remodeling after in vivo immune activation show that marvelD3, occludin, and tricellulin have distinct but overlapping functions at the tight junction. Although marvelD3 is able to partially compensate for occludin or tricellulin loss, it cannot fully restore function. We conclude that marvelD3, occludin, and tricellulin define the tight junction-associated MARVEL protein family. The data further suggest that these proteins are best considered as a group with both redundant and unique contributions to epithelial function and tight junction regulation.

Exploring the effects of cell seeding density on the differentiation of human pluripotent stem cells to brain microvascular endothelial cells.

PubMed

Wilson, Hannah K; Canfield, Scott G; Hjortness, Michael K; Palecek, Sean P; Shusta, Eric V

2015-05-21

Brain microvascular-like endothelial cells (BMECs) derived from human pluripotent stem cells (hPSCs) have significant promise as tools for drug screening and studying the structure and function of the BBB in health and disease. The density of hPSCs is a key factor in regulating cell fate and yield during differentiation. Prior reports of hPSC differentiation to BMECs have seeded hPSCs in aggregates, leading to non-uniform cell densities that may result in differentiation heterogeneity. Here we report a singularized-cell seeding approach compatible with hPSC-derived BMEC differentiation protocols and evaluate the effects of initial hPSC seeding density on the subsequent differentiation, yield, and blood-brain barrier (BBB) phenotype. A range of densities of hPSCs was seeded and differentiated, with the resultant endothelial cell yield quantified via VE-cadherin flow cytometry. Barrier phenotype of purified hPSC-derived BMECs was measured via transendothelial electrical resistance (TEER), and purification protocols were subsequently optimized to maximize TEER. Expression of characteristic vascular markers, tight junction proteins, and transporters was confirmed by immunocytochemistry and quantified by flow cytometry. P-glycoprotein and MRP-family transporter activity was assessed by intracellular accumulation assay. The initial hPSC seeding density of approximately 30,000 cells/cm(2) served to maximize the yield of VE-cadherin+ BMECs per input hPSC. BMECs displayed the highest TEER (>2,000 Ω × cm(2)) within this same range of initial seeding densities, although optimization of the BMEC purification method could minimize the seeding density dependence for some lines. Localization and expression levels of tight junction proteins as well as efflux transporter activity were largely independent of hPSC seeding density. Finally, the utility of the singularized-cell seeding approach was demonstrated by scaling the differentiation and purification process down from 6-well to 96-well culture without impacting BBB phenotype. Given the yield and barrier dependence on initial seeding density, the singularized-cell seeding approach reported here should enhance the reproducibility and scalability of hPSC-derived BBB models, particularly for the application to new pluripotent stem cell lines.

Energy spectrum and electrical conductivity of graphene with a nitrogen impurity

NASA Astrophysics Data System (ADS)

Repetskii, S. P.; Vyshivanaya, I. G.; Skotnikov, V. A.; Yatsenyuk, A. A.

2015-04-01

The electronic structure of graphene with a nitrogen impurity has been studied based on the model of tight binding using exchange-correlation potentials in the density-functional theory. Wave functions of 2 s and 2 p states of neutral noninteracting carbon atoms have been chosen as the basis. When studying the matrix elements of the Hamiltonian, the first three coordination shells have been taken into account. It has been established that the hybridization of electron-energy bands leads to the splitting of the electron energy spectrum near the Fermi level. Due to the overlap of the energy bands, the arising gap behaves as a quasi-gap, in which the density of the electron levels is much lower than in the rest of the spectrum. It has been established that the conductivity of graphene decreases with increasing nitrogen concentration. Since the increase in the nitrogen concentration leads to an increase in the density of states at the Fermi level, the decrease in the conductivity is due to a sharper decrease in the time of relaxation of the electron sates.

Ultrafast semi-metallic layer formation in detonating nitromethane

NASA Astrophysics Data System (ADS)

Reed, Evan; Manaa, M. Riad; Fried, Laurence; Glaesemann, Kurt; Joannopoulos, John

2008-03-01

We present the first quantum molecular dynamics simulations behind a detonation front (up to 0.2 ns) of the explosive nitromethane (CH3NO2) represented by the density-functional-based tight-binding method (DFTB). This simulation is enabled by our recently developed multi-scale shock wave molecular dynamics technique (MSST) that opens the door to longer duration simulations by several orders of magnitude. The electronic density of states around the Fermi energy initially increases as metastable material states are produced but then later decreases, perhaps unexpectedly. These changes indicate that the shock front is characterized by an increase in optical thickness and conductivity followed by a reduction around 100 picoseconds behind the front. We find that a significant population of intermediate metastable molecules are charged and charged species play an important role in the density of states evolution. The transient transformation to a semi-metallic state can be understood within the Anderson picture of metallization.

Theoretical prediction of low-density hexagonal ZnO hollow structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tuoc, Vu Ngoc, E-mail: tuoc.vungoc@hust.edu.vn; Huan, Tran Doan; Thao, Nguyen Thi

2016-10-14

Along with wurtzite and zinc blende, zinc oxide (ZnO) has been found in a large number of polymorphs with substantially different properties and, hence, applications. Therefore, predicting and synthesizing new classes of ZnO polymorphs are of great significance and have been gaining considerable interest. Herein, we perform a density functional theory based tight-binding study, predicting several new series of ZnO hollow structures using the bottom-up approach. The geometry of the building blocks allows for obtaining a variety of hexagonal, low-density nanoporous, and flexible ZnO hollow structures. Their stability is discussed by means of the free energy computed within the lattice-dynamicsmore » approach. Our calculations also indicate that all the reported hollow structures are wide band gap semiconductors in the same fashion with bulk ZnO. The electronic band structures of the ZnO hollow structures are finally examined in detail.« less

DFTB Parameters for the Periodic Table: Part 1, Electronic Structure.

PubMed

Wahiduzzaman, Mohammad; Oliveira, Augusto F; Philipsen, Pier; Zhechkov, Lyuben; van Lenthe, Erik; Witek, Henryk A; Heine, Thomas

2013-09-10

A parametrization scheme for the electronic part of the density-functional based tight-binding (DFTB) method that covers the periodic table is presented. A semiautomatic parametrization scheme has been developed that uses Kohn-Sham energies and band structure curvatures of real and fictitious homoatomic crystal structures as reference data. A confinement potential is used to tighten the Kohn-Sham orbitals, which includes two free parameters that are used to optimize the performance of the method. The method is tested on more than 100 systems and shows excellent overall performance.

Nonlinear susceptibilities of finite conjugated organic polymers

NASA Technical Reports Server (NTRS)

Beratan, David N.; Onuchic, Jose Nelson; Perry, Joseph W.

1987-01-01

Tight-binding calculations of the length dependence of the third-order molecular hyperpolarizability for polyenes and polyynes are reported. The pi-electron wave functions were determined by exploiting the limited translational symmetry of the molecules. Perturbation theory was used to calculate the longitudinal component of the electronic nonresonant hyperpolarizability. This is the first two-'band' calculation of third-order hyperpolarizabilities on finite pi-electron systems of varying length. In contrast to the results of the one-'band' models, the hyperpolarizability densities increase rapidly and then, after about 10-15 repeating units, approach an asymptotic value.

Inorganic nanotubes and fullerenes . Structure and properties of hypothetical phosphorus fullerenes

NASA Astrophysics Data System (ADS)

Seifert, G.; Heine, T.; Fowler, P. W.

The possibility of stable non-carbon fullerenes is discussed for the case of phosphorus fullerene-like cage structures. On the basis of Density Functional Tight Binding calculations it is shown that many such cages correspond to metastable structures, but with increasing nuclearity become less stable with respect to separate molecular P4 units. Stability rules, known for carbon fullerenes, such as the ``isolated pentagon rule'', do not reflect the different electronic and steric requirements of the phosphorus atom. The computational results tend to rule out phosphorus fullerenes.

Intestinal epithelial barrier function and tight junction proteins with heat and exercise

PubMed Central

Zuhl, Micah N.; Moseley, Pope L.

2015-01-01

A single layer of enterocytes and tight junctions (intercellular multiprotein complexes) form the intestinal epithelial barrier that controls transport of molecules through transcellular and paracellular pathways. A dysfunctional or “leaky” intestinal tight junction barrier allows augmented permeation of luminal antigens, endotoxins, and bacteria into the blood stream. Various substances and conditions have been shown to affect the maintenance of the intestinal epithelial tight junction barrier. The primary focus of the present review is to analyze the effects of exertional or nonexertional (passive hyperthermia) heat stress on tight junction barrier function in in vitro and in vivo (animals and humans) models. Our secondary focus is to review changes in tight junction proteins in response to exercise or hyperthermic conditions. Finally, we discuss some pharmacological or nutritional interventions that may affect the cellular mechanisms involved in maintaining homeostasis of the intestinal epithelial tight junction barrier during heat stress or exercise. PMID:26359485

Intestinal epithelial barrier function and tight junction proteins with heat and exercise.

PubMed

Dokladny, Karol; Zuhl, Micah N; Moseley, Pope L

2016-03-15

A single layer of enterocytes and tight junctions (intercellular multiprotein complexes) form the intestinal epithelial barrier that controls transport of molecules through transcellular and paracellular pathways. A dysfunctional or "leaky" intestinal tight junction barrier allows augmented permeation of luminal antigens, endotoxins, and bacteria into the blood stream. Various substances and conditions have been shown to affect the maintenance of the intestinal epithelial tight junction barrier. The primary focus of the present review is to analyze the effects of exertional or nonexertional (passive hyperthermia) heat stress on tight junction barrier function in in vitro and in vivo (animals and humans) models. Our secondary focus is to review changes in tight junction proteins in response to exercise or hyperthermic conditions. Finally, we discuss some pharmacological or nutritional interventions that may affect the cellular mechanisms involved in maintaining homeostasis of the intestinal epithelial tight junction barrier during heat stress or exercise. Copyright © 2016 the American Physiological Society.

Ischemia-reperfusion impairs blood-brain barrier function and alters tight junction protein expression in the ovine fetus

PubMed Central

Chen, Xiaodi; Threlkeld, Steven W.; Cummings, Erin E.; Juan, Ilona; Makeyev, Oleksandr; Besio, Walter G.; Gaitanis, John; Banks, William A.; Sadowska, Grazyna B.; Stonestreet, Barbara S.

2012-01-01

The blood-brain barrier is a restrictive interface between the brain parenchyma and the intravascular compartment. Tight junctions contribute to the integrity of the blood-brain barrier. Hypoxic-ischemic damage to the blood-brain barrier could be an important component of fetal brain injury. We hypothesized that increases in blood-brain barrier permeability after ischemia depend upon the duration of reperfusion and that decreases in tight junction proteins are associated with the ischemia-related impairment in blood-brain barrier function in the fetus. Blood-brain barrier function was quantified with the blood-to-brain transfer constant (Ki) and tight junction proteins by Western immunoblot in fetal sheep at 127 days-of-gestation without ischemia, and 4-, 24-, or 48-h after ischemia. The largest increase in Ki (P<0.05) was 4-h after ischemia. Occludin and claudin-5 expressions decreased at 4-h, but returned toward control levels 24- and 48-h after ischemia. Zonula occludens-1 and -2 decreased after ischemia. Inverse correlations between Ki and tight junction proteins suggest that the decreases in tight junction proteins contribute to impaired blood-brain barrier function after ischemia. We conclude that impaired blood-brain barrier function is an important component of hypoxic-ischemic brain injury in the fetus, and that increases in quantitatively measured barrier permeability (Ki) change as a function of the duration of reperfusion after ischemia. The largest increase in permeability occurs 4-h after ischemia and blood-brain barrier function improves early after injury because the blood-brain barrier is less permeable 24- and 48- than 4-h after ischemia. Changes in the tight junction molecular composition are associated with increases in blood-brain barrier permeability after ischemia. PMID:22986172

Bcc and Fcc transition metals and alloys: a central role for the Jahn-Teller effect in explaining their ideal and distorted structures.

PubMed

Lee, Stephen; Hoffmann, Roald

2002-05-01

Transition metal elements, alloys, and intermetallic compounds often adopt the body centered cubic (bcc) and face centered cubic (fcc) structures. By comparing quantitative density functional with qualitative tight-binding calculations, we analyze the electronic factors which make the bcc and fcc structures energetically favorable. To do so, we develop a tight-binding function, DeltaE(star), a function that measures the energetic effects of transferring electrons within wave vector stars. This function allows one to connect distortions in solids to the Jahn-Teller effect in molecules and to provide an orbital perspective on structure determining deformations in alloys. We illustrate its use by considering first a two-dimensional square net. We then turn to three-dimensional fcc and bcc structures, and distortions of these. Using DeltaE(star), we rationalize the differences in energy of these structures. We are able to deduce which orbitals are responsible for instabilities in seven to nine valence electron per atom (e(-)/a) bcc systems and five and six e(-)/a fcc structures. Finally we demonstrate that these results account for the bcc and fcc type structures found in both the elements and binary intermetallic compounds of group 4 through 9 transition metal atoms. The outline of a theory of metal structure deformations based on loss of point group operation rather than translational symmetry is presented.

Stability and electronic properties of oxygen-doped ZnS polytypes: DFTB study

NASA Astrophysics Data System (ADS)

Popov, Ilya S.; Vorokh, Andrey S.; Enyashin, Andrey N.

2018-06-01

Synthesis from aqueous solutions is an affordable method for fabrication of II-VI semiconductors. However, application of this method often imposes a disorder of crystal lattice, manifesting as a rich variety of polytypes arising from wurtzite and zinc blende phases. The origin of this disordering still remains debatable. Here, the influence of the most likely impurity at water environment - substitutional oxygen - on the polytypic equilibrium of zinc sulphide is studied by means of density-functional tight-binding method. According to calculations, the inclusion of such oxygen does not affect the polytypic equilibrium. Apart of thermodynamic stability, the electronic and elastic properties of ZnS polytypes are studied as the function of oxygen distribution.

A proposed simulation method for directed self-assembly of nanographene

NASA Astrophysics Data System (ADS)

Geraets, J. A.; Baldwin, J. P. C.; Twarock, R.; Hancock, Y.

2017-09-01

A methodology for predictive kinetic self-assembly modeling of bottom-up chemical synthesis of nanographene is proposed. The method maintains physical transparency in using a novel array format to efficiently store molecule information and by using array operations to determine reaction possibilities. Within a minimal model approach, the parameter space for the bond activation energies (i.e. molecule functionalization) at fixed reaction temperature and initial molecule concentrations is explored. Directed self-assembly of nanographene from functionalized tetrabenzanthracene and benzene is studied with regions in the activation energy phase-space showing length-to-width ratio tunability. The degree of defects and reaction reproducibility in the simulations is also determined, with the rate of functionalized benzene addition providing additional control of the dimension and quality of the nanographene. Comparison of the reaction energetics to available density functional theory data suggests the synthesis may be experimentally tenable using aryl-halide cross-coupling and noble metal surface-assisted catalysis. With full access to the intermediate reaction network and with dynamic coupling to density functional theory-informed tight-binding simulation, the method is proposed as a computationally efficient means towards detailed simulation-driven design of new nanographene systems.

Micro-structure and Air-tightness of Squeeze Casting Motor housing for New Energy Vehicle

NASA Astrophysics Data System (ADS)

Jiang, Y. F.; Kang, Z. Q.; Jiang, W. F.; Wang, K. W.; Sha, D. L.; Li, M. L.; Sun, J.

2018-05-01

In order to improve the performance of automobile parts, the influence of squeeze casting process parameters on casting defects, material structure and air-tightness of aluminum alloy motor housing for new energy vehicle was studied. The results show that the density of the castings increases with the increase in pressure and mold temperature. With increase in pouring temperature, it increases first and then decreases. Pressure has the greatest influence on the density of the castings. Under a certain pressure, with moderate increase in casting temperature and mold temperature, the grain growth begins to increase; the dendrites become less, the new α - Al grains are spherical and granular, the micro-structure is uniform. Also, with increase in pressure, this effect is more pronounced, the air-tightness of castings improve. In conclusion, when the pressure is 110MPa, pouring temperature is 680° C, mold temperature is 280° C, pressure holding for 30s, and punch speed of 0.1m/s, there is no clear shrinkage in the casting, the structure is uniform, the qualified rate of air-tightness of production reaches 86%, and the performance is excellent.

SOLPS modeling of the effect on plasma detachment of closing the lower divertor in DIII-D

DOE PAGES

Sang, C. F.; Stangeby, P. C.; Guo, H. Y.; ...

2016-12-15

SOLPS modeling has been carried out to assess the effect of tightly closing the lower divertor in DIII-D, which at present is almost fully open, on the achievement of cold dissipative/detached divertor conditions. To isolate the impact of other factors on the divertor plasma solution and to make direct comparisons, most of the parameters including the meshes were kept as similar as possible. Only the neutral baffling was modified to compare a fully open divertor with a tightly closed one. The modeling shows that the tightly closed divertor greatly improves trapping of recycling neutrals, thereby increasing radiative and charge exchangemore » losses in the divertor and reducing the electron temperature T et and deposited power density q dep at the target plate. Furthermore, the closed structure enables the divertor plasma to enter into highly dissipative and detached divertor conditions at a significantly lower upstream density. The effects of divertor closure on the neutral density and pressure, and their correlation with the divertor plasma conditions are also demonstrated. The effect of molecular D 2- ion D + elastic collisions and neutral-neutral collisions on the divertor plasma solution are assessed.« less

Impact of Donor Age on Corneal Endothelium-Descemet Membrane Layer Scroll Formation

PubMed Central

Bennett, Adam; Mahmoud, Shahira; Drury, Donna; Cavanagh, H. Dwight; McCulley, James P.; Petroll, W. Matthew; Mootha, V. Vinod

2014-01-01

Objectives To correlate corneal endothelium-Descemet membrane layer (EDM) parameters of scroll tightness with donor age, endothelial cell density, and history of diabetes. Methods EDM scrolls were harvested from 26 corneoscleral buttons using the SCUBA technique by a cornea-fellowship trained ophthalmologist masked to donor age. Two independent outcome parameters were used to characterize the scrolling severity of successfully harvested tissue: scroll width and tendency for EDM scroll formation (referred to as scroll rating on a 1 to 4 scale: incomplete scroll formation to tightly-scrolled). Results Mean donor age was 59 ± 17years (15–69). Mean endothelial cell density of EDM scroll was 2451 ± 626 cells/mm2 mm (range: 1307 – 3195). Using stepwise linear regression, a significant correlation was found between scroll width and donor age (R = 0.497, P < 0.05). Additionally, a significant inverse correlation was found between scroll width and endothelial cell density (R = −0.605, P < 0.05). There was no statistically significant correlation between a donor history of diabetes and the parameters of scrolling tendency. Conclusions Our data suggests that using older donors reduces EDM scroll tightness. PMID:25603436

The ZO-1–associated Y-box factor ZONAB regulates epithelial cell proliferation and cell density

PubMed Central

Balda, Maria S.; Garrett, Michelle D.; Matter, Karl

2003-01-01

Epithelial tight junctions regulate paracellular permeability, restrict apical/basolateral intramembrane diffusion of lipids, and have been proposed to participate in the control of epithelial cell proliferation and differentiation. Previously, we have identified ZO-1–associated nucleic acid binding proteins (ZONAB), a Y-box transcription factor whose nuclear localization and transcriptional activity is regulated by the tight junction–associated candidate tumor suppressor ZO-1. Now, we found that reduction of ZONAB expression using an antisense approach or by RNA interference strongly reduced proliferation of MDCK cells. Transfection of wild-type or ZONAB-binding fragments of ZO-1 reduced proliferation as well as nuclear ZONAB pools, indicating that promotion of proliferation by ZONAB requires its nuclear accumulation. Overexpression of ZONAB resulted in increased cell density in mature monolayers, and depletion of ZONAB or overexpression of ZO-1 reduced cell density. ZONAB was found to associate with cell division kinase (CDK) 4, and reduction of nuclear ZONAB levels resulted in reduced nuclear CDK4. Thus, our data indicate that tight junctions can regulate epithelial cell proliferation and cell density via a ZONAB/ZO-1–based pathway. Although this regulatory process may also involve regulation of transcription by ZONAB, our data suggest that one mechanism by which ZONAB and ZO-1 influence proliferation is by regulating the nuclear accumulation of CDK4. PMID:12566432

A local leaky-box model for the local stellar surface density-gas surface density-gas phase metallicity relation

NASA Astrophysics Data System (ADS)

Zhu, Guangtun Ben; Barrera-Ballesteros, Jorge K.; Heckman, Timothy M.; Zakamska, Nadia L.; Sánchez, Sebastian F.; Yan, Renbin; Brinkmann, Jonathan

2017-07-01

We revisit the relation between the stellar surface density, the gas surface density and the gas-phase metallicity of typical disc galaxies in the local Universe with the SDSS-IV/MaNGA survey, using the star formation rate surface density as an indicator for the gas surface density. We show that these three local parameters form a tight relationship, confirming previous works (e.g. by the PINGS and CALIFA surveys), but with a larger sample. We present a new local leaky-box model, assuming star-formation history and chemical evolution is localized except for outflowing materials. We derive closed-form solutions for the evolution of stellar surface density, gas surface density and gas-phase metallicity, and show that these parameters form a tight relation independent of initial gas density and time. We show that, with canonical values of model parameters, this predicted relation match the observed one well. In addition, we briefly describe a pathway to improving the current semi-analytic models of galaxy formation by incorporating the local leaky-box model in the cosmological context, which can potentially explain simultaneously multiple properties of Milky Way-type disc galaxies, such as the size growth and the global stellar mass-gas metallicity relation.

Polymer adsorption on silica and wettability of graphene oxide surfaces, experiments and simulations

NASA Astrophysics Data System (ADS)

Mortazavian, Hamid

Among the various classifications of polymer composites, studying polymers adsorbed to a surface such as silica is important due to their numerous applications. Adsorbed polymers usually show different properties than their bulk counterparts due to their interactions with the surface. In this study, we observed tightly- and loosely-bound polymer and mobile components in poly(vinyl acetate) (PVAc) on silica both with temperature-modulated differential scanning calorimetry (TMDSC) experiments and computer simulations. The more-mobile component which correlated to the region of low density at the air interface is reported for the first time using TMDSC thermograms. Pore size distribution and pore volume development of adsorbed PMMA samples showed different behavior below and above the tightly-bound amount of the polymer. The amount of tightly-bound polymer was obtained by a linear regression analysis of the ratio of the area under the two glass transitions. The values obtained vary from 0.52 to 0.86 mg PVAc/m2 silica depending upon the molecular mass for the amounts of PVAc and the specific surface area of fumed silica. Direct comparisons of the thermal properties and intermolecular interactions were performed between PVAc and poly(methyl methacrylate) (PMMA) with similar molecular masses and adsorbed amounts on silica. A larger amount of tightly-bound polymer and a greater change in glass transition were observed for adsorbed PMMA compared to adsorbed PVAc. These observations suggested that the interactions between PMMA and silica were stronger than those between PVAc and silica. Molecular modeling of these surface polymers showed that PMMA associates more strongly with silica than does PVAc through additional hydrogen-bonding interactions. Graphene oxide (GO) material surface characteristics make it easy to functionalize, making it a water repellant surface. To test the effect of chemical makeup and size of attached groups on the surface wettability of GO, we performed experimental water contact angle measurements and molecular modeling investigations on functionalized GO surfaces. Experimental and molecular simulation water contact angle measurements showed quantitative agreement for functionalizing groups with the same chain length at a variety of surface coverages.

Actinide electronic structure and atomic forces

NASA Astrophysics Data System (ADS)

Albers, R. C.; Rudin, Sven P.; Trinkle, Dallas R.; Jones, M. D.

2000-07-01

We have developed a new method[1] of fitting tight-binding parameterizations based on functional forms developed at the Naval Research Laboratory.[2] We have applied these methods to actinide metals and report our success using them (see below). The fitting procedure uses first-principles local-density-approximation (LDA) linear augmented plane-wave (LAPW) band structure techniques[3] to first calculate an electronic-structure band structure and total energy for fcc, bcc, and simple cubic crystal structures for the actinide of interest. The tight-binding parameterization is then chosen to fit the detailed energy eigenvalues of the bands along symmetry directions, and the symmetry of the parameterization is constrained to agree with the correct symmetry of the LDA band structure at each eigenvalue and k-vector that is fit to. By fitting to a range of different volumes and the three different crystal structures, we find that the resulting parameterization is robust and appears to accurately calculate other crystal structures and properties of interest.

New lessons from the H I size-mass relation of galaxies

NASA Astrophysics Data System (ADS)

Wang, Jing; Koribalski, Bärbel S.; Serra, Paolo; van der Hulst, Thijs; Roychowdhury, Sambit; Kamphuis, Peter; Chengalur, Jayaram N.

2016-08-01

We revisit the H I size-mass (D_{H I}-MH I) relation of galaxies with a sample of more than 500 nearby galaxies covering over five orders of magnitude in H I mass and more than 10 B-band magnitudes. The relation is remarkably tight with a scatter σ ˜ 0.06 dex, or 14 per cent. The scatter does not change as a function of galaxy luminosity, H I richness or morphological type. The relation is linked to the fact that dwarf and spiral galaxies have a homogeneous radial profile of H I surface density in the outer regions when the radius is normalized by DH I. The early-type disc galaxies typically have shallower H I radial profiles, indicating a different gas accretion history. We argue that the process of atomic-to-molecular gas conversion or star formation cannot explain the tightness of the DH I-MH I relation. This simple relation puts strong constraints on simulation models for galaxy formation.

Instability of superfluid Fermi gases induced by a rotonlike density mode in optical lattices

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yunomae, Yoshihiro; Yamamoto, Daisuke; Danshita, Ippei

2009-12-15

We study the stability of superfluid Fermi gases in deep optical lattices in the BCS-Bose-Einstein condensation (BEC) crossover at zero temperature. Within the tight-binding attractive Hubbard model, we calculate the spectrum of the low-energy Anderson-Bogoliubov (AB) mode as well as the single-particle excitations in the presence of superfluid flow in order to determine the critical velocities. To obtain the spectrum of the AB mode, we calculate the density response function in the generalized random-phase approximation applying the Green's function formalism developed by Cote and Griffin to the Hubbard model. We find that the spectrum of the AB mode is separatedmore » from the particle-hole continuum having the characteristic rotonlike minimum at short wavelength due to the strong charge-density-wave fluctuations. The energy of the rotonlike minimum decreases with increasing the lattice velocity and it reaches zero at the critical velocity which is smaller than the pair-breaking velocity. This indicates that the superfluid state is energetically unstable due to the spontaneous emission of the short-wavelength rotonlike excitations of the AB mode instead due to pair breaking. We determine the critical velocities as functions of the interaction strength across the BCS-BEC crossover regime.« less

Multi-level molecular modelling for plasma medicine

NASA Astrophysics Data System (ADS)

Bogaerts, Annemie; Khosravian, Narjes; Van der Paal, Jonas; Verlackt, Christof C. W.; Yusupov, Maksudbek; Kamaraj, Balu; Neyts, Erik C.

2016-02-01

Modelling at the molecular or atomic scale can be very useful for obtaining a better insight in plasma medicine. This paper gives an overview of different atomic/molecular scale modelling approaches that can be used to study the direct interaction of plasma species with biomolecules or the consequences of these interactions for the biomolecules on a somewhat longer time-scale. These approaches include density functional theory (DFT), density functional based tight binding (DFTB), classical reactive and non-reactive molecular dynamics (MD) and united-atom or coarse-grained MD, as well as hybrid quantum mechanics/molecular mechanics (QM/MM) methods. Specific examples will be given for three important types of biomolecules, present in human cells, i.e. proteins, DNA and phospholipids found in the cell membrane. The results show that each of these modelling approaches has its specific strengths and limitations, and is particularly useful for certain applications. A multi-level approach is therefore most suitable for obtaining a global picture of the plasma-biomolecule interactions.

Effects of oxidation on the plasmonic properties of aluminum nanoclusters.

PubMed

Douglas-Gallardo, Oscar A; Soldano, Germán J; Mariscal, Marcelo M; Sánchez, Cristián Gabriel

2017-11-16

The scouting of alternative plasmonic materials able to enhance and extend the optical properties of noble metal nanostructures is on the rise. Aluminum is endowed with a set of interesting properties which turn it into an attractive plasmonic material. Here we present the optical and electronic features of different aluminum nanostructures stemming from a multilevel computational study. Molecular Dynamics (MD) simulations using a reactive force field (ReaxFF), carefully validated with Density Functional Theory (DFT), were employed to mimic the oxidation of icosahedral aluminum nanoclusters. Resulting structures with different oxidation degrees were then studied through the Time-Dependent Density Functional Tight Binding (TD-DFTB) method. A similar approach was used in aluminum nanoclusters with a disordered structure to study how the loss of crystallinity affects the optical properties. To the best of our knowledge, this is the first report that addresses this issue from the fully atomistic time-dependent approach by means of two different and powerful simulation tools able to describe quantum and physicochemical properties associated with nanostructured particles.

Negative differential resistance and effect of defects and deformations in MoS{sub 2} armchair nanoribbon metal-oxide-semiconductor field effect transistor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sengupta, Amretashis, E-mail: amretashis@dese.iisc.ernet.in; Mahapatra, Santanu

In this work, we present a study on the negative differential resistance (NDR) behavior and the impact of various deformations (like ripple, twist, wrap) and defects like vacancies and edge roughness on the electronic properties of short-channel MoS{sub 2} armchair nanoribbon MOSFETs. The effect of deformation (3°–7° twist or wrap and 0.3–0.7 Å ripple amplitude) and defects on a 10 nm MoS2 ANR FET is evaluated by the density functional tight binding theory and the non-equilibrium Green's function approach. We study the channel density of states, transmission spectra, and the I{sub D}–V{sub D} characteristics of such devices under the varying conditions, withmore » focus on the NDR behavior. Our results show significant change in the NDR peak to valley ratio and the NDR window with such minor intrinsic deformations, especially with the ripple.« less

QM/QM approach to model energy disorder in amorphous organic semiconductors.

PubMed

Friederich, Pascal; Meded, Velimir; Symalla, Franz; Elstner, Marcus; Wenzel, Wolfgang

2015-02-10

It is an outstanding challenge to model the electronic properties of organic amorphous materials utilized in organic electronics. Computation of the charge carrier mobility is a challenging problem as it requires integration of morphological and electronic degrees of freedom in a coherent methodology and depends strongly on the distribution of polaron energies in the system. Here we represent a QM/QM model to compute the polaron energies combining density functional methods for molecules in the vicinity of the polaron with computationally efficient density functional based tight binding methods in the rest of the environment. For seven widely used amorphous organic semiconductor materials, we show that the calculations are accelerated up to 1 order of magnitude without any loss in accuracy. Considering that the quantum chemical step is the efficiency bottleneck of a workflow to model the carrier mobility, these results are an important step toward accurate and efficient disordered organic semiconductors simulations, a prerequisite for accelerated materials screening and consequent component optimization in the organic electronics industry.

The X3LYP extended density functional accurately describes H-bonding but fails completely for stacking.

PubMed

Cerný, Jirí; Hobza, Pavel

2005-04-21

The performance of the recently introduced X3LYP density functional which was claimed to significantly improve the accuracy for H-bonded and van der Waals complexes was tested for extended H-bonded and stacked complexes (nucleic acid base pairs and amino acid pairs). In the case of planar H-bonded complexes (guanine...cytosine, adenine...thymine) the DFT results nicely agree with accurate correlated ab initio results. For the stacked pairs (uracil dimer, cytosine dimer, adenine...thymine and guanine...cytosine) the DFT fails completely and it was even not able to localize any minimum at the stacked subspace of the potential energy surface. The geometry optimization of all these stacked clusters leads systematically to the planar H-bonded pairs. The amino acid pairs were investigated in the crystal geometry. DFT again strongly underestimates the accurate correlated ab initio stabilization energies and usually it was not able to describe the stabilization of a pair. The X3LYP functional thus behaves similarly to other current functionals. Stacking of nucleic acid bases as well as interaction of amino acids was described satisfactorily by using the tight-binding DFT method, which explicitly covers the London dispersion energy.

The role of adequate reference materials in density measurements in hemodialysis

NASA Astrophysics Data System (ADS)

Furtado, A.; Moutinho, J.; Moura, S.; Oliveira, F.; Filipe, E.

2015-02-01

In hemodialysis, oscillation-type density meters are used to measure the density of the acid component of the dialysate solutions used in the treatment of kidney patients. An incorrect density determination of this solution used in hemodialysis treatments can cause several and adverse events to patients. Therefore, despite the Fresenius Medical Care (FME) tight control of the density meters calibration results, this study shows the benefits of mimic the matrix usually measured to produce suitable reference materials for the density meter calibrations.

Ischemia-reperfusion impairs blood-brain barrier function and alters tight junction protein expression in the ovine fetus.

PubMed

Chen, X; Threlkeld, S W; Cummings, E E; Juan, I; Makeyev, O; Besio, W G; Gaitanis, J; Banks, W A; Sadowska, G B; Stonestreet, B S

2012-12-13

The blood-brain barrier is a restrictive interface between the brain parenchyma and the intravascular compartment. Tight junctions contribute to the integrity of the blood-brain barrier. Hypoxic-ischemic damage to the blood-brain barrier could be an important component of fetal brain injury. We hypothesized that increases in blood-brain barrier permeability after ischemia depend upon the duration of reperfusion and that decreases in tight junction proteins are associated with the ischemia-related impairment in blood-brain barrier function in the fetus. Blood-brain barrier function was quantified with the blood-to-brain transfer constant (K(i)) and tight junction proteins by Western immunoblot in fetal sheep at 127 days of gestation without ischemia, and 4, 24, or 48 h after ischemia. The largest increase in K(i) (P<0.05) was 4 h after ischemia. Occludin and claudin-5 expressions decreased at 4 h, but returned toward control levels 24 and 48 h after ischemia. Zonula occludens-1 and -2 decreased after ischemia. Inverse correlations between K(i) and tight junction proteins suggest that the decreases in tight junction proteins contribute to impaired blood-brain barrier function after ischemia. We conclude that impaired blood-brain barrier function is an important component of hypoxic-ischemic brain injury in the fetus, and that increases in quantitatively measured barrier permeability (K(i)) change as a function of the duration of reperfusion after ischemia. The largest increase in permeability occurs 4 h after ischemia and blood-brain barrier function improves early after injury because the blood-brain barrier is less permeable 24 and 48 than 4 h after ischemia. Changes in the tight junction molecular composition are associated with increases in blood-brain barrier permeability after ischemia. Copyright © 2012 IBRO. Published by Elsevier Ltd. All rights reserved.

Combined first-principles and model Hamiltonian study of the perovskite series R MnO 3 (R =La ,Pr ,Nd ,Sm ,Eu , and Gd )

NASA Astrophysics Data System (ADS)

Kováčik, Roman; Murthy, Sowmya Sathyanarayana; Quiroga, Carmen E.; Ederer, Claude; Franchini, Cesare

2016-02-01

We merge advanced ab initio schemes (standard density functional theory, hybrid functionals, and the G W approximation) with model Hamiltonian approaches (tight-binding and Heisenberg Hamiltonian) to study the evolution of the electronic, magnetic, and dielectric properties of the manganite family R MnO3 (R =La,Pr,Nd,Sm,Eu, and Gd) . The link between first principles and tight binding is established by downfolding the physically relevant subset of 3 d bands with eg character by means of maximally localized Wannier functions (MLWFs) using the VASP2WANNIER90 interface. The MLWFs are then used to construct a general tight-binding Hamiltonian written as a sum of the kinetic term, the Hund's rule coupling, the JT coupling, and the electron-electron interaction. The dispersion of the tight-binding (TB) eg bands at all levels are found to match closely the MLWFs. We provide a complete set of TB parameters which can serve as guidance for the interpretation of future studies based on many-body Hamiltonian approaches. In particular, we find that the Hund's rule coupling strength, the Jahn-Teller coupling strength, and the Hubbard interaction parameter U remain nearly constant for all the members of the R MnO3 series, whereas the nearest-neighbor hopping amplitudes show a monotonic attenuation as expected from the trend of the tolerance factor. Magnetic exchange interactions, computed by mapping a large set of hybrid functional total energies onto an Heisenberg Hamiltonian, clarify the origin of the A-type magnetic ordering observed in the early rare-earth manganite series as arising from a net negative out-of-plane interaction energy. The obtained exchange parameters are used to estimate the Néel temperature by means of Monte Carlo simulations. The resulting data capture well the monotonic decrease of the ordering temperature down the series from R =La to Gd, in agreement with experiments. This trend correlates well with the modulation of structural properties, in particular with the progressive reduction of the Mn-O-Mn bond angle which is associated with the quenching of the volume and the decrease of the tolerance factor due to the shrinkage of the ionic radii of R going from La to Gd.

In-surface confinement of topological insulator nanowire surface states

NASA Astrophysics Data System (ADS)

Chen, Fan W.; Jauregui, Luis A.; Tan, Yaohua; Manfra, Michael; Klimeck, Gerhard; Chen, Yong P.; Kubis, Tillmann

2015-09-01

The bandstructures of [110] and [001] Bi2Te3 nanowires are solved with the atomistic 20 band tight binding functionality of NEMO5. The theoretical results reveal: The popular assumption that all topological insulator (TI) wire surfaces are equivalent is inappropriate. The Fermi velocity of chemically distinct wire surfaces differs significantly which creates an effective in-surface confinement potential. As a result, topological insulator surface states prefer specific surfaces. Therefore, experiments have to be designed carefully not to probe surfaces unfavorable to the surface states (low density of states) and thereby be insensitive to the TI-effects.

Electronic properties of long DNA nanowires in dry and wet conditions

NASA Astrophysics Data System (ADS)

Mousavi, Hamze; Khodadadi, Jabbar; Grabowski, Marek

2015-11-01

The electronic behavior of the long disordered DNA nanowires in both dry and wet conditions is investigated through the band structure and density of states of a tight-binding Hamiltonian model for π-electrons of the backbone, using Green's functions approach. For a chosen set of parameters in the dry case, semiconducting behavior is reproduced. It is also shown that for sufficiently long strands, the order of the base pairs has no noticeable effect on the energy band-gap. Moreover, this semiconducting duplex shows metallic tendencies when interacting with the environment of polar molecules.

Understanding the electronic structure of CdSe quantum dot-fullerene (C{sub 60}) hybrid nanostructure for photovoltaic applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sarkar, Sunandan; Rajbanshi, Biplab; Sarkar, Pranab, E-mail: pranab.sarkar@visva-bharati.ac.in

2014-09-21

By using the density-functional tight binding method, we studied the electronic structure of CdSe quantum dot(QD)-buckminsterfullerene (C{sub 60}) hybrid systems as a function of both the size of the QD and concentration of the fullerene molecule. Our calculation reveals that the lowest unoccupied molecular orbital energy level of the hybrid CdSeQD-C{sub 60} systems lies on the fullerene moiety, whereas the highest occupied molecular orbital (HOMO) energy level lies either on the QD or the fullerene depending on size of the CdSe QD. We explored the possibility of engineering the energy level alignment by varying the size of the CdSe QD.more » With increase in size of the QD, the HOMO level is shifted upward and crosses the HOMO level of the C{sub 60}-thiol molecule resulting transition from the type-I to type-II band energy alignment. The density of states and charge density plot support these types of band gap engineering of the CdSe-C{sub 60} hybrid systems. This type II band alignment indicates the possibility of application of this nanohybrid for photovoltaic purpose.« less

DOS cones along atomic chains

NASA Astrophysics Data System (ADS)

Kwapiński, Tomasz

2017-03-01

The electron transport properties of a linear atomic chain are studied theoretically within the tight-binding Hamiltonian and the Green’s function method. Variations of the local density of states (DOS) along the chain are investigated. They are crucial in scanning tunnelling experiments and give important insight into the electron transport mechanism and charge distribution inside chains. It is found that depending on the chain parity the local DOS at the Fermi level can form cone-like structures (DOS cones) along the chain. The general condition for the local DOS oscillations is obtained and the linear behaviour of the local density function is confirmed analytically. DOS cones are characterized by a linear decay towards the chain which is in contrast to the propagation properties of charge density waves, end states and Friedel oscillations in one-dimensional systems. We find that DOS cones can appear due to non-resonant electron transport, the spin-orbit scattering or for chains fabricated on a substrate with localized electrons. It is also shown that for imperfect chains (e.g. with a reduced coupling strength between two neighboring sites) a diamond-like structure of the local DOS along the chain appears.

Magnetic field effects on charge structure factors of gapped graphene structure

NASA Astrophysics Data System (ADS)

Rezania, Hamed; Tawoose, Nasrin

2018-02-01

We present the behaviors of dynamical and static charge susceptibilities of undoped gapped graphene using the Green's function approach in the context of tight binding model Hamiltonian. Specially, the effects of magnetic field on the plasmon modes of gapped graphene structure are investigated via calculating correlation function of charge density operators. Our results show the increase of magnetic field leads to disappear high frequency plasmon mode for gapped case. We also show that low frequency plasmon mode has not affected by increase of magnetic field and chemical potential. Finally the temperature dependence of static charge structure factor of gapp graphene structure is studied. The effects of both magnetic field and gap parameter on the static structure factor are discusses in details.

Quasiparticle Energies and Band Gaps in Graphene Nanoribbons

NASA Astrophysics Data System (ADS)

Yang, Li; Park, Cheol-Hwan; Son, Young-Woo; Cohen, Marvin L.; Louie, Steven G.

2007-11-01

We present calculations of the quasiparticle energies and band gaps of graphene nanoribbons (GNRs) carried out using a first-principles many-electron Green’s function approach within the GW approximation. Because of the quasi-one-dimensional nature of a GNR, electron-electron interaction effects due to the enhanced screened Coulomb interaction and confinement geometry greatly influence the quasiparticle band gap. Compared with previous tight-binding and density functional theory studies, our calculated quasiparticle band gaps show significant self-energy corrections for both armchair and zigzag GNRs, in the range of 0.5 3.0 eV for ribbons of width 2.4 0.4 nm. The quasiparticle band gaps found here suggest that use of GNRs for electronic device components in ambient conditions may be viable.

Paracellular tightness and the functional expression of efflux transporters P-gp and BCRP in bEnd3 cells.

PubMed

Yang, Shu; Jin, Hong; Zhao, Zhigang

2018-04-23

Objective The blood-brain barrier (BBB), regulating brain homeostasis and limiting the entry of most drugs, is characterized by intercellular tight junctions and the presence of transporters. In this study, the paracellular tightness and functional expression of efflux transporters P-glycoprotein (P-gp) and breast cancer resistance protein (BCRP) were evaluated in mouse brain immortalized cell line bEnd3 to prove it as a useful BBB-mimicking system for biological and pharmacological research. Methods The presence of P-gp, BCRP and tight junction proteins occludin, claudin-5 and ZO-1 were validated by RT-PCR and Western blot. The tightness of bEnd3 monolayers was evaluated by measuring the permeability of hydrophilic marker Lucifer yellow. The P-gp functionality was identified by intracellular uptake assay using Rhodamine 123 (R123) as P-gp substrate and verapamil as P-gp inhibitor. The BCRP functionality was identified by flow cytometric analysis of mitoxantrone accumulation and fluorescence microscopic analysis of Hoechst 33342 accumulation using Ko-143 as BCRP inhibitor. Results The bEnd3 cells demonstrated the expression of P-gp, BCRP and tight junction proteins occludin, claudin-5 and ZO-1 at mRNA and protein levels. The permeability coefficient of Lucifer yellow was 1.3 ± 0.13 × 10 -3  cm/min, indicating the moderate paracellular tightness barrier formed by bEnd3 cells. The verapamil induced a higher cellular uptake of Rhodamine 123, and Ko-143 significantly elevated cellular accumulation of mitoxantrone and Hoechst 33342, suggesting the P-gp and BCRP functionality shown by bEnd3 cells. Conclusions The bEnd3 cell line represents a useful in vitro tool for studying BBB characteristics and drug transport mechanisms at the BBB.

Time-dependent quantum transport: An efficient method based on Liouville-von-Neumann equation for single-electron density matrix

NASA Astrophysics Data System (ADS)

Xie, Hang; Jiang, Feng; Tian, Heng; Zheng, Xiao; Kwok, Yanho; Chen, Shuguang; Yam, ChiYung; Yan, YiJing; Chen, Guanhua

2012-07-01

Basing on our hierarchical equations of motion for time-dependent quantum transport [X. Zheng, G. H. Chen, Y. Mo, S. K. Koo, H. Tian, C. Y. Yam, and Y. J. Yan, J. Chem. Phys. 133, 114101 (2010), 10.1063/1.3475566], we develop an efficient and accurate numerical algorithm to solve the Liouville-von-Neumann equation. We solve the real-time evolution of the reduced single-electron density matrix at the tight-binding level. Calculations are carried out to simulate the transient current through a linear chain of atoms, with each represented by a single orbital. The self-energy matrix is expanded in terms of multiple Lorentzian functions, and the Fermi distribution function is evaluated via the Padè spectrum decomposition. This Lorentzian-Padè decomposition scheme is employed to simulate the transient current. With sufficient Lorentzian functions used to fit the self-energy matrices, we show that the lead spectral function and the dynamics response can be treated accurately. Compared to the conventional master equation approaches, our method is much more efficient as the computational time scales cubically with the system size and linearly with the simulation time. As a result, the simulations of the transient currents through systems containing up to one hundred of atoms have been carried out. As density functional theory is also an effective one-particle theory, the Lorentzian-Padè decomposition scheme developed here can be generalized for first-principles simulation of realistic systems.

Ab initio molecular dynamics with nuclear quantum effects at classical cost: Ring polymer contraction for density functional theory.

PubMed

Marsalek, Ondrej; Markland, Thomas E

2016-02-07

Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding as a reference system, we show that our ring polymer contraction scheme gives rapid and systematic convergence to the full path integral density functional theory result. We demonstrate the efficiency of this approach in ab initio simulations of liquid water and the reactive protonated and deprotonated water dimer systems. We find that the vast majority of the nuclear quantum effects are accurately captured using contraction to just the ring polymer centroid, which requires the same number of density functional theory calculations as a classical simulation. Combined with a multiple time step scheme using the same reference system, which allows the time step to be increased, this approach is as fast as a typical classical ab initio molecular dynamics simulation and 35× faster than a full path integral calculation, while still exactly including the quantum sampling of nuclei. This development thus offers a route to routinely include nuclear quantum effects in ab initio molecular dynamics simulations at negligible computational cost.

Bile duct epithelial tight junctions and barrier function

PubMed Central

Rao, R.K.; Samak, G.

2013-01-01

Bile ducts play a crucial role in the formation and secretion of bile as well as excretion of circulating xenobiotic substances. In addition to its secretory and excretory functions, bile duct epithelium plays an important role in the formation of a barrier to the diffusion of toxic substances from bile into the hepatic interstitial tissue. Disruption of barrier function and toxic injury to liver cells appear to be involved in the pathogenesis of a variety of liver diseases such as primary sclerosing cholangitis, primary biliary cirrhosis and cholangiocarcinoma. Although the investigations into understanding the structure and regulation of tight junctions in gut, renal and endothelial tissues have expanded rapidly, very little is known about the structure and regulation of tight junctions in the bile duct epithelium. In this article we summarize the current understanding of physiology and pathophysiology of bile duct epithelium, the structure and regulation of tight junctions in canaliculi and bile duct epithelia and different mechanisms involved in the regulation of disruption and protection of bile duct epithelial tight junctions. This article will make a case for the need of future investigations toward our understanding of molecular organization and regulation of canalicular and bile duct epithelial tight junctions. PMID:24665411

Band gap engineering in finite elongated graphene nanoribbon heterojunctions: Tight-binding model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tayo, Benjamin O.

2015-08-15

A simple model based on the divide and conquer rule and tight-binding (TB) approximation is employed for studying the role of finite size effect on the electronic properties of elongated graphene nanoribbon (GNR) heterojunctions. In our model, the GNR heterojunction is divided into three parts: a left (L) part, middle (M) part, and right (R) part. The left part is a GNR of width W{sub L}, the middle part is a GNR of width W{sub M}, and the right part is a GNR of width W{sub R}. We assume that the left and right parts of the GNR heterojunction interactmore » with the middle part only. Under this approximation, the Hamiltonian of the system can be expressed as a block tridiagonal matrix. The matrix elements of the tridiagonal matrix are computed using real space nearest neighbor orthogonal TB approximation. The electronic structure of the GNR heterojunction is analyzed by computing the density of states. We demonstrate that for heterojunctions for which W{sub L} = W{sub R}, the band gap of the system can be tuned continuously by varying the length of the middle part, thus providing a new approach to band gap engineering in GNRs. Our TB results were compared with calculations employing divide and conquer rule in combination with density functional theory (DFT) and were found to agree nicely.« less

First-principles simulation and low-energy effective modeling of three-dimensional skyrmion in MnGe

NASA Astrophysics Data System (ADS)

Choi, Hongchul; Tai, Yuan-Yen; Zhu, Jian-Xin; T-4 Team

The skyrmion spin textures are mostly observed in two-dimensional (2D) space, which can be topologically mapped onto the surface of the sphere with an integer multiple of topological winding number. Recently, MnGe has been reported as a candidate of 3D skyrmion crystal, showing the variation of the skyrmion size along the z-direction. We have performed the first-principles simulation and constructed a tight-binding model with calculated electronic-structure information to investigate the 3D skyrmion phase in MnGe. Our first-principles study within density functional theory shows that the calculated magnetic moment is larger than that for MnSi (with different lattice constant), implying the possibility of a multiple magnetic transition under pressure. We have also found that the small-sized skyrmion could be stabilized in a 2D structure. Such a high density of the skyrmion is in good agreement with the experimental finding of large topological Hall effect. Finally, we will extend our study to consider the 3D skyrmion structure based on the constructed tight-binding model. This work was carried out under the auspices of the National Nuclear Security Administration of the U.S. Department of Energy at Los Alamos National Laboratory (LANL) under Contract No. DE-AC52-06NA25396, and was supported by the LANL LDRD Program.

The construction of a high-density linkage map for identifying SNP markers that are tightly linked to a nuclear-recessive major gene for male sterility in Cryptomeria japonica D. Don

PubMed Central

2012-01-01

Background High-density linkage maps facilitate the mapping of target genes and the construction of partial linkage maps around target loci to develop markers for marker-assisted selection (MAS). MAS is quite challenging in conifers because of their large, complex, and poorly-characterized genomes. Our goal was to construct a high-density linkage map to facilitate the identification of markers that are tightly linked to a major recessive male-sterile gene (ms1) for MAS in C. japonica, a species that is important in Japanese afforestation but which causes serious social pollinosis problems. Results We constructed a high-density saturated genetic linkage map for C. japonica using expressed sequence-derived co-dominant single nucleotide polymorphism (SNP) markers, most of which were genotyped using the GoldenGate genotyping assay. A total of 1261 markers were assigned to 11 linkage groups with an observed map length of 1405.2 cM and a mean distance between two adjacent markers of 1.1 cM; the number of linkage groups matched the basic chromosome number in C. japonica. Using this map, we located ms1 on the 9th linkage group and constructed a partial linkage map around the ms1 locus. This enabled us to identify a marker (hrmSNP970_sf) that is closely linked to the ms1 gene, being separated from it by only 0.5 cM. Conclusions Using the high-density map, we located the ms1 gene on the 9th linkage group and constructed a partial linkage map around the ms1 locus. The map distance between the ms1 gene and the tightly linked marker was only 0.5 cM. The identification of markers that are tightly linked to the ms1 gene will facilitate the early selection of male-sterile trees, which should expedite C. japonica breeding programs aimed at alleviating pollinosis problems without harming productivity. PMID:22424262

Mathematical model for determining the effects of intracytoplasmic inclusions on volume and density of microorganisms.

PubMed Central

Mas, J; Pedrós-Alió, C; Guerrero, R

1985-01-01

Procaryotic microorganisms accumulate several polymers in the form of intracellular inclusions as a strategy to increase survival in a changing environment. Such inclusions avoid osmotic pressure increases by tightly packaging certain macromolecules into the inclusion. In the present paper, a model describing changes in volume and density of the microbial cell as a function of the weight of the macromolecule forming the inclusion is derived from simple theoretical principles. The model is then tested by linear regression with experimental data from glycogen accumulation in Escherichia coli, poly-beta-hydroxybutyrate accumulation in Alcaligenes eutrophus, and sulfur accumulation in Chromatium spp. The model predicts a certain degree of hydration of the polymer in the inclusion and explains both the linear relationship between volume of the cell and weight of the polymer and the hyperbolic relationship between density of the cell and weight of the polymer. Other implications of the model are also discussed. PMID:3902798

Tight junction physiology of pleural mesothelium

PubMed Central

Markov, Alexander G.; Amasheh, Salah

2014-01-01

Pleura consists of visceral and parietal cell layers, producing a fluid, which is necessary for lubrication of the pleural space. Function of both mesothelial cell layers is necessary for the regulation of a constant pleural fluid volume and composition to facilitate lung movement during breathing. Recent studies have demonstrated that pleural mesothelial cells show a distinct expression pattern of tight junction proteins which are known to ubiquitously determine paracellular permeability. Most tight junction proteins provide a sealing function to epithelia, but some have been shown to have a paracellular channel function or ambiguous properties. Here we provide an in-depth review of the current knowledge concerning specific functional contribution of these proteins determining transport and barrier function of pleural mesothelium. PMID:25009499

Endocochlear potential generation is associated with intercellular communication in the stria vascularis: structural analysis in the viable dominant spotting mouse mutant.

PubMed

Carlisle, L; Steel, K; Forge, A

1990-11-01

Deafness in the viable dominant spotting mouse mutant is due to a primary defect of the stria vascularis which results in absence of the positive endocochlear potential in scala media. Endocochlear potentials were measured and the structure of stria vascularis of mutants with potentials close to zero was compared with that in normal littermate controls by use of morphometric methods. The stria vascularis was significantly thinner in mutants. Marginal cells were not significantly different from controls in terms of volume density or intramembrane particle density but the network density of tight junctions was significantly reduced in the mutants. A virtual absence of gap junctions between basal cells and marginal or intermediate cells was observed, but intramembrane particle density and junctional complexes between adjacent basal cells were not different from controls. The volume density of basal cells was significantly greater in mutants. Intermediate cells accounted for a significantly smaller volume density of the stria vascularis in mutants and had a lower density of intramembrane particles than controls. Melanocytes were not identified in the stria vascularis of mutants. These results suggest that communication between marginal, intermediate and basal cells might be important to the normal function of the stria vascularis.

Multi-scale predictive modeling of nano-material and realistic electron devices

NASA Astrophysics Data System (ADS)

Palaria, Amritanshu

Among the challenges faced in further miniaturization of electronic devices, heavy influence of the detailed atomic configuration of the material(s) involved, which often differs significantly from that of the bulk material(s), is prominent. Device design has therefore become highly interrelated with material engineering at the atomic level. This thesis aims at outlining, with examples, a multi-scale simulation procedure that allows one to integrate material and device aspects of nano-electronic design to predict behavior of novel devices with novel material. This is followed in four parts: (1) An approach that combines a higher time scale reactive force field analysis with density functional theory to predict structure of new material is demonstrated for the first time for nanowires. Novel stable structures for very small diameter silicon nanowires are predicted. (2) Density functional theory is used to show that the new nanowire structures derived in 1 above have properties different from diamond core wires even though the surface bonds in some may be similar to the surface of bulk silicon. (3) Electronic structure of relatively large-scale germanium sections of realistically strained Si/strained Ge/ strained Si nanowire heterostructures is computed using empirical tight binding and it is shown that the average non-homogeneous strain in these structures drives their interesting non-conventional electronic characteristics such as hole effective masses which decrease as the wire cross-section is reduced. (4) It is shown that tight binding, though empirical in nature, is not necessarily limited to the material and atomic structure for which the parameters have been empirically derived, but that simple changes may adapt the derived parameters to new bond environments. Si (100) surface electronic structure is obtained from bulk Si parameters.

Phononic crystals of spherical particles: A tight binding approach

NASA Astrophysics Data System (ADS)

Mattarelli, M.; Secchi, M.; Montagna, M.

2013-11-01

The vibrational dynamics of a fcc phononic crystal of spheres is studied and compared with that of a single free sphere, modelled either by a continuous homogeneous medium or by a finite cluster of atoms. For weak interaction among the spheres, the vibrational dynamics of the phononic crystal is described by shallow bands, with low degree of dispersion, corresponding to the acoustic spheroidal and torsional modes of the single sphere. The phonon displacements are therefore related to the vibrations of a sphere, as the electron wave functions in a crystal are related to the atomic wave functions in a tight binding model. Important dispersion is found for the two lowest phonon bands, which correspond to zero frequency free translation and rotation of a free sphere. Brillouin scattering spectra are calculated at some values of the exchanged wavevectors of the light, and compared with those of a single sphere. With weak interaction between particles, given the high acoustic impedance mismatch in dry systems, the density of phonon states consist of sharp bands separated by large gaps, which can be well accounted for by a single particle model. Based on the width of the frequency gaps, tunable with the particle size, and on the small number of dispersive acoustic phonons, such systems may provide excellent materials for application as sound or heat filters.

Controlled energy deposition and void-like modification inside transparent solids by two-color tightly focused femtosecond laser pulses

NASA Astrophysics Data System (ADS)

Potemkin, Fedor; Mareev, Evgeniy; Bezsudnova, Yulia; Platonenko, Victor; Bravy, Boris; Gordienko, Vyacheslav

2017-04-01

We report a bulk void-like micromodification of fused silica using two-color μJ-energy level tightly focused (NA = 0.5) co-propagating seeding (visible, 0.62 μm) and heating (near-IR, 1.24 μm) femtosecond laser pulses with online third harmonic diagnostics of created microplasmas as well as subsequent laser-induced void-like defects. It has been shown experimentally and theoretically that production of seeding electrons through multiphoton ionization by visible laser pulses paves the way for controllability of the energy deposition and laser-induced micromodification via carrier heating by delayed infrared laser pulses inside the material. Experimental results demonstrate wide possibilities to increase the density of energy deposited up to 6 kJ cm-3 inside the dielectric by tight focusing of two color fs-laser pulses and elliptical polarization for infrared heating fs-laser pulses. The developed theoretical approach predicts the enhancement of deposited energy density up to 9 kJ cm-3 using longer (mid-IR) wavelengths for heating laser pulses.

Claudins and the Modulation of Tight Junction Permeability

PubMed Central

Günzel, Dorothee

2013-01-01

Claudins are tight junction membrane proteins that are expressed in epithelia and endothelia and form paracellular barriers and pores that determine tight junction permeability. This review summarizes our current knowledge of this large protein family and discusses recent advances in our understanding of their structure and physiological functions. PMID:23589827

Density control in ITER: an iterative learning control and robust control approach

NASA Astrophysics Data System (ADS)

Ravensbergen, T.; de Vries, P. C.; Felici, F.; Blanken, T. C.; Nouailletas, R.; Zabeo, L.

2018-01-01

Plasma density control for next generation tokamaks, such as ITER, is challenging because of multiple reasons. The response of the usual gas valve actuators in future, larger fusion devices, might be too slow for feedback control. Both pellet fuelling and the use of feedforward-based control may help to solve this problem. Also, tight density limits arise during ramp-up, due to operational limits related to divertor detachment and radiative collapses. As the number of shots available for controller tuning will be limited in ITER, in this paper, iterative learning control (ILC) is proposed to determine optimal feedforward actuator inputs based on tracking errors, obtained in previous shots. This control method can take the actuator and density limits into account and can deal with large actuator delays. However, a purely feedforward-based density control may not be sufficient due to the presence of disturbances and shot-to-shot differences. Therefore, robust control synthesis is used to construct a robustly stabilizing feedback controller. In simulations, it is shown that this combined controller strategy is able to achieve good tracking performance in the presence of shot-to-shot differences, tight constraints, and model mismatches.

Systematically Ranking the Tightness of Membrane Association for Peripheral Membrane Proteins (PMPs)*

PubMed Central

Gao, Liyan; Ge, Haitao; Huang, Xiahe; Liu, Kehui; Zhang, Yuanya; Xu, Wu; Wang, Yingchun

2015-01-01

Large-scale quantitative evaluation of the tightness of membrane association for nontransmembrane proteins is important for identifying true peripheral membrane proteins with functional significance. Herein, we simultaneously ranked more than 1000 proteins of the photosynthetic model organism Synechocystis sp. PCC 6803 for their relative tightness of membrane association using a proteomic approach. Using multiple precisely ranked and experimentally verified peripheral subunits of photosynthetic protein complexes as the landmarks, we found that proteins involved in two-component signal transduction systems and transporters are overall tightly associated with the membranes, whereas the associations of ribosomal proteins are much weaker. Moreover, we found that hypothetical proteins containing the same domains generally have similar tightness. This work provided a global view of the structural organization of the membrane proteome with respect to divergent functions, and built the foundation for future investigation of the dynamic membrane proteome reorganization in response to different environmental or internal stimuli. PMID:25505158

Influence of the aggregate state on band structure and optical properties of C60 computed with different methods

NASA Astrophysics Data System (ADS)

Pal, Amrita; Arabnejad, Saeid; Yamashita, Koichi; Manzhos, Sergei

2018-05-01

C60 and C60 based molecules are efficient acceptors and electron transport layers for planar perovskite solar cells. While properties of these molecules are well studied by ab initio methods, those of solid C60, specifically its optical absorption properties, are not. We present a combined density functional theory-Density Functional Tight Binding (DFTB) study of the effect of solid state packing on the band structure and optical absorption of C60. The valence and conduction band edge energies of solid C60 differ on the order of 0.1 eV from single molecule frontier orbital energies. We show that calculations of optical properties using linear response time dependent-DFT(B) or the imaginary part of the dielectric constant (dipole approximation) can result in unrealistically large redshifts in the presence of intermolecular interactions compared to available experimental data. We show that optical spectra computed from the frequency-dependent real polarizability can better reproduce the effect of C60 aggregation on optical absorption, specifically with a generalized gradient approximation functional, and may be more suited to study effects of molecular aggregation.

Edge currents in frustrated Josephson junction ladders

NASA Astrophysics Data System (ADS)

Marques, A. M.; Santos, F. D. R.; Dias, R. G.

2016-09-01

We present a numerical study of quasi-1D frustrated Josephson junction ladders with diagonal couplings and open boundary conditions, in the large capacitance limit. We derive a correspondence between the energy of this Josephson junction ladder and the expectation value of the Hamiltonian of an analogous tight-binding model, and show how the overall superconducting state of the chain is equivalent to the minimum energy state of the tight-binding model in the subspace of one-particle states with uniform density. To satisfy the constraint of uniform density, the superconducting state of the ladder is written as a linear combination of the allowed k-states of the tight-binding model with open boundaries. Above a critical value of the parameter t (ratio between the intra-rung and inter-rung Josephson couplings) the ladder spontaneously develops currents at the edges, which spread to the bulk as t is increased until complete coverage is reached. Above a certain value of t, which varies with ladder size (t = 1 for an infinite-sized ladder), the edge currents are destroyed. The value t = 1 corresponds, in the tight-binding model, to the opening of a gap between two bands. We argue that the disappearance of the edge currents with this gap opening is not coincidental, and that this points to a topological origin for these edge current states.

The role of JAM-A in inflammatory bowel disease: unrevealing the ties that bind.

PubMed

Vetrano, Stefania; Danese, Silvio

2009-05-01

Tight junctions (TJ) are junctional proteins whose function is to maintain an intact intestinal epithelial barrier and regulate the paracellular movement of water and solutes. Altered TJ structure and epithelial permeability are observed in inflammatory bowel disease and seem to have an important role in the pathogenesis of these diseases. Junctional adhesion molecule-A (JAM-A) is a protein expressed at tight junctions of epithelial and endothelial cells, as well as on circulating leukocytes. Its function at tight junctions appears to be crucial as an extracellular adhesive molecule in the direct regulation of intestinal barrier function. This review focuses on the role of JAM-A in controlling mucosal homeostasis by regulating the integrity and permeability of epithelial barrier function.

Disorder and superfluid density in overdoped cuprate superconductors

NASA Astrophysics Data System (ADS)

Lee-Hone, N. R.; Dodge, J. S.; Broun, D. M.

2017-07-01

We calculate superfluid density for a dirty d -wave superconductor. The effects of impurity scattering are treated within the self-consistent t -matrix approximation, in weak-coupling BCS theory. Working from a realistic tight-binding parametrization of the Fermi surface, we find a superfluid density that is both correlated with Tc and linear in temperature, in good correspondence with recent experiments on overdoped La2 -xSrxCuO4 .

Tight binding simulation study on zigzag single-walled carbon nanotubes

NASA Astrophysics Data System (ADS)

Sharma, Deepa; Jaggi, Neena; Gupta, Vishu

2018-01-01

Tight binding simulation studies using the density functional tight binding (DFTB) model have been performed on various zigzag single-walled carbon-nanotubes (SWCNTs) to investigate their electronic properties using DFTB module of the Material Studio Software version 7.0. Various combinations of different eigen-solvers and charge mixing schemes available in the DFTB Module have been tried to chalk out the electronic structure. The analytically deduced values of the bandgap of (9, 0) SWCNT were compared with the experimentally determined value reported in the literature. On comparison, it was found that the tight binding approximations tend to drastically underestimate the bandgap values. However, the combination of Anderson charge mixing method with standard eigensolver when implemented using the smart algorithm was found to produce fairly close results. These optimized model parameters were then used to determine the band structures of various zigzag SWCNTs. (9, 0) Single-walled Nanotube which is extensively being used for sensing NH3, CH4 and NO2 has been picked up as a reference material since its experimental bandgap value has been reported in the literature. It has been found to exhibit a finite energy bandgap in contrast to its expected metallic nature. The study is of utmost significance as it not only probes and validates the simulation route for predicting suitable properties of nanomaterials but also throws light on the comparative efficacy of the different approximation and rationalization quantum mechanical techniques used in simulation studies. Such simulation studies if used intelligently prove to be immensely useful to the material scientists as they not only save time and effort but also pave the way to new experiments by making valuable predictions.

Generating Converged Accurate Free Energy Surfaces for Chemical Reactions with a Force-Matched Semiempirical Model.

PubMed

Kroonblawd, Matthew P; Pietrucci, Fabio; Saitta, Antonino Marco; Goldman, Nir

2018-04-10

We demonstrate the capability of creating robust density functional tight binding (DFTB) models for chemical reactivity in prebiotic mixtures through force matching to short time scale quantum free energy estimates. Molecular dynamics using density functional theory (DFT) is a highly accurate approach to generate free energy surfaces for chemical reactions, but the extreme computational cost often limits the time scales and range of thermodynamic states that can feasibly be studied. In contrast, DFTB is a semiempirical quantum method that affords up to a thousandfold reduction in cost and can recover DFT-level accuracy. Here, we show that a force-matched DFTB model for aqueous glycine condensation reactions yields free energy surfaces that are consistent with experimental observations of reaction energetics. Convergence analysis reveals that multiple nanoseconds of combined trajectory are needed to reach a steady-fluctuating free energy estimate for glycine condensation. Predictive accuracy of force-matched DFTB is demonstrated by direct comparison to DFT, with the two approaches yielding surfaces with large regions that differ by only a few kcal mol -1 .

Friction between Polymer Brushes

NASA Astrophysics Data System (ADS)

Sokoloff, Jeffrey

2006-03-01

A polymer brush consists of a surface with a fairly concentrated coating of polymer chains, each one of which has one of its ends tightly bound to the surface. They serve as extremely effective lubricant, producing friction coefficients as low as 0.001 or less! Polymer brushes are a promising way to reduce friction to extremely low values. They have the disadvantage, however, that they must be immersed in a liquid solvent in order to function as a lubricant. The presence of a solvent is believed to result in osmotic pressure which partially supports the load. The density profile of a polymer brush (i.e., the density of monomers as a function of distance from the surface to which the polymers are attached) is well established. What is not understood is how the interaction of polymer brush coated surfaces in contact with each other is able to account for the details of the observed low friction. For example, molecular dynamics studies generally do not predict static friction, whereas surface force apparatus measurements due to Tadmor, et. al., find that there is static friction. This is the topic of the present presentation.

Generating Converged Accurate Free Energy Surfaces for Chemical Reactions with a Force-Matched Semiempirical Model

DOE PAGES

Kroonblawd, Matthew P.; Pietrucci, Fabio; Saitta, Antonino Marco; ...

2018-03-15

Here, we demonstrate the capability of creating robust density functional tight binding (DFTB) models for chemical reactivity in prebiotic mixtures through force matching to short time scale quantum free energy estimates. Molecular dynamics using density functional theory (DFT) is a highly accurate approach to generate free energy surfaces for chemical reactions, but the extreme computational cost often limits the time scales and range of thermodynamic states that can feasibly be studied. In contrast, DFTB is a semiempirical quantum method that affords up to a thousandfold reduction in cost and can recover DFT-level accuracy. Here, we show that a force-matched DFTBmore » model for aqueous glycine condensation reactions yields free energy surfaces that are consistent with experimental observations of reaction energetics. Convergence analysis reveals that multiple nanoseconds of combined trajectory are needed to reach a steady-fluctuating free energy estimate for glycine condensation. Predictive accuracy of force-matched DFTB is demonstrated by direct comparison to DFT, with the two approaches yielding surfaces with large regions that differ by only a few kcal mol –1.« less

A review of theoretical study of graphene chemical vapor deposition synthesis on metals: nucleation, growth, and the role of hydrogen and oxygen

NASA Astrophysics Data System (ADS)

Rezwan Habib, Mohammad; Liang, Tao; Yu, Xuegong; Pi, Xiaodong; Liu, Yingchun; Xu, Mingsheng

2018-03-01

Graphene has attracted intense research interest due to its extraordinary properties and great application potential. Various methods have been proposed for the synthesis of graphene, among which chemical vapor deposition has drawn a great deal of attention for synthesizing large-area and high-quality graphene. Theoretical understanding of the synthesis mechanism is crucial for optimizing the experimental design for desired graphene production. In this review, we discuss the three fundamental steps of graphene synthesis in details, i.e. (1) decomposition of carbon feedstocks and formation of various active carbon species, (2) nucleation, and (3) attachment and extension. We provide a complete scenario of graphene synthesis on metal surfaces at atomistic level by means of density functional theory, molecular dynamics (MD), Monte Carlo (MC) and their combination and interface with other simulation methods such as quantum mechanical molecular dynamics, density functional tight binding molecular dynamics, and combination of MD and MC. We also address the latest investigation of the influences of the hydrogen and oxygen on the synthesis and the quality of the synthesized graphene.

Generating Converged Accurate Free Energy Surfaces for Chemical Reactions with a Force-Matched Semiempirical Model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kroonblawd, Matthew P.; Pietrucci, Fabio; Saitta, Antonino Marco

Here, we demonstrate the capability of creating robust density functional tight binding (DFTB) models for chemical reactivity in prebiotic mixtures through force matching to short time scale quantum free energy estimates. Molecular dynamics using density functional theory (DFT) is a highly accurate approach to generate free energy surfaces for chemical reactions, but the extreme computational cost often limits the time scales and range of thermodynamic states that can feasibly be studied. In contrast, DFTB is a semiempirical quantum method that affords up to a thousandfold reduction in cost and can recover DFT-level accuracy. Here, we show that a force-matched DFTBmore » model for aqueous glycine condensation reactions yields free energy surfaces that are consistent with experimental observations of reaction energetics. Convergence analysis reveals that multiple nanoseconds of combined trajectory are needed to reach a steady-fluctuating free energy estimate for glycine condensation. Predictive accuracy of force-matched DFTB is demonstrated by direct comparison to DFT, with the two approaches yielding surfaces with large regions that differ by only a few kcal mol –1.« less

Modeling electronic trap state distributions in nanocrystalline anatase

NASA Astrophysics Data System (ADS)

Le, Nam; Schweigert, Igor

The charge transport properties of nanocrystalline TiO2 films, and thus the catalytic performance of devices that incorporate them, are affected strongly by the spatial and energetic distribution of localized electronic trap states. Such traps may arise from a variety of defects: Ti interstitials, O vacancies, step edges at surfaces, and grain boundaries. We have developed a procedure for applying density functional theory (DFT) and density functional tight binding (DFTB) calculations to characterize distributions of localized states arising from multiple types of defects. We have applied the procedure to investigate how the morphologies of interfaces between pairs of attached anatase nanoparticles determine the energies of trap states therein. Our results complement recent experimental findings that subtle changes in the morphology of highly porous TiO2 aerogel networks can have a dramatic effect on catalytic performance, which was attributed to changes in the distribution of trap states. This work was supported by the U.S. Naval Research Laboratory via the National Research Council and by the Office of Naval Research through the U.S. Naval Research Laboratory.

Can Fe3+ and Al3+ ions serve as cationic bridges to facilitate the adsorption of anionic As(V) species on humic acids? A density functional theory study.

PubMed

Gorb, Leonid; Shukla, Manoj K

2017-03-01

A computational chemistry investigation was undertaken to shed light on the facilitatory role played by Fe 3+ and Al 3+ cations in the adsorption of anionic As(V) species by humic acids through the formation of so-called cationic bridges. Geometric and energetic parameters were obtained using density functional theory at the B3LYP/6-31G(d,p) level in conjunction with the polarizable continuum model (to account for the influence of bulk water). We found that, despite their similar molecular geometries, the adsorption energies of the As(V) species AsO 4 3- and H 2 AsO 4- differ when Fe 3+ , FeOH 2+ , Al 3+ , and AlOH 2+ participate in the bridge. We also found that effective adsorption of As(V) species by humic acids strongly depends on whether the considered cationic bridges are tightly coordinated by humic acids at the adsorption sites, as well as on the rigidity of these humic acid adsorption sites.

Ab initio molecular dynamics with nuclear quantum effects at classical cost: Ring polymer contraction for density functional theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marsalek, Ondrej; Markland, Thomas E., E-mail: tmarkland@stanford.edu

Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding asmore » a reference system, we show that our ring polymer contraction scheme gives rapid and systematic convergence to the full path integral density functional theory result. We demonstrate the efficiency of this approach in ab initio simulations of liquid water and the reactive protonated and deprotonated water dimer systems. We find that the vast majority of the nuclear quantum effects are accurately captured using contraction to just the ring polymer centroid, which requires the same number of density functional theory calculations as a classical simulation. Combined with a multiple time step scheme using the same reference system, which allows the time step to be increased, this approach is as fast as a typical classical ab initio molecular dynamics simulation and 35× faster than a full path integral calculation, while still exactly including the quantum sampling of nuclei. This development thus offers a route to routinely include nuclear quantum effects in ab initio molecular dynamics simulations at negligible computational cost.« less

A semi-metallic layer in detonating nitromethane

NASA Astrophysics Data System (ADS)

Reed, Evan; Manaa, Riad; Fried, Laurence; Glaesemann, Kurt; Joannopoulos, John

2007-06-01

We present the first ever glimpse behind a detonation front in a chemically reactive quantum molecular dynamics simulation (up to 0.2 ns) of the explosive nitromethane (CH3NO2) represented by the density-functional-based tight-binding method (DFTB). This simulation is enabled by our recently developed multi-scale shock wave molecular dynamics technique (MSST) that opens the door to longer duration simulations by several orders of magnitude. The electronic DOS around the Fermi energy initially increases as metastable material states are produced but then later decreases, perhaps unexpectedly. These changes indicate that the shock front is characterized by an increase in optical thickness followed by a reduction in optical thickness hundreds of picoseconds behind the front, explaining recent experimental observations. We find that a significant population of intermediate metastable molecules are charged and charged species play an important role in the density of states evolution and a possible Mott metal-insulator transition.

Effective lattice Hamiltonian for monolayer tin disulfide: Tailoring electronic structure with electric and magnetic fields

NASA Astrophysics Data System (ADS)

Yu, Jin; van Veen, Edo; Katsnelson, Mikhail I.; Yuan, Shengjun

2018-06-01

The electronic properties of monolayer tin dilsulfide (ML -Sn S2 ), a recently synthesized metal dichalcogenide, are studied by a combination of first-principles calculations and tight-binding (TB) approximation. An effective lattice Hamiltonian based on six hybrid s p -like orbitals with trigonal rotation symmetry are proposed to calculate the band structure and density of states for ML -Sn S2 , which demonstrates good quantitative agreement with relativistic density-functional-theory calculations in a wide energy range. We show that the proposed TB model can be easily applied to the case of an external electric field, yielding results consistent with those obtained from full Hamiltonian results. In the presence of a perpendicular magnetic field, highly degenerate equidistant Landau levels are obtained, showing typical two-dimensional electron gas behavior. Thus, the proposed TB model provides a simple way in describing properties in ML -Sn S2 .

Native State Volume Fluctuations in Proteins as a Mechanism for Dynamic Allostery.

PubMed

Law, Anthony B; Sapienza, Paul J; Zhang, Jun; Zuo, Xiaobing; Petit, Chad M

2017-03-15

Allostery enables tight regulation of protein function in the cellular environment. Although existing models of allostery are firmly rooted in the current structure-function paradigm, the mechanistic basis for allostery in the absence of structural change remains unclear. In this study, we show that a typical globular protein is able to undergo significant changes in volume under native conditions while exhibiting no additional changes in protein structure. These native state volume fluctuations were found to correlate with changes in internal motions that were previously recognized as a source of allosteric entropy. This finding offers a novel mechanistic basis for allostery in the absence of canonical structural change. The unexpected observation that function can be derived from expanded, low density protein states has broad implications for our understanding of allostery and suggests that the general concept of the native state be expanded to allow for more variable physical dimensions with looser packing.

Improvements on non-equilibrium and transport Green function techniques: The next-generation TRANSIESTA

NASA Astrophysics Data System (ADS)

Papior, Nick; Lorente, Nicolás; Frederiksen, Thomas; García, Alberto; Brandbyge, Mads

2017-03-01

We present novel methods implemented within the non-equilibrium Green function code (NEGF) TRANSIESTA based on density functional theory (DFT). Our flexible, next-generation DFT-NEGF code handles devices with one or multiple electrodes (Ne ≥ 1) with individual chemical potentials and electronic temperatures. We describe its novel methods for electrostatic gating, contour optimizations, and assertion of charge conservation, as well as the newly implemented algorithms for optimized and scalable matrix inversion, performance-critical pivoting, and hybrid parallelization. Additionally, a generic NEGF "post-processing" code (TBTRANS/PHTRANS) for electron and phonon transport is presented with several novelties such as Hamiltonian interpolations, Ne ≥ 1 electrode capability, bond-currents, generalized interface for user-defined tight-binding transport, transmission projection using eigenstates of a projected Hamiltonian, and fast inversion algorithms for large-scale simulations easily exceeding 106 atoms on workstation computers. The new features of both codes are demonstrated and bench-marked for relevant test systems.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Law, Anthony B.; Sapienza, Paul J.; Zhang, Jun

Allostery enables tight regulation of protein function in the cellular environment. While existing models of allostery are firmly rooted in the current structure-function paradigm, the mechanistic basis for allostery in the absence of structural change remains unclear. In this study, we show that a typical globular protein is able to undergo significant changes in volume under native conditions while exhibiting no additional changes in protein structure. These native state volume fluctuations were found to correlate with changes in internal motions that were previously recognized as a source of allosteric entropy. This finding offers a novel mechanistic basis for allostery inmore » the absence of canonical structural change. As a result, the unexpected observation that function can be derived from expanded, low density protein states has broad implications for our understanding of allostery and suggests that the general concept of the native state be expanded to allow for more variable physical dimensions with looser packing.« less

The effect of the gastrocnemius on the plantar fascia.

PubMed

Pascual Huerta, Javier

2014-12-01

Although anatomic and functional relationship has been established between the gastrocnemius muscle, via the Achilles tendon, and the plantar fascia, the exact role of gastrocnemius tightness in foot and plantar fascia problems is not completely understood. This article summarizes past and current literature linking these 2 structures and gives a mechanical explanation based on functional models of the relationship between gastrocnemius tightness and plantar fascia. The effect of gastrocnemius tightness on the sagittal behavior of the foot is also discussed. Copyright © 2014 Elsevier Inc. All rights reserved.

Tight junctions and the modulation of barrier function in disease

PubMed Central

2008-01-01

Tight junctions create a paracellular barrier in epithelial and endothelial cells protecting them from the external environment. Two different classes of integral membrane proteins constitute the tight junction strands in epithelial cells and endothelial cells, occludin and members of the claudin protein family. In addition, cytoplasmic scaffolding molecules associated with these junctions regulate diverse physiological processes like proliferation, cell polarity and regulated diffusion. In many diseases, disruption of this regulated barrier occurs. This review will briefly describe the molecular composition of the tight junctions and then present evidence of the link between tight junction dysfunction and disease. PMID:18415116

Relative distribution of cosmic rays and magnetic fields

NASA Astrophysics Data System (ADS)

Seta, Amit; Shukurov, Anvar; Wood, Toby S.; Bushby, Paul J.; Snodin, Andrew P.

2018-02-01

Synchrotron radiation from cosmic rays is a key observational probe of the galactic magnetic field. Interpreting synchrotron emission data requires knowledge of the cosmic ray number density, which is often assumed to be in energy equipartition (or otherwise tightly correlated) with the magnetic field energy. However, there is no compelling observational or theoretical reason to expect such a tight correlation to hold across all scales. We use test particle simulations, tracing the propagation of charged particles (protons) through a random magnetic field, to study the cosmic ray distribution at scales comparable to the correlation scale of the turbulent flow in the interstellar medium (≃100 pc in spiral galaxies). In these simulations, we find that there is no spatial correlation between the cosmic ray number density and the magnetic field energy density. In fact, their distributions are approximately statistically independent. We find that low-energy cosmic rays can become trapped between magnetic mirrors, whose location depends more on the structure of the field lines than on the field strength.

Transmembrane proteins of tight junctions.

PubMed

Chiba, Hideki; Osanai, Makoto; Murata, Masaki; Kojima, Takashi; Sawada, Norimasa

2008-03-01

Tight junctions contribute to the paracellular barrier, the fence dividing plasma membranes, and signal transduction, acting as a multifunctional complex in vertebrate epithelial and endothelial cells. The identification and characterization of the transmembrane proteins of tight junctions, claudins, junctional adhesion molecules (JAMs), occludin and tricellulin, have led to insights into the molecular nature of tight junctions. We provide an overview of recent progress in studies on these proteins and highlight their roles and regulation, as well as their functional significance in human diseases.

Tight junctions in inflammatory bowel diseases and inflammatory bowel disease associated colorectal cancer

PubMed Central

Landy, Jonathan; Ronde, Emma; English, Nick; Clark, Sue K; Hart, Ailsa L; Knight, Stella C; Ciclitira, Paul J; Al-Hassi, Hafid Omar

2016-01-01

Inflammatory bowel diseases are characterised by inflammation that compromises the integrity of the epithelial barrier. The intestinal epithelium is not only a static barrier but has evolved complex mechanisms to control and regulate bacterial interactions with the mucosal surface. Apical tight junction proteins are critical in the maintenance of epithelial barrier function and control of paracellular permeability. The characterisation of alterations in tight junction proteins as key players in epithelial barrier function in inflammatory bowel diseases is rapidly enhancing our understanding of critical mechanisms in disease pathogenesis as well as novel therapeutic opportunities. Here we give an overview of recent literature focusing on the role of tight junction proteins, in particular claudins, in inflammatory bowel diseases and inflammatory bowel disease associated colorectal cancer. PMID:27003989

Transferable tight-binding model for strained group IV and III-V materials and heterostructures

NASA Astrophysics Data System (ADS)

Tan, Yaohua; Povolotskyi, Michael; Kubis, Tillmann; Boykin, Timothy B.; Klimeck, Gerhard

2016-07-01

It is critical to capture the effect due to strain and material interface for device level transistor modeling. We introduce a transferable s p3d5s* tight-binding model with nearest-neighbor interactions for arbitrarily strained group IV and III-V materials. The tight-binding model is parametrized with respect to hybrid functional (HSE06) calculations for varieties of strained systems. The tight-binding calculations of ultrasmall superlattices formed by group IV and group III-V materials show good agreement with the corresponding HSE06 calculations. The application of the tight-binding model to superlattices demonstrates that the transferable tight-binding model with nearest-neighbor interactions can be obtained for group IV and III-V materials.

Modulation of Tight Junction Structure and Function by Kinases and Phosphatases Targeting Occludin

PubMed Central

Dörfel, Max Johannes; Huber, Otmar

2012-01-01

Tight junctions (TJs) typically represent the most apical contacts in epithelial and endothelial cell layers where they play an essential role in the separation of extracellular or luminal spaces from underlying tissues in the body. Depending on the protein composition, TJs define the barrier characteristics and in addition maintain cell polarity. Two major families of integral membrane proteins form the typical TJ strand network, the tight junction-associated MARVEL protein (TAMP) family members occludin, tricellulin, and MarvelD3 as well as a specific set of claudins. Occludin was the first identified member of these tetraspanins and is now widely accepted as a regulator of TJ assembly and function. Therefore, occludin itself has to be tightly regulated. Phosphorylation of occludin appears to be of central importance in this context. Here we want to summarize current knowledge on the kinases and phosphatases directly modifying occludin, and their role in the regulation of TJ structure, function, and dynamics. PMID:22315516

Possible involvement of gap junctions in the barrier function of tight junctions of brain and lung endothelial cells.

PubMed

Nagasawa, Kunihiko; Chiba, Hideki; Fujita, Hiroki; Kojima, Takashi; Saito, Tsuyoshi; Endo, Toshiaki; Sawada, Norimasa

2006-07-01

Gap-junction plaques are often observed with tight-junction strands of vascular endothelial cells but the molecular interaction and functional relationships between these two junctions remain obscure. We herein show that gap-junction proteins connexin40 (Cx40) and Cx43 are colocalized and coprecipitated with tight-junction molecules occludin, claudin-5, and ZO-1 in porcine blood-brain barrier (BBB) endothelial cells. Gap junction blockers 18beta-glycyrrhetinic acid (18beta-GA) and oleamide (OA) did not influence expression of Cx40, Cx43, occludin, claudin-5, junctional adhesion molecule (JAM)-A, JAM-B, JAM-C, or ZO-1, or their subcellular localization in the porcine BBB endothelial cells. In contrast, these gap-junction blocking agents inhibited the barrier function of tight junctions in cells, determined by measurement of transendothelial electrical resistance and paracellular flux of mannitol and inulin. 18beta-GA also significantly reduced the barrier property in rat lung endothelial (RLE) cells expressing doxycycline-induced claudin-1, but did not change the interaction between Cx43 and either claudin-1 or ZO-1, nor their expression levels or subcellular distribution. These findings suggest that Cx40- and/or Cx43-based gap junctions might be required to maintain the endothelial barrier function without altering the expression and localization of the tight-junction components analyzed. Copyright 2006 Wiley-Liss, Inc.

Effective mass in bilayer graphene at low carrier densities: The role of potential disorder and electron-electron interaction

NASA Astrophysics Data System (ADS)

Li, J.; Tan, L. Z.; Zou, K.; Stabile, A. A.; Seiwell, D. J.; Watanabe, K.; Taniguchi, T.; Louie, Steven G.; Zhu, J.

2016-10-01

In a two-dimensional electron gas, the electron-electron interaction generally becomes stronger at lower carrier densities and renormalizes the Fermi-liquid parameters, such as the effective mass of carriers. We combine experiment and theory to study the effective masses of electrons and holes me* and mh* in bilayer graphene in the low carrier density regime on the order of 1 ×1011c m-2 . Measurements use temperature-dependent low-field Shubnikov-de Haas oscillations observed in high-mobility hexagonal boron nitride supported samples. We find that while me* follows a tight-binding description in the whole density range, mh* starts to drop rapidly below the tight-binding description at a carrier density of n =6 ×1011c m-2 and exhibits a strong suppression of 30% when n reaches 2 ×1011c m-2 . Contributions from the electron-electron interaction alone, evaluated using several different approximations, cannot explain the experimental trend. Instead, the effect of the potential fluctuation and the resulting electron-hole puddles play a crucial role. Calculations including both the electron-electron interaction and disorder effects explain the experimental data qualitatively and quantitatively. This Rapid Communication reveals an unusual disorder effect unique to two-dimensional semimetallic systems.

Correlating Lithium Hydroxyl Accumulation with Capacity Retention in V2O5 Aerogel Cathodes.

PubMed

Wangoh, Linda W; Huang, Yiqing; Jezorek, Ryan L; Kehoe, Aoife B; Watson, Graeme W; Omenya, Fredrick; Quackenbush, Nicholas F; Chernova, Natasha A; Whittingham, M Stanley; Piper, Louis F J

2016-05-11

V2O5 aerogels are capable of reversibly intercalating more than 5 Li(+)/V2O5 but suffer from lifetime issues due to their poor capacity retention upon cycling. We employed a range of material characterization and electrochemical techniques along with atomic pair distribution function, X-ray photoelectron spectroscopy, and density functional theory to determine the origin of the capacity fading in V2O5 aerogel cathodes. In addition to the expected vanadium redox due to intercalation, we observed LiOH species that formed upon discharge and were only partially removed after charging, resulting in an accumulation of electrochemically inactive LiOH over each cycle. Our results indicate that the tightly bound water that is necessary for maintaining the aerogel structure is also inherently responsible for the capacity fade.

Correlating Lithium Hydroxyl Accumulation with Capacity Retention in V 2 O 5 Aerogel Cathodes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wangoh, Linda W.; Huang, Yiqing; Jezorek, Ryan L.

V 2O 5 aerogels are capable of reversibly intercalating more than 5 Li +/V 2O 5 but suffer from lifetime issues due to their poor capacity retention upon cycling. We employed a range of material characterization and electrochemical techniques along with atomic pair distribution function, X-ray photoelectron spectroscopy, and density functional theory to determine the origin of the capacity fading in V 2O 5 aerogel cathodes. In addition to the expected vanadium redox due to intercalation, we observed LiOH species that formed upon discharge and were only partially removed after charging, resulting in an accumulation of electrochemically inactive LiOH overmore » each cycle. Our results indicate that the tightly bound water that is necessary for maintaining the aerogel structure is also inherently responsible for the capacity fade.« less

Dark matter, long-range forces, and large-scale structure

NASA Technical Reports Server (NTRS)

Gradwohl, Ben-Ami; Frieman, Joshua A.

1992-01-01

If the dark matter in galaxies and clusters is nonbaryonic, it can interact with additional long-range fields that are invisible to experimental tests of the equivalence principle. We discuss the astrophysical and cosmological implications of a long-range force coupled only to the dark matter and find rather tight constraints on its strength. If the force is repulsive (attractive), the masses of galaxy groups and clusters (and the mean density of the universe inferred from them) have been systematically underestimated (overestimated). We explore the consequent effects on the two-point correlation function, large-scale velocity flows, and microwave background anisotropies, for models with initial scale-invariant adiabatic perturbations and cold dark matter.

Physical and Electronic Isolation of Carbon Nanotube Conductors

NASA Technical Reports Server (NTRS)

OKeeffe, James; Biegel, Bryan (Technical Monitor)

2001-01-01

Multi-walled nanotubes are proposed as a method to electrically and physically isolate nanoscale conductors from their surroundings. We use tight binding (TB) and density functional theory (DFT) to simulate the effects of an external electric field on multi-wall nanotubes. Two categories of multi-wall nanotube are investigated, those with metallic and semiconducting outer shells. In the metallic case, simulations show that the outer wall effectively screens the inner core from an applied electric field. This offers the ability to reduce crosstalk between nanotube conductors. A semiconducting outer shell is found not to perturb an electric field incident on the inner core, thereby providing physical isolation while allowing the tube to remain electrically coupled to its surroundings.

Multiple mobility edges in a 1D Aubry chain with Hubbard interaction in presence of electric field: Controlled electron transport

NASA Astrophysics Data System (ADS)

Saha, Srilekha; Maiti, Santanu K.; Karmakar, S. N.

2016-09-01

Electronic behavior of a 1D Aubry chain with Hubbard interaction is critically analyzed in presence of electric field. Multiple energy bands are generated as a result of Hubbard correlation and Aubry potential, and, within these bands localized states are developed under the application of electric field. Within a tight-binding framework we compute electronic transmission probability and average density of states using Green's function approach where the interaction parameter is treated under Hartree-Fock mean field scheme. From our analysis we find that selective transmission can be obtained by tuning injecting electron energy, and thus, the present model can be utilized as a controlled switching device.

Ionic Asymmetry and Solvent Excluded Volume Effects on Spherical Electric Double Layers: A Density Functional Approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Medasani, Bharat; Ovanesyan, Zaven; Thomas, Dennis G.

In this article we present a classical density functional theory for electrical double layers of spherical macroions that extends the capabilities of conventional approaches by accounting for electrostatic ion correlations, size asymmetry and excluded volume effects. The approach is based on a recent approximation introduced by Hansen-Goos and Roth for the hard sphere excess free energy of inhomogeneous fluids (J. Chem. Phys. 124, 154506). It accounts for the proper and efficient description of the effects of ionic asymmetry and solvent excluded volume, especially at high ion concentrations and size asymmetry ratios including those observed in experimental studies. Additionally, we utilizemore » a leading functional Taylor expansion approximation of the ion density profiles. In addition, we use the Mean Spherical Approximation for multi-component charged hard sphere fluids to account for the electrostatic ion correlation effects. These approximations are implemented in our theoretical formulation into a suitable decomposition of the excess free energy which plays a key role in capturing the complex interplay between charge correlations and excluded volume effects. We perform Monte Carlo simulations in various scenarios to validate the proposed approach, obtaining a good compromise between accuracy and computational cost. We use the proposed computational approach to study the effects of ion size, ion size asymmetry and solvent excluded volume on the ion profiles, integrated charge, mean electrostatic potential, and ionic coordination number around spherical macroions in various electrolyte mixtures. Our results show that both solvent hard sphere diameter and density play a dominant role in the distribution of ions around spherical macroions, mainly for experimental water molarity and size values where the counterion distribution is characterized by a tight binding to the macroion, similar to that predicted by the Stern model.« less

Proteomic and cellular localisation studies suggest non-tight junction cytoplasmic and nuclear roles for occludin in astrocytes.

PubMed

Morgan, Sarah V; Garwood, Claire J; Jennings, Luke; Simpson, Julie E; Castelli, Lydia M; Heath, Paul R; Mihaylov, Simeon R; Vaquéz-Villaseñor, Irina; Minshull, Thomas C; Ince, Paul G; Dickman, Mark J; Hautbergue, Guillaume M; Wharton, Stephen B

2018-05-08

Occludin is a component of tight junctions, which are essential structural components of the blood-brain barrier. However, occludin is expressed in cells without tight junctions, implying additional functions. We determined the expression and localisation of occludin in astrocytes in cell culture and in human brain tissue, and sought novel binding partners using a proteomic approach. Expression was investigated by immunocytochemistry and immunoblotting in the 1321N1 astrocytoma cell line and ScienCell human primary astrocytes, and by immunohistochemistry in human autopsy brain tissue. Recombinant N- and C-terminal occludin was used to pull-down proteins from 1321N1 cell lysates and protein-binding partners identified by mass spectrometry analysis. Occludin was expressed in both the cytoplasm and nucleus of astrocytes in vitro and in vivo. Mass spectrometry identified binding to nuclear and cytoplasmic proteins, particularly those related to RNA metabolism and nuclear function. Occludin is expressed in several subcellular compartments of brain cell-types that do not form tight junctions and the expression patterns in cell culture reflect those in human brain tissue, indicating they are suitable model systems. Proteomic analysis suggests that occludin has novel functions in neuroepithelial cells that are unrelated to tight junction formation. Further research will establish the roles of these functions in both cellular physiology and in disease states. © 2018 The Authors. European Journal of Neuroscience published by Federation of European Neuroscience Societies and John Wiley & Sons Ltd.

Transplantation of in vitro cultured endothelial progenitor cells repairs the blood-brain barrier and improves cognitive function of APP/PS1 transgenic AD mice.

PubMed

Zhang, Shishuang; Zhi, Yongle; Li, Fei; Huang, Shan; Gao, Huabin; Han, Zhaoli; Ge, Xintong; Li, Dai; Chen, Fanglian; Kong, Xiaodong; Lei, Ping

2018-04-15

To date, the pathogenesis of Alzheimer's disease (AD) remains unclear. It is well-known that excessive deposition of Aβ in the brain is a crucial part of the pathogenesis of AD. In recent years, the AD neurovascular unit hypothesis has attracted much attention. Impairment of the blood-brain barrier (BBB) leads to abnormal amyloid-β (Aβ) transport, and chronic cerebral hypoperfusion causes Aβ deposition throughout the onset and progression of AD. Endothelial progenitor cells (EPCs) are the universal cells for repairing blood vessels. Our previous studies have shown that a reduced number of EPCs in the peripheral blood results in cerebral vascular repair disorder, cerebral hypoperfusion and neurodegeneration, which might be related to the cognitive dysfunction of AD patients. This study was designed to confirm whether EPCs transplantation could repair the blood-brain barrier, stimulate angiogenesis and reduce Aβ deposition in AD. The expression of ZO-1, Occludin and Claudin-5 was up-regulated in APP/PS1 transgenic mice after hippocampal transplantation of EPCs. Consistent with previous studies, EPC transplants also increased the microvessel density. We observed that Aβ senile plaque deposition was decreased and hippocampal cell apoptosis was reduced after EPCs transplantation. The Morris water maze test showed that spatial learning and memory functions were significantly improved in mice transplanted with EPCs. Consequently, EPCs could up-regulate the expression of tight junction proteins, repair BBB tight junction function, stimulate angiogenesis, promote Aβ clearance, and decrease neuronal loss, ultimately improve cognitive function. Taken together, these data demonstrate EPCs may play an important role in the therapeutic implications for vascular dysfunction in AD. Copyright © 2018 Elsevier B.V. All rights reserved.

Model many-body Stoner Hamiltonian for binary FeCr alloys

NASA Astrophysics Data System (ADS)

Nguyen-Manh, D.; Dudarev, S. L.

2009-09-01

We derive a model tight-binding many-body d -electron Stoner Hamiltonian for FeCr binary alloys and investigate the sensitivity of its mean-field solutions to the choice of hopping integrals and the Stoner exchange parameters. By applying the local charge-neutrality condition within a self-consistent treatment we show that the negative enthalpy-of-mixing anomaly characterizing the alloy in the low chromium concentration limit is due entirely to the presence of the on-site exchange Stoner terms and that the occurrence of this anomaly is not specifically related to the choice of hopping integrals describing conventional chemical bonding between atoms in the alloy. The Bain transformation pathway computed, using the proposed model Hamiltonian, for the Fe15Cr alloy configuration is in excellent agreement with ab initio total-energy calculations. Our investigation also shows how the parameters of a tight-binding many-body model Hamiltonian for a magnetic alloy can be derived from the comparison of its mean-field solutions with other, more accurate, mean-field approximations (e.g., density-functional calculations), hence stimulating the development of large-scale computational algorithms for modeling radiation damage effects in magnetic alloys and steels.

A general intermolecular force field based on tight-binding quantum chemical calculations

NASA Astrophysics Data System (ADS)

Grimme, Stefan; Bannwarth, Christoph; Caldeweyher, Eike; Pisarek, Jana; Hansen, Andreas

2017-10-01

A black-box type procedure is presented for the generation of a molecule-specific, intermolecular potential energy function. The method uses quantum chemical (QC) information from our recently published extended tight-binding semi-empirical scheme (GFN-xTB) and can treat non-covalently bound complexes and aggregates with almost arbitrary chemical structure. The necessary QC information consists of the equilibrium structure, Mulliken atomic charges, charge centers of localized molecular orbitals, and also of frontier orbitals and orbital energies. The molecular pair potential includes model density dependent Pauli repulsion, penetration, as well as point charge electrostatics, the newly developed D4 dispersion energy model, Drude oscillators for polarization, and a charge-transfer term. Only one element-specific and about 20 global empirical parameters are needed to cover systems with nuclear charges up to radon (Z = 86). The method is tested for standard small molecule interaction energy benchmark sets where it provides accurate intermolecular energies and equilibrium distances. Examples for structures with a few hundred atoms including charged systems demonstrate the versatility of the approach. The method is implemented in a stand-alone computer code which enables rigid-body, global minimum energy searches for molecular aggregation or alignment.

Communication: Two-step explosion processes of highly charged fullerene cations C{sub 60}{sup q+} (q = 20–60)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yamazaki, Kaoru; Nakamura, Takashi; Kanno, Manabu

2014-09-28

To establish the fundamental understanding of the fragmentation dynamics of highly positive charged nano- and bio-materials, we carried out on-the-fly classical trajectory calculations on the fragmentation dynamics of C{sub 60}{sup q+} (q = 20–60). We used the UB3LYP/3-21G level of density functional theory and the self-consistent charge density-functional based tight-binding theory. For q ≥ 20, we found that a two-step explosion mechanism governs the fragmentation dynamics: C{sub 60}{sup q+} first ejects singly and multiply charged fast atomic cations C{sup z+} (z ≥ 1) via Coulomb explosions on a timescale of 10 fs to stabilize the remaining core cluster. Thermal evaporationsmore » of slow atomic and molecular fragments from the core cluster subsequently occur on a timescale of 100 fs to 1 ps. Increasing the charge q makes the fragments smaller. This two-step mechanism governs the fragmentation dynamics in the most likely case that the initial kinetic energy accumulated upon ionization to C{sub 60}{sup q+} by ion impact or X-ray free electron laser is larger than 100 eV.« less

Finding the best density functional approximation to describe interaction energies and structures of ionic liquids in molecular dynamics studies

NASA Astrophysics Data System (ADS)

Perlt, Eva; Ray, Promit; Hansen, Andreas; Malberg, Friedrich; Grimme, Stefan; Kirchner, Barbara

2018-05-01

Ionic liquids raise interesting but complicated questions for theoretical investigations due to the fact that a number of different inter-molecular interactions, e.g., hydrogen bonding, long-range Coulomb interactions, and dispersion interactions, need to be described properly. Here, we present a detailed study on the ionic liquids ethylammonium nitrate and 1-ethyl-3-methylimidazolium acetate, in which we compare different dispersion corrected density functional approximations to accurate local coupled cluster data in static calculations on ionic liquid clusters. The efficient new composite method B97-3c is tested and has been implemented in CP2K for future studies. Furthermore, tight-binding based approaches which may be used in large scale simulations are assessed. Subsequently, ab initio as well as classical molecular dynamics simulations are conducted and structural analyses are presented in order to shed light on the different short- and long-range structural patterns depending on the method and the system size considered in the simulation. Our results indicate the presence of strong hydrogen bonds in ionic liquids as well as the aggregation of alkyl side chains due to dispersion interactions.

Reconstructing the Initial Density Field of the Local Universe: Methods and Tests with Mock Catalogs

NASA Astrophysics Data System (ADS)

Wang, Huiyuan; Mo, H. J.; Yang, Xiaohu; van den Bosch, Frank C.

2013-07-01

Our research objective in this paper is to reconstruct an initial linear density field, which follows the multivariate Gaussian distribution with variances given by the linear power spectrum of the current cold dark matter model and evolves through gravitational instabilities to the present-day density field in the local universe. For this purpose, we develop a Hamiltonian Markov Chain Monte Carlo method to obtain the linear density field from a posterior probability function that consists of two components: a prior of a Gaussian density field with a given linear spectrum and a likelihood term that is given by the current density field. The present-day density field can be reconstructed from galaxy groups using the method developed in Wang et al. Using a realistic mock Sloan Digital Sky Survey DR7, obtained by populating dark matter halos in the Millennium simulation (MS) with galaxies, we show that our method can effectively and accurately recover both the amplitudes and phases of the initial, linear density field. To examine the accuracy of our method, we use N-body simulations to evolve these reconstructed initial conditions to the present day. The resimulated density field thus obtained accurately matches the original density field of the MS in the density range 0.3 \\lesssim \\rho /\\bar{\\rho } \\lesssim 20 without any significant bias. In particular, the Fourier phases of the resimulated density fields are tightly correlated with those of the original simulation down to a scale corresponding to a wavenumber of ~1 h Mpc-1, much smaller than the translinear scale, which corresponds to a wavenumber of ~0.15 h Mpc-1.

Temperature-dependent band structure of SrTiO3 interfaces

NASA Astrophysics Data System (ADS)

Raslan, Amany; Lafleur, Patrick; Atkinson, W. A.

2017-02-01

We build a theoretical model for the electronic properties of the two-dimensional (2D) electron gas that forms at the interface between insulating SrTiO3 and a number of polar cap layers, including LaTiO3, LaAlO3, and GdTiO3. The model treats conduction electrons within a tight-binding approximation and the dielectric polarization via a Landau-Devonshire free energy that incorporates strontium titanate's strongly nonlinear, nonlocal, and temperature-dependent dielectric response. The self-consistent band structure comprises a mix of quantum 2D states that are tightly bound to the interface and quasi-three-dimensional (3D) states that extend hundreds of unit cells into the SrTiO3 substrate. We find that there is a substantial shift of electrons away from the interface into the 3D tails as temperature is lowered from 300 K to 10 K. This shift is least important at high electron densities (˜1014cm-2 ) but becomes substantial at low densities; for example, the total electron density within 4 nm of the interface changes by a factor of two for 2D electron densities ˜1013cm-2 . We speculate that the quasi-3D tails form the low-density high-mobility component of the interfacial electron gas that is widely inferred from magnetoresistance measurements.

Accurate atomistic first-principles calculations of electronic stopping

DOE PAGES

Schleife, André; Kanai, Yosuke; Correa, Alfredo A.

2015-01-20

In this paper, we show that atomistic first-principles calculations based on real-time propagation within time-dependent density functional theory are capable of accurately describing electronic stopping of light projectile atoms in metal hosts over a wide range of projectile velocities. In particular, we employ a plane-wave pseudopotential scheme to solve time-dependent Kohn-Sham equations for representative systems of H and He projectiles in crystalline aluminum. This approach to simulate nonadiabatic electron-ion interaction provides an accurate framework that allows for quantitative comparison with experiment without introducing ad hoc parameters such as effective charges, or assumptions about the dielectric function. Finally, our work clearlymore » shows that this atomistic first-principles description of electronic stopping is able to disentangle contributions due to tightly bound semicore electrons and geometric aspects of the stopping geometry (channeling versus off-channeling) in a wide range of projectile velocities.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tokár, K.; Derian, R.; Mitas, L.

Using explicitly correlated fixed-node quantum Monte Carlo and density functional theory (DFT) methods, we study electronic properties, ground-state multiplets, ionization potentials, electron affinities, and low-energy fragmentation channels of charged half-sandwich and multidecker vanadium-benzene systems with up to 3 vanadium atoms, including both anions and cations. It is shown that, particularly in anions, electronic correlations play a crucial role; these effects are not systematically captured with any commonly used DFT functionals such as gradient corrected, hybrids, and range-separated hybrids. On the other hand, tightly bound cations can be described qualitatively by DFT. A comparison of DFT and quantum Monte Carlo providesmore » an in-depth understanding of the electronic structure and properties of these correlated systems. The calculations also serve as a benchmark study of 3d molecular anions that require a balanced many-body description of correlations at both short- and long-range distances.« less

Solvation of fluoro-acetonitrile in water by 2D-IR spectroscopy: A combined experimental-computational study

NASA Astrophysics Data System (ADS)

Cazade, Pierre-André; Tran, Halina; Bereau, Tristan; Das, Akshaya K.; Kläsi, Felix; Hamm, Peter; Meuwly, Markus

2015-06-01

The solvent dynamics around fluorinated acetonitrile is characterized by 2-dimensional infrared spectroscopy and atomistic simulations. The lineshape of the linear infrared spectrum is better captured by semiempirical (density functional tight binding) mixed quantum mechanical/molecular mechanics simulations, whereas force field simulations with multipolar interactions yield lineshapes that are significantly too narrow. For the solvent dynamics, a relatively slow time scale of 2 ps is found from the experiments and supported by the mixed quantum mechanical/molecular mechanics simulations. With multipolar force fields fitted to the available thermodynamical data, the time scale is considerably faster—on the 0.5 ps time scale. The simulations provide evidence for a well established CF-HOH hydrogen bond (population of 25%) which is found from the radial distribution function g(r) from both, force field and quantum mechanics/molecular mechanics simulations.

Proton transfer pathways, energy landscape, and kinetics in creatine-water systems.

PubMed

Ivchenko, Olga; Whittleston, Chris S; Carr, Joanne M; Imhof, Petra; Goerke, Steffen; Bachert, Peter; Wales, David J

2014-02-27

We study the exchange processes of the metabolite creatine, which is present in both tumorous and normal tissues and has NH2 and NH groups that can transfer protons to water. Creatine produces chemical exchange saturation transfer (CEST) contrast in magnetic resonance imaging (MRI). The proton transfer pathway from zwitterionic creatine to water is examined using a kinetic transition network constructed from the discrete path sampling approach and an approximate quantum-chemical energy function, employing the self-consistent-charge density-functional tight-binding (SCC-DFTB) method. The resulting potential energy surface is visualized by constructing disconnectivity graphs. The energy landscape consists of two distinct regions corresponding to the zwitterionic creatine structures and deprotonated creatine. The activation energy that characterizes the proton transfer from the creatine NH2 group to water was determined from an Arrhenius fit of rate constants as a function of temperature, obtained from harmonic transition state theory. The result is in reasonable agreement with values obtained in water exchange spectroscopy (WEX) experiments.

Native state volume fluctuations in proteins as a mechanism for dynamic allostery

DOE PAGES

Law, Anthony B.; Sapienza, Paul J.; Zhang, Jun; ...

2017-01-17

Allostery enables tight regulation of protein function in the cellular environment. While existing models of allostery are firmly rooted in the current structure-function paradigm, the mechanistic basis for allostery in the absence of structural change remains unclear. In this study, we show that a typical globular protein is able to undergo significant changes in volume under native conditions while exhibiting no additional changes in protein structure. These native state volume fluctuations were found to correlate with changes in internal motions that were previously recognized as a source of allosteric entropy. This finding offers a novel mechanistic basis for allostery inmore » the absence of canonical structural change. As a result, the unexpected observation that function can be derived from expanded, low density protein states has broad implications for our understanding of allostery and suggests that the general concept of the native state be expanded to allow for more variable physical dimensions with looser packing.« less

Calcium Channels and Oxidative Stress Mediate a Synergistic Disruption of Tight Junctions by Ethanol and Acetaldehyde in Caco-2 Cell Monolayers.

PubMed

Samak, Geetha; Gangwar, Ruchika; Meena, Avtar S; Rao, Roshan G; Shukla, Pradeep K; Manda, Bhargavi; Narayanan, Damodaran; Jaggar, Jonathan H; Rao, RadhaKrishna

2016-12-13

Ethanol is metabolized into acetaldehyde in most tissues. In this study, we investigated the synergistic effect of ethanol and acetaldehyde on the tight junction integrity in Caco-2 cell monolayers. Expression of alcohol dehydrogenase sensitized Caco-2 cells to ethanol-induced tight junction disruption and barrier dysfunction, whereas aldehyde dehydrogenase attenuated acetaldehyde-induced tight junction disruption. Ethanol up to 150 mM did not affect tight junction integrity or barrier function, but it dose-dependently increased acetaldehyde-mediated tight junction disruption and barrier dysfunction. Src kinase and MLCK inhibitors blocked this synergistic effect of ethanol and acetaldehyde on tight junction. Ethanol and acetaldehyde caused a rapid and synergistic elevation of intracellular calcium. Calcium depletion by BAPTA or Ca 2+ -free medium blocked ethanol and acetaldehyde-induced barrier dysfunction and tight junction disruption. Diltiazem and selective knockdown of TRPV6 or Ca V 1.3 channels, by shRNA blocked ethanol and acetaldehyde-induced tight junction disruption and barrier dysfunction. Ethanol and acetaldehyde induced a rapid and synergistic increase in reactive oxygen species by a calcium-dependent mechanism. N-acetyl-L-cysteine and cyclosporine A, blocked ethanol and acetaldehyde-induced barrier dysfunction and tight junction disruption. These results demonstrate that ethanol and acetaldehyde synergistically disrupt tight junctions by a mechanism involving calcium, oxidative stress, Src kinase and MLCK.

Probing Leader Cells in Endothelial Collective Migration by Plasma Lithography Geometric Confinement

PubMed Central

Yang, Yongliang; Jamilpour, Nima; Yao, Baoyin; Dean, Zachary S.; Riahi, Reza; Wong, Pak Kin

2016-01-01

When blood vessels are injured, leader cells emerge in the endothelium to heal the wound and restore the vasculature integrity. The characteristics of leader cells during endothelial collective migration under diverse physiological conditions, however, are poorly understood. Here we investigate the regulation and function of endothelial leader cells by plasma lithography geometric confinement generated. Endothelial leader cells display an aggressive phenotype, connect to follower cells via peripheral actin cables and discontinuous adherens junctions, and lead migrating clusters near the leading edge. Time-lapse microscopy, immunostaining, and particle image velocimetry reveal that the density of leader cells and the speed of migrating clusters are tightly regulated in a wide range of geometric patterns. By challenging the cells with converging, diverging and competing patterns, we show that the density of leader cells correlates with the size and coherence of the migrating clusters. Collectively, our data provide evidence that leader cells control endothelial collective migration by regualting the migrating clusters. PMID:26936382

Optical volume and mass measurements show that mammalian cells swell during mitosis

PubMed Central

Zlotek-Zlotkiewicz, Ewa; Monnier, Sylvain; Cappello, Giovanni; Le Berre, Mael

2015-01-01

The extent, mechanism, and function of cell volume changes during specific cellular events, such as cell migration and cell division, have been poorly studied, mostly because of a lack of adequate techniques. Here we unambiguously report that a large range of mammalian cell types display a significant increase in volume during mitosis (up to 30%). We further show that this increase in volume is tightly linked to the mitotic state of the cell and not to its spread or rounded shape and is independent of the presence of an intact actomyosin cortex. Importantly, this volume increase is not accompanied by an increase in dry mass and thus corresponds to a decrease in cell density. This mitotic swelling might have important consequences for mitotic progression: it might contribute to produce strong pushing forces, allowing mitotic cells to round up; it might also, by lowering cytoplasmic density, contribute to the large change of physicochemical properties observed in mitotic cells. PMID:26598614

Electronic transport in disordered MoS2 nanoribbons

NASA Astrophysics Data System (ADS)

Ridolfi, Emilia; Lima, Leandro R. F.; Mucciolo, Eduardo R.; Lewenkopf, Caio H.

2017-01-01

We study the electronic structure and transport properties of zigzag and armchair monolayer molybdenum disulfide nanoribbons using an 11-band tight-binding model that accurately reproduces the material's bulk band structure near the band gap. We study the electronic properties of pristine zigzag and armchair nanoribbons, paying particular attention to the edges states that appear within the MoS2 bulk gap. By analyzing both their orbital composition and their local density of states, we find that in zigzag-terminated nanoribbons these states can be localized at a single edge for certain energies independent of the nanoribbon width. We also study the effects of disorder in these systems using the recursive Green's function technique. We show that for the zigzag nanoribbons, the conductance due to the edge states is strongly suppressed by short-range disorder such as vacancies. In contrast, the local density of states still shows edge localization. We also show that long-range disorder has a small effect on the transport properties of nanoribbons within the bulk gap energy window.

Probing Leader Cells in Endothelial Collective Migration by Plasma Lithography Geometric Confinement.

PubMed

Yang, Yongliang; Jamilpour, Nima; Yao, Baoyin; Dean, Zachary S; Riahi, Reza; Wong, Pak Kin

2016-03-03

When blood vessels are injured, leader cells emerge in the endothelium to heal the wound and restore the vasculature integrity. The characteristics of leader cells during endothelial collective migration under diverse physiological conditions, however, are poorly understood. Here we investigate the regulation and function of endothelial leader cells by plasma lithography geometric confinement generated. Endothelial leader cells display an aggressive phenotype, connect to follower cells via peripheral actin cables and discontinuous adherens junctions, and lead migrating clusters near the leading edge. Time-lapse microscopy, immunostaining, and particle image velocimetry reveal that the density of leader cells and the speed of migrating clusters are tightly regulated in a wide range of geometric patterns. By challenging the cells with converging, diverging and competing patterns, we show that the density of leader cells correlates with the size and coherence of the migrating clusters. Collectively, our data provide evidence that leader cells control endothelial collective migration by regualting the migrating clusters.

Open-celled polyurethane foam

NASA Technical Reports Server (NTRS)

Russell, L. W.

1970-01-01

Open-celled polyurethane foam has a density of 8.3 pounds per cubic foot and a compressive strength of 295 to 325 psi. It is useful as a porous spacer in layered insulation and as an insulation material in vacuum tight systems.

Dielectric response of molecules in empirical tight-binding theory

NASA Astrophysics Data System (ADS)

Boykin, Timothy B.; Vogl, P.

2002-01-01

In this paper we generalize our previous approach to electromagnetic interactions within empirical tight-binding theory to encompass molecular solids and isolated molecules. In order to guarantee physically meaningful results, we rederive the expressions for relevant observables using commutation relations appropriate to the finite tight-binding Hilbert space. In carrying out this generalization, we examine in detail the consequences of various prescriptions for the position and momentum operators in tight binding. We show that attempting to fit parameters of the momentum matrix directly generally results in a momentum operator which is incompatible with the underlying tight-binding model, while adding extra position parameters results in numerous difficulties, including the loss of gauge invariance. We have applied our scheme, which we term the Peierls-coupling tight-binding method, to the optical dielectric function of the molecular solid PPP, showing that this approach successfully predicts its known optical properties even in the limit of isolated molecules.

Tightness of hamstring- and psoas major muscles. A prospective study of back pain in young men during their military service.

PubMed

Hellsing, A L

1988-01-01

Muscular tightness and the therapeutic effect of stretching has been widely discussed during the last few years in sports training and physiotherapy. Within a prospective study of back function and pain before and after compulsory military service, tightness of hamstring- and psoas muscles was assessed. Around 600 young men were examined three times over a period of four years. Tight hamstring muscles were found to be very common in this group. Only 43% of the right and 35% of the left legs reached an angle of at least 80 degrees from the couch during the straight-leg-raising test (Lasegue's test). The test of muscular tightness showed a significant test-retest reliability over all examinations. Tight hamstring- or psoas muscles could not be shown to correlate to current back pain or to the incidence of back pain during the follow-up period.

Configuration of separability and tests for multipartite entanglement in bell-type experiments.

PubMed

Nagata, Koji; Koashi, Masato; Imoto, Nobuyuki

2002-12-23

We derive tight quadratic inequalities for all kinds of hybrid separable-inseparable n-particle density operators on an arbitrary dimensional space. This methodology enables us to derive a tight quadratic inequality as tests for full n-partite entanglement in various Bell-type correlation experiments on the systems that may not be identified as a collection of qubits, e.g., those involving photons measured by incomplete detectors. It is also proved that when the two measured observables are assumed to precisely anticommute, a stronger quadratic inequality can be used as a witness of full n-partite entanglement.

Carbon dioxide is tightly bound in the [Co(Pyridine)(CO2)]- anionic complex

NASA Astrophysics Data System (ADS)

Graham, Jacob D.; Buytendyk, Allyson M.; Zhang, Xinxing; Kim, Seong K.; Bowen, Kit H.

2015-11-01

The [Co(Pyridine)(CO2)]- anionic complex was studied through the combination of photoelectron spectroscopy and density functional theory calculations. This complex was envisioned as a primitive model system for studying CO2 binding to negatively charged sites in metal organic frameworks. The vertical detachment energy (VDE) measured via the photoelectron spectrum is 2.7 eV. Our calculations imply a structure for [Co(Pyridine)(CO2)]- in which a central cobalt atom is bound to pyridine and CO2 moieties on either sides. This structure was validated by acceptable agreement between the calculated and measured VDE values. Based on our calculations, we found CO2 to be bound within the anionic complex by 1.4 eV.

Carbon dioxide is tightly bound in the [Co(Pyridine)(CO2)](-) anionic complex.

PubMed

Graham, Jacob D; Buytendyk, Allyson M; Zhang, Xinxing; Kim, Seong K; Bowen, Kit H

2015-11-14

The [Co(Pyridine)(CO2)](-) anionic complex was studied through the combination of photoelectron spectroscopy and density functional theory calculations. This complex was envisioned as a primitive model system for studying CO2 binding to negatively charged sites in metal organic frameworks. The vertical detachment energy (VDE) measured via the photoelectron spectrum is 2.7 eV. Our calculations imply a structure for [Co(Pyridine)(CO2)](-) in which a central cobalt atom is bound to pyridine and CO2 moieties on either sides. This structure was validated by acceptable agreement between the calculated and measured VDE values. Based on our calculations, we found CO2 to be bound within the anionic complex by 1.4 eV.

Surface alloy engineering in 2D trigonal lattice: giant Rashba spin splitting and two large topological gaps

NASA Astrophysics Data System (ADS)

Liu, Zhao; Jin, Yingdi; Yang, Yuchen; Wang, Z. F.; Yang, Jinlong

2018-02-01

We demonstrate that sp 2 based trigonal lattice can exhibit giant Rashba splitting and two large topological gaps simultaneously. First, an effective tight binding model is developed to describe the Rashba spin-orbit coupling (SOC) on a real surface and give a topological phase diagram based on two independent SOC parameters. Second, based on density functional theory calculations, it is proposed that Au/Si(111)-\\sqrt{3}× \\sqrt{3} surface with 1/3 monolayer Bi coverage is a good material candidate to realize both giant Rashba splitting and two large topological gaps. These results would inspire great research interests for searching two-dimensional topological insulator and manipulating Rashba spin splitting through surface alloy engineering.

Investigation of the effect of scattering centers on low dimensional nanowire channel

NASA Astrophysics Data System (ADS)

Cariappa, K. S.; Shukla, Raja; Sarkar, Niladri

2018-05-01

In this work, we studied the effect of scattering centers on the electron density profiles of a one dimensional Nanowire channel. Density Matrix Formalism is used for calculating the local electron densities at room temperature. Various scattering centers have been simulated in the channel. The nearest neighbor tight binding method is applied to construct the Hamiltonian of nanoscale devices. We invoke scattering centers by adding local scattering potentials to the Hamiltonian. This analysis could give an insight into the understanding and utilization of defects for device engineering.

Electronic compressibility of bilayer graphene

NASA Astrophysics Data System (ADS)

Henriksen, Erik

2011-03-01

We have recently measured the electronic compressibility of bilayer graphene, allowing exploration of the thermodynamic density of states as a function of applied electric and magnetic fields. Utilizing dual-gated field-effect devices, we can independently vary both the carrier density and the size of the tunable band gap. An oscillating voltage applied to a back gate generates corresponding signals in the top gate via electric fields lines which penetrate the graphene, thereby allowing a direct measurement of the inverse compressibility, K-1 , of the bilayer. We have mapped K-1 , which is proportional to the inverse density of states, as a function of the top and back gate voltages in zero and finite magnetic field. A sharp increase in K-1 near zero density is observed with increasing electric field strength, signaling the controlled opening of a band gap. At high magnetic fields, broad Landau level (LL) oscillations are observed, directly revealing the doubled degeneracy of the lowest LL and allowing for a determination of the disorder broadening of the levels. We compare our results to tight-binding calculations of the bilayer band structure, and to recent theoretical studies of the compressibility of bilayer graphene. Together, these clearly illustrate the unusual hyperbolic nature of the low energy band structure, reveal a sizeable electron-hole asymmetry, and suggest that many-body interactions play only a small role in bilayer-on-substrate devices. This work is a collaboration with J. P. Eisenstein of Caltech, and is supported by the NSF under Grant No. DMR-0552270 and the DOE under Grant No. DE-FG03-99ER45766.

Intracellular Ca2+ release mediates cationic but not anionic poly(amidoamine) (PAMAM) dendrimer-induced tight junction modulation.

PubMed

Avaritt, Brittany R; Swaan, Peter W

2014-09-01

Poly(amidoamine) (PAMAM) dendrimers show great promise for utilization as oral drug delivery vehicles. These polymers are capable of traversing epithelial barriers, and have been shown to translocate by both transcellular and paracellular routes. While many proof-of-concept studies have shown that PAMAM dendrimers improve intestinal transport, little information exists on the mechanisms of paracellular transport, specifically dendrimer-induced tight junction modulation. Using anionic G3.5 and cationic G4 PAMAM dendrimers with known absorption enhancers, we investigated tight junction modulation in Caco-2 monolayers by visualization and mannitol permeability and compared dendrimer-mediated tight junction modulation to that of established permeation enhancers. [(14)C]-Mannitol permeability in the presence and absence of phospholipase C-dependent signaling pathway inhibitors was also examined and indicated that this pathway may mediate dendrimer-induced changes in permeability. Differences between G3.5 and G4 in tight junction protein staining and permeability with inhibitors were evident, suggesting divergent mechanisms were responsible for tight junction modulation. These dissimilarities are further intimated by the intracellular calcium release caused by G4 but not G3.5. Based on our results, it is apparent that the underlying mechanisms of dendrimer permeability are complex, and the complexities are likely a result of the density and sign of the surface charges of PAMAM dendrimers. The results of this study will have implications on the future use of PAMAM dendrimers for oral drug delivery.

Multiply Reduced Oligofluorenes: Their Nature and Pairing with THF-Solvated Sodium Ions

DOE PAGES

Wu, Qin; Zaikowski, Lori; Kaur, Parmeet; ...

2016-07-01

Conjugated oligofluorenes are chemically reduced up to five charges in tetrahydrofuran solvent and confirmed with clear spectroscopic evidence. Stimulated by these experimental results, we have conducted a comprehensive computational study of the electronic structure and the solvation structure of representative oligofluorene anions with a focus on the pairing between sodium ions and these multianions. In addition, using density functional theory (DFT) methods and a solvation model of both explicit solvent molecules and implicit polarizable continuum, we first elucidate the structure of tightly solvated free sodium ions, and then explore the pairing of sodium ions either in contact with reduced oligofluorenesmore » or as solvent-separated ion pairs. Computed time-dependent-DFT absorption spectra are compared with experiments to assign the dominant ion pairing structure for each multianion. Computed ion pair binding energies further support our assignment. Lastly, the availability of different length and reducing level of oligofluorenes enables us to investigate the effects of total charge and charge density on the binding with sodium ions, and our results suggest both factors play important roles in ion pairing for small molecules. However, as the oligofluorene size grows, its charge density determines the binding strength with the sodium ion.« less

Shock-Compressed Hydrogen

NASA Astrophysics Data System (ADS)

Bickham, S. R.; Collins, L. A.; Kress, J. D.; Lenosky, T. J.

1999-06-01

To investigate recent gas-gun and laser experiments on hydrogen at elevated temperatures and high densities, we have performed quantum molecular dynamics simulations using a variety of sophisticated models, ranging from tight-binding(TB) to density functional(DF)(T.J. Lenosky, J.D. Kress, L.A. Collins, and I. Kwon Phys. Rev. B 55), R11907(1997) and references therein.. The TB models have been especially tailored to reproduce experimental findings, such as Diamond-Anvil Cell data, and ab initio calculations, such as H_2, H_3, and H4 potential energy surfaces. The DF calculations have employed the local-density approximation(LDA) as well as generalized gradient corrections(GGA) with large numbers of plane-waves ( ~10^5) that represent a very broad range of excited and continuum electronic states. Good agreement obtains among all these models. The simulations exhibit a rapidly rising electrical conductivity at low temperatures and high pressures in good agreement with the gas-gun results. This conduction property stems from a mobility of the electrons provided principally by the dissociated monomers. The Hugoniot for the conditions of the laser experiment, generated from the TB Equation-of-State, shows a maximum compression of around four instead of the observed six. We also report optical properties of the hydrogen media.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Qin; Zaikowski, Lori; Kaur, Parmeet

Conjugated oligofluorenes are chemically reduced up to five charges in tetrahydrofuran solvent and confirmed with clear spectroscopic evidence. Stimulated by these experimental results, we have conducted a comprehensive computational study of the electronic structure and the solvation structure of representative oligofluorene anions with a focus on the pairing between sodium ions and these multianions. In addition, using density functional theory (DFT) methods and a solvation model of both explicit solvent molecules and implicit polarizable continuum, we first elucidate the structure of tightly solvated free sodium ions, and then explore the pairing of sodium ions either in contact with reduced oligofluorenesmore » or as solvent-separated ion pairs. Computed time-dependent-DFT absorption spectra are compared with experiments to assign the dominant ion pairing structure for each multianion. Computed ion pair binding energies further support our assignment. Lastly, the availability of different length and reducing level of oligofluorenes enables us to investigate the effects of total charge and charge density on the binding with sodium ions, and our results suggest both factors play important roles in ion pairing for small molecules. However, as the oligofluorene size grows, its charge density determines the binding strength with the sodium ion.« less

Accurate donor electron wave functions from a multivalley effective mass theory.

NASA Astrophysics Data System (ADS)

Pendo, Luke; Hu, Xuedong

Multivalley effective mass (MEM) theories combine physical intuition with a marginal need for computational resources, but they tend to be insensitive to variations in the wavefunction. However, recent papers suggest full Bloch functions and suitable central cell donor potential corrections are essential to replicating qualitative and quantitative features of the wavefunction. In this talk, we consider a variational MEM method that can accurately predict both spectrum and wavefunction of isolated phosphorus donors. As per Gamble et. al, we employ a truncated series representation of the Bloch function with a tetrahedrally symmetric central cell correction. We use a dynamic dielectric constant, a feature commonly seen in tight-binding methods. Uniquely, we use a freely extensible basis of either all Slater- or all Gaussian-type functions. With a large basis able to capture the influence of higher energy eigenstates, this method is well positioned to consider the influence of external perturbations, such as electric field or applied strain, on the charge density. This work is supported by the US Army Research Office (W911NF1210609).

In tight junctions, claudins regulate the interactions between occludin, tricellulin and marvelD3, which, inversely, modulate claudin oligomerization.

PubMed

Cording, Jimmi; Berg, Johanna; Käding, Nadja; Bellmann, Christian; Tscheik, Christian; Westphal, Julie K; Milatz, Susanne; Günzel, Dorothee; Wolburg, Hartwig; Piontek, Jörg; Huber, Otmar; Blasig, Ingolf Ernst

2013-01-15

Tight junctions seal the paracellular cleft of epithelia and endothelia, form vital barriers between tissue compartments and consist of tight-junction-associated marvel proteins (TAMPs) and claudins. The function of TAMPs and the interaction with claudins are not understood. We therefore investigated the binding between the TAMPs occludin, tricellulin, and marvelD3 and their interaction with claudins in living tight-junction-free human embryonic kidney-293 cells. In contrast to claudins and occludin, tricellulin and marvelD3 showed no enrichment at cell-cell contacts indicating lack of homophilic trans-interaction between two opposing cell membranes. However, occludin, marvelD3 and tricellulin exhibited homophilic cis-interactions, along one plasma membrane, as measured by fluorescence resonance energy transfer. MarvelD3 also cis-interacted with occludin and tricellulin heterophilically. Classic claudins, such as claudin-1 to -5 may show cis-oligomerization with TAMPs, whereas the non-classic claudin-11 did not. Claudin-1 and -5 improved enrichment of occludin and tricellulin at cell-cell contacts. The low mobile claudin-1 reduced the membrane mobility of the highly mobile occludin and tricellulin, as studied by fluorescence recovery after photobleaching. Co-transfection of claudin-1 with TAMPs led to changes of the tight junction strand network of this claudin to a more physiological morphology, depicted by freeze-fracture electron microscopy. The results demonstrate multilateral interactions between the tight junction proteins, in which claudins determine the function of TAMPs and vice versa, and provide deeper insights into the tight junction assembly.

Dietary glucosylceramide enhances tight junction function in skin epidermis via induction of claudin-1.

PubMed

Kawada, Chinatsu; Hasegawa, Tatsuya; Watanabe, Mutsuto; Nomura, Yoshihiro

2013-01-01

Dietary glucosylceramide increased the expression of claudin-1 in UVB-irradiated mouse epidermis. Sphingosine and phytosphingosine, metabolites of glucosylceramide, increased trans-epithelial electrical resistance, and phytosphingosine increased claudin-1 mRNA expression in cultured keratinocytes. Our results indicate that the skin barrier improvement induced by dietary glucosylceramide might be due to enhancement of tight junction function, mediated by increased expression of claudin-1 induced by sphingoid metabolites.

High β produced by neutral beam injection in the START (Small Tight Aspect Ratio Tokamak) spherical tokamak

NASA Astrophysics Data System (ADS)

Sykes, Alan

1997-05-01

The world's first high-power auxiliary heating experiments in a tight aspect ratio (or spherical) tokamak have been performed on the Small Tight Aspect Ratio Tokomak (START) device [Sykes et al., Nucl. Fusion 32, 694 (1992)] at Culham Laboratory, using the 40 keV, 0.5 MW Neutral Beam Injector loaned by the Oak Ridge National Laboratory. Injection has been mainly of hydrogen into hydrogen or deuterium target plasmas, with a one-day campaign to explore D→D operation. In each case injection provides a combination of higher density operation and effective heating of both ions and electrons. The highest β values achieved to date in START are volume average βT˜11.5% and central beta βO˜50%. Already high, these values are expected to increase further with the use of higher beam power.

Adaptive tight frame based medical image reconstruction: a proof-of-concept study for computed tomography

NASA Astrophysics Data System (ADS)

Zhou, Weifeng; Cai, Jian-Feng; Gao, Hao

2013-12-01

A popular approach for medical image reconstruction has been through the sparsity regularization, assuming the targeted image can be well approximated by sparse coefficients under some properly designed system. The wavelet tight frame is such a widely used system due to its capability for sparsely approximating piecewise-smooth functions, such as medical images. However, using a fixed system may not always be optimal for reconstructing a variety of diversified images. Recently, the method based on the adaptive over-complete dictionary that is specific to structures of the targeted images has demonstrated its superiority for image processing. This work is to develop the adaptive wavelet tight frame method image reconstruction. The proposed scheme first constructs the adaptive wavelet tight frame that is task specific, and then reconstructs the image of interest by solving an l1-regularized minimization problem using the constructed adaptive tight frame system. The proof-of-concept study is performed for computed tomography (CT), and the simulation results suggest that the adaptive tight frame method improves the reconstructed CT image quality from the traditional tight frame method.

Two-Finger Tightness: What Is It? Measuring Torque and Reproducibility in a Simulated Model.

PubMed

Acker, William B; Tai, Bruce L; Belmont, Barry; Shih, Albert J; Irwin, Todd A; Holmes, James R

2016-05-01

Residents in training are often directed to insert screws using "two-finger tightness" to impart adequate torque but minimize the chance of a screw stripping in bone. This study seeks to quantify and describe two-finger tightness and to assess the variability of its application by residents in training. Cortical bone was simulated using a polyurethane foam block (30-pcf density) that was prepared with predrilled holes for tightening 3.5 × 14-mm long cortical screws and mounted to a custom-built apparatus on a load cell to capture torque data. Thirty-three residents in training, ranging from the first through fifth years of residency, along with 8 staff members, were directed to tighten 6 screws to two-finger tightness in the test block, and peak torque values were recorded. The participants were blinded to their torque values. Stripping torque (2.73 ± 0.56 N·m) was determined from 36 trials and served as a threshold for failed screw placement. The average torques varied substantially with regard to absolute torque values, thus poorly defining two-finger tightness. Junior residents less consistently reproduced torque compared with other groups (0.29 and 0.32, respectively). These data quantify absolute values of two-finger tightness but demonstrate considerable variability in absolute torque values, percentage of stripping torque, and ability to consistently reproduce given torque levels. Increased years in training are weakly correlated with reproducibility, but experience does not seem to affect absolute torque levels. These results question the usefulness of two-finger tightness as a teaching tool and highlight the need for improvement in resident motor skill training and development within a teaching curriculum. Torque measuring devices may be a useful simulation tools for this purpose.

Conductance of AFM Deformed Carbon Nanotubes

NASA Technical Reports Server (NTRS)

Svizhenko, Alexei; Maiti, Amitesh; Anatram, M. P.; Biegel, Bryan (Technical Monitor)

2002-01-01

This viewgraph presentation provides information on the electrical conductivity of carbon nanotubes upon deformation by atomic force microscopy (AFM). The density of states and conductance were computed using four orbital tight-binding method with various parameterizations. Different chiralities develop bandgap that varies with chirality.

Delayed astrocytic contact with cerebral blood vessels in FGF-2 deficient mice does not compromise permeability properties at the developing blood-brain barrier.

PubMed

Saunders, Norman R; Dziegielewska, Katarzyna M; Unsicker, Klaus; Ek, C Joakim

2016-11-01

The brain functions within a specialized environment tightly controlled by brain barrier mechanisms. Understanding the regulation of barrier formation is important for understanding brain development and may also lead to finding new ways to deliver pharmacotherapies to the brain; access of many potentially promising drugs is severely hindered by these barrier mechanisms. The cellular composition of the neurovascular unit of the blood-brain barrier proper and their effects on regulation of its function are beginning to be understood. One hallmark of the neurovascular unit in the adult is the astroglial foot processes that tightly surround cerebral blood vessels. However their role in barrier formation is still unclear. In this study we examined barrier function in newborn, juvenile and adult mice lacking fibroblast growth factor-2 (FGF-2), which has been shown to result in altered astroglial differentiation during development. We show that during development of FGF-2 deficient mice the astroglial contacts with cerebral blood vessels are delayed compared with wild-type animals. However, this delay did not result in changes to the permeability properties of the blood brain barrier as assessed by exclusion of either small or larger sized molecules at this interface. In addition cerebral vessels were positive for tight-junction proteins and we observed no difference in the ultrastructure of the tight-junctions. The results indicate that the direct contact of astroglia processes to cerebral blood vessels is not necessary for either the formation of the tight-junctions or for basic permeability properties and function of the blood-brain barrier. © 2016 Wiley Periodicals, Inc. Develop Neurobiol 76: 1201-1212, 2016. © 2016 Wiley Periodicals, Inc.

Resonant scattering due to adatoms in graphene: Top, bridge, and hollow positions

NASA Astrophysics Data System (ADS)

Irmer, Susanne; Kochan, Denis; Lee, Jeongsu; Fabian, Jaroslav

2018-02-01

We present a theoretical study of resonance characteristics in graphene from adatoms with s or pz character binding in top, bridge, and hollow positions. The adatoms are described by two tight-binding parameters: on-site energy and hybridization strength. We explore a wide range of different magnitudes of these parameters by employing T -matrix calculations in the single adatom limit and by tight-binding supercell calculations for dilute adatom coverage. We calculate the density of states and the momentum relaxation rate and extract the resonance level and resonance width. The top position with a large hybridization strength or, equivalently, small on-site energy, induces resonances close to zero energy. The bridge position, compared to top, is more sensitive to variation in the orbital tight-binding parameters. Resonances within the experimentally relevant energy window are found mainly for bridge adatoms with negative on-site energies. The effect of resonances from the top and bridge positions on the density of states and momentum relaxation rate is comparable and both positions give rise to a power-law decay of the resonant state in graphene. The hollow position with s orbital character is affected from destructive interference, which is seen from the very narrow resonance peaks in the density of states and momentum relaxation rate. The resonant state shows no clear tendency to a power-law decay around the impurity and its magnitude decreases strongly with lowering the adatom content in the supercell calculations. This is in contrast to the top and bridge positions. We conclude our study with a comparison to models of pointlike vacancies and strong midgap scatterers. The latter model gives rise to significantly higher momentum relaxation rates than caused by single adatoms.

Modulation of Intestinal Paracellular Transport by Bacterial Pathogens.

PubMed

Roxas, Jennifer Lising; Viswanathan, V K

2018-03-25

The passive and regulated movement of ions, solutes, and water via spaces between cells of the epithelial monolayer plays a critical role in the normal intestinal functioning. This paracellular pathway displays a high level of structural and functional specialization, with the membrane-spanning complexes of the tight junctions, adherens junctions, and desmosomes ensuring its integrity. Tight junction proteins, like occludin, tricellulin, and the claudin family isoforms, play prominent roles as barriers to unrestricted paracellular transport. The past decade has witnessed major advances in our understanding of the architecture and function of epithelial tight junctions. While it has been long appreciated that microbes, notably bacterial and viral pathogens, target and disrupt junctional complexes and alter paracellular permeability, the precise mechanisms remain to be defined. Notably, renewed efforts will be required to interpret the available data on pathogen-mediated barrier disruption in the context of the most recent findings on tight junction structure and function. While much of the focus has been on pathogen-induced dysregulation of junctional complexes, commensal microbiota and their products may influence paracellular permeability and contribute to the normal physiology of the gut. Finally, microbes and their products have become important tools in exploring host systems, including the junctional properties of epithelial cells. © 2018 American Physiological Society. Compr Physiol 8:823-842, 2018. Copyright © 2018 American Physiological Society. All rights reserved.

On the self-association potential of transmembrane tight junction proteins.

PubMed

Blasig, I E; Winkler, L; Lassowski, B; Mueller, S L; Zuleger, N; Krause, E; Krause, G; Gast, K; Kolbe, M; Piontek, J

2006-02-01

Tight junctions seal intercellular clefts via membrane-related strands, hence, maintaining important organ functions. We investigated the self-association of strand-forming transmembrane tight junction proteins. The regulatory tight junction protein occludin was differently tagged and cotransfected in eucaryotic cells. These occludins colocalized within the plasma membrane of the same cell, coprecipitated and exhibited fluorescence resonance energy transfer. Differently tagged strand-forming claudin-5 also colocalized in the plasma membrane of the same cell and showed fluorescence resonance energy transfer. This demonstrates self-association in intact cells both of occludin and claudin-5 in one plasma membrane. In search of dimerizing regions of occludin, dimerization of its cytosolic C-terminal coiledcoil domain was identified. In claudin-5, the second extracellular loop was detected as a dimer. Since the transmembrane junctional adhesion molecule also is known to dimerize, the assumption that homodimerization of transmembrane tight junction proteins may serve as a common structural feature in tight junction assembly is supported.

Gamma-ray generation in the interaction of two tightly focused laser pulses with a low-density target composed of electrons

NASA Astrophysics Data System (ADS)

Jirka, M.; Klimo, O.; Weber, S.; Bulanov, Sergei V.; Esirkepov, Timur Zh.; Korn, G.

2015-05-01

With the continuing development of laser systems, new important and so-far unexplored fields of research related to interaction of ultra-intense laser beams with matter are opening. At intensities of the order of 1022 W=cm2, electrons may be accelerated in the electromagnetic field of the laser wave and achieve such a high energy that they can enter the regime affected by the radiation reaction. Due to the non-linear Thomson and Compton scattering the accelerated electrons emit photons. The interaction of emitted photons with the laser field may result in effective generation of electron-positron pairs by means of the Breit-Wheeler process. In this work we study the influence of laser pulse polarization on gamma-ray generation during interaction of two colliding and tightly focused laser pulses with a low density target composed of electrons. This paper focuses on evolution of electron trajectories and key parameters χe (probability of photon emission) and χγ(probability of pair generation) in the laser field. These interactions are studied using 2D PIC simulations. It is shown that in the case of circularly polarized and tightly focused laser beams, electrons are not following circular trajectories at the magnetic node of the standing wave established in the focus, which leads to lowering the radiation emission efficiency.

Modelling realistic TiO2 nanospheres: A benchmark study of SCC-DFTB against hybrid DFT

NASA Astrophysics Data System (ADS)

Selli, Daniele; Fazio, Gianluca; Di Valentin, Cristiana

2017-10-01

TiO2 nanoparticles (NPs) are nowadays considered fundamental building blocks for many technological applications. Morphology is found to play a key role with spherical NPs presenting higher binding properties and chemical activity. From the experimental point of view, the characterization of these nano-objects is extremely complex, opening a large room for computational investigations. In this work, TiO2 spherical NPs of different sizes (from 300 to 4000 atoms) have been studied with a two-scale computational approach. Global optimization to obtain stable and equilibrated nanospheres was performed with a self-consistent charge density functional tight-binding (SCC-DFTB) simulated annealing process, causing a considerable atomic rearrangement within the nanospheres. Those SCC-DFTB relaxed structures have been then optimized at the DFT(B3LYP) level of theory. We present a systematic and comparative SCC-DFTB vs DFT(B3LYP) study of the structural properties, with particular emphasis on the surface-to-bulk sites ratio, coordination distribution of surface sites, and surface energy. From the electronic point of view, we compare HOMO-LUMO and Kohn-Sham gaps, total and projected density of states. Overall, the comparisons between DFTB and hybrid density functional theory show that DFTB provides a rather accurate geometrical and electronic description of these nanospheres of realistic size (up to a diameter of 4.4 nm) at an extremely reduced computational cost. This opens for new challenges in simulations of very large systems and more extended molecular dynamics.

Generalized nonequilibrium vertex correction method in coherent medium theory for quantum transport simulation of disordered nanoelectronics

NASA Astrophysics Data System (ADS)

Yan, Jiawei; Ke, Youqi

2016-07-01

Electron transport properties of nanoelectronics can be significantly influenced by the inevitable and randomly distributed impurities/defects. For theoretical simulation of disordered nanoscale electronics, one is interested in both the configurationally averaged transport property and its statistical fluctuation that tells device-to-device variability induced by disorder. However, due to the lack of an effective method to do disorder averaging under the nonequilibrium condition, the important effects of disorders on electron transport remain largely unexplored or poorly understood. In this work, we report a general formalism of Green's function based nonequilibrium effective medium theory to calculate the disordered nanoelectronics. In this method, based on a generalized coherent potential approximation for the Keldysh nonequilibrium Green's function, we developed a generalized nonequilibrium vertex correction method to calculate the average of a two-Keldysh-Green's-function correlator. We obtain nine nonequilibrium vertex correction terms, as a complete family, to express the average of any two-Green's-function correlator and find they can be solved by a set of linear equations. As an important result, the averaged nonequilibrium density matrix, averaged current, disorder-induced current fluctuation, and averaged shot noise, which involve different two-Green's-function correlators, can all be derived and computed in an effective and unified way. To test the general applicability of this method, we applied it to compute the transmission coefficient and its fluctuation with a square-lattice tight-binding model and compared with the exact results and other previously proposed approximations. Our results show very good agreement with the exact results for a wide range of disorder concentrations and energies. In addition, to incorporate with density functional theory to realize first-principles quantum transport simulation, we have also derived a general form of conditionally averaged nonequilibrium Green's function for multicomponent disorders.

Polymer-Cement Composites with Self-Healing Ability for Geothermal and Fossil Energy Applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Childers, M. Ian; Nguyen, Manh-Thuong; Rod, Kenton A.

Sealing of wellbores in geothermal and tight oil/gas reservoirs by filling the annulus with cement is a well-established practice. Failure of the cement as a result of physical and/or chemical stress is a common problem with serious environmental and financial consequences. Numerous alternative cement blends have been proposed for the oil and gas industry. Most of these possess poor mechanical properties, or are not designed to work in high temperature environments. This work reports on a novel polymer-cement composite with remarkable self-healing ability that maintains the required properties of typical wellbore cements and may be stable at most geothermal temperatures.more » We combine for the first time experimental analysis of physical and chemical properties with density functional theory simulations to evaluate cement performance. The thermal stability and mechanical strength are attributed to the formation of a number of chemical interactions between the polymer and cement matrix including covalent bonds, hydrogen bonding, and van der Waals interactions. Self-healing was demonstrated by sealing fractures with 0.3–0.5 mm apertures, 2 orders of magnitude larger than typical wellbore fractures. This polymer-cement composite represents a major advance in wellbore cementing that could improve the environmental safety and economics of enhanced geothermal energy and tight oil/gas production.« less

Oxygen holes and hybridization in the bismuthates

NASA Astrophysics Data System (ADS)

Khazraie, Arash; Foyevtsova, Kateryna; Elfimov, Ilya; Sawatzky, George A.

2018-02-01

Motivated by the recently renewed interest in the superconducting bismuth perovskites, we investigate the electronic structure of the parent compounds A BiO3 (A = Sr, Ba) using ab initio methods and tight-binding (TB) modeling. We use the density functional theory (DFT) in the local density approximation (LDA) to understand the role of various interactions in shaping the A BiO3 band structure near the Fermi level. It is established that interatomic hybridization involving Bi-6 s and O-2 p orbitals plays the most important role. Based on our DFT calculations, we derive a minimal TB model and demonstrate that it can describe the properties of the band structure as a function of lattice distortions, such as the opening of a charge gap with the onset of the breathing distortion and the associated condensation of holes onto a1 g-symmetric molecular orbitals formed by the O-2 pσ orbitals on collapsed octahedra. We also derive a single band model involving the hopping of an extended molecular orbital involving both Bi-6 s and a linear combination of six O-2 p orbitals which provides a very good description of the dispersion and band gaps of the low energy scale bands straddling the chemical potential.

Out-of-equilibrium dynamics of repulsive Fermi gases in quasiperiodic potentials: A density functional theory study

NASA Astrophysics Data System (ADS)

Ancilotto, Francesco; Rossini, Davide; Pilati, Sebastiano

2018-04-01

The dynamics of a one-dimensional two-component Fermi gas in the presence of a quasiperiodic optical lattice (OL) is investigated by means of a density functional theory approach. Inspired by the protocol implemented in recent cold-atom experiments—designed to identify the many-body localization transition—we analyze the relaxation of an initially prepared imbalance between the occupation number of odd and of even sites. For quasidisorder strength beyond the Anderson localization transition, the imbalance survives for long times, indicating the inability of the system to reach local equilibrium. The late-time value of the imbalance diminishes for increasing interaction strength. Close to the critical quasidisorder strength corresponding to the noninteracting (Anderson) transition, the interacting system displays an extremely slow relaxation dynamics, consistent with subdiffusive behavior. The amplitude of the imbalance fluctuations around its running average is found to decrease with time, and such damping is more effective with increasing interaction strengths. While our study addresses the setup with two equally intense OLs, very similar effects due to interactions have been observed also in recent cold-atom experiments performed in the tight-binding regime, i.e., where one of the two OLs is very deep and the other is much weaker.

[The effect of 18β-glycyrrhetinic acid on tight junctions of the nasal mucosa epithelial cells in rat models with allergic rhinitis].

PubMed

Ma, Yi; Gui, Yan; Wang, Youhu; Xi, Kehu; Chen, Xiaowan; Zhang, Fuhong; Ma, Chunxia; Hong, Hao; Liu, Xiangyi; Jiang, Ying; Dong, Ming; Yang, Guijun; Zhang, Xiaobing

2014-10-01

To observe 18β-glycyrrhetinic acid (GA) impact on ultrastructure of tight junctions (TJs) of nasal mucosa epithelial cells in rats models of allergic rhinitis (AR). Ninety-six Wistar rats were randomly divided into control group, model group, loratadine group, and 18β-glycyrrhetinic acid group, and each group had 24 rats. Ovalbumin was used to establish a rat AR model. The behavioral changes and the tight junctions of nasal epithelial were observed and compared in different groups after 2,4,6 and 10 weeks intervention. The length of TJs in allergic rhinitis model became shorter, electron-high-density plasma membrane became thicker, number of the integration loci reduced and gap of TJs widened or even ruptured. With the consistent effect of allergens,the changes of TJs in the model group aggravated gradually,and the changes of ultrastructure of TJs in 18β-glycyrrhetinic acid group was relieved apparently compared to model group and even were close to the control model with time. 18β-glycyrrhetinic acid can recover the ultrastructure of the tight junctions of AR rat nasal epithelial cells.

Spin fluctuations and superconductivity in a 3D tight-binding model for BaFe2As2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Graser, Siegfried; Kemper, Alexander F; Maier, Thomas A

2010-01-01

Despite the wealth of experimental data on the Fe-pnictide compounds of the KFe2As2 type, K=Ba, Ca, or Sr, the main theoretical work based on multiorbital tight-binding models has been restricted so far to the study of the related 1111 compounds. This can be ascribed to the more three-dimensional electronic structure found by ab initio calculations for the 122 materials, making this system less amenable to model development. In addition, the more complicated Brillouin zone BZ of the body-centered tetragonal symmetry does not allow a straightforward unfolding of the electronic band structure into an effective 1Fe/unit cell BZ. Here we presentmore » an effective five-orbital tight-binding fit of the full density functional theory band structure for BaFe2As2 including the kz dispersions. We compare the five-orbital spin fluctuation model to one previously studied for LaOFeAs and calculate the random-phase approximation enhanced susceptibility. Using the fluctuation ex- change approximation to determine the leading pairing instability, we then examine the differences between a strictly two-dimensional model calculation over a single kz cut of the BZ and a completely three-dimensional approach. We find pairing states quite similar to the 1111 materials, with generic quasi-isotropic pairing on the hole sheets and nodal states on the electron sheets at kz=0, which however are gapped as the system is hole doped. On the other hand, a substantial kz dependence of the order parameter remains, with most of the pairing strength deriving from processes near kz=?. These states exhibit a tendency for an enhanced anisotropy on the hole sheets and a reduced anisotropy on the electron sheets near the top of the BZ.« less

Tight junctions in cancer metastasis.

PubMed

Martin, Tracey A; Mason, Malcolm D; Jiang, Wen G

2011-01-01

Tight Junctions (TJ) are well known to function as a control for the paracellular diffusion of ions and certain molecules, it has however, become evident that the TJ has a vital role in maintaining cell to cell integrity. Loss of cohesion of the TJ structure can lead to invasion and ultimately to the metastasis of cancer cells. This review will discuss how modulation of expression of TJ molecules results in key changes in TJ barrier function leading to the progression of cancer and progression of metastasis.

a Fractal Permeability Model Coupling Boundary-Layer Effect for Tight Oil Reservoirs

NASA Astrophysics Data System (ADS)

Wang, Fuyong; Liu, Zhichao; Jiao, Liang; Wang, Congle; Guo, Hu

A fractal permeability model coupling non-flowing boundary-layer effect for tight oil reservoirs was proposed. Firstly, pore structures of tight formations were characterized with fractal theory. Then, with the empirical equation of boundary-layer thickness, Hagen-Poiseuille equation and fractal theory, a fractal torturous capillary tube model coupled with boundary-layer effect was developed, and verified with experimental data. Finally, the parameters influencing effective liquid permeability were quantitatively investigated. The research results show that effective liquid permeability of tight formations is not only decided by pore structures, but also affected by boundary-layer distributions, and effective liquid permeability is the function of fluid type, fluid viscosity, pressure gradient, fractal dimension, tortuosity fractal dimension, minimum pore radius and maximum pore radius. For the tight formations dominated with nanoscale pores, boundary-layer effect can significantly reduce effective liquid permeability, especially under low pressure gradient.

Improved Characterization and Modeling of Tight Oil Formations for CO 2 Enhanced Oil Recovery Potential and Storage Capacity Estimation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sorensen, James; Smith, Steven; Kurz, Bethany

Tight oil formations such as those in the Bakken petroleum system are known to hold hundreds of billions of barrels of oil in place; however, the primary recovery factor for these plays is typically less than 10%. Tight oil formations, including the Bakken Formation, therefore, may be attractive candidates for enhanced oil recovery (EOR) using CO 2. Multiphase fluid behavior and flow in fluid-rich shales can vary substantially depending on the size of pore throats, and properties such as fluid viscosity and density are much different in nanoscale pores than in macroscale pores. Thus it is critical to understand themore » nature and distribution of nano-, micro-, and macroscale pores and fracture networks. To address these issues, the Energy & Environmental Research Center (EERC) has been conducting a research program entitled “Improved Characterization and Modeling of Tight Oil Formations for CO 2 Enhanced Oil Recovery Potential and Storage Capacity Estimation.” The objectives of the project are 1) the use of advanced characterization methods to better understand and quantify the petrophysical and geomechanical factors that control CO 2 and oil mobility within tight oil formation samples, 2) the determination of CO 2 permeation and oil extraction rates in tight reservoir rocks and organic-rich shales of the Bakken, and 3) the integration of the laboratory-based CO 2 permeation and oil extraction data and the characterization data into geologic models and dynamic simulations to develop predictions of CO 2 storage resource and EOR in the Bakken tight oil formation. A combination of standard and advanced petrophysical characterization techniques were applied to characterize samples of Bakken Formation tight reservoir rock and shales from multiple wells. Techniques included advanced computer tomography (CT) imaging, scanning electron microscopy (SEM) techniques, whole-core and micro x-ray CT imaging, field emission (FE) SEM, and focused ion beam (FIB) SEM. Selected samples were also analyzed for geomechanical properties. X-ray CT imaging yielded information on the occurrence of fractures, bedding planes, fossils, and bioturbation in core, as well as data on bulk density and photoelectric factor logs, which were used to interpret porosity, organic content, and mineralogy. FESEM was used for characterization of nano- and microscale features, including nanoscale pore visualization and micropore and pore throat mineralogy. FIBSEM yielded micro- to nanoscale visualization of fracture networks, porosity and pore-size distribution, connected versus isolated porosity, and distribution of organics. Results from the characterization activities provide insight on nanoscale fracture properties, pore throat mineralogy and connectivity, rock matrix characteristics, mineralogy, and organic content. Laboratory experiments demonstrated that CO 2 can permeate the tight matrix of Bakken shale and nonshale reservoir samples and mobilize oil from those samples. Geologic models were created at scales ranging from the core plug to the reservoir, and dynamic simulations were conducted. The data from the characterization and laboratory-based activities were integrated into modeling research activities to determine the fundamental mechanisms controlling fluid transport in the Bakken, which support EOR scheme design and estimation of CO 2 storage potential in tight oil formations. Simulation results suggest a CO 2 storage resource estimate range of 169 million to 1.5 billion tonnes for the Bakken in North Dakota, possibly resulting in 1.8 billion to 16 billion barrels of incremental oil.« less

Basic concepts of quantum interference and electron transport in single-molecule electronics.

PubMed

Lambert, C J

2015-02-21

This tutorial outlines the basic theoretical concepts and tools which underpin the fundamentals of phase-coherent electron transport through single molecules. The key quantity of interest is the transmission coefficient T(E), which yields the electrical conductance, current-voltage relations, the thermopower S and the thermoelectric figure of merit ZT of single-molecule devices. Since T(E) is strongly affected by quantum interference (QI), three manifestations of QI in single-molecules are discussed, namely Mach-Zehnder interferometry, Breit-Wigner resonances and Fano resonances. A simple MATLAB code is provided, which allows the novice reader to explore QI in multi-branched structures described by a tight-binding (Hückel) Hamiltonian. More generally, the strengths and limitations of materials-specific transport modelling based on density functional theory are discussed.

Impact of the Topological Surface State on the Thermoelectric Transport in Sb2Te3 Thin Films.

PubMed

Hinsche, Nicki F; Zastrow, Sebastian; Gooth, Johannes; Pudewill, Laurens; Zierold, Robert; Rittweger, Florian; Rauch, Tomáš; Henk, Jürgen; Nielsch, Kornelius; Mertig, Ingrid

2015-04-28

Ab initio electronic structure calculations based on density functional theory and tight-binding methods for the thermoelectric properties of p-type Sb2Te3 films are presented. The thickness-dependent electrical conductivity and the thermopower are computed in the diffusive limit of transport based on the Boltzmann equation. Contributions of the bulk and the surface to the transport coefficients are separated, which enables to identify a clear impact of the topological surface state on the thermoelectric properties. When the charge carrier concentration is tuned, a crossover between a surface-state-dominant and a Fuchs-Sondheimer transport regime is achieved. The calculations are corroborated by thermoelectric transport measurements on Sb2Te3 films grown by atomic layer deposition.

Relaxation dynamics of C60

NASA Astrophysics Data System (ADS)

Walsh, Tiffany R.; Wales, David J.

1998-10-01

The relaxation dynamics of C60 from high-energy isomers to Buckminsterfullerene is examined using a master equation approach. An exhaustive catalog of the C60 fullerene isomers containing only five- and six-membered rings is combined with knowledge of the Stone-Wales rearrangements that connect all such isomers. Full geometry optimizations have been performed for all the minima and the transition states which connect them up to six Stone-Wales steps away from the global minimum. A density-functional tight-binding potential was employed to provide a quantum mechanical description of the bonding. The resulting picture of the potential energy landscape reveals a "weeping willow" structure which offers a clear explanation for the relatively long relaxation times observed experimentally. We also predict the most important transient local minima on the annealing pathway.

Regulation of tight junction assembly and epithelial morphogenesis by the heat shock protein Apg-2

PubMed Central

Aijaz, Saima; Sanchez-Heras, Elena; Balda, Maria S; Matter, Karl

2007-01-01

Background Tight junctions are required for epithelial barrier formation and participate in the regulation of signalling mechanisms that control proliferation and differentiation. ZO-1 is a tight junction-associated adaptor protein that regulates gene expression, junction assembly and epithelial morphogenesis. We have previously demonstrated that the heat shock protein Apg-2 binds ZO-1 and thereby regulates its role in cell proliferation. Here, we addressed the question whether Apg-2 is also important for junction formation and epithelial morphogenesis. Results We demonstrate that depletion of Apg-2 by RNAi in MDCK cells did not prevent formation of functional tight junctions. Similar to ZO-1, however, reduced expression of Apg-2 retarded de novo junction assembly if analysed in a Ca-switch model. Formation of functional junctions, as monitored by measuring transepithelial electrical resistance, and recruitment of tight and adherens junction markers were retarded. If cultured in three dimensional extracellular matrix gels, Apg-2 depleted cells, as previously shown for ZO-1 depleted cells, did not form hollow polarised cysts but poorly organised, irregular structures. Conclusion Our data indicate that Apg-2 regulates junction assembly and is required for normal epithelial morphogenesis in a three-dimensional culture system, suggesting that Apg-2 is an important regulator of epithelial differentiation. As the observed phenotypes are similar to those previously described for ZO-1 depleted cells and depletion of Apg-2 retards junctional recruitment of ZO-1, regulation of ZO-1 is likely to be an important functional role for Apg-2 during epithelial differentiation. PMID:18028534

Regulation of tight junction assembly and epithelial morphogenesis by the heat shock protein Apg-2.

PubMed

Aijaz, Saima; Sanchez-Heras, Elena; Balda, Maria S; Matter, Karl

2007-11-20

Tight junctions are required for epithelial barrier formation and participate in the regulation of signalling mechanisms that control proliferation and differentiation. ZO-1 is a tight junction-associated adaptor protein that regulates gene expression, junction assembly and epithelial morphogenesis. We have previously demonstrated that the heat shock protein Apg-2 binds ZO-1 and thereby regulates its role in cell proliferation. Here, we addressed the question whether Apg-2 is also important for junction formation and epithelial morphogenesis. We demonstrate that depletion of Apg-2 by RNAi in MDCK cells did not prevent formation of functional tight junctions. Similar to ZO-1, however, reduced expression of Apg-2 retarded de novo junction assembly if analysed in a Ca-switch model. Formation of functional junctions, as monitored by measuring transepithelial electrical resistance, and recruitment of tight and adherens junction markers were retarded. If cultured in three dimensional extracellular matrix gels, Apg-2 depleted cells, as previously shown for ZO-1 depleted cells, did not form hollow polarised cysts but poorly organised, irregular structures. Our data indicate that Apg-2 regulates junction assembly and is required for normal epithelial morphogenesis in a three-dimensional culture system, suggesting that Apg-2 is an important regulator of epithelial differentiation. As the observed phenotypes are similar to those previously described for ZO-1 depleted cells and depletion of Apg-2 retards junctional recruitment of ZO-1, regulation of ZO-1 is likely to be an important functional role for Apg-2 during epithelial differentiation.

Tight junction gene expression in gastrointestinal tract of dairy calves with coccidiosis and treated with glucagon-like peptide-2

USDA-ARS?s Scientific Manuscript database

Selective permeability of the intestinal epithelium and efficient nutrient absorption are important functions for proper growth and development of calves. Damage to the intestinal mucosa can give rise to harmful long-term health effects and reduce productivity of the mature animal. Tight junction pr...

Transversal Fluctuations of the ASEP, Stochastic Six Vertex Model, and Hall-Littlewood Gibbsian Line Ensembles

NASA Astrophysics Data System (ADS)

Corwin, Ivan; Dimitrov, Evgeni

2018-05-01

We consider the ASEP and the stochastic six vertex model started with step initial data. After a long time, T, it is known that the one-point height function fluctuations for these systems are of order T 1/3. We prove the KPZ prediction of T 2/3 scaling in space. Namely, we prove tightness (and Brownian absolute continuity of all subsequential limits) as T goes to infinity of the height function with spatial coordinate scaled by T 2/3 and fluctuations scaled by T 1/3. The starting point for proving these results is a connection discovered recently by Borodin-Bufetov-Wheeler between the stochastic six vertex height function and the Hall-Littlewood process (a certain measure on plane partitions). Interpreting this process as a line ensemble with a Gibbsian resampling invariance, we show that the one-point tightness of the top curve can be propagated to the tightness of the entire curve.

Influence of Gestational Age at Initiation of Antihypertensive Therapy: Secondary Analysis of CHIPS Trial Data (Control of Hypertension in Pregnancy Study).

PubMed

Pels, Anouk; Mol, Ben Willem J; Singer, Joel; Lee, Terry; von Dadelszen, Peter; Ganzevoort, Wessel; Asztalos, Elizabeth; Magee, Laura A

2018-06-01

For hypertensive women in CHIPS (Control of Hypertension in Pregnancy Study), we assessed whether the maternal benefits of tight control could be achieved, while minimizing any potentially negative effect on fetal growth, by delaying initiation of antihypertensive therapy until later in pregnancy. For the 981 women with nonsevere, chronic or gestational hypertension randomized to less-tight (target diastolic blood pressure, 100 mm Hg), or tight (target, 85 mm Hg) control, we used mixed-effects logistic regression to examine whether the effect of less-tight (versus tight) control on major outcomes was dependent on gestational age at randomization, adjusting for baseline factors as in the primary analysis and including an interaction term between gestational age at randomization and treatment allocation. Gestational age was considered categorically (quartiles) and continuously (linear or quadratic form), and the optimal functional form selected to provide the best fit to the data based on the Akaike information criterion. Randomization before (but not after) 24 weeks to less-tight (versus tight) control was associated with fewer babies with birth weight <10th centile ( P interaction =0.005), but more preterm birth ( P interaction =0.043), and no effect on perinatal death or high-level neonatal care >48 hours ( P interaction =0.354). For the mother, less-tight (versus tight) control was associated with more severe hypertension at all gestational ages but particularly so before 28 weeks ( P interaction =0.076). In women with nonsevere, chronic, or gestational hypertension, there seems to be no gestational age at which less-tight (versus tight) control is the preferred management strategy to optimize maternal or perinatal outcomes. URL: https://www.isrctn.com. Unique identifier: ISRCTN71416914. © 2018 The Authors.

Modeling of full-Heusler alloys within tight-binding approximation: Case study of Fe2MnAl

NASA Astrophysics Data System (ADS)

Azhar, A.; Majidi, M. A.; Nanto, D.

2017-07-01

Heusler alloys have been known for about a century, and predictions of magnetic moment values using Slater-Pauling rule have been successful for many such materials. However, such a simple counting rule has been found not to always work for all Heusler alloys. For instance, Fe2CuAl has been found to have magnetic moment of 3.30 µB per formula unit although the Slater-Pauling rule suggests the value of 2 µB. On the other hand, a recent experiment shows that a non-stoichiometric Heusler compound Fe2Mn0.5Cu0.5Al possesses magnetic moment of 4 µB, closer to the Slater-Pauling prediction for the stoichiometric compound. Such discrepancies signify that the theory to predict the magnetic moment of Heusler alloys in general is still far from being complete. Motivated by this issue, we propose to do a theoretical study on a full-Heusler alloy Fe2MnAl to understand the formation of magnetic moment microscopically. We model the system by constructing a density-functional-theory-based tight-binding Hamiltonian and incorporating Hubbard repulsive as well as spin-spin interactions for the electrons occupying the d-orbitals. Then, we solve the model using Green's function approach, and treat the interaction terms within the mean-field approximation. At this stage, we aim to formulate the computational algorithm for the overall calculation process. Our final goal is to compute the total magnetic moment per unit cell of this system and compare it with the experimental data.

Co-extrusion of electrolyte/anode functional layer/anode triple-layer ceramic hollow fibres for micro-tubular solid oxide fuel cells-electrochemical performance study

NASA Astrophysics Data System (ADS)

Li, Tao; Wu, Zhentao; Li, K.

2015-01-01

In this study, the effects of an anode functional layer (AFL) with controlled thickness on physical and electrochemical properties of a micro-tubular SOFC have been systematically studied. A series of electrolyte/AFL/anode triple-layer hollow fibres with controllable AFL thicknesses (16.9-52.7 μm) have been fabricated via a single-step phase-inversion assisted co-extrusion technique. Both robustness of the cell and gas-tightness of the electrolyte layer are considerably improved by introducing the AFL of this type. The fracture force of the sample with the thickest AFL (9.67 N) almost doubles when compared to the electrolyte/anode dual-layer counterpart (5.24 N). Gas-tightness of the electrolyte layer is also considerably increased as AFL contributes to better-matched sintering behaviours between different components. Moreover, the formation of an AFL simultaneously with electrolyte and anode significantly improves the cell performances. The sample with the thinnest AFL (approximately 16.9 μm, 6% of the total anode thickness) leads to a 30% (from 0.89 to 1.21 W cm-2) increase in maximum power density, due to increased triple-phase boundaries (TPB). However, further increase in TPB from a thicker AFL is less effective for improving the cell performance, due to the substantially increased fuel diffusion resistance and subsequently higher concentration polarization. This indicates that the control over the AFL thickness is critically important in avoiding offsetting the benefits of extended TPB and consequently decreased cell performances.

Plasmodesmata: channels for intercellular signaling during plant growth and development.

PubMed

Sevilem, Iris; Yadav, Shri Ram; Helariutta, Ykä

2015-01-01

Plants have evolved strategies for short- and long-distance communication to coordinate plant development and to adapt to changing environmental conditions. Plasmodesmata (PD) are intercellular nanochannels that provide an effective pathway for both selective and nonselective movement of various molecules that function in diverse biological processes. Numerous non-cell-autonomous proteins (NCAP) and small RNAs have been identified that have crucial roles in cell fate determination and organ patterning during development. Both the density and aperture size of PD are developmentally regulated, allowing formation of spatial symplastic domains for establishment of tissue-specific developmental programs. The PD size exclusion limit (SEL) is controlled by reversible deposition of callose, as well as by some PD-associated proteins. Although a large number of PD-associated proteins have been identified, many of their functions remain unknown. Despite the fact that PD are primarily membranous structures, surprisingly very little is known about their lipid composition. Thus, future studies in PD biology will provide deeper insights into the high-resolution structure and tightly regulated functions of PD and the evolution of PD-mediated cell-to-cell communication in plants.

Creating Perfused Functional Vascular Channels Using 3D Bio-Printing Technology

PubMed Central

Lee, Vivian K.; Kim, Diana Y.; Ngo, Haygan; Lee, Young; Seo, Lan; Yoo, Seung-Schik; Vincent, Peter A.; Dai, Guohao

2014-01-01

We developed a methodology using 3D bio-printing technology to create a functional in vitro vascular channel with perfused open lumen using only cells and biological matrices. The fabricated vasculature has a tight, confluent endothelium lining, presenting barrier function for both plasma protein and high-molecular weight dextran molecule. The fluidic vascular channel is capable of supporting the viability of tissue up to 5mm in distance at 5 million cells/mL density under the physiological flow condition. In static-cultured vascular channels, active angiogenic sprouting from the vessel surface was observed whereas physiological flow strongly suppressed this process. Gene expression analysis were reported in this study to show the potential of this vessel model in vascular biology research. The methods have great potential in vascularized tissue fabrication using 3D bio-printing technology as the vascular channel is simultaneously created while cells and matrix are printed around the channel in desired 3D patterns. It can also serve as a unique experimental tool for investigating fundamental mechanisms of vascular remodeling with extracellular matrix and maturation process under 3D flow condition. PMID:24965886

MacA, a periplasmic membrane fusion protein of the macrolide transporter MacAB-TolC, binds lipopolysaccharide core specifically and with high affinity.

PubMed

Lu, Shuo; Zgurskaya, Helen I

2013-11-01

The Escherichia coli MacAB-TolC transporter has been implicated in efflux of macrolide antibiotics and secretion of enterotoxin STII. In this study, we found that purified MacA, a periplasmic membrane fusion protein, contains one tightly bound rough core lipopolysaccharide (R-LPS) molecule per MacA molecule. R-LPS was bound specifically to MacA protein with affinity exceeding that of polymyxin B. Sequence analyses showed that MacA contains two high-density clusters of positively charged amino acid residues located in the cytoplasmic N-terminal domain and the periplasmic C-terminal domain. Substitutions in the C-terminal cluster reducing the positive-charge density completely abolished binding of R-LPS. At the same time, these substitutions significantly reduced the functionality of MacA in the protection of E. coli against macrolides in vivo and in the in vitro MacB ATPase stimulation assays. Taken together, our results suggest that R-LPS or a similar glycolipid is a physiological substrate of MacAB-TolC.

MacA, a Periplasmic Membrane Fusion Protein of the Macrolide Transporter MacAB-TolC, Binds Lipopolysaccharide Core Specifically and with High Affinity

PubMed Central

Lu, Shuo

2013-01-01

The Escherichia coli MacAB-TolC transporter has been implicated in efflux of macrolide antibiotics and secretion of enterotoxin STII. In this study, we found that purified MacA, a periplasmic membrane fusion protein, contains one tightly bound rough core lipopolysaccharide (R-LPS) molecule per MacA molecule. R-LPS was bound specifically to MacA protein with affinity exceeding that of polymyxin B. Sequence analyses showed that MacA contains two high-density clusters of positively charged amino acid residues located in the cytoplasmic N-terminal domain and the periplasmic C-terminal domain. Substitutions in the C-terminal cluster reducing the positive-charge density completely abolished binding of R-LPS. At the same time, these substitutions significantly reduced the functionality of MacA in the protection of E. coli against macrolides in vivo and in the in vitro MacB ATPase stimulation assays. Taken together, our results suggest that R-LPS or a similar glycolipid is a physiological substrate of MacAB-TolC. PMID:23974027

Velocities and rotational excitation of interstellar H2 toward Pi Scorpii

NASA Technical Reports Server (NTRS)

Jenkins, Edward B.; Lees, Joanna F.; Van Dishoeck, Ewine F.; Wilcots, Eric M.

1989-01-01

A spectrum of Pi Sco showing numerous atomic lines and 70 absorption features from the Lyman and Werner transitions of interstellar H2 in rotational level J from zero to five is presented. Their shapes of the composite column density profiles are very nearly Gaussian with a one-dimensional rms velocity dispersion of 3 km/s. The behavior of shifts in the inferred N(H2) as a function of velocity are consistent with the overall profiles being composed of nearly symmetrical, tightly paced assemblies of about seven unresolved components. The relative overall column densities in the higher J levels of H2 are consistent with a model where these states are populated by optical pumping through the Lyman and Werner transitions, powered by UV radiation from nearby stars. The slight narrowing of the high-J profiles may be due to small clumps of H2 at radial velocities some 5-8 km/s from the core of the profile are exposed to a pumping flux about 10 times lower than that for the material near the profile's center.

High-cell-density cultivation of recombinant Escherichia coli, purification and characterization of a self-sufficient biosynthetic octane ω-hydroxylase.

PubMed

Bordeaux, Mélanie; de Girval, Diane; Rullaud, Robin; Subileau, Maeva; Dubreucq, Eric; Drone, Jullien

2014-01-01

We have recently described the biocatalytic characterization of a self-sufficent biosynthetic alkane hydroxylase based on CYP153A13a from Alcanivorax borkumensis SK2 (thereafter A13-Red). Despite remarkable regio- and chemo-selectivity, A13-Red suffers of a difficult-to-reproduce expression and moderate operational stability. In this study, we focused our efforts on the production of A13-Red using high-cell-density cultivation (HCDC) of recombinant Escherichia coli. We achieved 455 mg (5,000 nmol) of functional enzyme per liter of culture. Tight control of cultivation parameters rendered the whole process highly reproducible compared with flask cultivations. We optimized the purification of the biocatalyst that can be performed in either two or three steps depending on the application needed to afford A13-Red up to 95 % homogeneous. We investigated different reaction conditions and found that the total turnover numbers of A13-Red during the in vitro hydroxylation of n-octane could reach up to 3,250 to produce 1-octanol (1.6 mM) over a period of 78 h.

X-ray Thomson Scattering in Warm Dense Matter without the Chihara Decomposition.

PubMed

Baczewski, A D; Shulenburger, L; Desjarlais, M P; Hansen, S B; Magyar, R J

2016-03-18

X-ray Thomson scattering is an important experimental technique used to measure the temperature, ionization state, structure, and density of warm dense matter (WDM). The fundamental property probed in these experiments is the electronic dynamic structure factor. In most models, this is decomposed into three terms [J. Chihara, J. Phys. F 17, 295 (1987)] representing the response of tightly bound, loosely bound, and free electrons. Accompanying this decomposition is the classification of electrons as either bound or free, which is useful for gapped and cold systems but becomes increasingly questionable as temperatures and pressures increase into the WDM regime. In this work we provide unambiguous first principles calculations of the dynamic structure factor of warm dense beryllium, independent of the Chihara form, by treating bound and free states under a single formalism. The computational approach is real-time finite-temperature time-dependent density functional theory (TDDFT) being applied here for the first time to WDM. We compare results from TDDFT to Chihara-based calculations for experimentally relevant conditions in shock-compressed beryllium.

JAM-C regulates tight junctions and integrin-mediated cell adhesion and migration.

PubMed

Mandicourt, Guillaume; Iden, Sandra; Ebnet, Klaus; Aurrand-Lions, Michel; Imhof, Beat A

2007-01-19

Junctional Adhesion Molecules (JAMs) have been described as major components of tight junctions in endothelial and epithelial cells. Tight junctions are crucial for the establishment and maintenance of cell polarity. During tumor development, they are remodeled, enabling neoplastic cells to escape from constraints imposed by intercellular junctions and to adopt a migratory behavior. Using a carcinoma cell line we tested whether JAM-C could affect tight junctions and migratory properties of tumor cells. We show that transfection of JAM-C improves the tight junctional barrier in tumor cells devoid of JAM-C expression. This is dependent on serine 281 in the cytoplasmic tail of JAM-C because serine mutation into alanine abolishes the specific localization of JAM-C in tight junctions and establishment of cell polarity. More importantly, the same mutation stimulates integrin-mediated cell migration and adhesion via the modulation of beta1 and beta3 integrin activation. These results highlight an unexpected function for JAM-C in controlling epithelial cell conversion from a static, polarized state to a pro-migratory phenotype.

Parametrization and Benchmark of Long-Range Corrected DFTB2 for Organic Molecules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vuong, Van Quan; Akkarapattiakal Kuriappan, Jissy; Kubillus, Maximilian

In this paper, we present the parametrization and benchmark of long-range corrected second-order density functional tight binding (DFTB), LC-DFTB2, for organic and biological molecules. The LC-DFTB2 model not only improves fundamental orbital energy gaps but also ameliorates the DFT self-interaction error and overpolarization problem, and further improves charge-transfer excited states significantly. Electronic parameters for the construction of the DFTB2 Hamiltonian as well as repulsive potentials were optimized for molecules containing C, H, N, and O chemical elements. We use a semiautomatic parametrization scheme based on a genetic algorithm. With the new parameters, LC-DFTB2 describes geometries and vibrational frequencies of organicmore » molecules similarly well as third-order DFTB3/3OB, the de facto standard parametrization based on a GGA functional. Finally, LC-DFTB2 performs well also for atomization and reaction energies, however, slightly less satisfactorily than DFTB3/3OB.« less

Parametrization and Benchmark of Long-Range Corrected DFTB2 for Organic Molecules

DOE PAGES

Vuong, Van Quan; Akkarapattiakal Kuriappan, Jissy; Kubillus, Maximilian; ...

2017-12-12

In this paper, we present the parametrization and benchmark of long-range corrected second-order density functional tight binding (DFTB), LC-DFTB2, for organic and biological molecules. The LC-DFTB2 model not only improves fundamental orbital energy gaps but also ameliorates the DFT self-interaction error and overpolarization problem, and further improves charge-transfer excited states significantly. Electronic parameters for the construction of the DFTB2 Hamiltonian as well as repulsive potentials were optimized for molecules containing C, H, N, and O chemical elements. We use a semiautomatic parametrization scheme based on a genetic algorithm. With the new parameters, LC-DFTB2 describes geometries and vibrational frequencies of organicmore » molecules similarly well as third-order DFTB3/3OB, the de facto standard parametrization based on a GGA functional. Finally, LC-DFTB2 performs well also for atomization and reaction energies, however, slightly less satisfactorily than DFTB3/3OB.« less

Simple extrapolation method to predict the electronic structure of conjugated polymers from calculations on oligomers

DOE PAGES

Larsen, Ross E.

2016-04-12

In this study, we introduce two simple tight-binding models, which we call fragment frontier orbital extrapolations (FFOE), to extrapolate important electronic properties to the polymer limit using electronic structure calculations on only a few small oligomers. In particular, we demonstrate by comparison to explicit density functional theory calculations that for long oligomers the energies of the highest occupied molecular orbital (HOMO), the lowest unoccupied molecular orbital (LUMO), and of the first electronic excited state are accurately described as a function of number of repeat units by a simple effective Hamiltonian parameterized from electronic structure calculations on monomers, dimers and, optionally,more » tetramers. For the alternating copolymer materials that currently comprise some of the most efficient polymer organic photovoltaic devices one can use these simple but rigorous models to extrapolate computed properties to the polymer limit based on calculations on a small number of low-molecular-weight oligomers.« less

Identification of two immortalized cell lines, ECV304 and bEnd3, for in vitro permeability studies of blood-brain barrier

PubMed Central

Mei, Shenghui; Jin, Hong; Zhu, Bin; Tian, Yue; Huo, Jiping; Cui, Xu; Guo, Anchen; Zhao, Zhigang

2017-01-01

To identify suitable cell lines for a mimetic system of in vivo blood-brain barrier (BBB) for drug permeability assessment, we characterized two immortalized cell lines, ECV304 and bEnd3 in the respect of the tightness, tight junction proteins, P-glycoprotein (P-gp) function and discriminative brain penetration. The ECV304 monoculture achieved higher transendothelial electrical resistance (TEER) and lower permeability to Lucifer yellow than bEnd3. However, co-culture with rat glioma C6 cells impaired the integrity of ECV304 and bEnd3 cell layers perhaps due to the heterogeneity among C6 cells in inducing BBB characteristics. The immunostaining of ZO-1 delivered distinct bands along cell borders on both cell lines while those of occludin and claudin-5 were diffused and weak. P-gp functionality was only proved in bEnd3 by Rhodamine 123 (R123) uptake assay. A permeability test of reference compounds displayed a similar rank order (digoxin < R123 < quinidine, verapamil < propranolol) in ECV304 and bEnd3 cells. In comparison with bEnd3, ECV304 developed tighter barrier for the passage of reference compounds and higher discrimination between transcellular and paracellular transport. However, the monoculture models of ECV304 and bEnd3 fail to achieve the sufficient tightness of in vitro BBB permeability models with high TEER and evident immunostaining of tight junction proteins. Further strategies to enhance the paracellular tightness of both cell lines to mimic in vivo BBB tight barrier deserve to be conducted. PMID:29059256

Identification of two immortalized cell lines, ECV304 and bEnd3, for in vitro permeability studies of blood-brain barrier.

PubMed

Yang, Shu; Mei, Shenghui; Jin, Hong; Zhu, Bin; Tian, Yue; Huo, Jiping; Cui, Xu; Guo, Anchen; Zhao, Zhigang

2017-01-01

To identify suitable cell lines for a mimetic system of in vivo blood-brain barrier (BBB) for drug permeability assessment, we characterized two immortalized cell lines, ECV304 and bEnd3 in the respect of the tightness, tight junction proteins, P-glycoprotein (P-gp) function and discriminative brain penetration. The ECV304 monoculture achieved higher transendothelial electrical resistance (TEER) and lower permeability to Lucifer yellow than bEnd3. However, co-culture with rat glioma C6 cells impaired the integrity of ECV304 and bEnd3 cell layers perhaps due to the heterogeneity among C6 cells in inducing BBB characteristics. The immunostaining of ZO-1 delivered distinct bands along cell borders on both cell lines while those of occludin and claudin-5 were diffused and weak. P-gp functionality was only proved in bEnd3 by Rhodamine 123 (R123) uptake assay. A permeability test of reference compounds displayed a similar rank order (digoxin < R123 < quinidine, verapamil < propranolol) in ECV304 and bEnd3 cells. In comparison with bEnd3, ECV304 developed tighter barrier for the passage of reference compounds and higher discrimination between transcellular and paracellular transport. However, the monoculture models of ECV304 and bEnd3 fail to achieve the sufficient tightness of in vitro BBB permeability models with high TEER and evident immunostaining of tight junction proteins. Further strategies to enhance the paracellular tightness of both cell lines to mimic in vivo BBB tight barrier deserve to be conducted.

Loss of tight junction barrier function and its role in cancer metastasis.

PubMed

Martin, Tracey A; Jiang, Wen G

2009-04-01

As the most apical structure between epithelial and endothelial cells, tight junctions (TJ) are well known as functioning as a control for the paracellular diffusion of ions and certain molecules. It has however, become increasingly apparent that the TJ has a vital role in maintaining cell to cell integrity and that the loss of cohesion of the structure can lead to invasion and thus metastasis of cancer cells. This article will present data showing how modulation of expression of TJ molecules results in key changes in TJ barrier function leading to the successful metastasis of a number of different cancer types.

Plant-derived triterpene celastrol ameliorates oxygen glucose deprivation-induced disruption of endothelial barrier assembly via inducing tight junction proteins.

PubMed

Luo, Dan; Zhao, Jia; Rong, Jianhui

2016-12-01

The integrity and functions of blood-brain barrier (BBB) are regulated by the expression and organization of tight junction proteins. The present study was designed to explore whether plant-derived triterpenoid celastrol could regulate tight junction integrity in murine brain endothelial bEnd3 cells. We disrupted the tight junctions between endothelial bEnd3 cells by oxygen glucose deprivation (OGD). We investigated the effects of celastrol on the permeability of endothelial monolayers by measuring transepithelial electrical resistance (TEER). To clarify the tight junction composition, we analyzed the expression of tight junction proteins by RT-PCR and Western blotting techniques. We found that celastrol recovered OGD-induced TEER loss in a concentration-dependent manner. Celastrol induced occludin, claudin-5 and zonula occludens-1 (ZO-1) in endothelial cells. As a result, celastrol effectively maintained tight junction integrity and inhibited macrophage migration through endothelial monolayers against OGD challenge. Further mechanistic studies revealed that celastrol induced the expression of occludin and ZO-1) via activating MAPKs and PI3K/Akt/mTOR pathway. We also observed that celastrol regulated claudin-5 expression through different mechanisms. The present study demonstrated that celastrol effectively protected tight junction integrity against OGD-induced damage. Thus, celastrol could be a drug candidate for the treatment of BBB dysfunction in various diseases. Copyright © 2016 Elsevier GmbH. All rights reserved.

Changes in intestinal tight junction permeability associated with industrial food additives explain the rising incidence of autoimmune disease.

PubMed

Lerner, Aaron; Matthias, Torsten

2015-06-01

The incidence of autoimmune diseases is increasing along with the expansion of industrial food processing and food additive consumption. The intestinal epithelial barrier, with its intercellular tight junction, controls the equilibrium between tolerance and immunity to non-self-antigens. As a result, particular attention is being placed on the role of tight junction dysfunction in the pathogenesis of AD. Tight junction leakage is enhanced by many luminal components, commonly used industrial food additives being some of them. Glucose, salt, emulsifiers, organic solvents, gluten, microbial transglutaminase, and nanoparticles are extensively and increasingly used by the food industry, claim the manufacturers, to improve the qualities of food. However, all of the aforementioned additives increase intestinal permeability by breaching the integrity of tight junction paracellular transfer. In fact, tight junction dysfunction is common in multiple autoimmune diseases and the central part played by the tight junction in autoimmune diseases pathogenesis is extensively described. It is hypothesized that commonly used industrial food additives abrogate human epithelial barrier function, thus, increasing intestinal permeability through the opened tight junction, resulting in entry of foreign immunogenic antigens and activation of the autoimmune cascade. Future research on food additives exposure-intestinal permeability-autoimmunity interplay will enhance our knowledge of the common mechanisms associated with autoimmune progression. Copyright © 2015. Published by Elsevier B.V.

Porous, Dexamethasone-loaded polyurethane coatings extend performance window of implantable glucose sensors in vivo.

PubMed

Vallejo-Heligon, Suzana G; Brown, Nga L; Reichert, William M; Klitzman, Bruce

2016-01-01

Continuous glucose sensors offer the promise of tight glycemic control for insulin dependent diabetics; however, utilization of such systems has been hindered by issues of tissue compatibility. Here we report on the in vivo performance of implanted glucose sensors coated with Dexamethasone-loaded (Dex-loaded) porous coatings employed to mediate the tissue-sensor interface. Two animal studies were conducted to (1) characterize the tissue modifying effects of the porous Dex-loaded coatings deployed on sensor surrogate implants and (2) investigate the effects of the same coatings on the in vivo performance of Medtronic MiniMed SOF-SENSOR™ glucose sensors. The tissue response to implants was evaluated by quantifying macrophage infiltration, blood vessel formation, and collagen density around implants. Sensor function was assessed by measuring changes in sensor sensitivity and time lag, calculating the Mean Absolute Relative Difference (MARD) for each sensor treatment, and performing functional glucose challenge test at relevant time points. Implants treated with porous Dex-loaded coatings diminished inflammation and enhanced vascularization of the tissue surrounding the implants. Functional sensors with Dex-loaded porous coatings showed enhanced sensor sensitivity over a 21-day period when compared to controls. Enhanced sensor sensitivity was accompanied with an increase in sensor signal lag and MARD score. These results indicate that Dex-loaded porous coatings were able to elicit an attenuated tissue response, and that such tissue microenvironment could be conducive towards extending the performance window of glucose sensors in vivo. In the present article, a coating to extend the functionality of implantable glucose sensors in vivo was developed. Our study showed that the delivery of an anti-inflammatory agent with the presentation of micro-sized topographical cues from coatings may lead to improved long-term glucose sensor function in vivo. We believe that improved function of sensors treated with the novel coatings was a result of the observed decreases in inflammatory cell density and increases in vessel density of the tissue adjacent to the devices. Furthermore, extending the in vivo functionality of implantable glucose sensors may lead to greater adoption of these devices by diabetic patients. Copyright © 2015 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Absorption of CO2 on Carbon-based Sensors: First-Principle Analysis

NASA Astrophysics Data System (ADS)

Tit, Nacir; Elezzi, Mohammed; Abdullah, Hasan; Bahlouli, Hocine; Yamani, Zain

We present first-principle investigation of the adsorption properties of CO and CO2 molecules on both graphene and carbon nano-tubes (CNTs) in presence of metal catalysis, mainly iron (Fe). The relaxations were carried out using the self-consistent-charge density-functional tight-binding (SCC-DFTB) code in neglect of heat effects. The results show the following: (1) Defected graphene is found to have high sensitivity and high selectivity towards chemisorption of CO molecules and weak physisorption with CO2 molecules. (2) In case of CNTs, the iron ``Fe'' catalyst plays an essential role in capturing CO2 molecules. The Fe ad-atoms on the surface of CNT introduce huge density of states at Fermi level, but the capture of CO2 molecules would reduce that density and consequently reduce conductivity and increase sensitivity. Concerning the selectivity, we have studied the sensitivity versus various gas molecules (such as: O2, N2, H2, H2O, and CO). Furthermore, to assess the effect of catalysis on sensitivity, we have studied the sensitivity of other metal catalysts (such as: Ni, Co, Ti, and Sc). We found that CNT-Fe is highly sensitive and selective towards detection of CO and CO2 molecules. CNT being conductive or semiconducting does not matter much on the adsorption properties.

Neural network evaluation of reflectometry density profiles for control purposes

NASA Astrophysics Data System (ADS)

Santos, J.; Nunes, F.; Manso, M.; Nunes, I.

1999-01-01

Broadband reflectometry is a diagnostic that is able to measure the density profile with high spatial and temporal resolutions, therefore it can be used to improve the performance of advanced tokamak operation modes and to supplement or correct the magnetics for plasma position control. To perform these tasks real-time processing is needed. Here we present a method that uses a neural network to make a fast evaluation of radial positions for selected density layers. Typical ASDEX Upgrade density profiles were used to generate the simulated network training and test sets. It is shown that the method has the potential to meet the tight timing requirements of control applications with the required accuracy. The network is also able to provide an accurate estimation of the position of density layers below the first density layer which is probed by an O-mode reflectometer, provided that it is trained with a realistic density profile model.

Electronic couplings for molecular charge transfer: Benchmarking CDFT, FODFT, and FODFTB against high-level ab initio calculations

NASA Astrophysics Data System (ADS)

Kubas, Adam; Hoffmann, Felix; Heck, Alexander; Oberhofer, Harald; Elstner, Marcus; Blumberger, Jochen

2014-03-01

We introduce a database (HAB11) of electronic coupling matrix elements (Hab) for electron transfer in 11 π-conjugated organic homo-dimer cations. High-level ab inito calculations at the multireference configuration interaction MRCI+Q level of theory, n-electron valence state perturbation theory NEVPT2, and (spin-component scaled) approximate coupled cluster model (SCS)-CC2 are reported for this database to assess the performance of three DFT methods of decreasing computational cost, including constrained density functional theory (CDFT), fragment-orbital DFT (FODFT), and self-consistent charge density functional tight-binding (FODFTB). We find that the CDFT approach in combination with a modified PBE functional containing 50% Hartree-Fock exchange gives best results for absolute Hab values (mean relative unsigned error = 5.3%) and exponential distance decay constants β (4.3%). CDFT in combination with pure PBE overestimates couplings by 38.7% due to a too diffuse excess charge distribution, whereas the economic FODFT and highly cost-effective FODFTB methods underestimate couplings by 37.6% and 42.4%, respectively, due to neglect of interaction between donor and acceptor. The errors are systematic, however, and can be significantly reduced by applying a uniform scaling factor for each method. Applications to dimers outside the database, specifically rotated thiophene dimers and larger acenes up to pentacene, suggests that the same scaling procedure significantly improves the FODFT and FODFTB results for larger π-conjugated systems relevant to organic semiconductors and DNA.

Error estimates for (semi-)empirical dispersion terms and large biomacromolecules.

PubMed

Korth, Martin

2013-10-14

The first-principles modeling of biomaterials has made tremendous advances over the last few years with the ongoing growth of computing power and impressive developments in the application of density functional theory (DFT) codes to large systems. One important step forward was the development of dispersion corrections for DFT methods, which account for the otherwise neglected dispersive van der Waals (vdW) interactions. Approaches at different levels of theory exist, with the most often used (semi-)empirical ones based on pair-wise interatomic C6R(-6) terms. Similar terms are now also used in connection with semiempirical QM (SQM) methods and density functional tight binding methods (SCC-DFTB). Their basic structure equals the attractive term in Lennard-Jones potentials, common to most force field approaches, but they usually use some type of cutoff function to make the mixing of the (long-range) dispersion term with the already existing (short-range) dispersion and exchange-repulsion effects from the electronic structure theory methods possible. All these dispersion approximations were found to perform accurately for smaller systems, but error estimates for larger systems are very rare and completely missing for really large biomolecules. We derive such estimates for the dispersion terms of DFT, SQM and MM methods using error statistics for smaller systems and dispersion contribution estimates for the PDBbind database of protein-ligand interactions. We find that dispersion terms will usually not be a limiting factor for reaching chemical accuracy, though some force fields and large ligand sizes are problematic.

Optical fingerprint of non-covalently functionalized transition metal dichalcogenides

NASA Astrophysics Data System (ADS)

Feierabend, Maja; Malic, Ermin; Knorr, Andreas; Berghäuser, Gunnar

2017-09-01

Atomically thin transition metal dichalcogenides (TMDs) hold promising potential for applications in optoelectronics. Due to their direct band gap and the extraordinarily strong Coulomb interaction, TMDs exhibit efficient light-matter coupling and tightly bound excitons. Moreover, large spin orbit coupling in combination with circular dichroism allows for spin and valley selective optical excitation. As atomically thin materials, they are very sensitive to changes in the surrounding environment. This motivates a functionalization approach, where external molecules are adsorbed to the materials surface to tailor its optical properties. Here, we apply the density matrix theory to investigate the potential of non-covalently functionalized monolayer TMDs. Considering exemplary molecules with a strong dipole moment, we predict spectral redshifts and the appearance of an additional side peak in the absorption spectrum of functionalized TMDs. We show that the molecular characteristics, e.g. coverage, orientation and dipole moment, crucially influence the optical properties of TMDs, leaving a unique optical fingerprint in the absorption spectrum. Furthermore, we find that the molecular dipole moments open a channel for coherent intervalley coupling between the high-symmetry K and K\\prime points which may create new possibilities for spin-valleytronics application.

The tight junction protein ZO-2 and Janus kinase 1 mediate intercellular communications in vascular smooth muscle cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tkachuk, Natalia; Tkachuk, Sergey; Patecki, Margret

2011-07-08

Highlights: {yields} The tight junction protein ZO-2 associates with Jak1 in vascular smooth muscle cells via ZO-2 N-terminal fragment. {yields} Jak1 mediates ZO-2 tyrosine phosphorylation and ZO-2 localization to the sites of homotypic intercellular contacts. {yields} The urokinase receptor uPAR regulates ZO-2/Jak1 functional association. {yields} The ZO-2/Jak1/uPAR signaling complex is required for vascular smooth muscle cells functional network formation. -- Abstract: Recent evidence points to a multifunctional role of ZO-2, the tight junction protein of the MAGUK (membrane-associated guanylate kinase-like) family. Though ZO-2 has been found in cell types lacking tight junction structures, such as vascular smooth muscle cells (VSMC),more » little is known about ZO-2 function in these cells. We provide evidence that ZO-2 mediates specific homotypic cell-to-cell contacts between VSMC. Using mass spectrometry we found that ZO-2 is associated with the non-receptor tyrosine kinase Jak1. By generating specific ZO-2 constructs we further found that the N-terminal fragment of ZO-2 molecule is responsible for this interaction. Adenovirus-based expression of Jak1 inactive mutant demonstrated that Jak1 mediates ZO-2 tyrosine phosphorylation. By means of RNA silencing, expression of Jak1 mutant form and fluorescently labeled ZO-2 fusion protein we further specified that active Jak1, but not Jak1 inactive mutant, mediates ZO-2 localization to the sites of intercellular contacts. We identified the urokinase receptor uPAR as a pre-requisite for these cellular events. Functional requirement of the revealed signaling complex for VSMC network formation was confirmed in experiments using Matrigel and in contraction assay. Our findings imply involvement of the ZO-2 tight junction independent signaling complex containing Jak1 and uPAR in VSMC intercellular communications. This mechanism may contribute to vascular remodeling in occlusive cardiovascular diseases and in arteriogenesis.« less

Computational design of nanoparticle drug delivery systems for selective targeting

NASA Astrophysics Data System (ADS)

Duncan, Gregg A.; Bevan, Michael A.

2015-09-01

Ligand-functionalized nanoparticles capable of selectively binding to diseased versus healthy cell populations are attractive for improved efficacy of nanoparticle-based drug and gene therapies. However, nanoparticles functionalized with high affinity targeting ligands may lead to undesired off-target binding to healthy cells. In this work, Monte Carlo simulations were used to quantitatively determine net surface interactions, binding valency, and selectivity between targeted nanoparticles and cell surfaces. Dissociation constant, KD, and target membrane protein density, ρR, are explored over a range representative of healthy and cancerous cell surfaces. Our findings show highly selective binding to diseased cell surfaces can be achieved with multiple, weaker affinity targeting ligands that can be further optimized by varying the targeting ligand density, ρL. Using the approach developed in this work, nanomedicines can be optimally designed for exclusively targeting diseased cells and tissues.Ligand-functionalized nanoparticles capable of selectively binding to diseased versus healthy cell populations are attractive for improved efficacy of nanoparticle-based drug and gene therapies. However, nanoparticles functionalized with high affinity targeting ligands may lead to undesired off-target binding to healthy cells. In this work, Monte Carlo simulations were used to quantitatively determine net surface interactions, binding valency, and selectivity between targeted nanoparticles and cell surfaces. Dissociation constant, KD, and target membrane protein density, ρR, are explored over a range representative of healthy and cancerous cell surfaces. Our findings show highly selective binding to diseased cell surfaces can be achieved with multiple, weaker affinity targeting ligands that can be further optimized by varying the targeting ligand density, ρL. Using the approach developed in this work, nanomedicines can be optimally designed for exclusively targeting diseased cells and tissues. Electronic supplementary information (ESI) available: Movie showing simulation renderings of targeted (ρL = 1820/μm2, KD = 120 μM) nanoparticle selective binding to cancer (ρR = 256/μm2) vs. healthy (ρR = 64/μm2) cell surfaces. Target membrane proteins have linear color scale depending on binding energy ranging from white when unbound (URL = 0) to red when tightly bound (URL = UM). See DOI: 10.1039/c5nr03691g

Histological assessment of the triangular fibrocartilage complex.

PubMed

Semisch, M; Hagert, E; Garcia-Elias, M; Lluch, A; Rein, S

2016-06-01

The morphological structure of the seven components of triangular fibrocartilage complexes of 11 cadaver wrists of elderly people was assessed microscopically, after staining with Hematoxylin-Eosin and Elastica van Gieson. The articular disc consisted of tight interlaced fibrocartilage without blood vessels except in its ulnar part. Volar and dorsal radioulnar ligaments showed densely parallel collagen bundles. The subsheath of the extensor carpi ulnaris muscle, the ulnotriquetral and ulnolunate ligament showed mainly mixed tight and loose parallel tissue. The ulnolunate ligament contained tighter parallel collagen bundles and clearly less elastic fibres than the ulnotriquetral ligament. The ulnocarpal meniscoid had an irregular morphological composition and loose connective tissue predominated. The structure of the articular disc indicates a buffering function. The tight structure of radioulnar and ulnolunate ligaments reflects a central stabilizing role, whereas the ulnotriquetral ligament and ulnocarpal meniscoid have less stabilizing functions. © The Author(s) 2015.

Ischemic preconditioning enhances integrity of coronary endothelial tight junctions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Zhao; Jin, Zhu-Qiu, E-mail: zhu-qiu.jin@sdstate.edu

2012-08-31

Highlights: Black-Right-Pointing-Pointer Cardiac tight junctions are present between coronary endothelial cells. Black-Right-Pointing-Pointer Ischemic preconditioning preserves the structural and functional integrity of tight junctions. Black-Right-Pointing-Pointer Myocardial edema is prevented in hearts subjected to ischemic preconditioning. Black-Right-Pointing-Pointer Ischemic preconditioning enhances translocation of ZO-2 from cytosol to cytoskeleton. -- Abstract: Ischemic preconditioning (IPC) is one of the most effective procedures known to protect hearts against ischemia/reperfusion (IR) injury. Tight junction (TJ) barriers occur between coronary endothelial cells. TJs provide barrier function to maintain the homeostasis of the inner environment of tissues. However, the effect of IPC on the structure and function of cardiacmore » TJs remains unknown. We tested the hypothesis that myocardial IR injury ruptures the structure of TJs and impairs endothelial permeability whereas IPC preserves the structural and functional integrity of TJs in the blood-heart barrier. Langendorff hearts from C57BL/6J mice were prepared and perfused with Krebs-Henseleit buffer. Cardiac function, creatine kinase release, and myocardial edema were measured. Cardiac TJ function was evaluated by measuring Evans blue-conjugated albumin (EBA) content in the extravascular compartment of hearts. Expression and translocation of zonula occludens (ZO)-2 in IR and IPC hearts were detected with Western blot. A subset of hearts was processed for the observation of ultra-structure of cardiac TJs with transmission electron microscopy. There were clear TJs between coronary endothelial cells of mouse hearts. IR caused the collapse of TJs whereas IPC sustained the structure of TJs. IR increased extravascular EBA content in the heart and myocardial edema but decreased the expression of ZO-2 in the cytoskeleton. IPC maintained the structure of TJs. Cardiac EBA content and edema were reduced in IPC hearts. IPC enhanced the translocation of ZO-2 from cytosol to cytoskeleton. In conclusion, TJs occur in normal mouse heart. IPC preserves the integrity of TJ structure and function that are vulnerable to IR injury.« less

The role of apical cell-cell junctions and associated cytoskeleton in mechanotransduction.

PubMed

Sluysmans, Sophie; Vasileva, Ekaterina; Spadaro, Domenica; Shah, Jimit; Rouaud, Florian; Citi, Sandra

2017-04-01

Tissues of multicellular organisms are characterised by several types of specialised cell-cell junctions. In vertebrate epithelia and endothelia, tight and adherens junctions (AJ) play critical roles in barrier and adhesion functions, and are connected to the actin and microtubule cytoskeletons. The interaction between junctions and the cytoskeleton is crucial for tissue development and physiology, and is involved in the molecular mechanisms governing cell shape, motility, growth and signalling. The machineries which functionally connect tight and AJ to the cytoskeleton comprise proteins which either bind directly to cytoskeletal filaments, or function as adaptors for regulators of the assembly and function of the cytoskeleton. In the last two decades, specific cytoskeleton-associated junctional molecules have been implicated in mechanotransduction, revealing the existence of multimolecular complexes that can sense mechanical cues and translate them into adaptation to tensile forces and biochemical signals. Here, we summarise the current knowledge about the machineries that link tight and AJ to actin filaments and microtubules, and the molecular basis for mechanotransduction at epithelial and endothelial AJ. © 2017 Société Française des Microscopies and Société de Biologie Cellulaire de France. Published by John Wiley & Sons Ltd.

Tuning the electronic properties of gated multilayer phosphorene: A self-consistent tight-binding study

NASA Astrophysics Data System (ADS)

Li, L. L.; Partoens, B.; Peeters, F. M.

2018-04-01

By taking account of the electric-field-induced charge screening, a self-consistent calculation within the framework of the tight-binding approach is employed to obtain the electronic band structure of gated multilayer phosphorene and the charge densities on the different phosphorene layers. We find charge density and screening anomalies in single-gated multilayer phosphorene and electron-hole bilayers in dual-gated multilayer phosphorene. Due to the unique puckered lattice structure, both intralayer and interlayer charge screenings are important in gated multilayer phosphorene. We find that the electric-field tuning of the band structure of multilayer phosphorene is distinctively different in the presence and absence of charge screening. For instance, it is shown that the unscreened band gap of multilayer phosphorene decreases dramatically with increasing electric-field strength. However, in the presence of charge screening, the magnitude of this band-gap decrease is significantly reduced and the reduction depends strongly on the number of phosphorene layers. Our theoretical results of the band-gap tuning are compared with recent experiments and good agreement is found.

Influence of strain on dislocation core in silicon

NASA Astrophysics Data System (ADS)

Pizzagalli, L.; Godet, J.; Brochard, S.

2018-05-01

First principles, density functional-based tight binding and semi-empirical interatomic potentials calculations are performed to analyse the influence of large strains on the structure and stability of a 60? dislocation in silicon. Such strains typically arise during the mechanical testing of nanostructures like nanopillars or nanoparticles. We focus on bi-axial strains in the plane normal to the dislocation line. Our calculations surprisingly reveal that the dislocation core structure largely depends on the applied strain, for strain levels of about 5%. In the particular case of bi-axial compression, the transformation of the dislocation to a locally disordered configuration occurs for similar strain magnitudes. The formation of an opening, however, requires larger strains, of about 7.5%. Furthermore, our results suggest that electronic structure methods should be favoured to model dislocation cores in case of large strains whenever possible.

Bandgap engineering of GaN nanowires

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ming, Bang-Ming; Yan, Hui; Wang, Ru-Zhi, E-mail: wrz@bjut.edu.cn, E-mail: yamcy@csrc.ac.cn

2016-05-15

Bandgap engineering has been a powerful technique for manipulating the electronic and optical properties of semiconductors. In this work, a systematic investigation of the electronic properties of [0001] GaN nanowires was carried out using the density functional based tight-binding method (DFTB). We studied the effects of geometric structure and uniaxial strain on the electronic properties of GaN nanowires with diameters ranging from 0.8 to 10 nm. Our results show that the band gap of GaN nanowires depends linearly on both the surface to volume ratio (S/V) and tensile strain. The band gap of GaN nanowires increases linearly with S/V, whilemore » it decreases linearly with increasing tensile strain. These linear relationships provide an effect way in designing GaN nanowires for their applications in novel nano-devices.« less

Fullerene-like Mo(W)(1-x)Re(x)S2 nanoparticles.

PubMed

Deepak, Francis Leonard; Popovitz-Biro, Ronit; Feldman, Yishay; Cohen, Hagai; Enyashin, Andrey; Seifert, Gotthard; Tenne, Reshef

2008-09-01

Inorganic fullerene-like (IF) Mo(1-x)Re(x)S(2) and W(1-x)Re(x)S(2) nanoparticles have been synthesized by a gas-phase reaction involving the respective metal halides with H(2)S. The IF-Mo(W)(1-x)Re(x)S(2) nanoparticles, containing up to 5 % Re, were characterized by a variety of experimental techniques. Analyses of the X-ray powder diffraction and different electron microscopy techniques show that the Re is doped in the MoS(2) host lattice. Interestingly, Re-doped MoS(2) nanotubes are present as well, although in small quantities ( approximately 5 %). XPS results confirm the nanoparticles to be more n-type arising from the effect of Re doping. Additionally, density-functional tight-binding (DFTB) calculations support the observed n-type behavior.

Observational data needs useful for modeling the coma

NASA Technical Reports Server (NTRS)

Huebner, W. F.; Giguere, P. T.

1981-01-01

A computer model of comet comae is described; results from assumed composition of frozen gases are summarized and compared to coma observations. Restrictions on relative abundance of some frozen constituents are illustrated. Modeling, when tightly coupled to observational data, can be important for comprehensive analysis of observations, for predicting undetected molecular species and for improved understanding of coma and nucleus. To accomplish this, total gas production rates and relative elemental abundances of H:C:N:O:S are needed as a function of heliocentric distance of the comet. Also needed are relative column densitites and column density profiles with well defined diaphragm range and pointing position on the coma. Production rates are less desirable since they are model dependent. Total number (or upper limits) of molecules in the coma and analysis of unidentified spectral lines are needed also.

Tight frames of k-plane ridgelets and the problem of representing objects that are smooth away from d-dimensional singularities in Rn

PubMed Central

Donoho, David L.

1999-01-01

For each pair (n, k) with 1 ≤ k < n, we construct a tight frame (ρλ : λ ∈ Λ) for L2 (Rn), which we call a frame of k-plane ridgelets. The intent is to efficiently represent functions that are smooth away from singularities along k-planes in Rn. We also develop tools to help decide whether k-plane ridgelets provide the desired efficient representation. We first construct a wavelet-like tight frame on the X-ray bundle χn,k—the fiber bundle having the Grassman manifold Gn,k of k-planes in Rn for base space, and for fibers the orthocomplements of those planes. This wavelet-like tight frame is the pushout to χn,k, via the smooth local coordinates of Gn,k, of an orthonormal basis of tensor Meyer wavelets on Euclidean space Rk(n−k) × Rn−k. We then use the X-ray isometry [Solmon, D. C. (1976) J. Math. Anal. Appl. 56, 61–83] to map this tight frame isometrically to a tight frame for L2(Rn)—the k-plane ridgelets. This construction makes analysis of a function f ∈ L2(Rn) by k-plane ridgelets identical to the analysis of the k-plane X-ray transform of f by an appropriate wavelet-like system for χn,k. As wavelets are typically effective at representing point singularities, it may be expected that these new systems will be effective at representing objects whose k-plane X-ray transform has a point singularity. Objects with discontinuities across hyperplanes are of this form, for k = n − 1. PMID:10051554

3D-fibroblast tissues constructed by a cell-coat technology enhance tight-junction formation of human colon epithelial cells.

PubMed

Matsusaki, Michiya; Hikimoto, Daichi; Nishiguchi, Akihiro; Kadowaki, Koji; Ohura, Kayoko; Imai, Teruko; Akashi, Mitsuru

2015-02-13

Caco-2, human colon carcinoma cell line, has been widely used as a model system for intestinal epithelial permeability because Caco-2 cells express tight-junctions, microvilli, and a number of enzymes and transporters characteristic of enterocytes. However, the functional differentiation and polarization of Caco-2 cells to express sufficient tight-junctions (a barrier) usually takes over 21 days in culture. This may be due to the cell culture environment, for example inflammation induced by plastic petri dishes. Three-dimensional (3D) sufficient cell microenvironments similar to in vivo natural conditions (proteins and cells), will promote rapid differentiation and higher functional expression of tight junctions. Herein we report for the first time an enhancement in tight-junction formation by 3D-cultures of Caco-2 cells on monolayered (1L) and eight layered (8L) normal human dermal fibroblasts (NHDF). Trans epithelial electric resistance (TEER) of Caco-2 cells was enhanced in the 3D-cultures, especially 8L-NHDF tissues, depending on culture times and only 10 days was enough to reach the same TEER value of Caco-2 monolayers after a 21 day incubation. Relative mRNA expression of tight-junction proteins of Caco-2 cells on 3D-cultures showed higher values than those in monolayer structures. Transporter gene expression patterns of Caco-2 cells on 3D-constructs were almost the same as those of Caco-2 monolayers, suggesting that there was no effect of 3D-cultures on transporter protein expression. The expression correlation between carboxylesterase 1 and 2 in 3D-cultures represented similar trends with human small intestines. The results of this study clearly represent a valuable application of 3D-Caco-2 tissues for pharmaceutical applications. Copyright © 2015 Elsevier Inc. All rights reserved.

How hormones influence composition and physiological function of the brain-blood barrier.

PubMed

Hampl, R; Bičíková, M; Sosvorová, L

2015-01-01

Hormones exert many actions in the brain. Their access and effects in the brain are regulated by the blood-brain barrier (BBB). Hormones as other substances may enter the brain and vice versa either by paracellular way requiring breaching tight junctions stitching the endothelial cells composing the BBB, or by passage through the cells (transcellular way). Hormones influence both ways through their receptors, both membrane and intracellular, present on/in the BBB. In the review the main examples are outlined how hormones influence the expression and function of proteins forming the tight junctions, as well as how they regulate expression and function of major protein transporters mediating transport of various substances including hormone themselves.

Claudin Loss-of-Function Disrupts Tight Junctions and Impairs Amelogenesis

PubMed Central

Bardet, Claire; Ribes, Sandy; Wu, Yong; Diallo, Mamadou Tidiane; Salmon, Benjamin; Breiderhoff, Tilman; Houillier, Pascal; Müller, Dominik; Chaussain, Catherine

2017-01-01

Claudins are a family of proteins that forms paracellular barriers and pores determining tight junctions (TJ) permeability. Claudin-16 and -19 are pore forming TJ proteins allowing calcium and magnesium reabsorption in the thick ascending limb of Henle's loop (TAL). Loss-of-function mutations in the encoding genes, initially identified to cause Familial Hypomagnesemia with Hypercalciuria and Nephrocalcinosis (FHHNC), were recently shown to be also involved in Amelogenesis Imperfecta (AI). In addition, both claudins were expressed in the murine tooth germ and Claudin-16 knockout (KO) mice displayed abnormal enamel formation. Claudin-3, an ubiquitous claudin expressed in epithelia including kidney, acts as a barrier-forming tight junction protein. We determined that, similarly to claudin-16 and claudin-19, claudin-3 was expressed in the tooth germ, more precisely in the TJ located at the apical end of secretory ameloblasts. The observation of Claudin-3 KO teeth revealed enamel defects associated to impaired TJ structure at the secretory ends of ameloblasts and accumulation of matrix proteins in the forming enamel. Thus, claudin-3 protein loss-of-function disturbs amelogenesis similarly to claudin-16 loss-of-function, highlighting the importance of claudin proteins for the TJ structure. These findings unravel that loss-of-function of either pore or barrier-forming TJ proteins leads to enamel defects. Hence, the major structural function of claudin proteins appears essential for amelogenesis. PMID:28596736

Claudin Loss-of-Function Disrupts Tight Junctions and Impairs Amelogenesis.

PubMed

Bardet, Claire; Ribes, Sandy; Wu, Yong; Diallo, Mamadou Tidiane; Salmon, Benjamin; Breiderhoff, Tilman; Houillier, Pascal; Müller, Dominik; Chaussain, Catherine

2017-01-01

Claudins are a family of proteins that forms paracellular barriers and pores determining tight junctions (TJ) permeability. Claudin-16 and -19 are pore forming TJ proteins allowing calcium and magnesium reabsorption in the thick ascending limb of Henle's loop (TAL). Loss-of-function mutations in the encoding genes, initially identified to cause Familial Hypomagnesemia with Hypercalciuria and Nephrocalcinosis (FHHNC), were recently shown to be also involved in Amelogenesis Imperfecta (AI). In addition, both claudins were expressed in the murine tooth germ and Claudin-16 knockout (KO) mice displayed abnormal enamel formation. Claudin-3, an ubiquitous claudin expressed in epithelia including kidney, acts as a barrier-forming tight junction protein. We determined that, similarly to claudin-16 and claudin-19, claudin-3 was expressed in the tooth germ, more precisely in the TJ located at the apical end of secretory ameloblasts. The observation of Claudin-3 KO teeth revealed enamel defects associated to impaired TJ structure at the secretory ends of ameloblasts and accumulation of matrix proteins in the forming enamel. Thus, claudin-3 protein loss-of-function disturbs amelogenesis similarly to claudin-16 loss-of-function, highlighting the importance of claudin proteins for the TJ structure. These findings unravel that loss-of-function of either pore or barrier-forming TJ proteins leads to enamel defects. Hence, the major structural function of claudin proteins appears essential for amelogenesis.

Long-range correction for tight-binding TD-DFT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Humeniuk, Alexander; Mitrić, Roland, E-mail: roland.mitric@uni-wuerzburg.de

2015-10-07

We present two improvements to the tight-binding approximation of time-dependent density functional theory (TD-DFTB): First, we add an exact Hartree-Fock exchange term, which is switched on at large distances, to the ground state Hamiltonian and similarly to the coupling matrix that enters the linear response equations for the calculation of excited electronic states. We show that the excitation energies of charge transfer states are improved relative to the standard approach without the long-range correction by testing the method on a set of molecules from the database in Peach et al. [J. Chem. Phys. 128, 044118 (2008)] which are known tomore » exhibit problematic charge transfer states. The degree of spatial overlap between occupied and virtual orbitals indicates where TD-DFTB and long-range corrected TD-DFTB (lc-TD-DFTB) can be expected to produce large errors. Second, we improve the calculation of oscillator strengths. The transition dipoles are obtained from Slater Koster files for the dipole matrix elements between valence orbitals. In particular, excitations localized on a single atom, which appear dark when using Mulliken transition charges, acquire a more realistic oscillator strength in this way. These extensions pave the way for using lc-TD-DFTB to describe the electronic structure of large chromophoric polymers, where uncorrected TD-DFTB fails to describe the high degree of conjugation and produces spurious low-lying charge transfer states.« less

Microstructure of cotton fibrous assemblies based on computed tomography

NASA Astrophysics Data System (ADS)

Jing, Hui; Yu, Weidong

2017-12-01

This paper describes for the first time the analysis of inner microstructure of cotton fibrous assemblies using computed tomography. Microstructure parameters such as packing density, fractal dimension as well as porosity including open porosity, closed porosity and total porosity are calculated based on 2D data from computed tomography. Values of packing density and fractal dimension are stable in random oriented fibrous assemblies, and there exists a satisfactory approximate linear relationship between them. Moreover, poles analysis indicates that porosity represents the tightness of fibrous assemblies and open poles are main existence.

Nonlinear properties of gated graphene in a strong electromagnetic field

DOE Office of Scientific and Technical Information (OSTI.GOV)

Avetisyan, A. A., E-mail: artakav@ysu.am; Djotyan, A. P., E-mail: adjotyan@ysu.am; Moulopoulos, K., E-mail: cos@ucy.ac.cy

We develop a microscopic theory of a strong electromagnetic field interaction with gated bilayer graphene. Quantum kinetic equations for density matrix are obtained using a tight binding approach within second quantized Hamiltonian in an intense laser field. We show that adiabatically changing the gate potentials with time may produce (at resonant photon energy) a full inversion of the electron population with high density between valence and conduction bands. In the linear regime, excitonic absorption of an electromagnetic radiation in a graphene monolayer with opened energy gap is also studied.

Many-body instabilities and mass generation in slow Dirac materials

NASA Astrophysics Data System (ADS)

Triola, Christopher; Zhu, Jian-Xin; Migliori, Albert; Balatsky, Alexander V.

2015-07-01

Some Kondo insulators are expected to possess topologically protected surface states with linear Dirac spectrum: the topological Kondo insulators. Because the bulk states of these systems typically have heavy effective electron masses, the surface states may exhibit extraordinarily small Fermi velocities that could force the effective fine structure constant of the surface states into the strong coupling regime. Using a tight-binding model, we study the many-body instabilities of these systems and identify regions of parameter space in which the system exhibits spin density wave and charge density wave order.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Morris, J.R.; Lu, Z.; Ring, D.M.

We have examined a variety of structures for the {l_brace}510{r_brace} symmetric tilt boundary in Si and Ge, using tight-binding and first-principles calculations. These calculations show that the observed structure in Si is the lowest-energy structure, despite the fact that it is more complicated than what is necessary to preserve fourfold coordination. Contrary to calculations using a Tersoff potential, first-principles calculations show that the energy depends strongly upon the structure. A recently developed tight-binding model for Si produces results in very good agreement with the first-principles calculations. Electronic density of states calculations based upon this model show no evidence of midgapmore » states and little evidence of electronic states localized to the grain boundary. {copyright} {ital 1998} {ital The American Physical Society}« less

Pharmaceutical Activation or Genetic Absence of ClC-2 Alters Tight Junctions During Experimental Colitis.

PubMed

Jin, Younggeon; Pridgen, Tiffany A; Blikslager, Anthony T

2015-12-01

We have previously reported that the ClC-2 chloride channel has an important role in regulation of tight junction barrier function during experimental colitis, and the pharmaceutical ClC-2 activator lubiprostone initiates intestinal barrier repair in ischemic-injured intestine. Thus, we hypothesized that pharmaceutical ClC-2 activation would have a protective and therapeutic effect in murine models of colitis, which would be absent in ClC-2 mice. We administered lubiprostone to wild-type or ClC-2 mice with dextran sulfate sodium (DSS) or 2, 4, 5-trinitrobenzene sulfonic acid-induced colitis. We determined the severity of colitis and assessed intestinal permeability. Selected tight junction proteins were analyzed by Western blotting and immunofluorescence/confocal microscopy, whereas proliferative and differentiated cells were examined with special staining and immunohistochemistry. Oral preventive or therapeutic administration of lubiprostone significantly reduced the severity of colitis and reduced intestinal permeability in both DSS and trinitrobenzene sulfonic acid-induced colitis. Preventive treatment with lubiprostone induced significant recovery of the expression and distribution of selected sealing tight junction proteins in mice with DSS-induced colitis. In addition, lubiprostone reduced crypt proliferation and increased the number of differentiated epithelial cells. Alternatively, when lubiprostone was administered to ClC-2 mice, the protective effect against DSS colitis was limited. This study suggests a central role for ClC-2 in restoration of barrier function and tight junction architecture in experimental murine colitis, which can be therapeutically targeted with lubiprostone.

Superfluid density and condensate fraction in the BCS-BEC crossover regime at finite temperatures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fukushima, N.; Ohashi, Y.; Faculty of Science and Technology, Keio University, Hiyoshi, Yokohama 223

2007-03-15

The superfluid density is a fundamental quantity describing the response to a rotation as well as in two-fluid collisional hydrodynamics. We present extensive calculations of the superfluid density {rho}{sub s} in the BCS-BEC crossover regime of a uniform superfluid Fermi gas at finite temperatures. We include strong-coupling or fluctuation effects on these quantities within a Gaussian approximation. We also incorporate the same fluctuation effects into the BCS single-particle excitations described by the superfluid order parameter {delta} and Fermi chemical potential {mu}, using the Nozieres-Schmitt-Rink approximation. This treatment is shown to be necessary for consistent treatment of {rho}{sub s} over themore » entire BCS-BEC crossover. We also calculate the condensate fraction N{sub c} as a function of the temperature, a quantity which is quite different from the superfluid density {rho}{sub s}. We show that the mean-field expression for the condensate fraction N{sub c} is a good approximation even in the strong-coupling BEC regime. Our numerical results show how {rho}{sub s} and N{sub c} depend on temperature, from the weak-coupling BCS region to the BEC region of tightly bound Cooper pair molecules. In a companion paper [Phys. Rev. A 74, 063626 (2006)], we derive an equivalent expression for {rho}{sub s} from the thermodynamic potential, which exhibits the role of the pairing fluctuations in a more explicit manner.« less

The role of cytosine methylation on charge transport through a DNA strand

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qi, Jianqing, E-mail: jqqi@uw.edu; Anantram, M. P., E-mail: anantmp@uw.edu; Govind, Niranjan, E-mail: niri.govind@pnnl.gov

Cytosine methylation has been found to play a crucial role in various biological processes, including a number of human diseases. The detection of this small modification remains challenging. In this work, we computationally explore the possibility of detecting methylated DNA strands through direct electrical conductance measurements. Using density functional theory and the Landauer-Büttiker method, we study the electronic properties and charge transport through an eight base-pair methylated DNA strand and its native counterpart. We first analyze the effect of cytosine methylation on the tight-binding parameters of two DNA strands and then model the transmission of the electrons and conductance throughmore » the strands both with and without decoherence. We find that the main difference of the tight-binding parameters between the native DNA and the methylated DNA lies in the on-site energies of (methylated) cytosine bases. The intra- and inter-strand hopping integrals between two nearest neighboring guanine base and (methylated) cytosine base also change with the addition of the methyl groups. Our calculations show that in the phase-coherent limit, the transmission of the methylated strand is close to the native strand when the energy is nearby the highest occupied molecular orbital level and larger than the native strand by 5 times in the bandgap. The trend in transmission also holds in the presence of the decoherence with the same rate. The lower conductance for the methylated strand in the experiment is suggested to be caused by the more stable structure due to the introduction of the methyl groups. We also study the role of the exchange-correlation functional and the effect of contact coupling by choosing coupling strengths ranging from weak to strong coupling limit.« less

The role of cytosine methylation on charge transport through a DNA strand

NASA Astrophysics Data System (ADS)

Qi, Jianqing; Govind, Niranjan; Anantram, M. P.

2015-09-01

Cytosine methylation has been found to play a crucial role in various biological processes, including a number of human diseases. The detection of this small modification remains challenging. In this work, we computationally explore the possibility of detecting methylated DNA strands through direct electrical conductance measurements. Using density functional theory and the Landauer-Büttiker method, we study the electronic properties and charge transport through an eight base-pair methylated DNA strand and its native counterpart. We first analyze the effect of cytosine methylation on the tight-binding parameters of two DNA strands and then model the transmission of the electrons and conductance through the strands both with and without decoherence. We find that the main difference of the tight-binding parameters between the native DNA and the methylated DNA lies in the on-site energies of (methylated) cytosine bases. The intra- and inter-strand hopping integrals between two nearest neighboring guanine base and (methylated) cytosine base also change with the addition of the methyl groups. Our calculations show that in the phase-coherent limit, the transmission of the methylated strand is close to the native strand when the energy is nearby the highest occupied molecular orbital level and larger than the native strand by 5 times in the bandgap. The trend in transmission also holds in the presence of the decoherence with the same rate. The lower conductance for the methylated strand in the experiment is suggested to be caused by the more stable structure due to the introduction of the methyl groups. We also study the role of the exchange-correlation functional and the effect of contact coupling by choosing coupling strengths ranging from weak to strong coupling limit.

Cadmium disorganises the scaffolding of gap and tight junction proteins in the hepatic cell line WIF B9.

PubMed

Boucherie, Sylviane; Decaens, Catherine; Verbavatz, Jean-Marc; Grosse, Brigitte; Erard, Marie; Merola, Fabienne; Cassio, Doris; Combettes, Laurent

2013-12-01

Hepatocytes, which perform the main functions of the liver, are particularly vulnerable to toxic agents such as cadmium, an environmental pollutant. To identify the molecular targets for cadmium in hepatocytes, we have studied the effects of CdCl2 on the hybrid cell line WIF-B9 that exhibits stable structural and functional hepatocytic polarity. We showed that the toxicity of CdCl2 (1 µM, 24 h) resulted in a reduction in direct intercellular communication (via gap junctions) and in an increase in paracellular permeability (decrease in the sealing of tight junctions). These effects were not related to changes in the expression of the key proteins involved, Cx32 and claudin 2, the first being constitutive of gap junctions and the second of tight junctions in this cell line. Using immunofluorescence experiments, we observed a change in the location of Cx32 and claudin 2: these two proteins were less often found in the tight junction network that closes the bile canaliculi (BC). In control cells, 'Proximity Ligation Assay' (PLA Duolink®) has confirmed in situ that molecules of claudin 2 and Cx32 are very close to each other at the BC (probably less than 16 nm). This was no longer the case after treatment with CdCl2 . Localisation of occludin and Cx32 relative to each other was not modified by CdCl2 , but CdCl2 increased the PLA signal between molecules of JAM-A and Cx32. Finally, examination of freeze-fracture replicas obtained from cultures treated with CdCl2 showed the disruption of the network of tight junctions and the depletion or the disintegration of the junctional plaques associated with tight junctions. This study demonstrates in situ the changes induced by cadmium on the organisation of cell-cell junctions and points out the importance of the association Cx32/claudin 2 for the maintenance of normal hepatocyte functions. © 2013 Société Française des Microscopies and Société de Biologie Cellulaire de France. Published by John Wiley & Sons Ltd.

Tight junction disruption: Helicobacter pylori and dysregulation of the gastric mucosal barrier

PubMed Central

Caron, Tyler J; Scott, Kathleen E; Fox, James G; Hagen, Susan J

2015-01-01

Long-term chronic infection with Helicobacter pylori (H. pylori) is a risk factor for gastric cancer development. In the multi-step process that leads to gastric cancer, tight junction dysfunction is thought to occur and serve as a risk factor by permitting the permeation of luminal contents across an otherwise tight mucosa. Mechanisms that regulate tight junction function and structure in the normal stomach, or dysfunction in the infected stomach, however, are largely unknown. Although conventional tight junction components are expressed in gastric epithelial cells, claudins regulate paracellular permeability and are likely the target of inflammation or H. pylori itself. There are 27 different claudin molecules, each with unique properties that render the mucosa an intact barrier that is permselective in a way that is consistent with cell physiology. Understanding the architecture of tight junctions in the normal stomach and then changes that occur during infection is important but challenging, because most of the reports that catalog claudin expression in gastric cancer pathogenesis are contradictory. Furthermore, the role of H. pylori virulence factors, such as cytotoxin-associated gene A and vacoulating cytotoxin, in regulating tight junction dysfunction during infection is inconsistent in different gastric cell lines and in vivo, likely because non-gastric epithelial cell cultures were initially used to unravel the details of their effects on the stomach. Hampering further study, as well, is the relative lack of cultured cell models that have tight junction claudins that are consistent with native tissues. This summary will review the current state of knowledge about gastric tight junctions, normally and in H. pylori infection, and make predictions about the consequences of claudin reorganization during H. pylori infection. PMID:26523106

TiO2-Based Indium Phosphide Metal-Oxide-Semiconductor Capacitor with High Capacitance Density.

PubMed

Cheng, Chun-Hu; Hsu, Hsiao-Hsuan; Chou, Kun-i

2015-04-01

We report a low-temperature InP p-MOS with a high capacitance density of 2.7 µF/cm2, low leakage current of 0.77 A/cm2 at 1 V and tight current distribution. The high-density and low-leakage InP MOS was achieved by using high-κ TiLaO dielectric and ultra-thin SiO2 buffer layer with a thickness of less than 0.5 nm. The obtained EOT can be aggressively scaled down to < 1 nm through the use of stacked TiLaO/SiO2 dielectric, which has the potential for the future application of high mobility III-V CMOS devices.

Spin-density wave state in simple hexagonal graphite

NASA Astrophysics Data System (ADS)

Mosoyan, K. S.; Rozhkov, A. V.; Sboychakov, A. O.; Rakhmanov, A. L.

2018-02-01

Simple hexagonal graphite, also known as AA graphite, is a metastable configuration of graphite. Using tight-binding approximation, it is easy to show that AA graphite is a metal with well-defined Fermi surface. The Fermi surface consists of two sheets, each shaped like a rugby ball. One sheet corresponds to electron states, another corresponds to hole states. The Fermi surface demonstrates good nesting: a suitable translation in the reciprocal space superposes one sheet onto another. In the presence of the electron-electron repulsion, a nested Fermi surface is unstable with respect to spin-density-wave ordering. This instability is studied using the mean-field theory at zero temperature, and the spin-density-wave order parameter is evaluated.

Cloudy Skies over AGN: Observations with Simbol-X

NASA Astrophysics Data System (ADS)

Salvati, M.; Risaliti, G.

2009-05-01

Recent time-resolved spectroscopic X-ray studies of bright obscured AGN show that column density variability on time scales of hours/days may be common, at least for sources with NH>1023 cm-2. This opens new oppurtunities in the analysis of the structure of the circumnuclear medium and of the X-ray source: resolving the variations due to single clouds covering/uncovering the X-ray source provides tight constraints on the source size, the clouds' size and distance, and their average number, density and column density. We show how Simbol-X will provide a breakthrough in this field, thanks to its broad band coverage, allowing (a) to precisely disentangle the continuum and NH variations, and (2) to extend the NH variability analysis to column densities >1023 cm-2.

ENVIRONMENTAL TECHNOLOGY VERIFICATION REPORT: STORMWATER SOURCE AREA TREATMENT DEVICE — BAYSAVER TECHNOLOGIES, INC. BAYSAVER SEPARATION SYSTEM, MODEL 10K

EPA Science Inventory

Verification testing of the BaySaver Separation System, Model 10K was conducted on a 10 acre drainage basin near downtown Griffin, Georgia. The system consists of two water tight pre-cast concrete manholes and a high-density polyethylene BaySaver Separator Unit. The BaySaver Mod...

Microwave emulations and tight-binding calculations of transport in polyacetylene

NASA Astrophysics Data System (ADS)

Stegmann, Thomas; Franco-Villafañe, John A.; Ortiz, Yenni P.; Kuhl, Ulrich; Mortessagne, Fabrice; Seligman, Thomas H.

2017-01-01

A novel approach to investigate the electron transport of cis- and trans-polyacetylene chains in the single-electron approximation is presented by using microwave emulation measurements and tight-binding calculations. In the emulation we take into account the different electronic couplings due to the double bonds leading to coupled dimer chains. The relative coupling constants are adjusted by DFT calculations. For sufficiently long chains a transport band gap is observed if the double bonds are present, whereas for identical couplings no band gap opens. The band gap can be observed also in relatively short chains, if additional edge atoms are absent, which cause strong resonance peaks within the band gap. The experimental results are in agreement with our tight-binding calculations using the nonequilibrium Green's function method. The tight-binding calculations show that it is crucial to include third nearest neighbor couplings to obtain the gap in the cis-polyacetylene.

Atomistic Design of CdSe/CdS Core-Shell Quantum Dots with Suppressed Auger Recombination.

PubMed

Jain, Ankit; Voznyy, Oleksandr; Hoogland, Sjoerd; Korkusinski, Marek; Hawrylak, Pawel; Sargent, Edward H

2016-10-12

We design quasi-type-II CdSe/CdS core-shell colloidal quantum dots (CQDs) exhibiting a suppressed Auger recombination rate. We do so using fully atomistic tight-binding wave functions and microscopic Coulomb interactions. The recombination rate as a function of the core and shell size and shape is tested against experiments. Because of a higher density of deep hole states and stronger hole confinement, Auger recombination is found to be up to six times faster for positive trions compared to negative ones in 4 nm core/10 nm shell CQDs. Soft-confinement at the interface results in weak suppression of Auger recombination compared to same-bandgap sharp-interface CQDs. We find that the suppression is due to increased volume of the core resulting in delocalization of the wave functions, rather than due to soft-confinement itself. We show that our results are consistent with previous effective mass models with the same system parameters. Increasing the dot volume remains the most efficient way to suppress Auger recombination. We predict that a 4-fold suppression of Auger recombination can be achieved in 10 nm CQDs by increasing the core volume by using rodlike cores embedded in thick shells.

Cholesterol overload impairing cerebellar function: the promise of natural products.

PubMed

El-Sayyad, Hassan I H

2015-05-01

The cerebellum is the part of the brain most involved in controlling motor and cognitive function. The surface becomes convoluted, forming folia that have a characteristic internal structure of three layers including molecular, Purkinje cell, and granular layer. This complex neural network gives rise to a massive signal-processing capability. Cholesterol is a major constituent, derived by de novo synthesis and the blood-brain barrier. Cholesterol is tightly regulated between neurons and glia-that is, astrocytes, microglia, and oligodendrocytes-and is essential for normal brain development. The axon is wrapped by myelin (cholesterol, phospholipids, and glycosphingolipids) and made up of membranes of oligodendrocytes, separated by periodic gaps in the myelin sheath, called nodes of Ranvier. Hypercholesterolemia is associated with increased oxidative stress and the development of neurotoxicity and Alzheimer's disease. Treatment with natural products has been found to support improved brain function and reduce low-density-lipoprotein cholesterol level. Fish oil is one such product; among the many plant products are: Morus alba leaves, fruit, and bark; pomegranate fruit and peel; Barley β - glucans; date palm; and Allium sativum. The therapeutic potential was discussed in relation with the antilipidemic drugs, statins (HMG-CoA reductase inhibitors). Copyright © 2015 Elsevier Inc. All rights reserved.

Analysis of noise in quorum sensing.

PubMed

Cox, Chris D; Peterson, Gregory D; Allen, Michael S; Lancaster, Joseph M; McCollum, James M; Austin, Derek; Yan, Ling; Sayler, Gary S; Simpson, Michael L

2003-01-01

Noise may play a pivotal role in gene circuit functionality, as demonstrated for the genetic switch in the bacterial phage lambda. Like the lambda switch, bacterial quorum sensing (QS) systems operate within a population and contain a bistable switching element, making it likely that noise plays a functional role in QS circuit operation. Therefore, a detailed analysis of the noise behavior of QS systems is needed. We have developed a set of tools generally applicable to the analysis of gene circuits, with an emphasis on investigations in the frequency domain (FD), that we apply here to the QS system in the marine bacterium Vibrio fischeri. We demonstrate that a tight coupling between exact stochastic simulation and FD analysis provides insights into the structure/function relationships in the QS circuit. Furthermore, we argue that a noise analysis is incomplete without consideration of the power spectral densities (PSDs) of the important molecular output signals. As an example we consider reversible reactions in the QS circuit, and show through analysis and exact stochastic simulation that these circuits make significant and dynamic modifications to the noise spectra. In particular, we demonstrate a "whitening" effect, which occurs as the noise is processed through these reversible reactions.

Exploiting the flexibility and the polarization of ferroelectric perovskite surfaces to achieve efficient photochemistry and enantiospecificity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rappe, Andrew

This research project explored the catalytic properties of complex surfaces of functional materials. The PI used first-principles density functional theory (DFT) calculations to explore a tightly integrated set of properties. The physical properties of complex functional materials that influence surface chemistry were explored, including bulk and surface electric dipoles, and surface conductivity. The energetic, compositional, electronic, and chemical properties of the surfaces of these materials were explored in detail, and connections between material properties and chemical reactivity were established. This project led to 28 publications, including Nat. Comm., JACS, 3 PRL, 7 PRB, 2 ACS Nano, 2 Nano Lett., 4more » JPCL, 2 JCP, Chem. Mater., ACS Appl. Mater. Interfaces, Phys. Rev. Appl., and a U.S. Patent on surface catalysts. The key accomplishments in this project involved work in six coordinated areas: pioneering ways to control bulk dipoles in order to dynamically affect catalysis, exploring novel ways of bringing charge to the surface for redox catalysis, nonstoichiometric surfaces offering new sites for heterogeneous catalysis, illustrating how surface catalysis responds to applied pressure, catalytic growth of carbon-based materials, and new computational methods allowing more accurate exploration of molecule-surface interactions« less

Quantum interference in coherent tunneling through branched molecular junctions containing ferrocene centers

NASA Astrophysics Data System (ADS)

Zhao, Xin; Kastlunger, Georg; Stadler, Robert

2017-08-01

In our theoretical study where we combine a nonequilibrium Green's function approach with density functional theory we investigate branched compounds containing ferrocene moieties in both branches which, due to their metal centers, are designed to allow for asymmetry induced by local charging. In these compounds the ferrocene moieties are connected to pyridyl anchor groups either directly or via acetylenic spacers in a metaconnection, where we also compare our results with those obtained for the respective single-branched molecules with both meta- and paraconnections between the metal center and the anchors. We find a destructive quantum interference (DQI) feature in the transmission function slightly below the lowest unoccupied molecular orbital, which dominates the conductance even for the uncharged branched compound with spacer groups inserted. In an analysis based on mapping the structural characteristics of the range of molecules in our article onto tight-binding models, we identify the structural source of the DQI minimum as the through-space coupling between the pyridyl anchor groups. We also find that local charging in one of the branches changes the conductance only by about one order of magnitude, which we explain in terms of the spatial distributions of the relevant molecular orbitals for the branched compounds.

Injuries of the Sternoclavicular Joint - An Innovative Approach in the Management of a Rare Injury: Tight Rope Fixation of the Costo-Clavicular Ligament.

PubMed

Unterkofler, Jan; Merschin, David; Langenbach, Andreas; Ekkernkamp, Axel; Schulz-Drost, Stefan

2017-01-01

Background: The costoclavicular ligament (CCL) provides the most tight stability within the sternoclavicular joint (SCJ), followed by the most cited sternoclavicular ligaments (SCL). Their disruption may cause severe instability of the SCJ. Different treatment options, such as the use of plates, wires or autologous tendons are associated with mainly limited functional outcome. Could a stabilization of CCL next to an anatomic fixation of the SCL provide sufficient reconstruction of the SCJ? Methods: A 58-year-old male showed severe anterior and painful instability of the SCJ following a fall on his shoulder 8 weeks ago. The SCJ had been reconstructed in an open procedure with stabilization of the CCL employing 2 tight ropes and anatomical suture of the SCL. Follow-up was carried out 78 weeks after operation. Results: The reduction of the SCJ was successful. X-ray proved the anatomic position of the SCJ. Pain was decreased in between the first 6 weeks. The patient showed uneventful follow-up and returned to work 6 months after the procedureas a hard working farmer. Conclusions: Innovative stabilization of the CCL with tight ropes additional to a suture of the SCL may enable anatomic reconstruction of the SCJ considering cosmetic and functional results. Celsius.

Cosmological constraints from Chandra observations of galaxy clusters.

PubMed

Allen, Steven W

2002-09-15

Chandra observations of rich, relaxed galaxy clusters allow the properties of the X-ray gas and the total gravitating mass to be determined precisely. Here, we present results for a sample of the most X-ray luminous, dynamically relaxed clusters known. We show that the Chandra data and independent gravitational lensing studies provide consistent answers on the mass distributions in the clusters. The mass profiles exhibit a form in good agreement with the predictions from numerical simulations. Combining Chandra results on the X-ray gas mass fractions in the clusters with independent measurements of the Hubble constant and the mean baryonic matter density in the Universe, we obtain a tight constraint on the mean total matter density of the Universe, Omega(m), and an interesting constraint on the cosmological constant, Omega(Lambda). We also describe the 'virial relations' linking the masses, X-ray temperatures and luminosities of galaxy clusters. These relations provide a key step in linking the observed number density and spatial distribution of clusters to the predictions from cosmological models. The Chandra data confirm the presence of a systematic offset of ca. 40% between the normalization of the observed mass-temperature relation and the predictions from standard simulations. This finding leads to a significant revision of the best-fit value of sigma(8) inferred from the observed temperature and luminosity functions of clusters.

Atomic and electronic structure transformations of silver nanoparticles under rapid cooling conditions.

PubMed

Lobato, I; Rojas, J; Landauro, C V; Torres, J

2009-02-04

The structural evolution and dynamics of silver nanodrops Ag(2869) (4.4 nm in diameter) under rapid cooling conditions have been studied by means of molecular dynamics simulations and electronic density of state calculations. The interaction of silver atoms is modelled by a tight-binding semiempirical interatomic potential proposed by Cleri and Rosato. The pair correlation functions and the pair analysis technique are used to reveal the structural transition in the process of solidification. It is shown that Ag nanoparticles evolve into different nanostructures under different cooling processes. At a cooling rate of 1.5625 × 10(13) K s(-1) the nanoparticles preserve an amorphous-like structure containing a large amount of 1551 and 1541 pairs which correspond to icosahedral symmetry. For a lower cooling rate (1.5625 × 10(12) K s(-1)), the nanoparticles transform into a crystal-like structure consisting mainly of 1421 and 1422 pairs which correspond to the face centred cubic and hexagonal close packed structures, respectively. The variations of the electronic density of states for the differently cooled nanoparticles are small, but in correspondence with the structural changes.

Investigation of electronic transport through a ladder-like graphene nanoribbon including random distributed impurities

NASA Astrophysics Data System (ADS)

Esmaili, Esmat; Mardaani, Mohammad; Rabani, Hassan

2018-01-01

The electronic transport of a ladder-like graphene nanoribbon which the on-site or hopping energies of a small part of it can be random is modeled by using the Green's function technique within the nearest neighbor tight-binding approach. We employ a unitary transformation in order to convert the Hamiltonian of the nanoribbon to the Hamiltonian of a tight-binding ladder-like network. In this case, the disturbed part of the system includes the second neighbor hopping interactions. While, the converted Hamiltonian of each ideal part is equivalent to the Hamiltonian of two periodic on-site chains. Therefore, we can insert the self-energies of the alternative on-site tight-binding chains to the inverse of the Green's function matrix of the ladder-like part. In this viewpoint, the conductance is constructed from two trans and cis contributions. The results show that increasing the disorder strength causes the increase and decrease of the conductance of the trans and cis contributions, respectively.

Dlg3 Trafficking and Apical Tight Junction Formation Is Regulated by Nedd4 and Nedd4-2 E3 Ubiquitin Ligases

PubMed Central

Van Campenhout, Claude A.; Eitelhuber, Andrea; Gloeckner, Christian J.; Giallonardo, Patrizia; Gegg, Moritz; Oller, Heide; Grant, Seth G.N.; Krappmann, Daniel; Ueffing, Marius; Lickert, Heiko

2011-01-01

Summary The Drosophila Discs large (Dlg) scaffolding protein acts as a tumor suppressor regulating basolateral epithelial polarity and proliferation. In mammals, four Dlg homologs have been identified; however, their functions in cell polarity remain poorly understood. Here, we demonstrate that the X-linked mental retardation gene product Dlg3 contributes to apical-basal polarity and epithelial junction formation in mouse organizer tissues, as well as to planar cell polarity in the inner ear. We purified complexes associated with Dlg3 in polarized epithelial cells, including proteins regulating directed trafficking and tight junction formation. Remarkably, of the four Dlg family members, Dlg3 exerts a distinct function by recruiting the ubiquitin ligases Nedd4 and Nedd4-2 through its PPxY motifs. We found that these interactions are required for Dlg3 monoubiquitination, apical membrane recruitment, and tight junction consolidation. Our findings reveal an unexpected evolutionary diversification of the vertebrate Dlg family in basolateral epithelium formation. PMID:21920314

An overview on genome organization of marine organisms.

PubMed

Costantini, Maria

2015-12-01

In this review we will concentrate on some general genome features of marine organisms and their evolution, ranging from vertebrate to invertebrates until unicellular organisms. Before genome sequencing, the ultracentrifugation in CsCl led to high resolution of mammalian DNA (without seeing at the sequence). The analytical profile of human DNA showed that the vertebrate genome is a mosaic of isochores, typically megabase-size DNA segments that belong in a small number of families characterized by different GC levels. The recent availability of a number of fully sequenced genomes allowed mapping very precisely the isochores, based on DNA sequences. Since isochores are tightly linked to biological properties such as gene density, replication timing and recombination, the new level of detail provided by the isochore map helped the understanding of genome structure, function and evolution. This led the current level of knowledge and to further insights. Copyright © 2015. Published by Elsevier B.V.

Heptagraphene: Tunable dirac cones in a graphitic structure

DOE PAGES

Lopez-Bezanilla, Alejandro; Martin, Ivar; Littlewood, Peter B.

2016-09-13

Here, we predict the existence and dynamical stability of heptagraphene, a new graphitic structure formed of rings of 10 carbon atoms bridged by carbene groups yielding seven-membered rings. Despite the rectangular unit cell, the band structure is topologically equivalent to that of strongly distorted graphene. Density-functional-theory calculations demonstrate that heptagraphene has Dirac cones on symmetry lines that are robust against biaxial strain but which open a gap under shear. At high deformation values bond reconstructions lead to different electronic band arrangements in dynamically stable configurations. Within a tight-binding framework this richness of the electronic behavior is identified as a directmore » consequence of the symmetry breaking within the cell which, unlike other graphitic structures, leads to band gap opening. A combined approach of chemical and physical modification of graphene unit cell unfurls the opportunity to design carbon-based systems in which one aims to tune an electronic band gap.« less

Predicting hydration free energies of amphetamine-type stimulants with a customized molecular model

NASA Astrophysics Data System (ADS)

Li, Jipeng; Fu, Jia; Huang, Xing; Lu, Diannan; Wu, Jianzhong

2016-09-01

Amphetamine-type stimulants (ATS) are a group of incitation and psychedelic drugs affecting the central nervous system. Physicochemical data for these compounds are essential for understanding the stimulating mechanism, for assessing their environmental impacts, and for developing new drug detection methods. However, experimental data are scarce due to tight regulation of such illicit drugs, yet conventional methods to estimate their properties are often unreliable. Here we introduce a tailor-made multiscale procedure for predicting the hydration free energies and the solvation structures of ATS molecules by a combination of first principles calculations and the classical density functional theory. We demonstrate that the multiscale procedure performs well for a training set with similar molecular characteristics and yields good agreement with a testing set not used in the training. The theoretical predictions serve as a benchmark for the missing experimental data and, importantly, provide microscopic insights into manipulating the hydrophobicity of ATS compounds by chemical modifications.

Molecular Growth Inside of Polycyclic Aromatic Hydrocarbon Clusters Induced by Ion Collisions.

PubMed

Delaunay, Rudy; Gatchell, Michael; Rousseau, Patrick; Domaracka, Alicja; Maclot, Sylvain; Wang, Yang; Stockett, Mark H; Chen, Tao; Adoui, Lamri; Alcamí, Manuel; Martín, Fernando; Zettergren, Henning; Cederquist, Henrik; Huber, Bernd A

2015-05-07

The present work combines experimental and theoretical studies of the collision between keV ion projectiles and clusters of pyrene, one of the simplest polycyclic aromatic hydrocarbons (PAHs). Intracluster growth processes induced by ion collisions lead to the formation of a wide range of new molecules with masses larger than that of the pyrene molecule. The efficiency of these processes is found to strongly depend on the mass and velocity of the incoming projectile. Classical molecular dynamics simulations of the entire collision process-from the ion impact (nuclear scattering) to the formation of new molecular species-reproduce the essential features of the measured molecular growth process and also yield estimates of the related absolute cross sections. More elaborate density functional tight binding calculations yield the same growth products as the classical simulations. The present results could be relevant to understand the physical chemistry of the PAH-rich upper atmosphere of Saturn's moon Titan.

Giant switchable Rashba effect in oxide heterostructures

DOE PAGES

Zhong, Zhicheng; Si, Liang; Zhang, Qinfang; ...

2015-03-01

One of the most fundamental phenomena and a reminder of the electron’s relativistic nature is the Rashba spin splitting for broken inversion symmetry. Usually this splitting is a tiny relativistic correction. Interfacing ferroelectric BaTiO₃ and a 5d (or 4d) transition metal oxide with a large spin-orbit coupling, Ba(Os,Ir,Ru)O₃, we show that giant Rashba spin splittings are indeed possible and even controllable by an external electric field. Based on density functional theory and a microscopic tight binding understanding, we conclude that the electric field is amplified and stored as a ferroelectric Ti-O distortion which, through the network of oxygen octahedra, inducesmore » a large (Os,Ir,Ru)-O distortion. The BaTiO₃/Ba(Os,Ru,Ir)O₃ heterostructure is hence the ideal test station for switching and studying the Rashba effect and allows applications at room temperature.« less

Thermal conductance of two interface materials and their applications in space systems

NASA Technical Reports Server (NTRS)

Scialdone, J. J.; Clatterbuck, C. H.; Wall, J. L.

1992-01-01

Two polymeric materials, the Cho-Therm 1671 elastomer and the CV-2946 conductive RTV silicone, have been evaluated. Tests were conducted in vacuum and in air, for many clamping pressures, power densities, and as a function of time. Results obtained show that the CV-2946 thermal conductance after 24 hour in vacuum is 0.62 W/sq cm C(4W/sq in C) when clamped with an average pressure of about 350 psi. The maximum conductance of Cho-Therm 1671 is 4.3 W/sq in C at the clamping pressure about 200 psi. After 72 h in vacuum, the conductance reaches a steady 3.4 W/sq in C, independent of clamping pressure. It is concluded that the tightly bolted, torqued fixtures do not buckle or distort and provide an optimum thermal conductance. The fixtures simulating an actual spacecraft configuration suffered severe bowing and separating, which caused considerable degradation of conductance values.

Black hole demographics from the M•-σ relation

NASA Astrophysics Data System (ADS)

Merritt, David; Ferrarese, Laura

2001-01-01

We analyse a sample of 32 galaxies for which a dynamical estimate of the mass of the hot stellar component, Mbulge, is available. For each of these galaxies, we calculate the mass of the central black hole, M•, using the tight empirical correlation between M• and bulge stellar velocity dispersion. The frequency function N[log(M•Mbulge)] is reasonably well described as a Gaussian with ~-2.90 and standard deviation ~0.45 the implied mean ratio of black hole mass to bulge mass is a factor of ~5 smaller than generally quoted in the literature. We present marginal evidence for a lower, average black hole mass fraction in more massive galaxies. The total mass density in black holes in the local Universe is estimated to be ~ 5×105MsolarMpc-3, consistent with that inferred from high-redshift (z~2) active galactic nuclei.

Importance of Electronic Correlations and Unusual Excitonic Effects in Formamidinium Lead Halide Perovskites

NASA Astrophysics Data System (ADS)

Whitcher, T. J.; Zhu, J.-X.; Chi, X.; Hu, H.; Zhao, Daming; Asmara, T. C.; Yu, X.; Breese, M. B. H.; Castro Neto, A. H.; Lam, Y. M.; Wee, A. T. S.; Chia, Elbert E. M.; Rusydi, A.

2018-04-01

Hybrid inorganic-organic perovskites have recently attracted much interest because of both rich fundamental sciences and potential applications such as the primary energy-harvesting material in solar cells. However, an understanding of electronic and optical properties, particularly the complex dielectric function, of these materials is still lacking. Here, we report on the electronic and optical properties of selective perovskites using temperature-dependent spectroscopic ellipsometry, x-ray absorption spectroscopy supported by first-principles calculations. Surprisingly, the perovskite FA0.85Cs0.15PbI2.9Br0.1 has a very high density of low-energy excitons that increases with increasing temperature even at room temperature, which is not seen in any other material. This is found to be due to the strong, unscreened electron-electron and partially screened electron-hole interactions, which then tightly connect low- and high-energy bands caused by doping.

Pressure dependence of critical temperature of bulk FeSe from spin fluctuation theory

NASA Astrophysics Data System (ADS)

Hirschfeld, Peter; Kreisel, Andreas; Wang, Yan; Tomic, Milan; Jeschke, Harald; Jacko, Anthony; Valenti, Roser; Maier, Thomas; Scalapino, Douglas

2013-03-01

The critical temperature of the 8K superconductor FeSe is extremely sensitive to pressure, rising to a maximum of 40K at about 10GPa. We test the ability of the current generation of fluctuation exchange pairing theories to account for this effect, by downfolding the density functional theory electronic structure for each pressure to a tight binding model. The Fermi surface found in such a procedure is then used with fixed Hubbard parameters to determine the pairing strength using the random phase approximation for the spin singlet pairing vertex. We find that the evolution of the Fermi surface captured by such an approach is alone not sufficient to explain the observed pressure dependence, and discuss alternative approaches. PJH, YW, AK were supported by DOE DE-FG02-05ER46236, the financial support of MT, HJ, and RV from the DFG Schwerpunktprogramm 1458 is kindly acknowledged.

Modeling Bi-induced changes in the electronic structure of GaAs1-xBix alloys

NASA Astrophysics Data System (ADS)

Virkkala, Ville; Havu, Ville; Tuomisto, Filip; Puska, Martti J.

2013-12-01

We suggested recently [V. Virkkala , Phys. Rev. BPRBMDO1098-012110.1103/PhysRevB.88.035204 88, 035204 (2013)] that the band-gap narrowing in dilute GaAs1-xNx alloys can be explained to result from the broadening of the localized N states due to the N-N interaction along the zigzag chains in the <110> directions. In that study our tight-binding modeling based on first-principles density-functional calculations took into account the random distribution of N atoms in a natural way. In this work we extend our modeling to GaAs1-xBix alloys. Our results indicate that Bi states mix with host material states. However, the states near the valence-band edge agglomerate along the zigzag chains originating from individual Bi atoms. This leads to Bi-Bi interactions in a random alloy broadening these states in energy and causing the band-gap narrowing.

Nanoscale organization of {beta}{sub 2}-adrenergic receptor-Venus fusion protein domains on the surface of mammalian cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vobornik, Dusan; Rouleau, Yanouchka; Haley, Jennifer

2009-04-24

Adrenergic receptors are a key component of nanoscale multiprotein complexes that are responsible for controlling the beat rate in a mammalian heart. We demonstrate the ability of near-field scanning optical microscopy (NSOM) to visualize {beta}{sub 2}-adrenergic receptors ({beta}{sub 2}AR) fused to the GFP analogue Venus at the nanoscale on HEK293 cells. The expression of the {beta}{sub 2}AR-Venus fusion protein was tightly controlled using a tetracycline-induced promoter. Both the size and density of the observed nanoscale domains are dependent on the level of induction and thus the level of protein expression. At concentrations between 100 and 700 ng/ml of inducer doxycycline,more » the size of domains containing the {beta}{sub 2}AR-Venus fusion protein appears to remain roughly constant, but the number of domains per cell increase. At 700 ng/ml doxycycline the functional receptors are organized into domains with an average diameter of 150 nm with a density similar to that observed for the native protein on primary murine cells. By contrast, larger micron-sized domains of {beta}{sub 2}AR are observed in the membrane of the HEK293 cells that stably overexpress {beta}{sub 2}AR-GFP and {beta}{sub 2}AR-eYFP. We conclude that precise chemical control of gene expression is highly advantageous for the use {beta}{sub 2}AR-Venus fusion proteins as models for {beta}{sub 2}AR function. These observations are critical for designing future cell models and assays based on {beta}{sub 2}AR, since the receptor biology is consistent with a relatively low density of nanoscale receptor domains.« less

Hepatic immunohistochemical localization of the tight junction protein ZO-1 in rat models of cholestasis.

PubMed Central

Anderson, J. M.; Glade, J. L.; Stevenson, B. R.; Boyer, J. L.; Mooseker, M. S.

1989-01-01

Structural alterations in hepatocyte tight junctions accompanying cholestasis were investigated using immunolocalization of ZO-1, the first known protein component of the tight junction. Disruption in the paracellular barrier function of the tight junction has been proposed to allow reflux of bile into the blood. Cholestasis was induced in 210 to 235 g male Sprague-Dawley rats either by five consecutive daily subcutaneous injections of 17-alpha-ethinyl estradiol (0.5 mg/kg/d in propylene glycol) or ligation of the common bile duct for 72 hours. The structural organization of the tight junction was assessed in each model by indirect immunofluorescent and immunoperoxidase staining for ZO-1 on frozen sections of liver and compared with controls. In control, sham-operated, and estradiol-injected animals, ZO-1 localizes in a uniform continuous manner along the margins of the canaliculi. In contrast, bile duct ligation results in the appearance of numerous discontinuities in ZO-1 staining accompanied by dilation or collapse of the lumenal space. Tissue content of the ZO-1 protein, as determined by quantitative immunoblotting, was unaffected in either cholestatic model compared with controls. These findings indicate that the molecular organization of the tight junction can be assessed from immunostaining patterns of ZO-1 in frozen sections of cholestatic livers. Under these experimental conditions, the organization of the tight junction at the level of the ZO-1 protein is altered by bile duct obstruction but not by ethinyl estradiol. Images Figure 1 Figure 2 PMID:2719075

Quasi one-dimensional band dispersion and surface metallization in long-range ordered polymeric wires

DOE PAGES

Vasseur, Guillaume; Fagot-Revurat, Yannick; Sicot, Muriel; ...

2016-01-04

We study the electronic structure of an ordered array of poly(para-phenylene) chains produced by surface-catalyzed dehalogenative polymerization of 1,4-dibromobenzene on copper (110). The quantization of unoccupied molecular states is measured as a function of oligomer length by scanning tunnelling spectroscopy, with Fermi level crossings observed for chains longer than ten phenyl rings. Angle-resolved photoelectron spectroscopy reveals a quasi-one-dimensional valence band as well as a direct gap of 1.15 eV, as the conduction band is partially filled through adsorption on the surface. Tight-binding modelling and ab initio density functional theory calculations lead to a full description of the organic band-structure, includingmore » the k-dispersion, the gap size and electron charge transfer mechanisms, highlighting a strong substrate-molecule interaction that drives the system into a metallic behaviour. In summary, we have fully characterized the band structure of a carbon-based conducting wire. This model system may be considered as a fingerprint of -conjugation of surface organic frameworks.« less

Non-local electron transport through normal and topological ladder-like atomic systems

NASA Astrophysics Data System (ADS)

Kurzyna, Marcin; Kwapiński, Tomasz

2018-05-01

We propose a locally protected ladder-like atomic system (nanoconductor) on a substrate that is insensitive to external perturbations. The system corresponds to coupled atomic chains fabricated on different surfaces. Electron transport properties of such conductors are studied theoretically using the model tight-binding Su-Schriffer-Hegger (SSH) Hamiltonian and Green's function formalism. We have found that the conductance of the system is almost insensitive to single adatoms and oscillates as a function of the side chain length with very large periods. Non-local character of the electron transport was observed also for topological SSH chains where nontrivial end states survive in the presence of disturbances as well as for different substrates. We have found that the careful inspection of the density of states or charge waves can provide the information about the atom energy levels and hopping amplitudes. Moreover, the ladder-like geometry allows one to distinguish between normal and topological zero-energy states. It is important that topological chains do not reveal Friedel oscillations which are observed in non-topological chains.

Invalidity of the Fermi liquid theory and magnetic phase transition in quasi-1D dopant-induced armchair-edged graphene nanoribbons

NASA Astrophysics Data System (ADS)

Hoi, Bui Dinh; Davoudiniya, Masoumeh; Yarmohammadi, Mohsen

2018-04-01

Based on theoretically tight-binding calculations considering nearest neighbors and Green's function technique, we show that the magnetic phase transition in both semiconducting and metallic armchair graphene nanoribbons with width ranging from 9.83 Å to 69.3 Å would be observed in the presence of injecting electrons by doping. This transition is explained by the temperature-dependent static charge susceptibility through calculation of the correlation function of charge density operators. This work showed that charge concentration of dopants in such system plays a crucial role in determining the magnetic phase. A variety of multicritical points such as transition temperatures and maximum susceptibility are compared in undoped and doped cases. Our findings show that there exist two different transition temperatures and maximum susceptibility depending on the ribbon width in doped structures. Another remarkable point refers to the invalidity (validity) of the Fermi liquid theory in nanoribbons-based systems at weak (strong) concentration of dopants. The obtained interesting results of magnetic phase transition in such system create a new potential for magnetic graphene nanoribbon-based devices.

First-principles simulations of doping-dependent mesoscale screening of adatoms in graphene

NASA Astrophysics Data System (ADS)

Mostofi, Arash; Corsetti, Fabiano; Wong, Dillon; Crommie, Michael; Lischner, Johannes

Adsorbed atoms and molecules play an important role in controlling and tuning the functional properties of 2D materials. Understanding and predicting this phenomenon from theory is challenging because of the need to capture both the local chemistry of the adsorbate-substrate interaction and its complex interplay with the long-range screening response of the substrate. To address this challenge, we have developed a first-principles multi-scale approach that combines linear-scaling density-functional theory, continuum screening theory and large-scale tight-binding simulations. Focussing on the case of a calcium adatom on graphene, we draw comparison between the effect of (i) non-linearity, (ii) intraband and interband transitions, and (iii) the exchange-correlation potential, thus providing insight into the relative importance of these different factors on the screening response. We also determine the charge transfer from the adatom to the graphene substrate (the key parameter used in continuum screening models), showing it to be significantly larger than previous estimates. AM and FC acknowledge support of the EPSRC under Grant EP/J015059/1, and JL under Grant EP/N005244/1.

Theoretical investigations on diamondoids (CnHm, n = 10-41): Nomenclature, structural stabilities, and gap distributions

NASA Astrophysics Data System (ADS)

Wang, Ya-Ting; Zhao, Yu-Jun; Liao, Ji-Hai; Yang, Xiao-Bao

2018-01-01

Combining the congruence check and the first-principles calculations, we have systematically investigated the structural stabilities and gap distributions of possible diamondoids (CnHm) with the carbon numbers (n) from 10 to 41. A simple method for the nomenclature is proposed, which can be used to distinguish and screen the candidates with high efficiency. Different from previous theoretical studies, the possible diamondoids can be enumerated according to our nomenclature, without any pre-determination from experiments. The structural stabilities and electronic properties have been studied by density functional based tight binding and first-principles methods, where a nearly linear correlation is found between the energy gaps obtained by these two methods. According to the formation energy of structures, we have determined the stable configurations as a function of chemical potential. The maximum and minimum energy gaps are found to be dominated by the shape of diamondoids for clusters with a given number of carbon atoms, while the gap decreases in general as the size increases due to the quantum confinement.

Rectification of graphene self-switching diodes: First-principles study

NASA Astrophysics Data System (ADS)

Ghaziasadi, Hassan; Jamasb, Shahriar; Nayebi, Payman; Fouladian, Majid

2018-05-01

The first principles calculations based on self-consistent charge density functional tight-binding have performed to investigate the electrical properties and rectification behavior of the graphene self-switching diodes (GSSD). The devices contained two structures called CG-GSSD and DG-GSSD which have metallic or semiconductor gates depending on their side gates have a single or double hydrogen edge functionalized. We have relaxed the devices and calculated I-V curves, transmission spectrums and maximum rectification ratios. We found that the DG-MSM devices are more favorable and more stable. Also, the DG-MSM devices have better maximum rectification ratios and current. Moreover, by changing the side gates widths and behaviors from semiconductor to metal, the threshold voltages under forward bias changed from +1.2 V to +0.3 V. Also, the maximum currents are obtained from 1.12 μA to 10.50 μA. Finally, the MSM and SSS type of all devices have minimum and maximum values of voltage threshold and maximum rectification ratios, but the 769-DG devices don't obey this rule.

Dark Energy Survey Year 1 Results: Methodology and Projections for Joint Analysis of Galaxy Clustering, Galaxy Lensing, and CMB Lensing Two-point Functions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Giannantonio, T.; et al.

Optical imaging surveys measure both the galaxy density and the gravitational lensing-induced shear fields across the sky. Recently, the Dark Energy Survey (DES) collaboration used a joint fit to two-point correlations between these observables to place tight constraints on cosmology (DES Collaboration et al. 2017). In this work, we develop the methodology to extend the DES Collaboration et al. (2017) analysis to include cross-correlations of the optical survey observables with gravitational lensing of the cosmic microwave background (CMB) as measured by the South Pole Telescope (SPT) and Planck. Using simulated analyses, we show how the resulting set of five two-pointmore » functions increases the robustness of the cosmological constraints to systematic errors in galaxy lensing shear calibration. Additionally, we show that contamination of the SPT+Planck CMB lensing map by the thermal Sunyaev-Zel'dovich effect is a potentially large source of systematic error for two-point function analyses, but show that it can be reduced to acceptable levels in our analysis by masking clusters of galaxies and imposing angular scale cuts on the two-point functions. The methodology developed here will be applied to the analysis of data from the DES, the SPT, and Planck in a companion work.« less

Use of herbicide to reduce stump-sprouting following thinning of an eastern black walnut agroforestry planting

Treesearch

W.D. " Dusty" Walter; H.E. " Gene" Garrett; Larry D. Godsey

2004-01-01

When establishing an agroforestry practice, the number of trees planted will often exceed the densities needed to achieve a final spacing or configuration. While tight spacings may facilitate certain growth parameters, such as height development, timely thinnings of plantings are required in order to maintain desirable growth rates. In managed plantations especially,...

Constraints on the magnetic fields in galaxies implied by the infrared-to-radio correlation

NASA Technical Reports Server (NTRS)

Helou, George; Bicay, M. D.

1990-01-01

A physical model is proposed for understanding the tight correlation between far-IR and nonthermal radio luminosities in star-forming galaxies. The approach suggests that the only constraint implied by the correlation is a universal relation whereby magnetic field strength scales with gas density to a power beta between 1/3 and 2/3, inclusive.

Dpb11 may function with RPA and DNA to initiate DNA replication.

PubMed

Bruck, Irina; Dhingra, Nalini; Martinez, Matthew P; Kaplan, Daniel L

2017-01-01

Dpb11 is required for the initiation of DNA replication in budding yeast. We found that Dpb11 binds tightly to single-stranded DNA (ssDNA) or branched DNA structures, while its human homolog, TopBP1, binds tightly to branched-DNA structures. We also found that Dpb11 binds stably to CDK-phosphorylated RPA, the eukaryotic ssDNA binding protein, in the presence of branched DNA. A Dpb11 mutant specifically defective for DNA binding did not exhibit tight binding to RPA in the presence of DNA, suggesting that Dpb11-interaction with DNA may promote the recruitment of RPA to melted DNA. We then characterized a mutant of Dpb11 that is specifically defective in DNA binding in budding yeast cells. Expression of dpb11-m1,2,3,5,ΔC results in a substantial decrease in RPA recruitment to origins, suggesting that Dpb11 interaction with DNA may be required for RPA recruitment to origins. Expression of dpb11-m1,2,3,5,ΔC also results in diminished GINS interaction with Mcm2-7 during S phase, while Cdc45 interaction with Mcm2-7 is like wild-type. The reduced GINS interaction with Mcm2-7 may be an indirect consequence of diminished origin melting. We propose that the tight interaction between Dpb11, CDK-phosphorylated RPA, and branched-DNA may be required for the essential function of stabilizing melted origin DNA in vivo. We also propose an alternative model, wherein Dpb11-DNA interaction is required for some other function in DNA replication initiation, such as helicase activation.

Anti-mouse CD52 monoclonal antibody ameliorates intestinal epithelial barrier function in interleukin-10 knockout mice with spontaneous chronic colitis.

PubMed

Wang, Honggang; Dong, Jianning; Shi, Peiliang; Liu, Jianhui; Zuo, Lugen; Li, Yi; Gong, Jianfeng; Gu, Lili; Zhao, Jie; Zhang, Liang; Zhang, Wei; Zhu, Weiming; Li, Ning; Li, Jieshou

2015-02-01

Intestinal inflammation causes tight junction changes and death of epithelial cells, and plays an important role in the development of Crohn's disease (CD). CD52 monoclonal antibody (CD52 mAb) directly targets the cell surface CD52 and is effective in depleting mature lymphocytes by cytolytic effects in vivo, leading to long-lasting changes in adaptive immunity. The aim of this study was to investigate the therapeutic effect of CD52 mAb on epithelial barrier function in animal models of IBD. Interleukin-10 knockout mice (IL-10(-/-) ) of 16 weeks with established colitis were treated with CD52 mAb once a week for 2 weeks. Severity of colitis, CD4(+) lymphocytes and cytokines in the lamina propria, epithelial expression of tight junction proteins, morphology of tight junctions, tumour necrosis factor-α (TNF-α)/TNF receptor 2 (TNFR2) mRNA expression, myosin light chain kinase (MLCK) expression and activity, as well as epithelial apoptosis in proximal colon were measured at the end of the experiment. CD52 mAb treatment effectively attenuated colitis associated with decreased lamina propria CD4(+) lymphocytes and interferon-γ/IL-17 responses in colonic mucosa in IL-10(-/-) mice. After CD52 mAb treatment, attenuation of colonic permeability, increased epithelial expression and correct localization of tight junction proteins (occludin and zona occludens protein-1), as well as ameliorated tight junction morphology were observed in IL-10(-/-) mice. CD52 mAb treatment also effectively suppressed the epithelial apoptosis, mucosa TNF-α mRNA expression, epithelial expression of long MLCK, TNFR2 and phosphorylation of MLC. Our results indicated that anti-CD52 therapy may inhibit TNF-α/TNFR2-mediated epithelial apoptosis and MLCK-dependent tight junction permeability by depleting activated T cells in the gut mucosa. © 2014 John Wiley & Sons Ltd.

INS/GNSS Tightly-Coupled Integration Using Quaternion-Based AUPF for USV.

PubMed

Xia, Guoqing; Wang, Guoqing

2016-08-02

This paper addresses the problem of integration of Inertial Navigation System (INS) and Global Navigation Satellite System (GNSS) for the purpose of developing a low-cost, robust and highly accurate navigation system for unmanned surface vehicles (USVs). A tightly-coupled integration approach is one of the most promising architectures to fuse the GNSS data with INS measurements. However, the resulting system and measurement models turn out to be nonlinear, and the sensor stochastic measurement errors are non-Gaussian and distributed in a practical system. Particle filter (PF), one of the most theoretical attractive non-linear/non-Gaussian estimation methods, is becoming more and more attractive in navigation applications. However, the large computation burden limits its practical usage. For the purpose of reducing the computational burden without degrading the system estimation accuracy, a quaternion-based adaptive unscented particle filter (AUPF), which combines the adaptive unscented Kalman filter (AUKF) with PF, has been proposed in this paper. The unscented Kalman filter (UKF) is used in the algorithm to improve the proposal distribution and generate a posterior estimates, which specify the PF importance density function for generating particles more intelligently. In addition, the computational complexity of the filter is reduced with the avoidance of the re-sampling step. Furthermore, a residual-based covariance matching technique is used to adapt the measurement error covariance. A trajectory simulator based on a dynamic model of USV is used to test the proposed algorithm. Results show that quaternion-based AUPF can significantly improve the overall navigation accuracy and reliability.

Band nesting, massive Dirac fermions, and valley Landé and Zeeman effects in transition metal dichalcogenides: A tight-binding model

NASA Astrophysics Data System (ADS)

Bieniek, Maciej; Korkusiński, Marek; Szulakowska, Ludmiła; Potasz, Paweł; Ozfidan, Isil; Hawrylak, Paweł

2018-02-01

We present here the minimal tight-binding model for a single layer of transition metal dichalcogenides (TMDCs) MX 2(M , metal; X , chalcogen) which illuminates the physics and captures band nesting, massive Dirac fermions, and valley Landé and Zeeman magnetic field effects. TMDCs share the hexagonal lattice with graphene but their electronic bands require much more complex atomic orbitals. Using symmetry arguments, a minimal basis consisting of three metal d orbitals and three chalcogen dimer p orbitals is constructed. The tunneling matrix elements between nearest-neighbor metal and chalcogen orbitals are explicitly derived at K ,-K , and Γ points of the Brillouin zone. The nearest-neighbor tunneling matrix elements connect specific metal and sulfur orbitals yielding an effective 6 ×6 Hamiltonian giving correct composition of metal and chalcogen orbitals but not the direct gap at K points. The direct gap at K , correct masses, and conduction band minima at Q points responsible for band nesting are obtained by inclusion of next-neighbor Mo-Mo tunneling. The parameters of the next-nearest-neighbor model are successfully fitted to MX 2(M =Mo ; X =S ) density functional ab initio calculations of the highest valence and lowest conduction band dispersion along K -Γ line in the Brillouin zone. The effective two-band massive Dirac Hamiltonian for MoS2, Landé g factors, and valley Zeeman splitting are obtained.

Pseudomonas aeruginosa elastase causes transient disruption of tight junctions and downregulation of PAR-2 in human nasal epithelial cells.

PubMed

Nomura, Kazuaki; Obata, Kazufumi; Keira, Takashi; Miyata, Ryo; Hirakawa, Satoshi; Takano, Ken-ichi; Kohno, Takayuki; Sawada, Norimasa; Himi, Tetsuo; Kojima, Takashi

2014-02-18

Pseudomonas aeruginosa causes chronic respiratory disease, and the elastase enzyme that it produces increases the permeability of airway epithelial cells owing to the disruption of tight junctions. P. aeruginosa is also implicated in prolonged chronic rhinosinusitis. However, the effects of P. aeruginosa elastase (PE) against the barrier formed by human nasal epithelial cells (HNECs) remain unknown. To investigate the mechanisms involved in the disruption of tight junctions by PE in HNECs, primary cultures of HNECs transfected with human telomerase reverse transcriptase (hTERT-HNECs) were used. The hTERT-HNECs were pretreated with inhibitors of various signal transduction pathways, PKC, MAPK, p38MAPK, PI3K, JNK, NF-κB, EGF receptor, proteasome, COX1 and COX2 before treatment with PE. Some cells were pretreated with siRNA and agonist of protease activated receptor-2 (PAR-2) before treatment with PE. Expression and structures of tight junctions were determined by Western blotting, real-time PCR, immunostaining and freeze-fracture. Transepithelial electrical resistance (TER) was examined as the epithelial barrier function. PE treatment transiently disrupted the epithelial barrier and downregulated the transmembrane proteins claudin-1 and -4, occludin, and tricellulin, but not the scaffold PDZ-expression proteins ZO-1 and -2 and adherens junction proteins E-cadherin and β-catenin. The transient downregulation of tight junction proteins was controlled via distinct signal transduction pathways such as the PKC, MAPK, PI3K, p38 MAPK, JNK, COX-1 and -2, and NF-κB pathways. Furthermore, treatment with PE transiently decreased PAR-2 expression, which also regulated the expression of the tight junction proteins. Treatment with a PAR-2 agonist prevented the downregulation of the tight junction proteins after PE treatment in HNECs. PE transiently disrupts tight junctions in HNECs and downregulates PAR-2. The transient disruption of tight junctions by PE might occur repeatedly during chronic rhinosinusitis.

Pseudomonas aeruginosa elastase causes transient disruption of tight junctions and downregulation of PAR-2 in human nasal epithelial cells

PubMed Central

2014-01-01

Background Pseudomonas aeruginosa causes chronic respiratory disease, and the elastase enzyme that it produces increases the permeability of airway epithelial cells owing to the disruption of tight junctions. P. aeruginosa is also implicated in prolonged chronic rhinosinusitis. However, the effects of P. aeruginosa elastase (PE) against the barrier formed by human nasal epithelial cells (HNECs) remain unknown. Methods To investigate the mechanisms involved in the disruption of tight junctions by PE in HNECs, primary cultures of HNECs transfected with human telomerase reverse transcriptase (hTERT-HNECs) were used. The hTERT-HNECs were pretreated with inhibitors of various signal transduction pathways, PKC, MAPK, p38MAPK, PI3K, JNK, NF-κB, EGF receptor, proteasome, COX1 and COX2 before treatment with PE. Some cells were pretreated with siRNA and agonist of protease activated receptor-2 (PAR-2) before treatment with PE. Expression and structures of tight junctions were determined by Western blotting, real-time PCR, immunostaining and freeze-fracture. Transepithelial electrical resistance (TER) was examined as the epithelial barrier function. Results PE treatment transiently disrupted the epithelial barrier and downregulated the transmembrane proteins claudin-1 and -4, occludin, and tricellulin, but not the scaffold PDZ-expression proteins ZO-1 and -2 and adherens junction proteins E-cadherin and β-catenin. The transient downregulation of tight junction proteins was controlled via distinct signal transduction pathways such as the PKC, MAPK, PI3K, p38 MAPK, JNK, COX-1 and -2, and NF-κB pathways. Furthermore, treatment with PE transiently decreased PAR-2 expression, which also regulated the expression of the tight junction proteins. Treatment with a PAR-2 agonist prevented the downregulation of the tight junction proteins after PE treatment in HNECs. Conclusions PE transiently disrupts tight junctions in HNECs and downregulates PAR-2. The transient disruption of tight junctions by PE might occur repeatedly during chronic rhinosinusitis. PMID:24548792

IGF-1 decreases portal vein endotoxin via regulating intestinal tight junctions and plays a role in attenuating portal hypertension of cirrhotic rats.

PubMed

Zhao, Tian-Yu; Su, Li-Ping; Ma, Chun-Ye; Zhai, Xiao-Han; Duan, Zhi-Jun; Zhu, Ying; Zhao, Gang; Li, Chun-Yan; Wang, Li-Xia; Yang, Dong

2015-07-08

Intestinal barrier dysfunction is not only the consequence of liver cirrhosis, but also an active participant in the development of liver cirrhosis. Previous studies showed that external administration of insulin-like growth factor 1 (IGF-1) improved intestinal barrier function in liver cirrhosis. However, the mechanism of IGF-1 on intestinal barrier in liver cirrhosis is not fully elucidated. The present study aims to investigate the mechanisms of IGF-1 improving intestinal barrier function via regulating tight junctions in intestines. We used carbon tetrachloride induced liver cirrhotic rats to investigate the effect of IGF-1 on intestinal claudin-1 and occludin expressions, serum alanine transaminase (ALT) and aspartate transaminase (AST) levels, severity of liver fibrosis, portal pressures, enterocytic apoptosis and lipopolysaccharides (LPS) levels in portal vein. The changes of IGF-1 in serum during the development of rat liver cirrhosis were also evaluated. Additionally, we assessed the effect of IGF-1 on claudin-1 and occludin expressions, changes of transepithelial electrical resistance (TEER) and apoptosis in Caco-2 cells to confirm in vivo findings. Serum IGF-1 levels were decreased in the development of rat liver cirrhosis, and external administration of IGF-1 restored serum IGF-1 levels. External administration of IGF-1 reduced serum ALT and AST levels, severity of liver fibrosis, LPS levels in portal vein, enterocytic apoptosis and portal pressure in cirrhotic rats. External administration of IGF-1 increased the expressions of claudin-1 and occludin in enterocytes, and attenuated tight junction dysfunction in intestines of cirrhotic rats. LPS decreased TEER in Caco-2 cell monolayer. LPS also decreased claudin-1 and occludin expressions and increased apoptosis in Caco-2 cells. Furthermore, IGF-1 attenuated the effect of LPS on TEER, claudin-1 expression, occludin expression and apoptosis in Caco-2 cells. Tight junction dysfunction develops during the development of liver cirrhosis, and endotoxemia will develop subsequently. Correspondingly, increased endotoxin in portal system worsens tight junction dysfunction via decreasing intestinal occludin and claudin-1 expressions and increasing enterocytic apoptosis. Endotoxemia and intestinal barrier dysfunction form a vicious circle. External administration of IGF-1 breaks this vicious circle. Improvement of tight junctions might be one possible mechanism of the restoration of intestinal barrier function mediated by IGF-1.

The N and C Termini of ZO-1 Are Surrounded by Distinct Proteins and Functional Protein Networks*

PubMed Central

Van Itallie, Christina M.; Aponte, Angel; Tietgens, Amber Jean; Gucek, Marjan; Fredriksson, Karin; Anderson, James Melvin

2013-01-01

The proteins and functional protein networks of the tight junction remain incompletely defined. Among the currently known proteins are barrier-forming proteins like occludin and the claudin family; scaffolding proteins like ZO-1; and some cytoskeletal, signaling, and cell polarity proteins. To define a more complete list of proteins and infer their functional implications, we identified the proteins that are within molecular dimensions of ZO-1 by fusing biotin ligase to either its N or C terminus, expressing these fusion proteins in Madin-Darby canine kidney epithelial cells, and purifying and identifying the resulting biotinylated proteins by mass spectrometry. Of a predicted proteome of ∼9000, we identified more than 400 proteins tagged by biotin ligase fused to ZO-1, with both identical and distinct proteins near the N- and C-terminal ends. Those proximal to the N terminus were enriched in transmembrane tight junction proteins, and those proximal to the C terminus were enriched in cytoskeletal proteins. We also identified many unexpected but easily rationalized proteins and verified partial colocalization of three of these proteins with ZO-1 as examples. In addition, functional networks of interacting proteins were tagged, such as the basolateral but not apical polarity network. These results provide a rich inventory of proteins and potential novel insights into functions and protein networks that should catalyze further understanding of tight junction biology. Unexpectedly, the technique demonstrates high spatial resolution, which could be generally applied to defining other subcellular protein compartmentalization. PMID:23553632

Altered Expression of ZO-1 and ZO-2 in Sertoli Cells and Loss of Blood-Testis Barrier Integrity in Testicular Carcinoma In Situ1

PubMed Central

Fink, Cornelia; Weigel, Roswitha; Hembes, Tanja; Lauke-Wettwer, Heidrun; Kliesch, Sabine; Bergmann, Martin; Brehm, Ralph H

2006-01-01

Abstract Carcinoma in situ (CIS) is the noninvasive precursor of most human testicular germ cell tumors. In normal seminiferous epithelium, specialized tight junctions between Sertoli cells constitute the major component of the blood-testis barrier. Sertoli cells associated with CIS exhibit impaired maturation status, but their functional significance remains unknown. The aim was to determine whether the blood-testis barrier is morphologically and/or functionally altered. We investigated the expression and distribution pattern of the tight junction proteins zonula occludens (ZO) 1 and 2 in normal seminiferous tubules compared to tubules showing CIS. In normal tubules, ZO-1 and ZO-2 immunostaining was observed at the blood-testis barrier region of adjacent Sertoli cells. Within CIS tubules, ZO-1 and ZO-2 immunoreactivity was reduced at the blood-testis barrier region, but spread to stain the Sertoli cell cytoplasm. Western blot analysis confirmed ZO-1 and ZO-2, and their respective mRNA were shown by RT-PCR. Additionally, we assessed the functional integrity of the blood-testis barrier by lanthanum tracer study. Lanthanum permeated tight junctions in CIS tubules, indicating disruption of the blood-testis barrier. In conclusion, Sertoli cells associated with CIS show an altered distribution of ZO-1 and ZO-2 and lose their blood-testis barrier function. PMID:17217619

Textural and mineralogical study of sandstones from the onshore Gulf of Alaska Tertiary Province, southern Alaska

USGS Publications Warehouse

Winkler, Gary R.; McLean, Hugh; Plafker, George

1976-01-01

Petrographic examination of 74 outcrop samples of Paleocene through Pliocene age from the onshore Gulf of Alaska Tertiary Province indicates that sandstones of the province characteristically are texturally immature and mineralogically unstable. Diagenetic alteration of framework grains throughout the stratigraphic sequence has produced widespread zeolite cement or phyllosilicate grain coatings and pseudomatrix. Multiple deformation and deep burial of the older Tertiary sequence--the Orca Group, the shale of Haydon Peak, and the Kulthieth and Tokun Formations--caused extensive alteration and grain interpenetration, resulting in low porosity values. Less intense deformation and intermediate depth of burial of the younger Tertiary sequence--the Katalla, Poul Creek, Redwood, and Yakataga Formations--has resulted in a greater range in textural properties. Most sandstone samples in the younger Tertiary sequence are poorly sorted, tightly packed, and have strongly appressed framework grains, but some are less tightly packed and contain less matrix. Soft and mineralogically unstable framework grains have undergone considerable alteration, reducing pore space even in the youngest rocks. Measurements of porosity, permeability, grain density, and sonic velocity of outcrop samples of the younger Tertiary sequence indicate a modest up-section improvement in sandstone reservoir characteristics. Nonetheless porosity and permeability values typically are below 16 percent and 15 millidarcies respectively and grain densities are consistently high, about 2.7 gm/cc. Low permeability and porosity values, and high grain densities and sonic velocities appear to be typical of most outcrop areas throughout the onshore Gulf of Alaska Tertiary Province.

The role of microtubules in contractile ring function.

PubMed

Conrad, A H; Paulsen, A Q; Conrad, G W

1992-05-01

During cytokinesis, a cortical contractile ring forms around a cell, constricts to a stable tight neck and terminates in separation of the daughter cells. At first cleavage, Ilyanassa obsoleta embryos form two contractile rings simultaneously. The cleavage furrow (CF), in the animal hemisphere between the spindle poles, constricts to a stable tight neck and separates the daughter cells. The third polar lobe constriction (PLC-3), in the vegetal hemisphere below the spindle, constricts to a transient tight neck, but then relaxes, allowing the polar lobe cytoplasm to merge with one daughter cell. Eggs exposed to taxol, a drug that stabilizes microtubules, before the CF or the PLC-3 develop, fail to form CFs, but form stabilized tight PLCs. Eggs exposed to taxol at the time of PLC-3 formation develop varied numbers of constriction rings in their animal hemispheres and one PLC in their vegetal hemisphere, none of which relax. Eggs exposed to taxol after PLC-3 initiation form stabilized tight CFs and PLCs. At maximum constriction, control embryos display immunolocalization of nonextractable alpha-tubulin in their CFs, but not in their PLCs, and reveal, via electron microscopy, many microtubules extending through their CFs, but not through their PLCs. Embryos which form stabilized tightly constricted CFs and PLCs in the presence of taxol display immunolocalization of nonextractable alpha-tubulin in both constrictions and show many polymerized microtubules extending through both CFs and PLCs. These results suggest that the extension of microtubules through a tight contractile ring may be important for stabilizing that constriction and facilitating subsequent cytokinesis.

The role of microtubules in contractile ring function

NASA Technical Reports Server (NTRS)

Conrad, A. H.; Paulsen, A. Q.; Conrad, G. W.; Spooner, B. S. (Principal Investigator)

1992-01-01

During cytokinesis, a cortical contractile ring forms around a cell, constricts to a stable tight neck and terminates in separation of the daughter cells. At first cleavage, Ilyanassa obsoleta embryos form two contractile rings simultaneously. The cleavage furrow (CF), in the animal hemisphere between the spindle poles, constricts to a stable tight neck and separates the daughter cells. The third polar lobe constriction (PLC-3), in the vegetal hemisphere below the spindle, constricts to a transient tight neck, but then relaxes, allowing the polar lobe cytoplasm to merge with one daughter cell. Eggs exposed to taxol, a drug that stabilizes microtubules, before the CF or the PLC-3 develop, fail to form CFs, but form stabilized tight PLCs. Eggs exposed to taxol at the time of PLC-3 formation develop varied numbers of constriction rings in their animal hemispheres and one PLC in their vegetal hemisphere, none of which relax. Eggs exposed to taxol after PLC-3 initiation form stabilized tight CFs and PLCs. At maximum constriction, control embryos display immunolocalization of nonextractable alpha-tubulin in their CFs, but not in their PLCs, and reveal, via electron microscopy, many microtubules extending through their CFs, but not through their PLCs. Embryos which form stabilized tightly constricted CFs and PLCs in the presence of taxol display immunolocalization of nonextractable alpha-tubulin in both constrictions and show many polymerized microtubules extending through both CFs and PLCs. These results suggest that the extension of microtubules through a tight contractile ring may be important for stabilizing that constriction and facilitating subsequent cytokinesis.

FAST TRACK COMMUNICATION: Finite-temperature magnetism in bcc Fe under compression

NASA Astrophysics Data System (ADS)

Sha, Xianwei; Cohen, R. E.

2010-09-01

We investigate the contributions of finite-temperature magnetic fluctuations to the thermodynamic properties of bcc Fe as functions of pressure. First, we apply a tight-binding total-energy model parameterized to first-principles linearized augmented plane-wave computations to examine various ferromagnetic, anti-ferromagnetic, and noncollinear spin spiral states at zero temperature. The tight-binding data are fit to a generalized Heisenberg Hamiltonian to describe the magnetic energy functional based on local moments. We then use Monte Carlo simulations to compute the magnetic susceptibility, the Curie temperature, heat capacity, and magnetic free energy. Including the finite-temperature magnetism improves the agreement with experiment for the calculated thermal expansion coefficients.

Irsogladine maleate regulates gap junctional intercellular communication-dependent epithelial barrier in human nasal epithelial cells.

PubMed

Miyata, Ryo; Nomura, Kazuaki; Kakuki, Takuya; Takano, Ken-Ichi; Kohno, Takayuki; Konno, Takumi; Sawada, Norimasa; Himi, Tetsuo; Kojima, Takashi

2015-04-01

The airway epithelium of the human nasal mucosa acts as the first physical barrier that protects against inhaled substances and pathogens. Irsogladine maleate (IM) is an enhancer of gastric mucosal protective factors via upregulation of gap junctional intercellular communication (GJIC). GJIC is thought to participate in the formation of functional tight junctions. However, the effects of IM on GJIC and the epithelial barrier in human nasal epithelial cells (HNECs) remain unknown. To investigate the effects of IM on GJIC and the tight junctional barrier in HNECs, primary cultures of HNECs transfected with human telomerase reverse transcriptase (hTERT-HNECs) were treated with IM and the GJIC inhibitors oleamide and 18β-GA. Some cells were pretreated with IM before treatment with TLR3 ligand poly(I:C) to examine whether IM prevented the changes via TLR3-mediated signal pathways. In hTERT-HNECs, GJIC blockers reduced the expression of tight junction molecules claudin-1, -4, -7, occludin, tricellulin, and JAM-A. IM induced GJIC activity and enhanced the expression of claudin-1, -4, and JAM-A at the protein and mRNA levels with an increase of barrier function. GJIC blockers prevented the increase of the tight junction proteins induced by IM. Furthermore, IM prevented the reduction of JAM-A but not induction of IL-8 and TNF-α induced by poly(I:C). In conclusion, IM can maintain the GJIC-dependent tight junctional barrier via regulation of GJIC in upper airway nasal epithelium. Therefore, it is possible that IM may be useful as a nasal spray to prevent the disruption of the epithelial barrier by viral infections and exposure to allergens in human nasal mucosa.

miR-Let7A Controls the Cell Death and Tight Junction Density of Brain Endothelial Cells under High Glucose Condition

PubMed Central

Song, Juhyun; Yoon, So Ra

2017-01-01

Hyperglycemia-induced stress in the brain of patients with diabetes triggers the disruption of blood-brain barrier (BBB), leading to diverse neurological diseases including stroke and dementia. Recently, the role of microRNA becomes an interest in the research for deciphering the mechanism of brain endothelial cell damage under hyperglycemia. Therefore, we investigated whether mircoRNA Let7A (miR-Let7A) controls the damage of brain endothelial (bEnd.3) cells against high glucose condition. Cell viability, cell death marker expressions (p-53, Bax, and cleaved poly ADP-ribose polymerase), the loss of tight junction proteins (ZO-1 and claudin-5), proinflammatory response (interleukin-6, tumor necrosis factor-α), inducible nitric oxide synthase, and nitrite production were confirmed using MTT, reverse transcription-PCR, quantitative-PCR, Western blotting, immunofluorescence, and Griess reagent assay. miR-Let7A overexpression significantly prevented cell death and loss of tight junction proteins and attenuated proinflammatory response and nitrite production in the bEnd.3 cells under high glucose condition. Taken together, we suggest that miR-Let7A may attenuate brain endothelial cell damage by controlling cell death signaling, loss of tight junction proteins, and proinflammatory response against high glucose stress. In the future, the manipulation of miR-Let7A may be a novel solution in controlling BBB disruption which leads to the central nervous system diseases. PMID:28680530

miR-Let7A Controls the Cell Death and Tight Junction Density of Brain Endothelial Cells under High Glucose Condition.

PubMed

Song, Juhyun; Yoon, So Ra; Kim, Oh Yoen

2017-01-01

Hyperglycemia-induced stress in the brain of patients with diabetes triggers the disruption of blood-brain barrier (BBB), leading to diverse neurological diseases including stroke and dementia. Recently, the role of microRNA becomes an interest in the research for deciphering the mechanism of brain endothelial cell damage under hyperglycemia. Therefore, we investigated whether mircoRNA Let7A (miR-Let7A) controls the damage of brain endothelial (bEnd.3) cells against high glucose condition. Cell viability, cell death marker expressions (p-53, Bax, and cleaved poly ADP-ribose polymerase), the loss of tight junction proteins (ZO-1 and claudin-5), proinflammatory response (interleukin-6, tumor necrosis factor- α ), inducible nitric oxide synthase, and nitrite production were confirmed using MTT, reverse transcription-PCR, quantitative-PCR, Western blotting, immunofluorescence, and Griess reagent assay. miR-Let7A overexpression significantly prevented cell death and loss of tight junction proteins and attenuated proinflammatory response and nitrite production in the bEnd.3 cells under high glucose condition. Taken together, we suggest that miR-Let7A may attenuate brain endothelial cell damage by controlling cell death signaling, loss of tight junction proteins, and proinflammatory response against high glucose stress. In the future, the manipulation of miR-Let7A may be a novel solution in controlling BBB disruption which leads to the central nervous system diseases.

Multi-layer thin-film electrolytes for metal supported solid oxide fuel cells

NASA Astrophysics Data System (ADS)

Haydn, Markus; Ortner, Kai; Franco, Thomas; Uhlenbruck, Sven; Menzler, Norbert H.; Stöver, Detlev; Bräuer, Günter; Venskutonis, Andreas; Sigl, Lorenz S.; Buchkremer, Hans-Peter; Vaßen, Robert

2014-06-01

A key to the development of metal-supported solid oxide fuel cells (MSCs) is the manufacturing of gas-tight thin-film electrolytes, which separate the cathode from the anode. This paper focuses the electrolyte manufacturing on the basis of 8YSZ (8 mol.-% Y2O3 stabilized ZrO2). The electrolyte layers are applied by a physical vapor deposition (PVD) gas flow sputtering (GFS) process. The gas-tightness of the electrolyte is significantly improved when sequential oxidic and metallic thin-film multi-layers are deposited, which interrupt the columnar grain structure of single-layer electrolytes. Such electrolytes with two or eight oxide/metal layers and a total thickness of about 4 μm obtain leakage rates of less than 3 × 10-4 hPa dm3 s-1 cm-2 (Δp: 100 hPa) at room temperature and therefore fulfill the gas tightness requirements. They are also highly tolerant with respect to surface flaws and particulate impurities which can be present on the graded anode underground. MSC cell tests with double-layer and multilayer electrolytes feature high power densities more than 1.4 W cm-2 at 850 °C and underline the high potential of MSC cells.

Preliminary design study of small long life boiling water reactor (BWR) with tight lattice thorium nitride fuel

DOE Office of Scientific and Technical Information (OSTI.GOV)

Trianti, Nuri, E-mail: nuri.trianti@gmail.com, E-mail: szaki@fi.itba.c.id; Su'ud, Zaki, E-mail: nuri.trianti@gmail.com, E-mail: szaki@fi.itba.c.id; Arif, Idam, E-mail: nuri.trianti@gmail.com, E-mail: szaki@fi.itba.c.id

2014-09-30

Neutronic performance of small long-life boiling water reactors (BWR) with thorium nitride based fuel has been performed. A recent study conducted on BWR in tight lattice environments (with a lower moderator percentage) produces small power reactor which has some specifications, i.e. 10 years operation time, power density of 19.1 watt/cc and maximum excess reactivity of about 4%. This excess reactivity value is smaller than standard reactivity of conventional BWR. The use of hexagonal geometry on the fuel cell of BWR provides a substantial effect on the criticality of the reactor to obtain a longer operating time. Supported by a tightmore » concept lattice where the volume fraction of the fuel is greater than the moderator and fuel, Thorium Nitride give good results for fuel cell design on small long life BWR. The excess reactivity of the reactor can be reduced with the addition of gadolinium as burnable poisons. Therefore the hexagonal tight lattice fuel cell design of small long life BWR that has a criticality more than 20 years of operating time has been obtained.« less

Perspectives from ab-initio and tight-binding: Applications to transition metal compounds and superlattices

NASA Astrophysics Data System (ADS)

Venkataraman, Vijay Shankar

The experimental and theoretical study of transition metal compounds have occupied condensed matter physicists for the best part of the last century. The rich variety of physical behaviour exhibited by these compounds owes its origin to the subtle balance of the energy scales at play for the d orbitals. In this thesis, we study three different systems comprised of transition metal atoms from the third, the fourth, and the fifth group of the periodic table using a combination of ab-initio density functional theory (DFT) computations and effective tight-binding models for the electronic properties. We first consider the electronic properties of artificially fabricated perovskite superlattices of the form [(SrIrO3)m / SrTiO3] with integer m denoting the number of layers of SrIrO3. After discussing the results of experiments undertaken by our collaborators, we present the results of our DFT calculations and build tight-binding models for the m = 1 and m = 2 superlattices. The active ingredient is found to be the 5d orbitals with significant spin-orbit coupling. We then study the energies of magnetic ground states within DFT and compare and contrast our results with those obtained for the bulk Ruddlesden-Popper iridates. Together with experimental measurements, our results suggest that these superlattices are an exciting venue to probe the magnetism and metal-insulator transitions that occur from the intricate balance of the spin-orbit coupling and electron interactions, as has been reported for their bulk counterparts. Next, we consider alpha-RuCl3, a honeycomb lattice compound. We first show using DFT calculations in conjunction with experiments performed by our collaborators, how spin-orbit coupling in the 4d orbitals of Ru is essential to understand the insulating state realized in this compound. Then, in the latter half of the chapter, we study the magnetic ground states of a two-dimensional analogue of alpha-RuCl3 in weak and strong-coupling regimes obtained from a tight-binding model for the 4d orbitals. We further compare these results with energies obtained from DFT calculations. We obtain a zig-zag magnetic ground state for this compound, in all the three approaches. Within DFT, we find that correlations enhance the spin-orbit coupling in this compound and that the anisotropic Kitaev interactions between the spins are dominant in a strong-coupling model. Then, we move on to study the electronic band structures of the higher manganese silicides, which are good thermoelectric materials. Using results from DFT calculations on Mn4Si7 and structural arguments, we construct an effective tight-binding model for the first three members of this series - Mn4Si7, Mn11Si19, and Mn15Si26.

Functional analysis of tight junction organization.

PubMed

DiBona, D R

1985-01-01

The functional basis of tight junction design has been examined from the point of view that this rate-limiting barrier to paracellular transport is a multicompartment system. Review of the osmotic sensitivity of these structures points to the need for this sort of analysis for meaningful correlation of structure and function under a range of conditions. A similar conclusion is drawn with respect to results from voltage-clamping protocols where reversal of spontaneous transmural potential difference elicits parallel changes in both structure and function in much the same way as does reversal of naturally occurring osmotic gradients. In each case, it becomes necessary to regard the junction as a functionally polarized structure to account for observations of its rectifying properties. Lastly, the details of experimentally-induced junction deformation are examined in light of current theories of its organization; arguments are presented in favor of the view that the primary components of intramembranous organization (as viewed with freeze-fracture techniques) are lipidic rather than proteinaceous.

Waves generated in the plasma plume of helicon magnetic nozzle

DOE Office of Scientific and Technical Information (OSTI.GOV)

Singh, Nagendra; Rao, Sathyanarayan; Ranganath, Praveen

2013-03-15

Experimental measurements have shown that the plasma plume created in a helicon plasma device contains a conical structure in the plasma density and a U-shaped double layer (US-DL) tightly confined near the throat where plasma begins to expand from the source. Recently reported two-dimensional particle-in-cell simulations verified these density and US-DL features of the plasma plume. Simulations also showed that the plasma in the plume develops non-thermal feature consisting of radial ion beams with large densities near the conical surface of the density structure. The plasma waves that are generated by the radial ion beams affecting the structure of themore » plasma plume are studied here. We find that most intense waves persist in the high-density regions of the conical density structure, where the transversely accelerated ions in the radial electric fields in the plume are reflected setting up counter-streaming. The waves generated are primarily ion Bernstein modes. The nonlinear evolution of the waves leads to magnetic field-aligned striations in the fields and the plasma near the conical surface of the density structure.« less

Tight-binding analysis of Si and GaAs ultrathin bodies with subatomic wave-function resolution

NASA Astrophysics Data System (ADS)

Tan, Yaohua P.; Povolotskyi, Michael; Kubis, Tillmann; Boykin, Timothy B.; Klimeck, Gerhard

2015-08-01

Empirical tight-binding (ETB) methods are widely used in atomistic device simulations. Traditional ways of generating the ETB parameters rely on direct fitting to bulk experiments or theoretical electronic bands. However, ETB calculations based on existing parameters lead to unphysical results in ultrasmall structures like the As-terminated GaAs ultrathin bodies (UTBs). In this work, it is shown that more transferable ETB parameters with a short interaction range can be obtained by a process of mapping ab initio bands and wave functions to ETB models. This process enables the calibration of not only the ETB energy bands but also the ETB wave functions with corresponding ab initio calculations. Based on the mapping process, ETB models of Si and GaAs are parameterized with respect to hybrid functional calculations. Highly localized ETB basis functions are obtained. Both the ETB energy bands and wave functions with subatomic resolution of UTBs show good agreement with the corresponding hybrid functional calculations. The ETB methods can then be used to explain realistically extended devices in nonequilibrium that cannot be tackled with ab initio methods.

Extreme plasma states in laser-governed vacuum breakdown.

PubMed

Efimenko, Evgeny S; Bashinov, Aleksei V; Bastrakov, Sergei I; Gonoskov, Arkady A; Muraviev, Alexander A; Meyerov, Iosif B; Kim, Arkady V; Sergeev, Alexander M

2018-02-05

Triggering vacuum breakdown at laser facility is expected to provide rapid electron-positron pair production for studies in laboratory astrophysics and fundamental physics. However, the density of the produced plasma may cease to increase at a relativistic critical density, when the plasma becomes opaque. Here, we identify the opportunity of breaking this limit using optimal beam configuration of petawatt-class lasers. Tightly focused laser fields allow generating plasma in a small focal volume much less than λ 3 and creating extreme plasma states in terms of density and produced currents. These states can be regarded to be a new object of nonlinear plasma physics. Using 3D QED-PIC simulations we demonstrate a possibility of reaching densities over 10 25  cm -3 , which is an order of magnitude higher than expected earlier. Controlling the process via initial target parameters provides an opportunity to reach the discovered plasma states at the upcoming laser facilities.

Generation of a sub-half-wavelength focal spot with purely transverse spin angular momentum

NASA Astrophysics Data System (ADS)

Hang, Li; Fu, Jian; Yu, Xiaochang; Wang, Ying; Chen, Peifeng

2017-11-01

We theoretically demonstrate that optical focus fields with purely transverse spin angular momentum (SAM) can be obtained when a kind of special incident fields is focused by a high numerical aperture (NA) aplanatic lens (AL). When the incident pupil fields are refracted by an AL, two transverse Cartesian components of the electric fields at the exit pupil plane do not have the same order of sinusoidal or cosinoidal components, resulting in zero longitudinal SAMs of the focal fields. An incident field satisfying above conditions is then proposed. Using the Richard-Wolf vectorial diffraction theory, the energy density and SAM density distributions of the tightly focused beam are calculated and the results clearly validate the proposed theory. In addition, a sub-half-wavelength focal spot with purely transverse SAM can be achieved and a flattop energy density distribution parallel to z-axis can be observed around the maximum energy density point.

Scaffolding proteins in the development and maintenance of the epidermal permeability barrier.

PubMed

Crawford, Melissa; Dagnino, Lina

2017-10-02

The skin of mammals and other terrestrial vertebrates protects the organism against the external environment, preventing heat, water and electrolyte loss, as well as entry of chemicals and pathogens. Impairments in the epidermal permeability barrier function are associated with the genesis and/or progression of a variety of pathological conditions, including genetic inflammatory diseases, microbial and viral infections, and photodamage induced by UV radiation. In mammals, the outside-in epidermal permeability barrier is provided by the joint action of the outermost cornified layer, together with assembled tight junctions in granular keratinocytes found in the layers underneath. Tight junctions serve as both outside-in and inside-out barriers, and impede paracellular movements of ions, water, macromolecules and microorganisms. At the molecular level, tight junctions consist of integral membrane proteins that form an extracellular seal between adjacent cells, and associate with cytoplasmic scaffold proteins that serve as links with the actin cytoskeleton. In this review, we address the roles that scaffold proteins play specifically in the establishment and maintenance of the epidermal permeability barrier, and how various pathologies alter or impair their functions.

Up-regulation of the tight-junction protein ZO-1 by substance P and IGF-1 in A431 cells.

PubMed

Ko, Ji-Ae; Murata, Shizuka; Nishida, Teruo

2009-08-01

The formation of a barrier by tight junctions is important in epithelia of various tissues. Substance P (SP) and insulin-like growth factor (IGF)-1 synergistically promote barrier function in the corneal epithelium. We have now examined the effects of SP and IGF-1 on expression of the tight-junction protein zonula occludens (ZO)-1 in A431 human epidermoid carcinoma cells. Reverse transcription-polymerase chain reaction (RT-PCR) and immunoblot analyses revealed that SP and IGF-1 increased the amounts of ZO-1 mRNA and protein in these cells in a concentration-dependent manner, with neither SP nor IGF-1 alone having such an effect. The SP- and IGF-1-induced up-regulation of ZO-1 was accompanied by phosphorylation of extracellular signal-regulated kinase (ERK), and both of these effects were blocked by PD98059, an inhibitor of ERK activation. SP and IGF-1 also increased the transepithelial electrical resistance (TER) (an indicator of barrier function) of an A431 cell monolayer in a manner sensitive to PD98059. Our results thus suggest that the synergistic induction of ZO-1 expression by SP and IGF-1 may promote barrier function in skin epithelial cells. (c) 2009 John Wiley & Sons, Ltd.

Integrin-Linked Kinase Is Indispensable for Keratinocyte Differentiation and Epidermal Barrier Function.

PubMed

Sayedyahossein, Samar; Rudkouskaya, Alena; Leclerc, Valerie; Dagnino, Lina

2016-02-01

A functional permeability barrier is essential to prevent the passage of water and electrolytes, macromolecules, and pathogens through the epidermis. This is accomplished in terminally differentiated keratinocytes through formation of a cornified envelope and the assembly of tight intercellular junctions. Integrin-linked kinase (ILK) is a scaffold protein essential for hair follicle morphogenesis and epidermal attachment to the basement membrane. However, the biological functions of ILK in differentiated keratinocytes remain poorly understood. Furthermore, whether ILK is implicated in keratinocyte differentiation and intercellular junction formation has remained an unresolved issue. Here we describe a pivotal role for ILK in keratinocyte differentiation responses to increased extracellular Ca(2+), regulation of adherens and tight junction assembly, and the formation of an outside-in permeability barrier toward macromolecules. In the absence of ILK, the calcium sensing receptor, E-cadherin, and ZO-1 fail to translocate to the cell membrane, through mechanisms that involve abnormalities in microtubules and in RhoA activation. In situ, ILK-deficient epidermis exhibits reduced tight junction formation and increased outside-in permeability to a dextran tracer, indicating reduced barrier properties toward macromolecules. Therefore, ILK is an essential component of keratinocyte differentiation programs that contribute to epidermal integrity and the establishment of its barrier properties. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Dpb11 may function with RPA and DNA to initiate DNA replication

PubMed Central

Bruck, Irina; Dhingra, Nalini; Martinez, Matthew P.

2017-01-01

Dpb11 is required for the initiation of DNA replication in budding yeast. We found that Dpb11 binds tightly to single-stranded DNA (ssDNA) or branched DNA structures, while its human homolog, TopBP1, binds tightly to branched-DNA structures. We also found that Dpb11 binds stably to CDK-phosphorylated RPA, the eukaryotic ssDNA binding protein, in the presence of branched DNA. A Dpb11 mutant specifically defective for DNA binding did not exhibit tight binding to RPA in the presence of DNA, suggesting that Dpb11-interaction with DNA may promote the recruitment of RPA to melted DNA. We then characterized a mutant of Dpb11 that is specifically defective in DNA binding in budding yeast cells. Expression of dpb11-m1,2,3,5,ΔC results in a substantial decrease in RPA recruitment to origins, suggesting that Dpb11 interaction with DNA may be required for RPA recruitment to origins. Expression of dpb11-m1,2,3,5,ΔC also results in diminished GINS interaction with Mcm2-7 during S phase, while Cdc45 interaction with Mcm2-7 is like wild-type. The reduced GINS interaction with Mcm2-7 may be an indirect consequence of diminished origin melting. We propose that the tight interaction between Dpb11, CDK-phosphorylated RPA, and branched-DNA may be required for the essential function of stabilizing melted origin DNA in vivo. We also propose an alternative model, wherein Dpb11-DNA interaction is required for some other function in DNA replication initiation, such as helicase activation. PMID:28467467

Becoming angular momentum density flow through nonlinear mass transfer into a gravitating spheroidal body

NASA Astrophysics Data System (ADS)

Krot, A. M.

2009-04-01

A statistical theory for a cosmological body forming based on the spheroidal body model has been proposed in the works [1]-[4]. This work studies a slowly evolving process of gravitational condensation of a spheroidal body from an infinitely distributed gas-dust substance in space. The equation for an initial evolution of mass density function of a gas-dust cloud is considered here. It is found this equation coincides completely with the analogous equation for a slowly gravitational compressed spheroidal body [5]. A conductive flow in dissipative systems was investigated by I. Prigogine in his works (see, for example, [6], [7]). As it has been found in [2], [5], there exists a conductive antidiffusion flow in a slowly compressible gravitating spheroidal body. Applying the equation of continuity to this conductive flow density we obtain a linear antidiffusion equation [5]. However, if an intensity of conductive flow density increases sharply then the linear antidiffusion equation becomes a nonlinear one. Really, it was pointed to [6] analogous linear equations of diffusion or thermal conductivity transform in nonlinear equations respectively. In this case, the equation of continuity describes a nonlinear mass flow being a source of instabilities into a gravitating spheroidal body because the gravitational compression factor G is a function of not only time but a mass density. Using integral substitution we can reduce a nonlinear antidiffusion equation to the linear antidiffusion equation relative to a new function. If the factor G can be considered as a specific angular momentum then the new function is an angular momentum density. Thus, a nonlinear momentum density flow induces a flow of angular momentum density because streamlines of moving continuous substance come close into a gravitating spheroidal body. Really, the streamline approach leads to more tight interactions of "liquid particles" that implies a superposition of their specific angular momentums. This superposition forms an antidiffusion flow of an angular momentum density into a gravitating spheroidal body. References: [1] Krot, A.M. The statistical model of gravitational interaction of particles. Achievement in Modern Radioelectronics (spec.issue"Cosmic Radiophysics", Moscow), 1996, no.8, pp. 66-81 (in Russian). [2] Krot, A.M. Statistical description of gravitational field: a new approach. Proc. SPIE's 14th Annual Intern.Symp. "AeroSense", Orlando, Florida, USA, 2000, vol.4038, pp.1318-1329. [3] Krot, A.M. The statistical model of rotating and gravitating spheroidal body with the point of view of general relativity. Proc.35th COSPAR Scientific Assembly, Paris, France, 2004, Abstract A-00162. [4] Krot, A. The statistical approach to exploring formation of Solar system. Proc.EGU General Assembly, Vienna, Austria, 2006, Geophys.Res.Abstracts, vol.8, A-00216; SRef-ID: 1607-7962/gra/. [5] Krot, A.M. A statistical approach to investigate the formation of the solar system. Chaos, Solitons and Fractals, 2008, doi:10.1016/j.chaos.2008.06.014. [6] Glansdorff, P. and Prigogine, I. Thermodynamic Theory of Structure, Stability and Fluctuations. London, 1971. [7] Nicolis, G. and Prigogine, I. Self-organization in Nonequilibrium Systems:From Dissipative Structures to Order through Fluctuation. John Willey and Sons, New York etc., 1977.

BH-DFTB/DFT calculations for iron clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aktürk, Abdurrahman; Sebetci, Ali, E-mail: asebetci@mevlana.edu.tr

2016-05-15

We present a study on the structural, electronic, and magnetic properties of Fe{sub n}(n  =  2  −  20) clusters by performing density functional tight binding (DFTB) calculations within a basin hopping (BH) global optimization search followed by density functional theory (DFT) investigations. The structures, total energies and total spin magnetic moments are calculated and compared with previously reported theoretical and experimental results. Two basis sets SDD with ECP and 6-31G** are employed in the DFT calculations together with BLYP GGA exchange-correlation functional. The results indicate that the offered BH-DFTB/DFT strategy collects all the global minima of which different minima havemore » been reported in the previous studies by different groups. Small Fe clusters have three kinds of packing; icosahedral (Fe{sub 9−13}), centered hexagonal antiprism (Fe{sub 14−17}, Fe{sub 20}), and truncated decahedral (Fe{sub 17(2)}, Fe{sub 18−19}). It is obtained in a qualitative agreement with the time of flight mass spectra that the magic numbers for the small Fe clusters are 7, 13, 15, and 19 and with the collision induced dissociation experiments that the sizes 6, 7, 13, 15, and 19 are thermodynamically more stable than their neighboring sizes. The spin magnetic moment per atom of Fe{sub n}(n = 2 − 20) clusters is between 2.4 and 3.6 μ{sub B} for the most of the sizes. The antiferromagnetic coupling between the central and the surface atoms of the Fe{sub 13} icosahedron, which have already been reported by experimental and theoretical studies, is verified by our calculations as well. The quantitative disagreements between the calculations and measurements of the magnetic moments of the individual sizes are still to be resolved.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Xingchen; Salahub, Dennis R.

There is no doubt that a huge gap exists in understanding heterogeneous catalysis between a cluster model of a few atoms and a bulk model of periodic slabs. Nanoparticles, which are crucial in heterogeneous catalysis in industry, lie in the middle of the gap. We present here our work on the computational modelling of molybdenum carbide nanoparticles (MCNPs) as the catalysts for the upgrading of oil sands in the in-situ environment, using benzene hydrogenation as a model reaction. With a cluster model, efforts were first made to understand the mechanism of the reaction with a density functional theory (DFT) studymore » on the adsorption of benzene and its hydrogenation product – cyclohexane, as well as the cyclic hydrogenation reaction intermediates on the Mo{sub 2}C(0001) surface. From the thermodynamic data, along with literature information, it was found that the benzene hydrogenation reaction on molybdenum carbide happens most likely through a Langmuir-Hinshelwood mechanism with the gradual lifting up of the benzene molecule. The electron localization function (ELF) was then used to help understand the nature of the interactions between the MCNPs, identifying strong multi-center interactions between the adsorbates and the MCNPs. To enable the treatment of larger nanoparticles, a fast semi-empirical density functional tight-binding (DFTB) method was parameterized. With this method, the potential energy profiles of benzene hydrogenation reactions on different sizes of MCNPs are calculated. The study was then extended to consider a MCNP embedded in solvent (benzene), using a quantum mechanical (DFTB) / molecular mechanical approach. Calculations on the free energies profiles with the umbrella sampling method show that the entropy of the MCNPs and the solvent are essential in understanding the catalytic activity of the transition metal related nanoparticles for solid/liquid heterogeneous catalysis.« less

Design of an advanced bundle divertor for the Demonstration Tokamak Hybrid Reactor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, T.F.; Lee, A.Y.; Ruck, G.W.

1979-01-25

The conclusion of this work is that a bundle divertor, using an improved method of designing the magnetic field configuration, is feasible for the Demonstration Tokamak Hybrid Reactor (DTHR) investigated by Westinghouse. The most significant achievement of this design is the reduction in current density (1 kA/cm/sup 2/) in the divertor coils in comparison to the overall averaged current densities per tesla of field to be nulled for DITE (25 kA/cm/sup 2/) and for ISX-B/sup 2/ (11 kA/cm/sup 2/). Therefore, superconducting magnets can be built into the tight space available with a sound mechanical structure.

Large Eddy Simulation of a Forced Round Turbulent Buoyant Plume in Neutral Surroundings

NASA Technical Reports Server (NTRS)

Basu, A. J.; Mansour, N. N.; Koga, Dennis (Technical Monitor)

1999-01-01

Buoyant flows play an important role in various technological and environmental issues. For example, dispersal of pollutants, smoke, or volcano exhaust in the atmosphere, vertical motion of air, formation of clouds and other weather systems, and flows in cooling towers and fires are all determined primarily by buoyancy effects. The buoyancy force in such flows can originate from either a heat source or due to different densities between a fluid and its surroundings. Whatever the cause, the flow can be understood by studying the effects of the tight coupling between the thermal and the velocity fields since density differences can be characterized as temperature differences.

Comparison of Conjugate Gradient Density Matrix Search and Chebyshev Expansion Methods for Avoiding Diagonalization in Large-Scale Electronic Structure Calculations

NASA Technical Reports Server (NTRS)

Bates, Kevin R.; Daniels, Andrew D.; Scuseria, Gustavo E.

1998-01-01

We report a comparison of two linear-scaling methods which avoid the diagonalization bottleneck of traditional electronic structure algorithms. The Chebyshev expansion method (CEM) is implemented for carbon tight-binding calculations of large systems and its memory and timing requirements compared to those of our previously implemented conjugate gradient density matrix search (CG-DMS). Benchmark calculations are carried out on icosahedral fullerenes from C60 to C8640 and the linear scaling memory and CPU requirements of the CEM demonstrated. We show that the CPU requisites of the CEM and CG-DMS are similar for calculations with comparable accuracy.

Magnetic and Electric Transverse Spin Density of Spatially Confined Light

NASA Astrophysics Data System (ADS)

Neugebauer, Martin; Eismann, Jörg S.; Bauer, Thomas; Banzer, Peter

2018-04-01

When a beam of light is laterally confined, its field distribution can exhibit points where the local magnetic and electric field vectors spin in a plane containing the propagation direction of the electromagnetic wave. The phenomenon indicates the presence of a nonzero transverse spin density. Here, we experimentally investigate this transverse spin density of both magnetic and electric fields, occurring in highly confined structured fields of light. Our scheme relies on the utilization of a high-refractive-index nanoparticle as a local field probe, exhibiting magnetic and electric dipole resonances in the visible spectral range. Because of the directional emission of dipole moments that spin around an axis parallel to a nearby dielectric interface, such a probe particle is capable of locally sensing the magnetic and electric transverse spin density of a tightly focused beam impinging under normal incidence with respect to said interface. We exploit the achieved experimental results to emphasize the difference between magnetic and electric transverse spin densities.

The mechanism of transforming diamond nanowires to carbon nanostructures.

PubMed

Sorkin, Anastassia; Su, Haibin

2014-01-24

The transformation of diamond nanowires (DNWs) with different diameters and geometries upon heating is investigated with density-functional-based tight-binding molecular dynamics. DNWs of {100} and {111} oriented cross-section with projected average line density between 7 and 20 atoms Å(-1) transform into carbon nanotubes (CNTs) under gradual heating up to 3500-4000 K. DNWs with projected average line density larger than 25 atoms Å(-1) transform into double-wall CNTs. The route of transformation into CNTs clearly exhibits three stages, with the intriguing intermediate structural motif of a carbon nanoscroll (CNS). Moreover, the morphology plays an important role in the transformation involving the CNS as one important intermediate motif to form CNTs. When starting with [Formula: see text] oriented DNWs with a square cross-section consisting of two {111} facets facing each other, one interesting structure with 'nano-bookshelf' shape emerges: a number of graphene 'shelves' located inside the CNT, bonding to the CNT walls with sp(3) hybridized atoms. The nano-bookshelf structures exist in a wide range of temperatures up to 3,000 K. The further transformation from nano-bookshelf structures depends on the strength of the joints connecting shelves with CNT walls. Notably, the nano-bookshelf structure can evolve into two end products: one is CNT via the CNS pathway, the other is graphene transformed directly from the nano-bookshelf structure at high temperature. This work sheds light on the microscopic insight of carbon nanostructure formation mechanisms with the featured motifs highlighted in the pathways.

iAID: an improved auxin-inducible degron system for the construction of a 'tight' conditional mutant in the budding yeast Saccharomyces cerevisiae.

PubMed

Tanaka, Seiji; Miyazawa-Onami, Mayumi; Iida, Tetsushi; Araki, Hiroyuki

2015-08-01

Isolation of a 'tight' conditional mutant of a gene of interest is an effective way of studying the functions of essential genes. Strategies that use ubiquitin-mediated protein degradation to eliminate the product of a gene of interest, such as heat-inducible degron (td) and auxin-inducible degron (AID), are powerful methods for constructing conditional mutants. However, these methods do not work with some genes. Here, we describe an improved AID system (iAID) for isolating tight conditional mutants in the budding yeast Saccharomyces cerevisiae. In this method, transcriptional repression by the 'Tet-OFF' promoter is combined with proteolytic elimination of the target protein by the AID system. To provide examples, we describe the construction of tight mutants of the replication factors Dpb11 and Mcm10, dpb11-iAID, and mcm10-iAID. Because Dpb11 and Mcm10 are required for the initiation of DNA replication, their tight mutants are unable to enter S phase. This is the case for dpb11-iAID and mcm10-iAID cells after the addition of tetracycline and auxin. Both the 'Tet-OFF' promoter and the AID system have been shown to work in model eukaryotes other than budding yeast. Therefore, the iAID system is not only useful in budding yeast, but also can be applied to other model systems to isolate tight conditional mutants. Copyright © 2015 John Wiley & Sons, Ltd.

MicroRNAs as regulators of drug transporters, drug-metabolizing enzymes, and tight junctions: implication for intestinal barrier function.

PubMed

Ikemura, Kenji; Iwamoto, Takuya; Okuda, Masahiro

2014-08-01

Drug transporters, drug-metabolizing enzymes, and tight junctions in the small intestine function as an absorption barrier and sometimes as a facilitator of orally administered drugs. The expression of these proteins often fluctuates and thereby causes individual pharmacokinetic variability. MicroRNAs (miRNAs), which are small non-coding RNAs, have recently emerged as a new class of gene regulator. MiRNAs post-transcriptionally regulate gene expression by binding to target mRNA to suppress its translation or regulate its degradation. They have been shown to be key regulators of proteins associated with pharmacokinetics. Moreover, the role of miRNAs on the expression of some proteins expressed in the small intestine has recently been clarified. In this review, we summarize current knowledge regarding the role of miRNAs in the regulation of drug transporters, drug-metabolizing enzymes, and tight junctions as well as its implication for intestinal barrier function. MiRNAs play vital roles in the differentiation, architecture, and barrier function of intestinal epithelial cells, and directly and/or indirectly regulate the expression and function of proteins associated with drug absorption in intestinal epithelial cells. Moreover, the variation of miRNA expression caused by pathological and physiological conditions as well as genetic factors should affect the expression of these proteins. Therefore, miRNAs could be significant factors affecting inter- and intra-individual variations in the pharmacokinetics and intestinal absorption of drugs. Overall, miRNAs could be promising targets for personalized pharmacotherapy or other attractive therapies through intestinal absorption of drugs. Copyright © 2014 Elsevier Inc. All rights reserved.

Estrogen Modulates Expression of Tight Junction Proteins in Rat Vagina

PubMed Central

Oh, Kyung-Jin; Ahn, Kyuyoun

2016-01-01

Background. The objectives of this study were to investigate the localization of tight junctions and the modulation of zonula occludens- (ZO-) 1, occludin and claudin-1 expression by estrogen in castrated female rat vagina. Female Sprague-Dawley rats (230–240 g, n = 45) were divided into three groups and subjected to a sham operation (control group, n = 15), bilateral ovariectomy (Ovx group, n = 15), or bilateral ovariectomy followed by daily subcutaneous injection of 17β-estradiol (50 μg/kg/day, Ovx + Est group, n = 15). The cellular localization and expression of ZO-1, occludin, and claudin-1 were determined in each group by immunohistochemistry and western blot. Results. Expression of ZO-1 was diffuse in all groups, with the highest intensity in the superficial epithelium in the control group. Occludin was localized in the intermediate and basal epithelium. Claudin-1 was most intense in the superficial layer of the vaginal epithelium in the control group. Expression of ZO-1, occludin, and claudin-1 was significantly decreased after ovariectomy and was restored to the level of the control after estrogen replacement. Conclusions. Tight junctions are distinctly localized in rat vagina, and estrogen modulates the expression of tight junctions. Further researches are needed to clarify the functional role of tight junctions in vaginal lubrication. PMID:27127786

Estrogen Modulates Expression of Tight Junction Proteins in Rat Vagina.

PubMed

Oh, Kyung-Jin; Lee, Hyun-Suk; Ahn, Kyuyoun; Park, Kwangsung

2016-01-01

Background. The objectives of this study were to investigate the localization of tight junctions and the modulation of zonula occludens- (ZO-) 1, occludin and claudin-1 expression by estrogen in castrated female rat vagina. Female Sprague-Dawley rats (230-240 g, n = 45) were divided into three groups and subjected to a sham operation (control group, n = 15), bilateral ovariectomy (Ovx group, n = 15), or bilateral ovariectomy followed by daily subcutaneous injection of 17β-estradiol (50 μg/kg/day, Ovx + Est group, n = 15). The cellular localization and expression of ZO-1, occludin, and claudin-1 were determined in each group by immunohistochemistry and western blot. Results. Expression of ZO-1 was diffuse in all groups, with the highest intensity in the superficial epithelium in the control group. Occludin was localized in the intermediate and basal epithelium. Claudin-1 was most intense in the superficial layer of the vaginal epithelium in the control group. Expression of ZO-1, occludin, and claudin-1 was significantly decreased after ovariectomy and was restored to the level of the control after estrogen replacement. Conclusions. Tight junctions are distinctly localized in rat vagina, and estrogen modulates the expression of tight junctions. Further researches are needed to clarify the functional role of tight junctions in vaginal lubrication.

Carbon Nanotube Field Emission Arrays

DTIC Science & Technology

2011-06-01

K , and M [14]. Using the tight binding energy model, the energy dispersion relations for graphene can be calculated for the triangle formed from...The corresponding reciprocal lattice vectors, b1 and b2, and Brillouin zone of graphene [14]. 19 graphene band structure is the six K ...points where the two bands are degenerate and the Fermi level passes. It has been shown through thorough calculations that at T = 0 K , the density

The Effect of Nozzle Design and Operating Conditions on the Atomization and Distribution of Fuel Sprays

NASA Technical Reports Server (NTRS)

Lee, Dana W

1933-01-01

The atomization and distribution characteristics of fuel sprays from automatic injection valves for compression-ignition engines were determined by catching the fuel drops on smoked-glass plates, and then measuring and counting the impressions made in the lampblack. The experiments were made in an air-tight chamber in which the air density was raised to values corresponding to engine conditions.

Partially acoustic dark matter, interacting dark radiation, and large scale structure

NASA Astrophysics Data System (ADS)

Chacko, Zackaria; Cui, Yanou; Hong, Sungwoo; Okui, Takemichi; Tsai, Yuhsinz

2016-12-01

The standard paradigm of collisionless cold dark matter is in tension with measurements on large scales. In particular, the best fit values of the Hubble rate H 0 and the matter density perturbation σ 8 inferred from the cosmic microwave background seem inconsistent with the results from direct measurements. We show that both problems can be solved in a framework in which dark matter consists of two distinct components, a dominant component and a subdominant component. The primary component is cold and collisionless. The secondary component is also cold, but interacts strongly with dark radiation, which itself forms a tightly coupled fluid. The growth of density perturbations in the subdominant component is inhibited by dark acoustic oscillations due to its coupling to the dark radiation, solving the σ 8 problem, while the presence of tightly coupled dark radiation ameliorates the H 0 problem. The subdominant component of dark matter and dark radiation continue to remain in thermal equilibrium until late times, inhibiting the formation of a dark disk. We present an example of a simple model that naturally realizes this scenario in which both constituents of dark matter are thermal WIMPs. Our scenario can be tested by future stage-IV experiments designed to probe the CMB and large scale structure.

Comparison of ultrastructure, tight junction-related protein expression and barrier function of human corneal epithelial cells cultivated on amniotic membrane with and without air-lifting.

PubMed

Ban, Yuriko; Cooper, Leanne J; Fullwood, Nigel J; Nakamura, Takahiro; Tsuzuki, Masakatsu; Koizumi, Noriko; Dota, Atsuyoshi; Mochida, Chikako; Kinoshita, Shigeru

2003-06-01

To evaluate the usefulness of the air-lifting technique for culturing corneal limbal epithelial cells on amniotic membrane (AM) for use in ocular surface reconstruction. A cultured sheet that has a good barrier function should be better for this purpose. In corneal epithelium, tight junctions (TJ) play a vital role in the barrier function. The TJ complex includes the integral transmembrane proteins occludin and the claudins, and some membrane-associated proteins such as ZO-1. In this paper, we investigated the barrier function and the expression of TJ related proteins. Corneal limbal epithelium obtained from donor corneas and cultivated on acellular AM was divided into two groups. These were the non-air-lifting (Non-AL) group, which was continuously submerged in medium, and the air-lifting (AL) group, which was submerged in medium for 3 weeks, then exposed to air by lowering the medium level. Morphology and the permeability to horseradish peroxidase (HRP) were determined by electron microscopy. Tight junction (TJ)-related protein and mRNA expression changes were assessed by immunoblotting and reverse transcription-polymerase chain reaction. The cultures of both groups formed 4-5-layer-thick, well-stratified epithelium. The AL cultures had tightly packed epithelial cells with all the HRP/diaminobenzidine (DAB) reaction product accumulated on the apical surface of the superficial cells. The Non-AL culture, by contrast, had more loosely packed epithelial cells with larger intercellular spaces. The HRP/DAB reaction product penetrated the intercellular space to a depth of 3-4 cell layers. Statistically, there was a significant difference in intercellular spaces and desmosome count in the superficial cells between the groups. With AL, TJ-related proteins localized at the apical portion of the lateral membrane. TJ-related protein and mRNA amounts were not changed by AL while claudin subtype expression became more consistent and closer to that of in vivo corneal epithelium. The AL technique reduces intercellular spaces in the superficial cells and promotes the formation of the barrier function. It is useful in culturing corneal epithelial cells for use in ocular surface reconstruction.

Mechanism and comparison of needle-type non-thermal direct and indirect atmospheric pressure plasma jets on the degradation of dyes

NASA Astrophysics Data System (ADS)

Attri, Pankaj; Yusupov, Maksudbek; Park, Ji Hoon; Lingamdinne, Lakshmi Prasanna; Koduru, Janardhan Reddy; Shiratani, Masaharu; Choi, Eun Ha; Bogaerts, Annemie

2016-10-01

Purified water supply for human use, agriculture and industry is the major global priority nowadays. The advanced oxidation process based on atmospheric pressure non-thermal plasma (NTP) has been used for purification of wastewater, although the underlying mechanisms of degradation of organic pollutants are still unknown. In this study we employ two needle-type atmospheric pressure non-thermal plasma jets, i.e., indirect (ID-APPJ) and direct (D-APPJ) jets operating at Ar feed gas, for the treatment of methylene blue, methyl orange and congo red dyes, for two different times (i.e., 20 min and 30 min). Specifically, we study the decolorization/degradation of all three dyes using the above mentioned plasma sources, by means of UV-Vis spectroscopy, HPLC and a density meter. We also employ mass spectroscopy to verify whether only decolorization or also degradation takes place after treatment of the dyes by the NTP jets. Additionally, we analyze the interaction of OH radicals with all three dyes using reactive molecular dynamics simulations, based on the density functional-tight binding method. This investigation represents the first report on the degradation of these three different dyes by two types of NTP setups, analyzed by various methods, and based on both experimental and computational studies.

Structure and vibrational spectra of low-energy silicon clusters

NASA Astrophysics Data System (ADS)

Sieck, A.; Porezag, D.; Frauenheim, Th.; Pederson, M. R.; Jackson, K.

1997-12-01

We have identified low-energy structures of silicon clusters with 9 to 14 atoms using a nonorthogonal tight-binding method (TB) based on density-functional theory (DF). We have further investigated the resulting structures with an accurate all-electron first-principles technique. The results for cohesive energies, cluster geometries, and highest occupied to lowest unoccupied molecular orbital (HOMO-LUMO) gaps show an overall good agreement between DF-TB and self-consistent-field (SCF) DF theory. For Si9 and Si14, we have found equilibrium structures, whereas for Si11, Si12, and Si13, we present clusters with energies close to that of the corresponding ground-state structure recently proposed in the literature. The bonding scheme of clusters in this size range is different from the bulk tetrahedral symmetry. The most stable structures, characterized by low energies and large HOMO-LUMO gaps, have similar common subunits. To aid in their experimental identification, we have computed the full vibrational spectra of the structures, along with the Raman activities, IR intensities, and static polarizabilities, using SCF-DF theory within the local-density approximation (LDA). This method has already been successfully applied to the determination of Raman and IR spectra of silicon clusters with 3-8, 10, 13, 20, and 21 atoms.

Bona-fide method for the determination of short range order and transport properties in a ferro-aluminosilicate slag

PubMed Central

Karalis, Konstantinos T.; Dellis, Dimitrios; Antipas, Georgios S. E.; Xenidis, Anthimos

2016-01-01

The thermodynamics, structural and transport properties (density, melting point, heat capacity, thermal expansion coefficient, viscosity and electrical conductivity) of a ferro-aluminosilicate slag have been studied in the solid and liquid state (1273–2273 K) using molecular dynamics. The simulations were based on a Buckingham-type potential, which was extended here, to account for the presence of Cr and Cu. The potential was optimized by fitting pair distribution function partials to values determined by Reverse Monte Carlo modelling of X-ray and neutron diffraction experiments. The resulting short range order features and ring statistics were in tight agreement with experimental data and created consensus for the accurate prediction of transport properties. Accordingly, calculations yielded rational values both for the average heat capacity, equal to 1668.58 J/(kg·K), and for the viscosity, in the range of 4.09–87.64 cP. The potential was consistent in predicting accurate values for mass density (i.e. 2961.50 kg/m3 vs. an experimental value of 2940 kg/m3) and for electrical conductivity (5.3–233 S/m within a temperature range of 1273.15–2273.15 K). PMID:27455915

Electronic transport in the quantum spin Hall state due to the presence of adatoms in graphene

NASA Astrophysics Data System (ADS)

Lima, Leandro; Lewenkopf, Caio

Heavy adatoms, even at low concentrations, are predicted to turn a graphene sheet into a topological insulator with substantial gap. The adatoms mediate the spin-orbit coupling that is fundamental to the quantum spin Hall effect. The adatoms act as local spin-orbit scatterer inducing hopping processes between distant carbon atoms giving origin to transverse spin currents. Although there are effective models that describe spectral properties of such systems with great detail, quantitative theoretical work for the transport counterpart is still lacking. We developed a multiprobe recursive Green's function technique with spin resolution to analyze the transport properties for large geometries. We use an effective tight-binding Hamiltonian to describe the problem of adatoms randomly placed at the center of the honeycomb hexagons, which is the case for most transition metals. Our choice of current and voltage probes is favorable to experiments since it filters the contribution of only one spin orientation, leading to a quantized spin Hall conductance of e2 / h . We also discuss the electronic propagation in the system by imaging the local density of states and the electronic current densities. The authors acknowledge the Brazilian agencies CNPq, CAPES, FAPERJ and INCT de Nanoestruturas de Carbono for financial support.

Density impact on performance of composite Si/graphite electrodes

DOE PAGES

Dufek, Eric J.; Picker, Michael; Petkovic, Lucia M.

2016-01-27

The ability of alkali-substituted binders for composite Si and graphite negative electrodes to minimize capacity fade for lithium ion batteries is investigated. Polymer films and electrodes are described and characterized by FTIR following immersion in electrolyte (1:2 EC:DMC) for 24 h. FTIR analysis following electrode formation displayed similar alkali-ion dependent shifts in peak location suggesting that changes in the vibrational structure of the binder are maintained after electrode formation. The Si and graphite composite electrodes prepared using the alkali-substituted polyacrylates were also exposed to electrochemical cycling and it has been found that the performance of the Na-substituted binder is superiormore » to a comparable density K-substituted system. However, in comparing performance across many different electrode densities attention needs to be placed on making comparisons at similar densities, as low density electrodes tend to exhibit lower capacity fade over cycling. This is highlighted by a 6% difference between a low density K-substituted electrode and a high density Na-substituted sample. As a result, this low variance between the two systems makes it difficult to quickly make a direct evaluation of binder performance unless electrode density is tightly controlled.« less

Oncostatin M induces upregulation of claudin-2 in rodent hepatocytes coinciding with changes in morphology and function of tight junctions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Imamura, Masafumi; Department of Pathology, Sapporo Medical University School of Medicine, S1. W17. Sapporo 060-8556; Kojima, Takashi

2007-05-15

In rodent livers, integral tight junction (TJ) proteins claudin-1, -2, -3, -5 and -14 are detected and play crucial roles in the barrier to keep bile in bile canaculi away from the blood circulation. Claudin-2 shows a lobular gradient increasing from periportal to pericentral hepatocytes, whereas claudin-1 and -3 are expressed in the whole liver lobule. Although claudin-2 expression induces cation-selective channels in tight junctions of epithelial cells, the physiological functions and regulation of claudin-2 in hepatocytes remain unclear. Oncostatin M (OSM) is a multifunctional cytokine implicated in the differentiation of hepatocytes that induces formation of E-cadherin-based adherens junctions inmore » fetal hepatocytes. In this study, we examined whether OSM could induce expression and function of claudin-2 in rodent hepatocytes, immortalized mouse and primary cultured proliferative rat hepatocytes. In the immortalized mouse and primary cultured proliferative rat hepatocytes, treatment with OSM markedly increased mRNA and protein of claudin-2 together with formation of developed networks of TJ strands. The increase of claudin-2 enhanced the paracellular barrier function which depended on molecular size. The increase of claudin-2 expression induced by OSM in rodent hepatocytes was regulated through distinct signaling pathways including PKC. These results suggest that expression of claudin-2 in rodent hepatocytes may play a specific role as controlling the size of paracellular permeability in the barrier to keep bile in bile canaculi.« less

Network organization is globally atypical in autism: A graph theory study of intrinsic functional connectivity.

PubMed

Keown, Christopher L; Datko, Michael C; Chen, Colleen P; Maximo, José Omar; Jahedi, Afrooz; Müller, Ralph-Axel

2017-01-01

Despite abundant evidence of brain network anomalies in autism spectrum disorder (ASD), findings have varied from broad functional underconnectivity to broad overconnectivity. Rather than pursuing overly simplifying general hypotheses ('under' vs. 'over'), we tested the hypothesis of atypical network distribution in ASD (i.e., participation of unusual loci in distributed functional networks). We used a selective high-quality data subset from the ABIDE datashare (including 111 ASD and 174 typically developing [TD] participants) and several graph theory metrics. Resting state functional MRI data were preprocessed and analyzed for detection of low-frequency intrinsic signal correlations. Groups were tightly matched for available demographics and head motion. As hypothesized, the Rand Index (reflecting how similar network organization was to a normative set of networks) was significantly lower in ASD than TD participants. This was accounted for by globally reduced cohesion and density, but increased dispersion of networks. While differences in hub architecture did not survive correction, rich club connectivity (among the hubs) was increased in the ASD group. Our findings support the model of reduced network integration (connectivity with networks) and differentiation (or segregation; based on connectivity outside network boundaries) in ASD. While the findings applied at the global level, they were not equally robust across all networks and in one case (greater cohesion within ventral attention network in ASD) even reversed.

Proton acceleration by multi-terawatt interaction with a near-critical density hydrogen jet

NASA Astrophysics Data System (ADS)

Goers, Andy; Feder, Linus; Hine, George; Salehi, Fatholah; Woodbury, Daniel; Su, J. J.; Papadopoulos, Dennis; Zigler, Arie; Milchberg, Howard

2016-10-01

We investigate the high intensity laser interaction with thin, near critical density plasmas as a means of efficient acceleration of MeV protons. A promising mechanism is magnetic vortex acceleration, where the ponderomotive force of a tightly focused laser pulse drives a relativistic electron current which generates a strong azimuthal magnetic field. The rapid expansion of this azimuthal magnetic field at the back side of the target can accelerate plasma ions to MeV scale energies. Compared to typical ion acceleration experiments utilizing a laser- thin solid foil interaction, magnetic vortex acceleration in near critical density plasma may be realized in a high density gas jet, making it attractive for applications requiring high repetition rates. We present preliminary experiments studying laser-plasma interaction and proton acceleration in a thin (< 200 μm) near-critical density hydrogen gas jet delivering electron densities 1020 -1021 cm-3 . This research was funded by the United States Department of Energy and the Defense Advanced Research Projects Agency (DARPA) under Contract Number W911-NF-15-C-0217, issued by the Army Research Office.

Accumulation of Amyloid β-Protein in the Low-Density Membrane Domain Accurately Reflects the Extent of β-Amyloid Deposition in the Brain

PubMed Central

Oshima, Noriko; Morishima-Kawashima, Maho; Yamaguchi, Haruyasu; Yoshimura, Masahiro; Sugihara, Shiro; Khan, Karen; Games, Dora; Schenk, Dale; Ihara, Yasuo

2001-01-01

To learn more about the process of amyloid β-protein (Aβ) deposition in the brain, human prefrontal cortices were fractionated by sucrose density gradient centrifugation, and the Aβ content in each fraction was quantified by a two-site enzyme-linked immunosorbent assay. The fractionation protocol revealed two pools of insoluble Aβ. One corresponded to a low-density membrane domain; the other was primarily composed of extracellular Aβ deposits in those cases in which Aβ accumulated to significant levels. Aβ42 levels in the low-density membrane domain were proportional to the extent of total Aβ42 accumulation, which is known to correlate well with overall amyloid burden. In PDAPP mice that form senile plaques and accumulate Aβ in a similar manner to aging humans, Aβ42 accumulation in the low-density membrane domain also increased as Aβ deposition progressed with aging. These observations indicate that the Aβ42 associated with low-density membrane domains is tightly coupled with the process of extracellular Aβ deposition. PMID:11395399

An environment-dependent semi-empirical tight binding model suitable for electron transport in bulk metals, metal alloys, metallic interfaces, and metallic nanostructures. II. Application—Effect of quantum confinement and homogeneous strain on Cu conductance

NASA Astrophysics Data System (ADS)

Hegde, Ganesh; Povolotskyi, Michael; Kubis, Tillmann; Charles, James; Klimeck, Gerhard

2014-03-01

The Semi-Empirical tight binding model developed in Part I Hegde et al. [J. Appl. Phys. 115, 123703 (2014)] is applied to metal transport problems of current relevance in Part II. A systematic study of the effect of quantum confinement, transport orientation, and homogeneous strain on electronic transport properties of Cu is carried out. It is found that quantum confinement from bulk to nanowire boundary conditions leads to significant anisotropy in conductance of Cu along different transport orientations. Compressive homogeneous strain is found to reduce resistivity by increasing the density of conducting modes in Cu. The [110] transport orientation in Cu nanowires is found to be the most favorable for mitigating conductivity degradation since it shows least reduction in conductance with confinement and responds most favorably to compressive strain.

Dual functions of a small regulatory subunit in the mitochondrial calcium uniporter complex.

PubMed

Tsai, Ming-Feng; Phillips, Charles B; Ranaghan, Matthew; Tsai, Chen-Wei; Wu, Yujiao; Willliams, Carole; Miller, Christopher

2016-04-21

Mitochondrial Ca(2+) uptake, a process crucial for bioenergetics and Ca(2+) signaling, is catalyzed by the mitochondrial calcium uniporter. The uniporter is a multi-subunit Ca(2+)-activated Ca(2+) channel, with the Ca(2+) pore formed by the MCU protein and Ca(2+)-dependent activation mediated by MICU subunits. Recently, a mitochondrial inner membrane protein EMRE was identified as a uniporter subunit absolutely required for Ca(2+) permeation. However, the molecular mechanism and regulatory purpose of EMRE remain largely unexplored. Here, we determine the transmembrane orientation of EMRE, and show that its known MCU-activating function is mediated by the interaction of transmembrane helices from both proteins. We also reveal a second function of EMRE: to maintain tight MICU regulation of the MCU pore, a role that requires EMRE to bind MICU1 using its conserved C-terminal polyaspartate tail. This dual functionality of EMRE ensures that all transport-competent uniporters are tightly regulated, responding appropriately to a dynamic intracellular Ca(2+) landscape.

B-spline tight frame based force matching method

NASA Astrophysics Data System (ADS)

Yang, Jianbin; Zhu, Guanhua; Tong, Dudu; Lu, Lanyuan; Shen, Zuowei

2018-06-01

In molecular dynamics simulations, compared with popular all-atom force field approaches, coarse-grained (CG) methods are frequently used for the rapid investigations of long time- and length-scale processes in many important biological and soft matter studies. The typical task in coarse-graining is to derive interaction force functions between different CG site types in terms of their distance, bond angle or dihedral angle. In this paper, an ℓ1-regularized least squares model is applied to form the force functions, which makes additional use of the B-spline wavelet frame transform in order to preserve the important features of force functions. The B-spline tight frames system has a simple explicit expression which is useful for representing our force functions. Moreover, the redundancy of the system offers more resilience to the effects of noise and is useful in the case of lossy data. Numerical results for molecular systems involving pairwise non-bonded, three and four-body bonded interactions are obtained to demonstrate the effectiveness of our approach.

Modelling of Lyman-alpha emitting galaxies and ionized bubbles at the epoch of reionization

NASA Astrophysics Data System (ADS)

Yajima, Hidenobu; Sugimura, Kazuyuki; Hasegawa, Kenji

2018-07-01

Understanding {Ly{α}} emitting galaxies (LAEs) can be a key to reveal cosmic reionization and galaxy formation in the early Universe. Based on halo merger trees and {Ly{α}} radiation transfer calculations, we model redshift evolution of LAEs and their observational properties at z ≥ 6. We consider ionized bubbles associated with individual LAEs and IGM (integer-galactic medium) transmission of {Ly{α}} photons. We find that {Ly{α}} luminosity tightly correlates with halo mass and stellar mass, while the relation with star formation rate has a large dispersion. Comparing our models with the observed luminosity function by Konno et al., we suggest that LAEs at z ˜ 7 have galactic wind of V_out ≳ 100 km s^{-1} and H I column density of N_HI ≳ 10^{20} cm^{-2}. Number density of bright LAEs rapidly decreases as redshift increases, due to both lower star formation rate and smaller H II bubbles. Our model predicts future wide deep surveys with next-generation telescopes, such as James Webb Space Telescope, European Extremely Large Telescope, and Thirty Metre Telescope, can detect LAEs at z ˜ 10 with a number density of n_LAE ˜ {a few } × 10^{-6} Mpc^{-3} for the flux sensitivity of 10^{-18} erg cm^{-2} s^{-1}. When giant H II bubbles are formed by clustering LAEs, the number density of observable LAEs can increase by a factor of few. By combining these surveys with future 21-cm observations, it could be possible to detect both LAEs with L_{Lyα }≳ 10^{42} erg s^{-1} and their associated giant H II bubbles with the size {≳ } 250 kpc at z ˜ 10.

Modelling of Lyman-alpha emitting galaxies and ionized bubbles at the epoch of reionization

NASA Astrophysics Data System (ADS)

Yajima, Hidenobu; Sugimura, Kazuyuki; Hasegawa, Kenji

2018-04-01

Understanding {Ly{α }} emitting galaxies (LAEs) can be a key to reveal cosmic reionization and galaxy formation in the early Universe. Based on halo merger trees and {Ly{α }} radiation transfer calculations, we model redshift evolution of LAEs and their observational properties at z ≥ 6. We consider ionized bubbles associated with individual LAEs and IGM transmission of {Ly{α }} photons. We find that {Ly{α }} luminosity tightly correlates with halo mass and stellar mass, while the relation with star formation rate has a large dispersion. Comparing our models with the observed luminosity function by Konno et al., we suggest that LAEs at z ˜ 7 have galactic wind of V_out ≳ 100 km s^{-1} and HI column density of N_HI ≳ 10^{20} cm^{-2}. Number density of bright LAEs rapidly decreases as redshift increases, due to both lower star formation rate and smaller HII bubbles. Our model predicts future wide deep surveys with next generation telescopes, such as JWST, E-ELT and TMT, can detect LAEs at z ˜ 10 with a number density of n_LAE ˜ a few × 10^{-6} Mpc^{-3} for the flux sensitivity of 10^{-18} erg cm^{-2} s^{-1}. When giant HII bubbles are formed by clustering LAEs, the number density of observable LAEs can increase by a factor of few. By combining these surveys with future 21-cm observations, it could be possible to detect both LAEs with L_{Lyα }≳ 10^{42} erg s^{-1} and their associated giant HII bubbles with the size ≳ 250 kpc at z ˜ 10.

Carbon aerogels by pyrolysis of TEMPO-oxidized cellulose

NASA Astrophysics Data System (ADS)

Zhang, Sizhao; Feng, Jian; Feng, Junzong; Jiang, Yonggang; Ding, Feng

2018-05-01

Although carbon aerogels derived from naturally occurring materials have been developed extensively, a reasonable synthetic approach using cellulose-resource remains unclear. Here, we report a strategy to prepare carbon aerogels originated from cellulose position-selectively oxidized by TEMPO-oxidized process. Contrary to non-TEMPO-oxidized cellulose-derived carbon aerogels (NCCA) with relative loose structure, TEMPO-oxidized cellulose-derived carbon aerogels (TCCA) with tight fibrillar-continuous network are monitored, suggesting the importance of TEMPO-oxidized modification towards creating the architecture of subsequently produced carbon aerogels. TCCA endows a higher BET area despite owning slightly dense bulk density comparing with that of NCCA. The structural texture of TCCA could be maintained in a way in comparison to TEMPO-oxidized cellulose-derived aerogel, due to the integration and aggregation effect by losing the electric double layer repulsion via ionization of the surface carboxyl groups. FTIR and XPS analyses signify the evidence of non-functionalized carbon-skeleton network formation in terms of TCCA. Further, the mechanism concerning the creation of carbon aerogels is also established. These findings not only provide new insights into the production of carbon aerogels but also open up a new opportunity in the field of functional carbon materials.

Tracking of plus-ends reveals microtubule functional diversity in different cell types

NASA Astrophysics Data System (ADS)

Shaebani, M. Reza; Pasula, Aravind; Ott, Albrecht; Santen, Ludger

2016-07-01

Many cellular processes are tightly connected to the dynamics of microtubules (MTs). While in neuronal axons MTs mainly regulate intracellular trafficking, they participate in cytoskeleton reorganization in many other eukaryotic cells, enabling the cell to efficiently adapt to changes in the environment. We show that the functional differences of MTs in different cell types and regions is reflected in the dynamic properties of MT tips. Using plus-end tracking proteins EB1 to monitor growing MT plus-ends, we show that MT dynamics and life cycle in axons of human neurons significantly differ from that of fibroblast cells. The density of plus-ends, as well as the rescue and catastrophe frequencies increase while the growth rate decreases toward the fibroblast cell margin. This results in a rather stable filamentous network structure and maintains the connection between nucleus and membrane. In contrast, plus-ends are uniformly distributed along the axons and exhibit diverse polymerization run times and spatially homogeneous rescue and catastrophe frequencies, leading to MT segments of various lengths. The probability distributions of the excursion length of polymerization and the MT length both follow nearly exponential tails, in agreement with the analytical predictions of a two-state model of MT dynamics.

Micro solid oxide fuel cell fabricated on porous stainless steel: a new strategy for enhanced thermal cycling ability

PubMed Central

Kim, Kun Joong; Park, Byung Hyun; Kim, Sun Jae; Lee, Younki; Bae, Hongyeul; Choi, Gyeong Man

2016-01-01

Miniaturized solid oxide fuel cells (micro-SOFCs) are being extensively studied as a promising alternative to Li batteries for next generation portable power. A new micro-SOFC is designed and fabricated which shows enhanced thermal robustness by employing oxide-based thin-film electrode and porous stainless steel (STS) substrate. To deposit gas-tight thin-film electrolyte on STS, nano-porous composite oxide is proposed and applied as a new contact layer on STS. The micro-SOFC fabricated on composite oxide- STS dual layer substrate shows the peak power density of 560 mW cm−2 at 550 °C and maintains this power density during rapid thermal cycles. This cell may be suitable for portable electronic device that requires high power-density and fast thermal cycling. PMID:26928921

Micro solid oxide fuel cell fabricated on porous stainless steel: a new strategy for enhanced thermal cycling ability.

PubMed

Kim, Kun Joong; Park, Byung Hyun; Kim, Sun Jae; Lee, Younki; Bae, Hongyeul; Choi, Gyeong Man

2016-03-01

Miniaturized solid oxide fuel cells (micro-SOFCs) are being extensively studied as a promising alternative to Li batteries for next generation portable power. A new micro-SOFC is designed and fabricated which shows enhanced thermal robustness by employing oxide-based thin-film electrode and porous stainless steel (STS) substrate. To deposit gas-tight thin-film electrolyte on STS, nano-porous composite oxide is proposed and applied as a new contact layer on STS. The micro-SOFC fabricated on composite oxide- STS dual layer substrate shows the peak power density of 560 mW cm(-2) at 550 °C and maintains this power density during rapid thermal cycles. This cell may be suitable for portable electronic device that requires high power-density and fast thermal cycling.

Interrupting an Imminent Body Current Fault and Restoring Full Power in Milliseconds on a DIII-D National Fusion Facility Gyrotron

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ponce, Dan; Brambila, Rigo E.; Cengher, Mirela

The ECH Group at DIII-D has installed in-house engineered, FPGA-based, high voltage reference waveform generators on its gyrotron control systems to enhance the capabilities of the systems and replace obsolete equipment. The new hardware, named D-Wavegen, outputs 16-bit signals every microsecond and can respond to events and anomalies in real-time. These generators have been reliably pausing gyrotron rf output during periods of DIII-D plasma density that exceed the fault density trip level and restarting the rf output if the density falls below the trip level. While tightly monitoring gyrotron body current and internal pressure, D-Wavegen has also been reliably restarting,more » in a little over 10ms, gyrotrons that spontaneously ceased rf generation.« less

Interrupting an Imminent Body Current Fault and Restoring Full Power in Milliseconds on a DIII-D National Fusion Facility Gyrotron

DOE PAGES

Ponce, Dan; Brambila, Rigo E.; Cengher, Mirela; ...

2017-10-19

The ECH Group at DIII-D has installed in-house engineered, FPGA-based, high voltage reference waveform generators on its gyrotron control systems to enhance the capabilities of the systems and replace obsolete equipment. The new hardware, named D-Wavegen, outputs 16-bit signals every microsecond and can respond to events and anomalies in real-time. These generators have been reliably pausing gyrotron rf output during periods of DIII-D plasma density that exceed the fault density trip level and restarting the rf output if the density falls below the trip level. While tightly monitoring gyrotron body current and internal pressure, D-Wavegen has also been reliably restarting,more » in a little over 10ms, gyrotrons that spontaneously ceased rf generation.« less

Nonlinear Thomson scattering of a relativistically strong tightly focused ultrashort laser pulse

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vais, O. E.; Bochkarev, S. G., E-mail: bochkar@sci.lebedev.ru; Bychenkov, V. Yu.

The problem of nonlinear Thomson scattering of a relativistically strong linearly polarized ultrashort laser pulse tightly focused into a spot with a diameter of D{sub F} ≳ λ (where λ is the laser wavelength) is solved. The energy, spectral, and angular distributions of radiation generated due to Thomson scattering from test electrons located in the focal region are found. The characteristics of scattered radiation are studied as functions of the tightness of laser focusing and the initial position of test particles relative to the center of the focal region for a given laser pulse energy. It is demonstrated that themore » ultratight focusing is not optimal for obtaining the brightest and hardest source of secondary electromagnetic radiation. The hardest and shortest radiation pulse is generated when the beam waist diameter is ≃10λ.« less

Myosin light chain kinase knockout improves gut barrier function and confers a survival advantage in polymicrobial sepsis.

PubMed

Lorentz, C Adam; Liang, Zhe; Meng, Mei; Chen, Ching-Wen; Yoseph, Benyam P; Breed, Elise R; Mittal, Rohit; Klingensmith, Nathan J; Farris, Alton B; Burd, Eileen M; Koval, Michael; Ford, Mandy L; Coopersmith, Craig M

2017-06-07

Sepsis-induced intestinal hyperpermeability is mediated by disruption of the epithelial tight junction, which is closely associated with the peri-junctional actin-myosin ring. Myosin light chain kinase (MLCK) phosphorylates the myosin regulatory light chain, resulting in increased permeability. The purpose of this study was to determine whether genetic deletion of MLCK would alter gut barrier function and survival from sepsis. MLCK -/- and wild type (WT) mice were subjected to cecal ligation and puncture and assayed for both survival and mechanistic studies. Survival was significantly increased in MLCK -/- mice (95% vs. 24%, p<0.0001). Intestinal permeability increased in septic WT mice compared to unmanipulated mice. In contrast, permeability in septic MLCK -/- mice was similar to that seen in unmanipulated animals. Improved gut barrier function in MLCK -/- mice was associated with increases in the tight junction mediators ZO-1 and claudin 15 without alterations in claudin 1, 2, 3, 4, 5, 7, 8, 13, occludin or JAM-A. Other components of intestinal integrity (apoptosis, proliferation and villus length) were unaffected by MLCK deletion as were local peritoneal inflammation and distant lung injury. Systemic IL-10 was decreased greater than 10-fold in MLCK -/- mice; however, survival was similar between septic MLCK -/- mice given exogenous IL-10 or vehicle. These data demonstrate that deletion of MLCK improves survival following sepsis, associated with normalization of intestinal permeability and selected tight junction proteins.

Hyaluronan 35kDa treatment protects mice from Citrobacter rodentium infection and induces epithelial tight junction protein ZO-1 in vivo.

PubMed

Kim, Yeojung; Kessler, Sean P; Obery, Dana R; Homer, Craig R; McDonald, Christine; de la Motte, Carol A

2017-10-01

Maintaining a healthy intestinal barrier, the primary physical barrier between intestinal microbiota and the underlying lamina propria, is critical for optimal health. Epithelial integrity is essential for the prevention of the entrance of luminal contents, such as bacteria and their products, through the large intestinal barrier. In this study, we investigated the protective functions of biosynthetic, specific sized, hyaluronan around 35kDa (HA35) on intestinal epithelium in healthy mice, as well as mice infected Citrobacter rodentium, an established model that mimics infection with a serious human pathogen, enteropathogenic E. coli (EPEC). Our results reveal that treatment with HA35 protects mice from Citrobacter infection and enhances the epithelial barrier function. In particular, we have found that HA35 induces the expression of tight junction protein zonula occludens (ZO)-1 in both healthy and Citrobacter infected mice, as demonstrated by immunoflurorescence and Western blot analyses. Furthermore, we determined that HA35 treatment enhances ZO-1 expression and reduces intestinal permeability at the early stages of dextran sulfate sodium (DSS)-induced colitis in mice. Together, our data demonstrate that the expression and functionality of tight junctions, are increased by HA35 treatment, suggesting a novel mechanism for the protection from Citrobacter infection. Copyright © 2016 Elsevier B.V. All rights reserved.

Hypoxic Stress and Inflammatory Pain Disrupt Blood-Brain Barrier Tight Junctions: Implications for Drug Delivery to the Central Nervous System.

PubMed

Lochhead, Jeffrey J; Ronaldson, Patrick T; Davis, Thomas P

2017-07-01

A functional blood-brain barrier (BBB) is necessary to maintain central nervous system (CNS) homeostasis. Many diseases affecting the CNS, however, alter the functional integrity of the BBB. It has been shown that various diseases and physiological stressors can impact the BBB's ability to selectively restrict passage of substances from the blood to the brain. Modifications of the BBB's permeability properties can potentially contribute to the pathophysiology of CNS diseases and result in altered brain delivery of therapeutic agents. Hypoxia and/or inflammation are central components of a number of diseases affecting the CNS. A number of studies indicate hypoxia or inflammatory pain increase BBB paracellular permeability, induce changes in the expression and/or localization of tight junction proteins, and affect CNS drug uptake. In this review, we look at what is currently known with regard to BBB disruption following a hypoxic or inflammatory insult in vivo. Potential mechanisms involved in altering tight junction components at the BBB are also discussed. A more detailed understanding of the mediators involved in changing BBB functional integrity in response to hypoxia or inflammatory pain could potentially lead to new treatments for CNS diseases with hypoxic or inflammatory components. Additionally, greater insight into the mechanisms involved in TJ rearrangement at the BBB may lead to novel strategies to pharmacologically increase delivery of drugs to the CNS.

A novel immunotoxin reveals a new role for CD321 in endothelial cells

PubMed Central

Kim, Jia; Hokaiwado, Shintaro; Nawa, Makiko; Okamoto, Hayato; Kogiso, Tomohiko; Watabe, Tetsuro; Hattori, Nobutaka

2017-01-01

There are currently several antibody therapies that directly target tumors, and antibody-drug conjugates represent a novel moiety as next generation therapeutics. Here, we used a unique screening probe, DT3C, to identify functional antibodies that recognized surface molecules and functional epitopes, and which provided toxin delivery capability. Accordingly, we generated the 90G4 antibody, which induced DT3C-dependent cytotoxicity in endothelial cells. Molecular analysis revealed that 90G4 recognized CD321, a protein localized at tight junctions. Although CD321 plays a pivotal role in inflammation and lymphocyte trans-endothelial migration, little is known about its mechanism of action in endothelial cells. Targeting of CD321 by the 90G4 immunotoxin induced cell death. Moreover, 90G4 immunotoxin caused cytotoxicity primarily in migratory endothelial cells, but not in those forming sheets, suggesting a critical role for CD321 in tumor angiogenesis. We also found that hypoxia triggered redistribution of CD321 to a punctate localization on the basal side of cells, resulting in functional impairment of tight junctions and increased motility. Thus, our findings raise the intriguing possibility that endothelial CD321 presented cellular localization in tight junction as well as multifunctional dynamics in several conditions, leading to illuminate the importance of widely-expressed CD321 as a potential target for antitumor therapy. PMID:29028806

Cosmology and astrophysics from relaxed galaxy clusters - III. Thermodynamic profiles and scaling relations

NASA Astrophysics Data System (ADS)

Mantz, A. B.; Allen, S. W.; Morris, R. G.; Schmidt, R. W.

2016-03-01

This is the third in a series of papers studying the astrophysics and cosmology of massive, dynamically relaxed galaxy clusters. Our sample comprises 40 clusters identified as being dynamically relaxed and hot (I.e. massive) in Papers I and II of this series. Here we consider the thermodynamics of the intracluster medium, in particular the profiles of density, temperature and related quantities, as well as integrated measurements of gas mass, average temperature, total luminosity and centre-excluded luminosity. We fit power-law scaling relations of each of these quantities as a function of redshift and cluster mass, which can be measured precisely and with minimal bias for these relaxed clusters using hydrostatic arguments. For the thermodynamic profiles, we jointly model the density and temperature and their intrinsic scatter as a function of radius, thus also capturing the behaviour of the gas pressure and entropy. For the integrated quantities, we also jointly fit a multidimensional intrinsic covariance. Our results reinforce the view that simple hydrodynamical models provide a good description of relaxed clusters outside their centres, but that additional heating and cooling processes are important in the inner regions (radii r ≲ 0.5 r2500 ≈ 0.15 r500). The thermodynamic profiles remain regular, with small intrinsic scatter, down to the smallest radii where deprojection is straightforward (˜20 kpc); within this radius, even the most relaxed systems show clear departures from spherical symmetry. Our results suggest that heating and cooling are continuously regulated in a tight feedback loop, allowing the cluster atmosphere to remain stratified on these scales.

Acene-modified triphenylamine dyes for dye-sensitized solar cells: a computational study.

PubMed

Fan, Wenjie; Tan, Dazhi; Deng, Wei-Qiao

2012-06-04

A series of metal-free acene-modified triphenylamine dyes (benzene to pentacene, denoted as TPA-AC1 to TPA-AC5) are investigated as organic sensitizers for application in dye-sensitized solar cells (DSSCs). A combination of density functional theory (DFT), density functional tight-binding (DFTB), and time-dependent DFT (TDDFT) approaches is employed. The effects of acene units on the spectra and electrochemical properties of the acene-modified TPA organic dyes are demonstrated. The dye/(TiO(2))(46) anatase nanoparticle systems are also simulated to show the electronic structures at the interface. The results show that from TPA-AC1 to TPA-AC5 with increasing sizes of the acenes, the absorption and fluorescence spectra are systematically broadened and red-shifted, but the oscillator strength and electron injection properties are reduced. The molecular orbital contributions show increasing localization on the bridging acene units from TPA-AC1 to TPA-AC5. From the theoretical examination of some key parameters including free enthalpy related to the electron injection, light-harvesting efficiency, and the shift of semiconductor conduction band, TPA-AC3 with an anthracene moiety demonstrates a balance of the above crucial factors. TPA-AC3 is expected to be a promising dye with desirable energetic and spectroscopic parameters in the DSSC field, which is consistent with recent experimental work. This study is expected to deepen our understanding of TPA-based organic dyes and assist the molecular design of new metal-free dyes for the further optimization of DSSCs. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

First-principles modeling of the thermoelectric properties of SrTiO3/SrRuO3 superlattices

NASA Astrophysics Data System (ADS)

García-Fernández, Pablo; Verissimo-Alves, Marcos; Bilc, Daniel I.; Ghosez, Philippe; Junquera, Javier

2012-08-01

Using a combination of first-principles simulations, based on density functional theory and Boltzmann's semiclassical theory, we have calculated the transport and thermoelectric properties of the half-metallic two-dimensional electron gas confined in single SrRuO3 layers of SrTiO3/SrRuO3 periodic superlattices. Close to the Fermi energy, we find that the semiconducting majority-spin channel displays a very large in-plane component of the Seebeck tensor at room temperature, S˜ 1500 μV/K, and the minority-spin channel shows good in-plane conductivity, σ=2.5 (mΩ cm)-1. However, we find that the total power factor and thermoelectric figure of merit for reduced doping is too small for practical applications. Our results support that the confinement of the electronic motion is not the only thing that matters to describe the main features of the transport and thermoelectric properties with respect the chemical doping, but the shape of the electronic density of states, which in our case departs from the free-electron behavior, is also important. The evolution of the electronic structure, electrical conductivity, Seebeck coefficient, and power factor as a function of the chemical potential is explained by a simplified tight-binding model. We find that the electron gas in our system is composed by a pair of one-dimensional electron gases orthogonal to each other. This reflects the fact the physical dimensionality of the electronic system (1D) can be even smaller than that of the spacial confinement of the carriers (2D).

Could tight junctions regulate the barrier function of the aged skin?

PubMed

Svoboda, Marek; Bílková, Zuzana; Muthný, Tomáš

2016-03-01

The skin is known to be the largest organ in human organism creating interface with outer environment. The skin provides protective barrier against pathogens, physical and chemical insults, and against uncontrolled loss of water. The barrier function was primarily attributed to the stratum corneum (SC) but recent studies confirmed that epidermal tight junctions (TJs) also play important role in maintaining barrier properties of the skin. Independent observations indicate that barrier function and its recovery is impaired in aged skin. However, trans-epidermal water loss (TEWL) values remains rather unchanged in elderly population. UV radiation as major factor of photoageing impairs TJ proteins, but TJs have great self-regenerative potential. Since it may be possible that TJs can compensate TEWL in elderly due to its regenerative and compensatory capabilities, important question remains to be answered: how are TJs regulated during skin ageing? This review provides an insight into TJs functioning as epidermal barrier and summarizes current knowledge about the impact of ageing on the barrier function of the skin and epidermal TJs. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Tunable molecular plasmons in polycyclic aromatic hydrocarbons.

PubMed

Manjavacas, Alejandro; Marchesin, Federico; Thongrattanasiri, Sukosin; Koval, Peter; Nordlander, Peter; Sánchez-Portal, Daniel; García de Abajo, F Javier

2013-04-23

We show that chemically synthesized polycyclic aromatic hydrocarbons (PAHs) exhibit molecular plasmon resonances that are remarkably sensitive to the net charge state of the molecule and the atomic structure of the edges. These molecules can be regarded as nanometer-sized forms of graphene, from which they inherit their high electrical tunability. Specifically, the addition or removal of a single electron switches on/off these molecular plasmons. Our first-principles time-dependent density-functional theory (TDDFT) calculations are in good agreement with a simpler tight-binding approach that can be easily extended to much larger systems. These fundamental insights enable the development of novel plasmonic devices based upon chemically available molecules, which, unlike colloidal or lithographic nanostructures, are free from structural imperfections. We further show a strong interaction between plasmons in neighboring molecules, quantified in significant energy shifts and field enhancement, and enabling molecular-based plasmonic designs. Our findings suggest new paradigms for electro-optical modulation and switching, single-electron detection, and sensing using individual molecules.

Strong interlayer coupling in phosphorene/graphene van der Waals heterostructure: A first-principles investigation

NASA Astrophysics Data System (ADS)

Hu, Xue-Rong; Zheng, Ji-Ming; Ren, Zhao-Yu

2018-04-01

Based on first-principles calculations within the framework of density functional theory, we study the electronic properties of phosphorene/graphene heterostructures. Band gaps with different sizes are observed in the heterostructure, and charges transfer from graphene to phosphorene, causing the Fermi level of the heterostructure to shift downward with respect to the Dirac point of graphene. Significantly, strong coupling between two layers is discovered in the band spectrum even though it has a van der Waals heterostructure. A tight-binding Hamiltonian model is used to reveal that the resonance of the Bloch states between the phosphorene and graphene layers in certain K points combines with the symmetry matching between band states, which explains the reason for the strong coupling in such heterostructures. This work may enhance the understanding of interlayer interaction and composition mechanisms in van der Waals heterostructures consisting of two-dimensional layered nanomaterials, and may indicate potential reference information for nanoelectronic and optoelectronic applications.

The role of solitons on the tunneling magnetoresistance through a double-stranded DNA molecule

NASA Astrophysics Data System (ADS)

Ashhadi, M.

2018-07-01

We have studied the role of solitons on the spin-dependent transport properties of through a double-stranded DNA (dsDNA) molecule attached to two the semi-infinite ferromagnetic (FM) electrodes. The work is based on a tight-binding Hamiltonian model within the framework of a generalized Green's function technique and relies on the Landauer-Bütikker formalism as the basis for studying the current-voltage characteristic of this system. The conductance properties of the spin system are studied for a ladder model for poly (dG)-poly (dC) DNA molecule. Our calculations indicate that the presence of a homogeneous distribution of the solitons along the molecular, as a sublattice of the correlated solitons, gives rise to significant enhancement in the density of states within the bandgap and large enhancement in conductance and the current-voltage characteristic. It is also shown that tunnel magnetoresistance (TMR) decreases in compared with TMR obtained in the absence of solitons.

Fragmentation network of doubly charged methionine: Interpretation using graph theory

NASA Astrophysics Data System (ADS)

Ha, D. T.; Yamazaki, K.; Wang, Y.; Alcamí, M.; Maeda, S.; Kono, H.; Martín, F.; Kukk, E.

2016-09-01

The fragmentation of doubly charged gas-phase methionine (HO2CCH(NH2)CH2CH2SCH3) is systematically studied using the self-consistent charge density functional tight-binding molecular dynamics (MD) simulation method. We applied graph theory to analyze the large number of the calculated MD trajectories, which appears to be a highly effective and convenient means of extracting versatile information from the large data. The present theoretical results strongly concur with the earlier studied experimental ones. Essentially, the dication dissociates into acidic group CO2H and basic group C4NSH10. The former may carry a single or no charge and stays intact in most cases, whereas the latter may hold either a single or a double charge and tends to dissociate into smaller fragments. The decay of the basic group is observed to follow the Arrhenius law. The dissociation pathways to CO2H and C4NSH10 and subsequent fragmentations are also supported by ab initio calculations.

Structural, electronic properties and stability of metatitanic acid (H 2TiO 3) nanotubes

NASA Astrophysics Data System (ADS)

Enyashin, A. N.; Denisova, T. A.; Ivanovskii, A. L.

2009-12-01

Quite recently, metatitanic acid (H 2TiO 3) has been successfully prepared, which extended the family of known titanic acids H 2Ti nO 2n+1 ( n = 2, 3 and 4). Here the atomic models for nanotubes (NTs) of metatitanic acid are designed and their cohesive and electronic properties are considered depending on their chirality and radii by means of density-functional theory-tight-binding (DFTB) method. Our main findings are that the proposed H 2TiO 3 tubes are stable and that all these NTs will be the insulators (independently from their chirality and the diameters) with forbidden gaps at about ˜4.6 eV. We have found also that aforementioned properties of predicted H 2TiO 3 NTs are very similar with those of recently prepared fabricated nanotubes of polytitanic acids; thus, it is possible to expect that the proposed H 2TiO 3 tubular materials may be fabricated.

Specific arrangement of alpha-helical coiled coils in the core domain of the bacterial flagellar hook for the universal joint function.

PubMed

Fujii, Takashi; Kato, Takayuki; Namba, Keiichi

2009-11-11

The bacterial flagellar hook is a short, highly curved tubular structure connecting the rotary motor to the filament acting as a helical propeller. The bending flexibility of the hook allows it to work as a universal joint. A partial atomic model of the hook revealed a sliding intersubunit domain interaction along the protofilament to produce bending flexibility. However, it remained unclear how the tightly packed inner core domains can still permit axial extension and compression. We report advances in cryoEM image analysis for high-resolution, high-throughput structural analysis and a density map of the hook that reveals most of the secondary structures, including the terminal alpha helices forming a coiled coil. The orientations and axial packing interactions of these two alpha helices are distinctly different from those of the filament, allowing them to have a room for axial compression and extension for bending flexibility without impairing the mechanical stability of the hook.

Chemical control of orbital polarization in artificially structured transition-metal oxides: La2NiXO6 (X=B,Al,Ga,In) from first principles

NASA Astrophysics Data System (ADS)

Han, M. J.; Marianetti, C. A.; Millis, A. J.

2010-10-01

The application of modern layer-by-layer growth techniques to transition-metal oxide materials raises the possibility of creating new classes of materials with rationally designed correlated electron properties. An important step toward this goal is the demonstration that electronic structure can be controlled by atomic composition. In compounds with partially occupied transition-metal d shells, one important aspect of the electronic structure is the relative occupancy of different d orbitals. Previous work has established that strain and quantum confinement can be used to influence orbital occupancy. In this paper we demonstrate a different modality for orbital control in transition-metal oxide heterostructures, using density-functional band calculations supplemented by a tight-binding analysis to show that the choice of nontransition-metal counterion X in transition-metal oxide heterostructures composed of alternating LaNiO3 and LaXO3 units strongly affects orbital occupancy, changing the magnitude and in some cases the sign of the orbital polarization.

Engineering and manipulating exciton wave packets

NASA Astrophysics Data System (ADS)

Zang, Xiaoning; Montangero, Simone; Carr, Lincoln D.; Lusk, Mark T.

2017-05-01

When a semiconductor absorbs light, the resulting electron-hole superposition amounts to a uncontrolled quantum ripple that eventually degenerates into diffusion. If the conformation of these excitonic superpositions could be engineered, though, they would constitute a new means of transporting information and energy. We show that properly designed laser pulses can be used to create such excitonic wave packets. They can be formed with a prescribed speed, direction, and spectral make-up that allows them to be selectively passed, rejected, or even dissociated using superlattices. Their coherence also provides a handle for manipulation using active, external controls. Energy and information can be conveniently processed and subsequently removed at a distant site by reversing the original procedure to produce a stimulated emission. The ability to create, manage, and remove structured excitons comprises the foundation for optoexcitonic circuits with application to a wide range of quantum information, energy, and light-flow technologies. The paradigm is demonstrated using both tight-binding and time-domain density functional theory simulations.

Electronic and magnetic behaviors of B, N, and 3d transition metal substitutions in germanium carbide monolayer

NASA Astrophysics Data System (ADS)

Xu, Zhuo; Li, Yangping; Liu, Zhengtang; Liu, Shengzhong (Frank)

2018-04-01

The structural, electronic, and magnetic behaviors of two-dimensional GeC (2D-GeC) with single vacancy, substitutional B, N, and 3d transition metal atoms (Sc, Ti, V, Cr, Mn, Fe, Co, and Ni) are investigated based on the density functional theory. These impurities are tightly bonded to the surrounding atoms and found energetically more favorable at Ge sub-lattice site. In addition, the electronic band structures and magnetic properties of the doped systems indicate that (i) tunable electronic structures and magnetic moments of 2D-GeC can be obtained depending on different dopant species and sub-lattice sites, (ii) systems such as VC@Sc, VC@Fe, VC@Co, VGe@Fe, and VGe@Co are found to be half-metals, while the other systems all show semiconductor behavior. Simple models of the impurity-vacancy interaction is put forwards to illustrate the origin of the electronic structures and magnetic moments.

A global reaction route mapping-based kinetic Monte Carlo algorithm

NASA Astrophysics Data System (ADS)

Mitchell, Izaac; Irle, Stephan; Page, Alister J.

2016-07-01

We propose a new on-the-fly kinetic Monte Carlo (KMC) method that is based on exhaustive potential energy surface searching carried out with the global reaction route mapping (GRRM) algorithm. Starting from any given equilibrium state, this GRRM-KMC algorithm performs a one-step GRRM search to identify all surrounding transition states. Intrinsic reaction coordinate pathways are then calculated to identify potential subsequent equilibrium states. Harmonic transition state theory is used to calculate rate constants for all potential pathways, before a standard KMC accept/reject selection is performed. The selected pathway is then used to propagate the system forward in time, which is calculated on the basis of 1st order kinetics. The GRRM-KMC algorithm is validated here in two challenging contexts: intramolecular proton transfer in malonaldehyde and surface carbon diffusion on an iron nanoparticle. We demonstrate that in both cases the GRRM-KMC method is capable of reproducing the 1st order kinetics observed during independent quantum chemical molecular dynamics simulations using the density-functional tight-binding potential.

Twisted molecular excitons as mediators for changing the angular momentum of light

NASA Astrophysics Data System (ADS)

Zang, Xiaoning; Lusk, Mark T.

2017-07-01

Molecules with CN or CN h symmetry can absorb quanta of optical angular momentum to generate twisted excitons with well-defined quasiangular momenta of their own. Angular momentum is conserved in such interactions at the level of a paraxial approximation for the light beam. A sequence of absorption events can thus be used to create a range of excitonic angular momenta. Subsequent decay can produce radiation with a single angular momentum equal to that accumulated. Such molecules can thus be viewed as mediators for changing the angular momentum of light. This sidesteps the need to exploit nonlinear light-matter interactions based on higher-order susceptibilities. A tight-binding paradigm is used to verify angular momentum conservation and demonstrate how it can be exploited to change the angular momentum of light. The approach is then extended to a time-dependent density functional theory setting where the key results are shown to hold in a many-body, multilevel setting.

A high-throughput screening approach for the optoelectronic properties of conjugated polymers.

PubMed

Wilbraham, Liam; Berardo, Enrico; Turcani, Lukas; Jelfs, Kim E; Zwijnenburg, Martijn A

2018-06-25

We propose a general high-throughput virtual screening approach for the optical and electronic properties of conjugated polymers. This approach makes use of the recently developed xTB family of low-computational-cost density functional tight-binding methods from Grimme and co-workers, calibrated here to (TD-)DFT data computed for a representative diverse set of (co-)polymers. Parameters drawn from the resulting calibration using a linear model can then be applied to the xTB derived results for new polymers, thus generating near DFT-quality data with orders of magnitude reduction in computational cost. As a result, after an initial computational investment for calibration, this approach can be used to quickly and accurately screen on the order of thousands of polymers for target applications. We also demonstrate that the (opto)electronic properties of the conjugated polymers show only a very minor variation when considering different conformers and that the results of high-throughput screening are therefore expected to be relatively insensitive with respect to the conformer search methodology applied.

Enhanced thermopower in ZnO two-dimensional electron gas

PubMed Central

Shimizu, Sunao; Bahramy, Mohammad Saeed; Iizuka, Takahiko; Ono, Shimpei; Miwa, Kazumoto; Tokura, Yoshinori; Iwasa, Yoshihiro

2016-01-01

Control of dimensionality has proven to be an effective way to manipulate the electronic properties of materials, thereby enabling exotic quantum phenomena, such as superconductivity, quantum Hall effects, and valleytronic effects. Another example is thermoelectricity, which has been theoretically proposed to be favorably controllable by reducing the dimensionality. Here, we verify this proposal by performing a systematic study on a gate-tuned 2D electron gas (2DEG) system formed at the surface of ZnO. Combining state-of-the-art electric-double-layer transistor experiments and realistic tight-binding calculations, we show that, for a wide range of carrier densities, the 2DEG channel comprises a single subband, and its effective thickness can be reduced to ∼ 1 nm at sufficiently high gate biases. We also demonstrate that the thermoelectric performance of the 2DEG region is significantly higher than that of bulk ZnO. Our approach opens up a route to exploit the peculiar behavior of 2DEG electronic states and realize thermoelectric devices with advanced functionalities. PMID:27222585

Dissipative time-dependent quantum transport theory.

PubMed

Zhang, Yu; Yam, Chi Yung; Chen, GuanHua

2013-04-28

A dissipative time-dependent quantum transport theory is developed to treat the transient current through molecular or nanoscopic devices in presence of electron-phonon interaction. The dissipation via phonon is taken into account by introducing a self-energy for the electron-phonon coupling in addition to the self-energy caused by the electrodes. Based on this, a numerical method is proposed. For practical implementation, the lowest order expansion is employed for the weak electron-phonon coupling case and the wide-band limit approximation is adopted for device and electrodes coupling. The corresponding hierarchical equation of motion is derived, which leads to an efficient and accurate time-dependent treatment of inelastic effect on transport for the weak electron-phonon interaction. The resulting method is applied to a one-level model system and a gold wire described by tight-binding model to demonstrate its validity and the importance of electron-phonon interaction for the quantum transport. As it is based on the effective single-electron model, the method can be readily extended to time-dependent density functional theory.

Insulator-semimetallic transition in quasi-1D charged impurity-infected armchair boron-nitride nanoribbons

NASA Astrophysics Data System (ADS)

Dinh Hoi, Bui; Yarmohammadi, Mohsen

2018-04-01

We address control of electronic phase transition in charged impurity-infected armchair-edged boron-nitride nanoribbons (ABNNRs) with the local variation of Fermi energy. In particular, the density of states of disordered ribbons produces the main features in the context of pretty simple tight-binding model and Green's functions approach. To this end, the Born approximation has been implemented to find the effect of π-band electron-impurity interactions. A modulation of the π-band depending on the impurity concentrations and scattering potentials leads to the phase transition from insulator to semimetallic. We present here a detailed physical meaning of this transition by studying the treatment of massive Dirac fermions. From our findings, it is found that the ribbon width plays a crucial role in determining the electronic phase of disordered ABNNRs. The obtained results in controllable gap engineering are useful for future experiments. Also, the observations in this study have also fueled interest in the electronic properties of other 2D materials.

A global reaction route mapping-based kinetic Monte Carlo algorithm.

PubMed

Mitchell, Izaac; Irle, Stephan; Page, Alister J

2016-07-14

We propose a new on-the-fly kinetic Monte Carlo (KMC) method that is based on exhaustive potential energy surface searching carried out with the global reaction route mapping (GRRM) algorithm. Starting from any given equilibrium state, this GRRM-KMC algorithm performs a one-step GRRM search to identify all surrounding transition states. Intrinsic reaction coordinate pathways are then calculated to identify potential subsequent equilibrium states. Harmonic transition state theory is used to calculate rate constants for all potential pathways, before a standard KMC accept/reject selection is performed. The selected pathway is then used to propagate the system forward in time, which is calculated on the basis of 1st order kinetics. The GRRM-KMC algorithm is validated here in two challenging contexts: intramolecular proton transfer in malonaldehyde and surface carbon diffusion on an iron nanoparticle. We demonstrate that in both cases the GRRM-KMC method is capable of reproducing the 1st order kinetics observed during independent quantum chemical molecular dynamics simulations using the density-functional tight-binding potential.

Chemisorption of hydrogen atoms and hydroxyl groups on stretched graphene: A coupled QM/QM study

NASA Astrophysics Data System (ADS)

Katin, Konstantin P.; Prudkovskiy, Vladimir S.; Maslov, Mikhail M.

2017-09-01

Using the density functional theory coupled with the nonorthogonal tight-binding model, we analyze the chemisorption of hydrogen atoms and hydroxyl groups on the unstrained and stretched graphene sheets. Drawback of finite cluster model of graphene for the chemisorption energy calculation in comparison with the QM/QM approach applied is discussed. It is shown that the chemisorption energy for the hydroxyl group is sufficiently lower than for hydrogen at stretching up to 7.5%. The simultaneous paired chemisorption of hydrogen and hydroxyl groups on the same hexagon has also been examined. Adsorption of two radicals in ortho and para positions is found to be more energetically favorable than those in meta position at any stretching considered. In addition the energy difference between adsorbent pairs in ortho and para positions decreases as the stretching rises. It could be concluded that the graphene stretching leads to the loss of preferred mutual arrangement of two radicals on its surface.

Angular momentum transport with twisted exciton wave packets

NASA Astrophysics Data System (ADS)

Zang, Xiaoning; Lusk, Mark T.

2017-10-01

A chain of cofacial molecules with CN or CN h symmetry supports excitonic states with a screwlike structure. These can be quantified with the combination of an axial wave number and an azimuthal winding number. Combinations of these states can be used to construct excitonic wave packets that spiral down the chain with well-determined linear and angular momenta. These twisted exciton wave packets can be created and annihilated using laser pulses, and their angular momentum can be optically modified during transit. This allows for the creation of optoexcitonic circuits in which information, encoded in the angular momentum of light, is converted into excitonic wave packets that can be manipulated, transported, and then reemitted. A tight-binding paradigm is used to demonstrate the key ideas. The approach is then extended to quantify the evolution of twisted exciton wave packets in a many-body, multilevel time-domain density functional theory setting. In both settings, numerical methods are developed that allow the site-to-site transfer of angular momentum to be quantified.

Nature of a single doped hole in two-leg Hubbard and t - J ladders

DOE PAGES

Liu, Shenxiu; Jiang, Hong -Chen; Devereaux, Thomas P.

2016-10-15

In this study, we have systematically studied the single-hole problem in two-leg Hubbard and t–J ladders by large-scale density-matrix renormalization-group calculations. We found that the doped holes in both models behave similarly, while the three-site correlated hopping term is not important in determining the ground-state properties. For more insights, we have also calculated the elementary excitations, i.e., the energy gaps to the excited states of the system. In the strong-rung limit, we found that the doped hole behaves as a Bloch quasiparticle in both systems where the spin and charge of the doped hole are tightly bound together. In themore » isotropic limit, while the hole still behaves like a quasiparticle in the long-wavelength limit, our results show that its spin and charge components are only loosely bound together inside the quasiparticle, whose internal structure can lead to a visible residual effect which dramatically changes the local structure of the ground-state wave function.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Shenxiu; Jiang, Hong -Chen; Devereaux, Thomas P.

In this study, we have systematically studied the single-hole problem in two-leg Hubbard and t–J ladders by large-scale density-matrix renormalization-group calculations. We found that the doped holes in both models behave similarly, while the three-site correlated hopping term is not important in determining the ground-state properties. For more insights, we have also calculated the elementary excitations, i.e., the energy gaps to the excited states of the system. In the strong-rung limit, we found that the doped hole behaves as a Bloch quasiparticle in both systems where the spin and charge of the doped hole are tightly bound together. In themore » isotropic limit, while the hole still behaves like a quasiparticle in the long-wavelength limit, our results show that its spin and charge components are only loosely bound together inside the quasiparticle, whose internal structure can lead to a visible residual effect which dramatically changes the local structure of the ground-state wave function.« less

Genome-Wide Reprogramming of Transcript Architecture by Temperature Specifies the Developmental States of the Human Pathogen Histoplasma

PubMed Central

Gilmore, Sarah A.; Voorhies, Mark; Gebhart, Dana; Sil, Anita

2015-01-01

Eukaryotic cells integrate layers of gene regulation to coordinate complex cellular processes; however, mechanisms of post-transcriptional gene regulation remain poorly studied. The human fungal pathogen Histoplasma capsulatum (Hc) responds to environmental or host temperature by initiating unique transcriptional programs to specify multicellular (hyphae) or unicellular (yeast) developmental states that function in infectivity or pathogenesis, respectively. Here we used recent advances in next-generation sequencing to uncover a novel re-programming of transcript length between Hc developmental cell types. We found that ~2% percent of Hc transcripts exhibit 5’ leader sequences that differ markedly in length between morphogenetic states. Ribosome density and mRNA abundance measurements of differential leader transcripts revealed nuanced transcriptional and translational regulation. One such class of regulated longer leader transcripts exhibited tight transcriptional and translational repression. Further examination of these dually repressed genes revealed that some control Hc morphology and that their strict regulation is necessary for the pathogen to make appropriate developmental decisions in response to temperature. PMID:26177267

Origin of the Surface-Induced First Hyperpolarizability in the C60/SiO2 System: SCC-DFTB Insight.

PubMed

Nénon, Sébastien; Champagne, Benoît

2014-01-02

Using the self-consistent charge density functional tight binding (SCC-DFTB) method, C60 molecules physisorbed on an α-quartz slab are shown to display a first hyperpolarizability, whereas, owing to their symmetry, both the α-quartz slab and C60 molecule have no first hyperpolarizabilities. A larger first hyperpolarizability is achieved when the lowest-lying (five- or six-membered) ring is situated in between two hydroxyl rows, rather than on top, because this situation favors orbital overlaps and charge transfer. Further analysis has demonstrated that (i) the first hyperpolarizability originates from the MO overlap and field-induced charge transfers from the neighboring substrate/adsorbate moieties but not to geometric relaxation of the C60 molecules at the interface and that (ii) larger first hyperpolarizabilities are associated with low surface coverage and with small distances between C60 and the surface. This contribution is a clear illustration of the emergence of second-order nonlinear optical responses (first hyperpolarizability) as a result of breaking the centrosymmetry.

Diverse magnetic quantization in bilayer silicene

NASA Astrophysics Data System (ADS)

Do, Thi-Nga; Shih, Po-Hsin; Gumbs, Godfrey; Huang, Danhong; Chiu, Chih-Wei; Lin, Ming-Fa

2018-03-01

The generalized tight-binding model is developed to investigate the rich and unique electronic properties of A B -bt (bottom-top) bilayer silicene under uniform perpendicular electric and magnetic fields. The first pair of conduction and valence bands, with an observable energy gap, displays unusual energy dispersions. Each group of conduction/valence Landau levels (LLs) is further classified into four subgroups, i.e., the sublattice- and spin-dominated LL subgroups. The magnetic-field-dependent LL energy spectra exhibit irregular behavior corresponding to the critical points of the band structure. Moreover, the electric field can induce many LL anticrossings. The main features of the LLs are uncovered with many van Hove singularities in the density-of-states and nonuniform delta-function-like peaks in the magnetoabsorption spectra. The feature-rich magnetic quantization directly reflects the geometric symmetries, intralayer and interlayer atomic interactions, spin-orbital couplings, and field effects. The results of this work can be applied to novel designs of Si-based nanoelectronics and nanodevices with enhanced mobilities.

Genome-Wide Reprogramming of Transcript Architecture by Temperature Specifies the Developmental States of the Human Pathogen Histoplasma.

PubMed

Gilmore, Sarah A; Voorhies, Mark; Gebhart, Dana; Sil, Anita

2015-07-01

Eukaryotic cells integrate layers of gene regulation to coordinate complex cellular processes; however, mechanisms of post-transcriptional gene regulation remain poorly studied. The human fungal pathogen Histoplasma capsulatum (Hc) responds to environmental or host temperature by initiating unique transcriptional programs to specify multicellular (hyphae) or unicellular (yeast) developmental states that function in infectivity or pathogenesis, respectively. Here we used recent advances in next-generation sequencing to uncover a novel re-programming of transcript length between Hc developmental cell types. We found that ~2% percent of Hc transcripts exhibit 5' leader sequences that differ markedly in length between morphogenetic states. Ribosome density and mRNA abundance measurements of differential leader transcripts revealed nuanced transcriptional and translational regulation. One such class of regulated longer leader transcripts exhibited tight transcriptional and translational repression. Further examination of these dually repressed genes revealed that some control Hc morphology and that their strict regulation is necessary for the pathogen to make appropriate developmental decisions in response to temperature.

Intermediate band formation in a δ-doped like QW superlattices of GaAs/AlxGa1-xAs for solar cell design

NASA Astrophysics Data System (ADS)

Del Río-De Santiago, A.; Martínez-Orozco, J. C.; Rodríguez-Magdaleno, K. A.; Contreras-Solorio, D. A.; Rodríguez-Vargas, I.; Ungan, F.

2018-03-01

It is reported a numerical computation of the local density of states for a δ-doped like QW superlattices of AlxGa1-xAs, as a possible heterostructure that, being integrated into a solar cell device design, can provide an intermediate band of allowed states to assist the absorption of photons with lower energies than that of the energy gap of the solar-cell constituent materials. This work was performed using the nearest neighbors sp3s* tight-binding model including spin. The confining potential caused by the ionized donor impurities in δ-doped impurities seeding that was obtained analytically within the lines of the Thomas-Fermi approximation was reproduced here by the Al concentration x variation. This potential is considered as an external perturbation in the tight-binding methodology and it is included in the diagonal terms of the tight-binding Hamiltonian. Special attention is paid to the width of the intermediate band caused by the change in the considered aluminium concentration x, the inter-well distance between δ-doped like QW wells and the number of them in the superlattice. In general we can conclude that this kind of superlattices can be suitable for intermediate band formation for possible intermediate-band solar cell design.

Conductance signatures of electron confinement induced by strained nanobubbles in graphene

NASA Astrophysics Data System (ADS)

Bahamon, Dario A.; Qi, Zenan; Park, Harold S.; Pereira, Vitor M.; Campbell, David K.

2015-09-01

We investigate the impact of strained nanobubbles on the conductance characteristics of graphene nanoribbons using a combined molecular dynamics - tight-binding simulation scheme. We describe in detail how the conductance, density of states, and current density of zigzag or armchair graphene nanoribbons are modified by the presence of a nanobubble. In particular, we establish that low-energy electrons can be confined in the vicinity of or within the nanobubbles by the delicate interplay among the pseudomagnetic field pattern created by the shape of the bubble, mode mixing, and substrate interaction. The coupling between confined evanescent states and propagating modes can be enhanced under different clamping conditions, which translates into Fano resonances in the conductance traces.

Bond-order potential for magnetic body-centered-cubic iron and its transferability

NASA Astrophysics Data System (ADS)

Lin, Yi-Shen; Mrovec, M.; Vitek, V.

2016-06-01

We derived and thoroughly tested a bond-order potential (BOP) for body-centered-cubic (bcc) magnetic iron that can be employed in atomistic calculations of a broad variety of crystal defects that control structural, mechanical, and thermodynamic properties of this technologically important metal. The constructed BOP reflects correctly the mixed nearly free electron and covalent bonding arising from the partially filled d band as well as the ferromagnetism that is actually responsible for the stability of the bcc structure of iron at low temperatures. The covalent part of the cohesive energy is determined within the tight-binding bond model with the Green's function of the Schrödinger equation determined using the method of continued fractions terminated at a sufficient level of the moments of the density of states. This makes the BOP an O (N ) method usable for very large numbers of particles. Only d d bonds are included explicitly, but the effect of s electrons on the covalent energy is included via their screening of the corresponding d d bonds. The magnetic part of the cohesive energy is included using the Stoner model of itinerant magnetism. The repulsive part of the cohesive energy is represented, as in any tight-binding scheme, by an empirical formula. Its functional form is physically justified by studies of the repulsion in face-centered-cubic (fcc) solid argon under very high pressure where the repulsion originates from overlapping s and p closed-shell electrons just as it does from closed-shell s electrons in transition metals squeezed into the ion core under the influence of the large covalent d bonding. Testing of the transferability of the developed BOP to environments significantly different from those of the ideal bcc lattice was carried out by studying crystal structures and magnetic states alternative to the ferromagnetic bcc lattice, vacancies, divacancies, self-interstitial atoms (SIAs), paths continuously transforming the bcc structure to different less symmetric structures and phonons. The results of these calculations are compared with either experiments or calculations based on the density functional theory (DFT), and they all show very good agreement. Importantly, the lowest energy configuration of SIAs agrees with DFT calculations that show that it is an exception within bcc transition metals controlled by magnetism. Moreover, the migration energy of interstitials is significantly lower than that of vacancies, which is essential for correct analysis of the effects of irradiation. Finally, the core structure and glide of ½ <111 > screw dislocations that control the plastic flow in single crystals of bcc metals was explored. The results fully agree with available DFT based studies and with experimental observations of the slip geometry of bcc iron at low temperatures.

Usefulness of the convexity apparent hyperperfusion sign in 123I-iodoamphetamine brain perfusion SPECT for the diagnosis of idiopathic normal pressure hydrocephalus.

PubMed

Ohmichi, Takuma; Kondo, Masaki; Itsukage, Masahiro; Koizumi, Hidetaka; Matsushima, Shigenori; Kuriyama, Nagato; Ishii, Kazunari; Mori, Etsuro; Yamada, Kei; Mizuno, Toshiki; Tokuda, Takahiko

2018-03-16

OBJECTIVE The gold standard for the diagnosis of idiopathic normal pressure hydrocephalus (iNPH) is the CSF removal test. For elderly patients, however, a less invasive diagnostic method is required. On MRI, high-convexity tightness was reported to be an important finding for the diagnosis of iNPH. On SPECT, patients with iNPH often show hyperperfusion of the high-convexity area. The authors tested 2 hypotheses regarding the SPECT finding: 1) it is relative hyperperfusion reflecting the increased gray matter density of the convexity, and 2) it is useful for the diagnosis of iNPH. The authors termed the SPECT finding the convexity apparent hyperperfusion (CAPPAH) sign. METHODS Two clinical studies were conducted. In study 1, SPECT was performed for 20 patients suspected of having iNPH, and regional cerebral blood flow (rCBF) of the high-convexity area was examined using quantitative analysis. Clinical differences between patients with the CAPPAH sign (CAP) and those without it (NCAP) were also compared. In study 2, the CAPPAH sign was retrospectively assessed in 30 patients with iNPH and 19 healthy controls using SPECT images and 3D stereotactic surface projection. RESULTS In study 1, rCBF of the high-convexity area of the CAP group was calculated as 35.2-43.7 ml/min/100 g, which is not higher than normal values of rCBF determined by SPECT. The NCAP group showed lower cognitive function and weaker responses to the removal of CSF than the CAP group. In study 2, the CAPPAH sign was positive only in patients with iNPH (24/30) and not in controls (sensitivity 80%, specificity 100%). The coincidence rate between tight high convexity on MRI and the CAPPAH sign was very high (28/30). CONCLUSIONS Patients with iNPH showed hyperperfusion of the high-convexity area on SPECT; however, the presence of the CAPPAH sign did not indicate real hyperperfusion of rCBF in the high-convexity area. The authors speculated that patients with iNPH without the CAPPAH sign, despite showing tight high convexity on MRI, might have comorbidities such as Alzheimer's disease.

Decursin inhibits VEGF-mediated inner blood-retinal barrier breakdown by suppression of VEGFR-2 activation.

PubMed

Kim, Jin Hyoung; Kim, Jeong Hun; Lee, You Mie; Ahn, Eun-Mi; Kim, Kyu-Won; Yu, Young Suk

2009-09-01

The blood-retinal barrier (BRB) is essential for the normal structural and functional integrity of the retina, whose breakdown could cause the serious vision loss. Vascular endothelial growth factor (VEGF), as a permeable factor, induces alteration of tight junction proteins to result in BRB breakdown. Herein, we demonstrated that decursin inhibits VEGF-mediated inner BRB breakdown through suppression of VEGFR-2 signaling pathway. In retinal endothelial cells, decursin inhibited VEGF-mediated hyperpermeability. Decursin prevented VEGF-mediated loss of tight junction proteins including zonula occludens-1 (ZO-1), ZO-2, and occludin in retinal endothelial cells, which was also supported by restoration of tight junction proteins in intercellular junction. In addition, decursin significantly inhibited VEGF-mediated vascular leakage from retinal vessels, which was accompanied by prevention of loss of tight junction proteins in retinal vessels. Decursin significantly suppressed VEGF-induced VEGFR-2 phosphrylation that consequently led to inhibition of extracellular signal-regulated kinase (ERK) 1/2 activation. Moreover, decursin induced no cytotoxicity to retinal endothelial cells and no retinal toxicity under therapeutic concentrations. Therefore, our results suggest that decursin prevents VEGF-mediated BRB breakdown through blocking of loss of tight junction proteins, which might be regulated by suppression of VEGFR-2 activation. As a novel inhibitor to BRB breakdown, decursin could be applied to variable retinopathies with BRB breakdown.

Uropathogenic E. coli Promote a Paracellular Urothelial Barrier Defect Characterized by Altered Tight Junction Integrity, Epithelial Cell Sloughing and Cytokine Release

PubMed Central

Wood, M. W.; Breitschwerdt, E. B.; Nordone, S. K.; Linder, K. E.; Gookin, J. L.

2013-01-01

Summary The urinary bladder is a common site of bacterial infection with a majority of cases attributed to uropathogenic Escherichia coli. Sequels of urinary tract infections (UTIs) include the loss of urothelial barrier function and subsequent clinical morbidity secondary to the permeation of urine potassium, urea and ammonia into the subepithelium. To date there has been limited research describing the mechanism by which this urothelial permeability defect develops. The present study models acute uropathogenic E. coli infection in vitro using intact canine bladder mucosa mounted in Ussing chambers to determine whether infection induces primarily a transcellular or paracellular permeability defect. The Ussing chamber sustains tissue viability while physically separating submucosal and lumen influences, so this model is ideal for quantitative measurement of transepithelial electrical resistance (TER) to assess alterations of urothelial barrier function. Using this model, changes in both tissue ultrastructure and TER indicated that uropathogenic E. coli infection promotes a paracellular permeability defect associated with the failure of umbrella cell tight junction formation and umbrella cell sloughing. In addition, bacterial interaction with the urothelium promoted secretion of cytokines from the urinary bladder with bioactivity capable of modulating epithelial barrier function including tumour necrosis factor-α, interleukin (IL)-6 and IL-15. IL-15 secretion by the infected bladder mucosa is a novel finding and, because IL-15 plays key roles in reconstitution of tight junction function in damaged intestine, this study points to a potential role for IL-15 in UTI-induced urothelial injury. PMID:22014415

Do galaxy global relationships emerge from local ones? The SDSS IV MaNGA surface mass density-metallicity relation

NASA Astrophysics Data System (ADS)

Barrera-Ballesteros, Jorge K.; Heckman, Timothy M.; Zhu, Guangtun B.; Zakamska, Nadia L.; Sánchez, Sebastian F.; Law, David; Wake, David; Green, Jenny E.; Bizyaev, Dmitry; Oravetz, Daniel; Simmons, Audrey; Malanushenko, Elena; Pan, Kaike; Roman Lopes, Alexandre; Lane, Richard R.

2016-12-01

We present the stellar surface mass density versus gas metallicity (Σ*-Z) relation for more than 500 000 spatially resolved star-forming resolution elements (spaxels) from a sample of 653 disc galaxies included in the SDSS IV MaNGA survey. We find a tight relation between these local properties, with higher metallicities as the surface density increases. This relation extends over three orders of magnitude in the surface mass density and a factor of 4 in metallicity. We show that this local relationship can simultaneously reproduce two well-known properties of disc galaxies: their global mass-metallicity relationship and their radial metallicity gradients. We also find that the Σ*-Z relation is largely independent of the galaxy's total stellar mass and specific star formation rate (sSFR), except at low stellar mass and high sSFR. These results suggest that in the present-day universe local properties play a key role in determining the gas-phase metallicity in typical disc galaxies.

The complete influenza hemagglutinin fusion domain adopts a tight helical hairpin arrangement at the lipid:water interface.

PubMed

Lorieau, Justin L; Louis, John M; Bax, Ad

2010-06-22

All but five of the N-terminal 23 residues of the HA2 domain of the influenza virus glycoprotein hemagglutinin (HA) are strictly conserved across all 16 serotypes of HA genes. The structure and function of this HA2 fusion peptide (HAfp) continues to be the focus of extensive biophysical, computational, and functional analysis, but most of these analyses are of peptides that do not include the strictly conserved residues Trp(21)-Tyr(22)-Gly(23). The heteronuclear triple resonance NMR study reported here of full length HAfp of sero subtype H1, solubilized in dodecylphosphatidyl choline, reveals a remarkably tight helical hairpin structure, with its N-terminal alpha-helix (Gly(1)-Gly(12)) packed tightly against its second alpha-helix (Trp(14)-Gly(23)), with six of the seven conserved Gly residues at the interhelical interface. The seventh conserved Gly residue in position 13 adopts a positive angle, enabling the hairpin turn that links the two helices. The structure is stabilized by multiple interhelical C(alpha)H to C=O hydrogen bonds, characterized by strong interhelical H(N)-H(alpha) and H(alpha)-H(alpha) NOE contacts. Many of the previously identified mutations that make HA2 nonfusogenic are also incompatible with the tight antiparallel hairpin arrangement of the HAfp helices.(15)N relaxation analysis indicates the structure to be highly ordered on the nanosecond time scale, and NOE analysis indicates HAfp is located at the water-lipid interface, with its hydrophobic surface facing the lipid environment, and the Gly-rich side of the helix-helix interface exposed to solvent.

Genome-wide linkage mapping of QTL for black point reaction in bread wheat (Triticum aestivum L.).

PubMed

Liu, Jindong; He, Zhonghu; Wu, Ling; Bai, Bin; Wen, Weie; Xie, Chaojie; Xia, Xianchun

2016-11-01

Nine QTL for black point resistance in wheat were identified using a RIL population derived from a Linmai 2/Zhong 892 cross and 90K SNP assay. Black point, discoloration of the embryo end of the grain, downgrades wheat grain quality leading to significant economic losses to the wheat industry. The availability of molecular markers will accelerate improvement of black point resistance in wheat breeding. The aims of this study were to identify quantitative trait loci (QTL) for black point resistance and tightly linked molecular markers, and to search for candidate genes using a high-density genetic linkage map of wheat. A recombinant inbred line (RIL) population derived from the cross Linmai 2/Zhong 892 was evaluated for black point reaction during the 2011-2012, 2012-2013 and 2013-2014 cropping seasons, providing data for seven environments. A high-density linkage map was constructed by genotyping the RILs with the wheat 90K single nucleotide polymorphism (SNP) chip. Composite interval mapping detected nine QTL on chromosomes 2AL, 2BL, 3AL, 3BL, 5AS, 6A, 7AL (2) and 7BS, designated as QBp.caas-2AL, QBp.caas-2BL, QBp.caas-3AL, QBp.caas-3BL, QBp.caas-5AS, QBp.caas-6A, QBp.caas-7AL.1, QBp.caas-7AL.2 and QBp.caas-7BS, respectively. All resistance alleles, except for QBp.caas-7AL.1 from Linmai 2, were contributed by Zhong 892. QBp.caas-3BL, QBp.caas-5AS, QBp.caas-7AL.1, QBp.caas-7AL.2 and QBp.caas-7BS probably represent new loci for black point resistance. Sequences of tightly linked SNPs were used to survey wheat and related cereal genomes identifying three candidate genes for black point resistance. The tightly linked SNP markers can be used in marker-assisted breeding in combination with the kompetitive allele specific PCR technique to improve black point resistance.

Neutronic fuel element fabrication

DOEpatents

Korton, George

2004-02-24

This disclosure describes a method for metallurgically bonding a complete leak-tight enclosure to a matrix-type fuel element penetrated longitudinally by a multiplicity of coolant channels. Coolant tubes containing solid filler pins are disposed in the coolant channels. A leak-tight metal enclosure is then formed about the entire assembly of fuel matrix, coolant tubes and pins. The completely enclosed and sealed assembly is exposed to a high temperature and pressure gas environment to effect a metallurgical bond between all contacting surfaces therein. The ends of the assembly are then machined away to expose the pin ends which are chemically leached from the coolant tubes to leave the coolant tubes with internal coolant passageways. The invention described herein was made in the course of, or under, a contract with the U.S. Atomic Energy Commission. It relates generally to fuel elements for neutronic reactors and more particularly to a method for providing a leak-tight metal enclosure for a high-performance matrix-type fuel element penetrated longitudinally by a multiplicity of coolant tubes. The planned utilization of nuclear energy in high-performance, compact-propulsion and mobile power-generation systems has necessitated the development of fuel elements capable of operating at high power densities. High power densities in turn require fuel elements having high thermal conductivities and good fuel retention capabilities at high temperatures. A metal clad fuel element containing a ceramic phase of fuel intimately mixed with and bonded to a continuous refractory metal matrix has been found to satisfy the above requirements. Metal coolant tubes penetrate the matrix to afford internal cooling to the fuel element while providing positive fuel retention and containment of fission products generated within the fuel matrix. Metal header plates are bonded to the coolant tubes at each end of the fuel element and a metal cladding or can completes the fuel-matrix enclosure by encompassing the sides of the fuel element between the header plates.

Quantitative features in the computed tomography of healthy lungs.

PubMed Central

Fromson, B H; Denison, D M

1988-01-01

This study set out to determine whether quantitative features of lung computed tomography scans could be identified that would lead to a tightly defined normal range for use in assessing patients. Fourteen normal subjects with apparently healthy lungs were studied. A technique was developed for rapid and automatic extraction of lung field data from the computed tomography scans. The Hounsfield unit histograms were constructed and, when normalised for predicted lung volumes, shown to be consistent in shape for all the subjects. A three dimensional presentation of the data in the form of a "net plot" was devised, and from this a logarithmic relationship between the area of each lung slice and its mean density was derived (r = 0.9, n = 545, p less than 0.0001). The residual density, calculated as the difference between measured density and density predicted from the relationship with area, was shown to be normally distributed with a mean of 0 and a standard deviation of 25 Hounsfield units (chi 2 test: p less than 0.05). A presentation combining this residual density with the net plot is described. PMID:3353883

Axisymmetric Density Waves in Saturn's Rings

NASA Astrophysics Data System (ADS)

Hedman, Matthew; Nicholson, Philip

2018-04-01

Density waves in Saturn's rings are typically tightly wrapped spiral patterns generated by resonances with either Saturn's moons or structures inside the planet. However, between the Barnard and Bessel Gaps in the Cassini Division (i.e. between 120,240 and 120,300 km), there are density variations that appear to form an axisymmetric density wave, which consists of concentric regions of varying density that propagate radially through the rings. Such a wave requires some process that forces ring particles at all longitudes to pass through pericenter at the same time, and so cannot be generated by satellite resonances. Instead this particular wave appears to be excited by interference between a nearby satellite resonance and normal mode oscillations on the inner edge of the Barnard Gap. Similar axisymmetric waves may exist within the Dawes ringlet and the outermost part of the B ring, which are also just interior to resonantly confined edges that exhibit a large number of normal modes. These waves may therefore provide new insights into how resonant perturbations near an edge can propagate through a disk of material.

Syringomyelia

MedlinePlus

... are symptoms, they may include: Headache Loss of muscle mass ( wasting , atrophy), often in the arms and hands Spasms or tightness in the leg or hand and arm muscles Muscle function loss , loss of ability to use ...

Physiological roles of claudins in kidney tubule paracellular transport.

PubMed

Muto, Shigeaki

2017-01-01

The paracellular pathways in renal tubular epithelia such as the proximal tubules, which reabsorb the largest fraction of filtered solutes and water and are leaky epithelia, are important routes for transepithelial transport of solutes and water. Movement occurs passively via an extracellular route through the tight junction between cells. The characteristics of paracellular transport vary among different nephron segments with leaky or tighter epithelia. Claudins expressed at tight junctions form pores and barriers for paracellular transport. Claudins are from a multigene family, comprising at least 27 members in mammals. Multiple claudins are expressed at tight junctions of individual nephron segments in a nephron segment-specific manner. Over the last decade, there have been advances in our understanding of the structure and functions of claudins. This paper is a review of our current knowledge of claudins, with special emphasis on their physiological roles in proximal tubule paracellular solute and water transport. Copyright © 2017 the American Physiological Society.

The mechanism of transforming diamond nanowires to carbon nanostructures

NASA Astrophysics Data System (ADS)

Sorkin, Anastassia; Su, Haibin

2014-01-01

The transformation of diamond nanowires (DNWs) with different diameters and geometries upon heating is investigated with density-functional-based tight-binding molecular dynamics. DNWs of <100> and <111> oriented cross-section with projected average line density between 7 and 20 atoms Å-1 transform into carbon nanotubes (CNTs) under gradual heating up to 3500-4000 K. DNWs with projected average line density larger than 25 atoms Å-1 transform into double-wall CNTs. The route of transformation into CNTs clearly exhibits three stages, with the intriguing intermediate structural motif of a carbon nanoscroll (CNS). Moreover, the morphology plays an important role in the transformation involving the CNS as one important intermediate motif to form CNTs. When starting with \\langle \\bar {2}1 1\\rangle oriented DNWs with a square cross-section consisting of two {111} facets facing each other, one interesting structure with ‘nano-bookshelf’ shape emerges: a number of graphene ‘shelves’ located inside the CNT, bonding to the CNT walls with sp3 hybridized atoms. The nano-bookshelf structures exist in a wide range of temperatures up to 3000 K. The further transformation from nano-bookshelf structures depends on the strength of the joints connecting shelves with CNT walls. Notably, the nano-bookshelf structure can evolve into two end products: one is CNT via the CNS pathway, the other is graphene transformed directly from the nano-bookshelf structure at high temperature. This work sheds light on the microscopic insight of carbon nanostructure formation mechanisms with the featured motifs highlighted in the pathways.

Linear and non-linear bias: predictions versus measurements

NASA Astrophysics Data System (ADS)

Hoffmann, K.; Bel, J.; Gaztañaga, E.

2017-02-01

We study the linear and non-linear bias parameters which determine the mapping between the distributions of galaxies and the full matter density fields, comparing different measurements and predictions. Associating galaxies with dark matter haloes in the Marenostrum Institut de Ciències de l'Espai (MICE) Grand Challenge N-body simulation, we directly measure the bias parameters by comparing the smoothed density fluctuations of haloes and matter in the same region at different positions as a function of smoothing scale. Alternatively, we measure the bias parameters by matching the probability distributions of halo and matter density fluctuations, which can be applied to observations. These direct bias measurements are compared to corresponding measurements from two-point and different third-order correlations, as well as predictions from the peak-background model, which we presented in previous papers using the same data. We find an overall variation of the linear bias measurements and predictions of ˜5 per cent with respect to results from two-point correlations for different halo samples with masses between ˜1012and1015 h-1 M⊙ at the redshifts z = 0.0 and 0.5. Variations between the second- and third-order bias parameters from the different methods show larger variations, but with consistent trends in mass and redshift. The various bias measurements reveal a tight relation between the linear and the quadratic bias parameters, which is consistent with results from the literature based on simulations with different cosmologies. Such a universal relation might improve constraints on cosmological models, derived from second-order clustering statistics at small scales or higher order clustering statistics.

Drag reduction by Acinetobacter calcoaceticus BD4.

PubMed

Sar, N; Rosenberg, E

1987-09-01

The encapsulated bacterium Acinetobacter calcoaceticus BD4 at a density of 3.6 X 10(9) cells per ml reduced the friction of turbulent water in a narrow pipe by 55%. This drag reduction was due to the tightly bound polysaccharide capsules (0.4 mg per ml) of culture. Capsule-deficient mutants of BD4 failed to reduce drag. The cell-bound polysaccharide demonstrated a threefold-higher drag-reducing activity than the polymer which was free in solution.

Consequences of Femtosecond Laser Filament Generation Conditions in Standoff Laser Induced Breakdown Spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harilal, Sivanandan S.; Yeak, J.; Brumfield, Brian E.

2016-08-08

We investigate the role of femtosecond laser focusing conditions on ablation properties and its implications on analytical merits and standoff detection applications. Femtosecond laser pulses can be used for ablation either by tightly focusing or by using filaments generated during its propagation. We evaluated the persistence of atomic, and molecular emission features as well as time evolution of the fundamental properties (temperature and density) of ablation plumes generated using different methods.

Tight-Binding Approach to Computational Materials Science, Symposium Held December 1-3, 1997, Boston, Massachusetts, USA. Volume 491

DTIC Science & Technology

1998-01-01

to their large unit size and to experimental difficulties in determining geometries of carbon-based complex materials because of the weak X - ray ...qualitative relationship between the calculated local density of states and the experimental X - ray pho- toelectron spectra (XPS) and the Bremsstrahlung...from interaction schemes and allows complete data sets from different sources (neutron or X - ray diffraction, chemical constraints) to be fitted. In

Advantages and Challenges of 10-Gbps Transmission on High-Density Interconnect Boards

NASA Astrophysics Data System (ADS)

Yee, Chang Fei; Jambek, Asral Bahari; Al-Hadi, Azremi Abdullah

2016-06-01

This paper provides a brief introduction to high-density interconnect (HDI) technology and its implementation on printed circuit boards (PCBs). The advantages and challenges of implementing 10-Gbps signal transmission on high-density interconnect boards are discussed in detail. The advantages (e.g., smaller via dimension and via stub removal) and challenges (e.g., crosstalk due to smaller interpair separation) of HDI are studied by analyzing the S-parameter, time-domain reflectometry (TDR), and transmission-line eye diagrams obtained by three-dimensional electromagnetic modeling (3DEM) and two-dimensional electromagnetic modeling (2DEM) using Mentor Graphics HyperLynx and Keysight Advanced Design System (ADS) electronic computer-aided design (ECAD) software. HDI outperforms conventional PCB technology in terms of signal integrity, but proper routing topology should be applied to overcome the challenge posed by crosstalk due to the tight spacing between traces.

Dark energy in the dark ages

NASA Astrophysics Data System (ADS)

Linder, Eric V.

2006-08-01

Non-negligible dark energy density at high redshifts would indicate dark energy physics distinct from a cosmological constant or "reasonable" canonical scalar fields. Such dark energy can be constrained tightly through investigation of the growth of structure, with limits of ≲2% of total energy density at z ≫ 1 for many models. Intermediate dark energy can have effects distinct from its energy density; the dark ages acceleration can be constrained to last less than 5% of a Hubble e-fold time, exacerbating the coincidence problem. Both the total linear growth, or equivalently σ8, and the shape and evolution of the nonlinear mass power spectrum for z < 2 (using the Linder-White nonlinear mapping prescription) provide important windows. Probes of growth, such as weak gravitational lensing, can interact with supernovae and CMB distance measurements to scan dark energy behavior over the entire range z = 0-1100.

Ion/proton-conducting apparatus and method

DOEpatents

Yates, Matthew; Xue, Wei

2014-12-23

A c-axis-oriented HAP thin film synthesized by seeded growth on a palladium hydrogen membrane substrate. An exemplary synthetic process includes electrochemical seeding on the substrate, and secondary and tertiary hydrothermal treatments under conditions that favor growth along c-axes and a-axes in sequence. By adjusting corresponding synthetic conditions, an HAP this film can be grown to a controllable thickness with a dense coverage on the underlying substrate. The thin films have relatively high proton conductivity under hydrogen atmosphere and high temperature conditions. The c-axis oriented films may be integrated into fuel cells for application in the intermediate temperature range of 200-600.degree. C. The electrochemical-hydrothermal deposition technique may be applied to create other oriented crystal materials having optimized properties, useful for separations and catalysis as well as electronic and electrochemical applications, electrochemical membrane reactors, and in chemical sensors. Additional high-density and gas-tight HAP film compositions may be deposited using a two-step deposition method that includes an electrochemical deposition method followed by a hydrothermal deposition method. The two-step method uses a single hydrothermal deposition solution composition. The method may be used to deposit HAP films including but not limited to at least doped HAP films, and more particularly including carbonated HAP films. In addition, the high-density and gas-tight HAP films may be used in proton exchange membrane fuel cells.

Well test mathematical model for fractures network in tight oil reservoirs

NASA Astrophysics Data System (ADS)

Diwu, Pengxiang; Liu, Tongjing; Jiang, Baoyi; Wang, Rui; Yang, Peidie; Yang, Jiping; Wang, Zhaoming

2018-02-01

Well test, especially build-up test, has been applied widely in the development of tight oil reservoirs, since it is the only available low cost way to directly quantify flow ability and formation heterogeneity parameters. However, because of the fractures network near wellbore, generated from artificial fracturing linking up natural factures, traditional infinite and finite conductivity fracture models usually result in significantly deviation in field application. In this work, considering the random distribution of natural fractures, physical model of fractures network is proposed, and it shows a composite model feature in the large scale. Consequently, a nonhomogeneous composite mathematical model is established with threshold pressure gradient. To solve this model semi-analytically, we proposed a solution approach including Laplace transform and virtual argument Bessel function, and this method is verified by comparing with existing analytical solution. The matching data of typical type curves generated from semi-analytical solution indicates that the proposed physical and mathematical model can describe the type curves characteristic in typical tight oil reservoirs, which have up warping in late-term rather than parallel lines with slope 1/2 or 1/4. It means the composite model could be used into pressure interpretation of artificial fracturing wells in tight oil reservoir.

Manufactured aluminum oxide nanoparticles decrease expression of tight junction proteins in brain vasculature.

PubMed

Chen, Lei; Yokel, Robert A; Hennig, Bernhard; Toborek, Michal

2008-12-01

Manufactured nanoparticles of aluminum oxide (nano-alumina) have been widely used in the environment; however, their potential toxicity provides a growing concern for human health. The present study focuses on the hypothesis that nano-alumina can affect the blood-brain barrier and induce endothelial toxicity. In the first series of experiments, human brain microvascular endothelial cells (HBMEC) were exposed to alumina and control nanoparticles in dose- and time-responsive manners. Treatment with nano-alumina markedly reduced HBMEC viability, altered mitochondrial potential, increased cellular oxidation, and decreased tight junction protein expression as compared to control nanoparticles. Alterations of tight junction protein levels were prevented by cellular enrichment with glutathione. In the second series of experiments, rats were infused with nano-alumina at the dose of 29 mg/kg and the brains were stained for expression of tight junction proteins. Treatment with nano-alumina resulted in a marked fragmentation and disruption of integrity of claudin-5 and occludin. These results indicate that cerebral vasculature can be affected by nano-alumina. In addition, our data indicate that alterations of mitochondrial functions may be the underlying mechanism of nano-alumina toxicity.

Exciton-phonon cooperative mechanism of the triple-q charge-density-wave and antiferroelectric electron polarization in TiSe2

NASA Astrophysics Data System (ADS)

Kaneko, Tatsuya; Ohta, Yukinori; Yunoki, Seiji

2018-04-01

We investigate the microscopic mechanisms of the charge-density-wave (CDW) formation in a monolayer TiSe2 using a realistic multiorbital d -p model with electron-phonon coupling and intersite Coulomb (excitonic) interactions. First, we estimate the tight-binding bands of Ti 3 d and Se 4 p orbitals in the monolayer TiSe2 on the basis of the first-principles band-structure calculations. We thereby show orbital textures of the undistorted band structure near the Fermi level. Next, we derive the electron-phonon coupling using the tight-binding approximation and show that the softening occurs in the transverse phonon mode at the M point of the Brillouin zone. The stability of the triple-q CDW state is thus examined to show that the transverse phonon modes at the M1, M2, and M3 points are frozen simultaneously. Then, we introduce the intersite Coulomb interactions between the nearest-neighbor Ti and Se atoms that lead to the excitonic instability between the valence Se 4 p and conduction Ti 3 d bands. Treating the intersite Coulomb interactions in the mean-field approximation, we show that the electron-phonon and excitonic interactions cooperatively stabilize the triple-q CDW state in TiSe2. We also calculate a single-particle spectrum in the CDW state and reproduce the band folding spectra observed in photoemission spectroscopies. Finally, to clarify the nature of the CDW state, we examine the electronic charge density distribution and show that the CDW state in TiSe2 is of a bond type and induces a vortexlike antiferroelectric polarization in the kagome network of Ti atoms.

A UNIVERSAL NEUTRAL GAS PROFILE FOR NEARBY DISK GALAXIES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bigiel, F.; Blitz, L., E-mail: bigiel@uni-heidelberg.de

2012-09-10

Based on sensitive CO measurements from HERACLES and H I data from THINGS, we show that the azimuthally averaged radial distribution of the neutral gas surface density ({Sigma}{sub HI}+ {Sigma}{sub H2}) in 33 nearby spiral galaxies exhibits a well-constrained universal exponential distribution beyond 0.2 Multiplication-Sign r{sub 25} (inside of which the scatter is large) with less than a factor of two scatter out to two optical radii r{sub 25}. Scaling the radius to r{sub 25} and the total gas surface density to the surface density at the transition radius, i.e., where {Sigma}{sub HI} and {Sigma}{sub H2} are equal, as wellmore » as removing galaxies that are interacting with their environment, yields a tightly constrained exponential fit with average scale length 0.61 {+-} 0.06 r{sub 25}. In this case, the scatter reduces to less than 40% across the optical disks (and remains below a factor of two at larger radii). We show that the tight exponential distribution of neutral gas implies that the total neutral gas mass of nearby disk galaxies depends primarily on the size of the stellar disk (influenced to some degree by the great variability of {Sigma}{sub H2} inside 0.2 Multiplication-Sign r{sub 25}). The derived prescription predicts the total gas mass in our sub-sample of 17 non-interacting disk galaxies to within a factor of two. Given the short timescale over which star formation depletes the H{sub 2} content of these galaxies and the large range of r{sub 25} in our sample, there appears to be some mechanism leading to these largely self-similar radial gas distributions in nearby disk galaxies.« less

MicroRNA-205 targets tight junction-related proteins during urothelial cellular differentiation.

PubMed

Chung, Pei-Jung Katy; Chi, Lang-Ming; Chen, Chien-Lun; Liang, Chih-Lung; Lin, Chung-Tzu; Chang, Yu-Xun; Chen, Chun-Hsien; Chang, Yu-Sun

2014-09-01

The mammalian bladder urothelium classified as basal, intermediate, and terminally differentiated umbrella cells offers one of the most effective permeability barrier functions known to exist in nature because of the formation of apical uroplakin plaques and tight junctions. To improve our understanding of urothelial differentiation, we analyzed the microRNA (miRNA) expression profiles of mouse urinary tissues and by TaqMan miRNA analysis of microdissected urothelial layers and in situ miRNA-specific hybridization to determine the dependence of these miRNAs on the differentiation stage. Our in situ hybridization studies revealed that miR-205 was enriched in the undifferentiated basal and intermediate cell layers. We then used a quantitative proteomics approach to identify miR-205 target genes in primary cultured urothelial cells subjected to antagomir-mediated knockdown of specific miRNAs. Twenty-four genes were reproducibly regulated by miR-205; eleven of them were annotated as cell junction- and tight junction-related molecules. Western blot analysis demonstrated that antagomir-induced silencing of miR-205 in primary cultured urothelial cells elevated the expression levels of Tjp1, Cgnl1, and Cdc42. Ectopic expression of miR-205 in MDCK cells inhibited the expression of tight junction proteins and the formation of tight junctions. miR-205- knockdown urothelial cells showed alterations in keratin synthesis and increases of uroplakin Ia and Ib, which are the urothelial differentiation products. These results suggest that miR-205 may contribute a role in regulation of urothelial differentiation by modulating the expression of tight junction-related molecules. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Minimal Effects of VEGF and Anti-VEGF Drugs on the Permeability or Selectivity of RPE Tight Junctions

PubMed Central

Peng, Shaomin; Adelman, Ron A.

2010-01-01

Purpose. Bevacizumab and ranibizumab are currently used to treat age-related macular degeneration by neutralizing vascular endothelial growth factor (VEGF). In this study, the potential side effects on the outer blood–retinal barrier were examined. Methods. Human fetal RPE (hfRPE) cells were used because they are highly differentiated in culture. The claudin composition of RPE tight junctions was determined by RT-PCR, immunoblot analysis, and immunofluorescence. ELISA assays monitored the secretion and trafficking of VEGF and a fluid-phase marker, methylpolyethylene glycol (mPEG). Tight junction functions were assessed by the conductance of K+ and Na+ (derived from the transepithelial electrical resistance, TER) and the flux of NaCl and mPEG. Results. Claudin-3, claudin-10, and claudin-19 were detected in RPE tight junctions. VEGF was secreted in equal amounts across the apical and basolateral membranes, but the apical membrane was more active in endocytosing and degrading VEGF. Exogenous VEGF and mPEG crossed the RPE monolayer by transcytosis, predominantly in the apical-to-basal direction. RPE tight junctions were selective for K+, but did not discriminate between Na+ and Cl−. VEGF, bevacizumab, and ranibizumab had minimal effects on TER, permeation of mPEG, and selectivity for K+, Na+, and Cl−. They had minimal effects on the expression and distribution of the claudins. Conclusions. RPE has mechanisms for maintaining low concentrations of VEGF in the subretinal space that include endocytosis and degradation and fluid-phase transcytosis in the apical-to-basal direction. RPE tight junctions are selective for K+ over Na+ and Cl−. Permeability and selectivity of the junctions are not affected by VEGF, bevacizumab, or ranibizumab. PMID:20042644

Bayesian inference of galaxy formation from the K-band luminosity function of galaxies: tensions between theory and observation

NASA Astrophysics Data System (ADS)

Lu, Yu; Mo, H. J.; Katz, Neal; Weinberg, Martin D.

2012-04-01

We conduct Bayesian model inferences from the observed K-band luminosity function of galaxies in the local Universe, using the semi-analytic model (SAM) of galaxy formation introduced in Lu et al. The prior distributions for the 14 free parameters include a large range of possible models. We find that some of the free parameters, e.g. the characteristic scales for quenching star formation in both high-mass and low-mass haloes, are already tightly constrained by the single data set. The posterior distribution includes the model parameters adopted in other SAMs. By marginalizing over the posterior distribution, we make predictions that include the full inferential uncertainties for the colour-magnitude relation, the Tully-Fisher relation, the conditional stellar mass function of galaxies in haloes of different masses, the H I mass function, the redshift evolution of the stellar mass function of galaxies and the global star formation history. Using posterior predictive checking with the available observational results, we find that the model family (i) predicts a Tully-Fisher relation that is curved; (ii) significantly overpredicts the satellite fraction; (iii) vastly overpredicts the H I mass function; (iv) predicts high-z stellar mass functions that have too many low-mass galaxies and too few high-mass ones and (v) predicts a redshift evolution of the stellar mass density and the star formation history that are in moderate disagreement. These results suggest that some important processes are still missing in the current model family, and we discuss a number of possible solutions to solve the discrepancies, such as interactions between galaxies and dark matter haloes, tidal stripping, the bimodal accretion of gas, preheating and a redshift-dependent initial mass function.

The Role of Neuronal Signaling in Controlling Cerebral Blood Flow

ERIC Educational Resources Information Center

Drake, Carrie T.; Iadecola, Costantino

2007-01-01

Well-regulated blood flow within the brain is vital to normal function. The brain's requirement for sufficient blood flow is ensured by a tight link between neural activity and blood flow. The link between regional synaptic activity and regional cerebral blood flow, termed functional hyperemia, is the basis for several modern imaging techniques…

The tight binding model study of the role of band filling on the charge gap in graphene-on-substrate in paramagnetic state

NASA Astrophysics Data System (ADS)

Panda, Rudrashish; Sahu, Sivabrata; Rout, G. C.

2017-05-01

We communicate here a tight binding theoretical model study of the band filling effect on the charge gap in graphene-on-substrate. The Hamiltonian consists of nearest neighbor electron hopping and substrate induced gap. Besides this the Coulomb interaction is considered here within mean-field approximation in the paramagnetic limit. The electron occupancies at two sublattices are calculated by Green's function technique and are solved self consistently. Finally the charge gap i.e. Δ ¯=U [ < na > -< nb > ] is calculated and computed numerically. The results are reported.

Scattering matrix of arbitrary tight-binding Hamiltonians

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ramírez, C., E-mail: carlos@ciencias.unam.mx; Medina-Amayo, L.A.

2017-03-15

A novel efficient method to calculate the scattering matrix (SM) of arbitrary tight-binding Hamiltonians is proposed, including cases with multiterminal structures. In particular, the SM of two kinds of fundamental structures is given, which can be used to obtain the SM of bigger systems iteratively. Also, a procedure to obtain the SM of layer-composed periodic leads is described. This method allows renormalization approaches, which permits computations over macroscopic length systems without introducing additional approximations. Finally, the transmission coefficient of a ring-shaped multiterminal system and the transmission function of a square-lattice nanoribbon with a reduced width region are calculated.

Therapeutic Nanodevices

NASA Astrophysics Data System (ADS)

Lee, Stephen C.; Ruegsegger, Mark; Barnes, Philip D.; Smith, Bryan R.; Ferrari, Mauro

Therapeutic nanotechnology offers minimally invasive therapies with high densities of function concentrated in small volumes, features that may reduce patient morbidity and mortality. Unlike other areas of nanotechnology, novel physical properties associated with nanoscale dimensionality are not the raison d'etre of therapeutic nanotechnology, whereas the aggregation of multiple biochemical (or comparably precise) functions into controlled nanoarchitectures is. Multifunctionality is a hallmark of emerging nanotherapeutic devices, and multifunctionality can allow nanotherapeutic devices to perform multi-step work processes, with each functional component contributing to one or more nanodevice subroutine such that, in aggregate, subroutines sum to a cogent work process. Cannonical nanotherapeutic subroutines include tethering (targeting) to sites of disease, dispensing measured doses of drug (or bioactive compound), detection of residual disease after therapy and communication with an external clinician/operator. Emerging nanotherapeutics thus blur the boundaries between medical devices and traditional pharmaceuticals. Assembly of therapeutic nanodevices generally exploits either (bio)material self assembly properties or chemoselective bioconjugation techniques, or both. Given the complexity, composition, and the necessity for their tight chemical and structural definition inherent in the nature of nanotherapeutics, their cost of goods (COGs) might exceed that of (already expensive) biologics. Early therapeutic nanodevices will likely be applied to disease states which exhibit significant unmet patient need (cancer and cardiovascular disease), while application to other disease states well-served by conventional therapy may await perfection of nanotherapeutic design and assembly protocols.

Therapeutic Nanodevices

NASA Astrophysics Data System (ADS)

Lee, Stephen; Ruegsegger, Mark; Barnes, Philip; Smith, Bryan; Ferrari, Mauro

Therapeutic nanotechnology offers minimally invasive therapies with high densities of function concentrated in small volumes, features that may reduce patient morbidity and mortality. Unlike other areas of nanotechnology, novel physical properties associated with nanoscale dimensionality are not the raison d'être of therapeutic nanotechnology, whereas the aggregation of multiple biochemical (or comparably precise) functions into controlled nanoarchitectures is. Multifunctionality is a hallmark of emerging nanotherapeutic devices, and multifunctionality can allow nanotherapeutic devices to perform multistep work processes, with each functional component contributing to one or more nanodevice subroutine such that, in aggregate, subroutines sum to a cogent work process. Cannonical nanotherapeutic subroutines include tethering (targeting) to sites of disease, dispensing measured doses of drug (or bioactive compound), detection of residual disease after therapy and communication with an external clinician/operator. Emerging nanotherapeutics thus blur the boundaries between medical devices and traditional pharmaceuticals. Assembly of therapeutic nanodevices generally exploits either (bio)material self-assembly properties or chemoselective bioconjugation techniques, or both. Given the complexity, composition, and the necessity for their tight chemical and structural definition inherent in the nature of nanotherapeutics, their cost of goods (COGs) might exceed that of (already expensive) biologics. Early therapeutic nanodevices will likely be applied to disease states which exhibit significant unmet patient need (cancer and cardiovascular disease), while application to other disease states well-served by conventional therapy may await perfection of nanotherapeutic design and assembly protocols.

SnO2/Reduced Graphene Oxide Interlayer Mitigating the Shuttle Effect of Li-S Batteries.

PubMed

Hu, Nana; Lv, Xingshuai; Dai, Ying; Fan, Linlin; Xiong, Dongbin; Li, Xifei

2018-06-06

The short cycle life of lithium-sulfur batteries (LSBs) plagues its practical application. In this study, a uniform SnO 2 /reduced graphene oxide (denoted as SnO 2 /rGO) composite is successfully designed onto the commercial polypropylene separator for use of interlayer of LSBs to decrease the charge-transfer resistance and trap the soluble lithium polysulfides (LPSs). As a result, the assembled devices using the separator modified with the functional interlayer (SnO 2 /rGO) exhibit improved cycle performance; for instance, over 200 cycles at 1C, the discharge capacity of the cells reaches 734 mAh g -1 . The cells also display high rate capability, with the average discharge capacity of 541.9 mAh g -1 at 5C. Additionally, the mechanism of anchoring behavior of the SnO 2 /rGO interlayer was systematically investigated using density functional theory calculations. The results demonstrate that the improved performance is related to the ability of SnO 2 /rGO to effectively absorb S 8 cluster and LPS. The strong Li-O/Sn-S/O-S bonds and tight chemical adsorption between LPS and SnO 2 mitigate the shuttle effect of LSBs. This study demonstrates that engineering the functional interlayer of metal oxide and carbon materials in LSBs may be an easy way to improve their rate capacity and cycling life.

Development of High vacuum facility for baking and cool down experiments for SST-1 Tokamak components

NASA Astrophysics Data System (ADS)

Khan, Ziauddin; Pathan, Firozkhan S.; Yuvakiran, Paravastu; George, Siju; Manthena, Himabindu; Raval, Dilip C.; Thankey, Prashant L.; Dhanani, Kalpesh R.; Gupta, Manoj Kumar; Pradhan, Subrata

2012-11-01

SST-1 Tokamak, a steady state super-conducting device, is under refurbishment to demonstrate the plasma discharge for the duration of 1000 second. The major fabricated components of SST-1 like vacuum vessel, thermal shields, superconducting magnets etc have to be tested for their functional parameters. During machine operation, vacuum vessel will be baked at 150 °C, thermal shields will be operated at 85 K and magnet system will be operated at 4.5 K. All these components must have helium leak tightness under these conditions so far as the machine operation is concerned. In order to validate the helium leak tightness of these components, in-house high vacuum chamber is fabricated. This paper describes the analysis, design and fabrication of high vacuum chamber to demonstrate these functionalities. Also some results will be presented.

The Effect of Diacutaneous Fibrolysis on Patellar Position Measured Using Ultrasound Scanning in Patellofemoral Pain Syndrome Patients.

PubMed

Fanlo-Mazas, Pablo; Bueno-Gracia, Elena; de Escudero-Zapico, Alazne Ruiz; Tricás-Moreno, José Miguel; Lucha-López, María Orosia

2018-04-13

Tightness or lack of flexibility of flexibility of several muscles of the thigh has been associated with patellofemoral-join pain. A tight iliotibial band can lead to laterally located patella and an abnormal patellar tracking pattern. Diacutaneous fibrolysis is commonly used to reduce muscle tightness, but no studies have evaluated the effects of this technique in the treatment of patellofemoral pain syndrome patients. To assess the effect of diacutaneous fibrolysis on patellar position in patients with patellofemoral pain syndrome. A single-group, pretest-posttest clinical trial. University of Zaragoza. 46 subjects with patellofemoral pain (20 males, 26 females (age 27.8 ± 6.9 years)). 3 sessions of diacutaneous fibrolysis. Patellar position measurement using real time ultrasound scanning, pain intensity measured with visual analogue scale and function measured with the Anterior Knee Pain Scale. The application of three sessions of diacutaneous fibrolysis significantly increased the patellar position at post-treatment evaluation (p<0.001) and at one-week follow-up (p<0.001). There was not a significance difference on patellar position between post-treatment and follow-up measurements (p=0.283). There were also a statistically significant decrease in pain and increase in function at post-treatment and at one-week follow-up measurements (p<0.001). This study found that patellar position, pain intensity and function were significantly improved after three sessions of diacutaneous fibrolysis and at one week follow up.

Myosin Light Chain Kinase Mediates Intestinal Barrier Disruption following Burn Injury

PubMed Central

Chen, Chuanli; Wang, Pei; Su, Qin; Wang, Shiliang; Wang, Fengjun

2012-01-01

Background Severe burn injury results in the loss of intestinal barrier function, however, the underlying mechanism remains unclear. Myosin light chain (MLC) phosphorylation mediated by MLC kinase (MLCK) is critical to the pathophysiological regulation of intestinal barrier function. We hypothesized that the MLCK-dependent MLC phosphorylation mediates the regulation of intestinal barrier function following burn injury, and that MLCK inhibition attenuates the burn-induced intestinal barrier disfunction. Methodology/Principal Findings Male balb/c mice were assigned randomly to either sham burn (control) or 30% total body surface area (TBSA) full thickness burn without or with intraperitoneal injection of ML-9 (2 mg/kg), an MLCK inhibitor. In vivo intestinal permeability to fluorescein isothiocyanate (FITC)-dextran was measured. Intestinal mucosa injury was assessed histologically. Tight junction proteins ZO-1, occludin and claudin-1 was analyzed by immunofluorescent assay. Expression of MLCK and phosphorylated MLC in ileal mucosa was assessed by Western blot. Intestinal permeability was increased significantly after burn injury, which was accompanied by mucosa injury, tight junction protein alterations, and increase of both MLCK and MLC phosphorylation. Treatment with ML-9 attenuated the burn-caused increase of intestinal permeability, mucosa injury, tight junction protein alterations, and decreased MLC phosphorylation, but not MLCK expression. Conclusions/Significance The MLCK-dependent MLC phosphorylation mediates intestinal epithelial barrier dysfunction after severe burn injury. It is suggested that MLCK-dependent MLC phosphorylation may be a critical target for the therapeutic treatment of intestinal epithelial barrier disruption after severe burn injury. PMID:22529961

Tight junction proteins contribute to barrier properties in human pleura.

PubMed

Markov, Alexander G; Voronkova, Maria A; Volgin, George N; Yablonsky, Piotr K; Fromm, Michael; Amasheh, Salah

2011-03-15

The permeability of pleural mesothelium helps to control the volume and composition of the liquid lubricating pleural surfaces. Information on pleural barrier function in health and disease, however, is scarce. Tissue specimens of human pleura were mounted in Ussing chambers for measurement of transmesothelial resistance. Expression of tight junction (TJ) proteins was studied by Western blots and immune fluorescence confocal microscopy. Both visceral and parietal pleura showed barrier properties represented by transmesothelial resistance. Occludin, claudin-1, -3, -5, and -7, were detected in visceral pleura. In parietal pleura, the same TJ proteins were detected, except claudin-7. In tissues from patients with pleural inflammation these tightening claudins were decreased and in visceral pleura claudin-2, a paracellular channel former, became apparent. We report that barrier function in human pleura coincides with expression of claudins known to be key determinants of epithelial barrier properties. In inflamed tissue, claudin expression indicates a reduced barrier function. Copyright © 2010 Elsevier B.V. All rights reserved.

Community structure in networks of functional connectivity: resolving functional organization in the rat brain with pharmacological MRI.

PubMed

Schwarz, Adam J; Gozzi, Alessandro; Bifone, Angelo

2009-08-01

In the study of functional connectivity, fMRI data can be represented mathematically as a network of nodes and links, where image voxels represent the nodes and the connections between them reflect a degree of correlation or similarity in their response. Here we show that, within this framework, functional imaging data can be partitioned into 'communities' of tightly interconnected voxels corresponding to maximum modularity within the overall network. We evaluated this approach systematically in application to networks constructed from pharmacological MRI (phMRI) of the rat brain in response to acute challenge with three different compounds with distinct mechanisms of action (d-amphetamine, fluoxetine, and nicotine) as well as vehicle (physiological saline). This approach resulted in bilaterally symmetric sub-networks corresponding to meaningful anatomical and functional connectivity pathways consistent with the purported mechanism of action of each drug. Interestingly, common features across all three networks revealed two groups of tightly coupled brain structures that responded as functional units independent of the specific neurotransmitter systems stimulated by the drug challenge, including a network involving the prefrontal cortex and sub-cortical regions extending from the striatum to the amygdala. This finding suggests that each of these networks includes general underlying features of the functional organization of the rat brain.

Small angle slot divertor concept for long pulse advanced tokamaks

NASA Astrophysics Data System (ADS)

Guo, H. Y.; Sang, C. F.; Stangeby, P. C.; Lao, L. L.; Taylor, T. S.; Thomas, D. M.

2017-04-01

SOLPS-EIRENE edge code analysis shows that a gas-tight slot divertor geometry with a small-angle (glancing-incidence) target, named the small angle slot (SAS) divertor, can achieve cold, dissipative/detached divertor conditions at relatively low values of plasma density at the outside midplane separatrix. SAS exhibits the following key features: (1) strong enhancement of the buildup of neutral density in a localized region near the plasma strike point on the divertor target; (2) spreading of the cooling front across the divertor target with the slot gradually flaring out from the strike point, thus effectively reducing both heat flux and erosion on the entire divertor target surface. Such a divertor may potentially provide a power and particle handling solution for long pulse advanced tokamaks.

Correlation Decay in Fermionic Lattice Systems with Power-Law Interactions at Nonzero Temperature

NASA Astrophysics Data System (ADS)

Hernández-Santana, Senaida; Gogolin, Christian; Cirac, J. Ignacio; Acín, Antonio

2017-09-01

We study correlations in fermionic lattice systems with long-range interactions in thermal equilibrium. We prove a bound on the correlation decay between anticommuting operators and generalize a long-range Lieb-Robinson-type bound. Our results show that in these systems of spatial dimension D with, not necessarily translation invariant, two-site interactions decaying algebraically with the distance with an exponent α ≥2 D , correlations between such operators decay at least algebraically to 0 with an exponent arbitrarily close to α at any nonzero temperature. Our bound is asymptotically tight, which we demonstrate by a high temperature expansion and by numerically analyzing density-density correlations in the one-dimensional quadratic (free, exactly solvable) Kitaev chain with long-range pairing.

Biological samples on the ISS-EXPOSE facility for the ROSE/PUR experiment

NASA Astrophysics Data System (ADS)

Rontó, Gy.; Bérces, A.; Fekete, A.; Kerékgyártó, T.; Lammer, H.; Kargl, G.; Kömle, N. I.

2002-11-01

Three types of samples, bacteriophage T7, isolated phage DNA, polycrystalline uracil thin films were prepared in sandwich form that were closed vacuum-tightly with inert gaseous environment. The response of the samples to the following selected space environmental conditions was investigated: temperature (-20 - +40°C), vacuum, short wavelength UV irradiation. Uracil thin layer samples proved to be insensitive for temperature. In the vacuum chamber the structure of the samples in sandwich arrangement did not change. Irradiation with germicidal and Deuterium lamps caused a decrease in the optical density of the uracil layers and the decrease showed a saturation tendency in both cases. The dose-effect curves at germicidal lamp possess a saturation level at a lower optical density than at Deuterium.

Quantum molecular dynamics simulations of dense matter

DOE Office of Scientific and Technical Information (OSTI.GOV)

Collins, L.; Kress, J.; Troullier, N.

1997-12-31

The authors have developed a quantum molecular dynamics (QMD) simulation method for investigating the properties of dense matter in a variety of environments. The technique treats a periodically-replicated reference cell containing N atoms in which the nuclei move according to the classical equations-of-motion. The interatomic forces are generated from the quantum mechanical interactions of the (between?) electrons and nuclei. To generate these forces, the authors employ several methods of varying sophistication from the tight-binding (TB) to elaborate density functional (DF) schemes. In the latter case, lengthy simulations on the order of 200 atoms are routinely performed, while for the TB,more » which requires no self-consistency, upwards to 1000 atoms are systematically treated. The QMD method has been applied to a variety cases: (1) fluid/plasma Hydrogen from liquid density to 20 times volume-compressed for temperatures of a thousand to a million degrees Kelvin; (2) isotopic hydrogenic mixtures, (3) liquid metals (Li, Na, K); (4) impurities such as Argon in dense hydrogen plasmas; and (5) metal/insulator transitions in rare gas systems (Ar,Kr) under high compressions. The advent of parallel versions of the methods, especially for fast eigensolvers, presage LDA simulations in the range of 500--1000 atoms and TB runs for tens of thousands of particles. This leap should allow treatment of shock chemistry as well as large-scale mixtures of species in highly transient environments.« less

Size versus electronic factors in transition metal carbide and TCP phase stability

NASA Astrophysics Data System (ADS)

Pettifor, D. G.; Seiser, B.; Margine, E. R.; Kolmogorov, A. N.; Drautz, R.

2013-09-01

The contributions of atomic size and electronic factors to the structural stability of transition metal carbides and topologically close-packed (TCP) phases are investigated. The hard-sphere model that has been used by Cottrell to rationalize the occurrence of the octahedral and trigonal local coordination polyhedra within the transition metal carbides is shown to have limitations in TiC since density functional theory (DFT) predicts that the second most metastable phase closest to the B1 (NaCl) ground state takes the B? (BN) structure type with 5-atom local coordination polyhedra with very short Ti-C bond lengths. The importance of electronic factors in the TCP phases is demonstrated by DFT predictions that the A15, ? and ? phases are stabilized between groups VI and VII of the elemental transition metals, whereas the ? and Laves phases are destabilized. The origin of this difference is related to the bimodal shape parameter of the electronic density of states by using the bond-order potential expansion of the structural energy within a canonical tight-binding model. The importance of the size factor in the TCP phases is illustrated by the DFT heats of formation for the binary systems Mo-Re, Mo-Ru, Nb-Re and Nb-Ru which show that the ? and Laves phases become more and more stable compared to A15, ? and ? as the size factor increases from Mo-Re through to Nb-Ru.

Chronic depletion of gonadal testosterone leads to blood-brain barrier dysfunction and inflammation in male mice.

PubMed

Atallah, Afnan; Mhaouty-Kodja, Sakina; Grange-Messent, Valérie

2017-09-01

A dysfunction in the blood-brain barrier (BBB) is associated with many neurological and metabolic disorders. Although sex steroid hormones have been shown to impact vascular tone, endothelial function, oxidative stress, and inflammatory responses, there are still no data on the role of testosterone in the regulation of BBB structure and function. In this context, we investigated the effects of gonadal testosterone depletion on the integrity of capillary BBB and the surrounding parenchyma in male mice. Our results show increased BBB permeability for different tracers and endogenous immunoglobulins in chronically testosterone-depleted male mice. These results were associated with disorganization of tight junction structures shown by electron tomography and a lower amount of tight junction proteins such as claudin-5 and ZO-1. BBB leakage was also accompanied by activation of astrocytes and microglia, and up-regulation of inflammatory molecules such as inducible nitric oxide synthase (iNOS), cyclooxygenase 2 (COX-2), interleukin 1 beta (IL-1β), and tumor necrosis factor (TNF). Supplementation of castrated male mice with testosterone restored BBB selective permeability, tight junction integrity, and almost completely abrogated the inflammatory features. The present demonstration that testosterone transiently impacts cerebrovascular physiology in adult male mice should help gain new insights into neurological and metabolic diseases linked to hypogonadism in men of all ages.

Poly(I:C) Induces Human Lung Endothelial Barrier Dysfunction by Disrupting Tight Junction Expression of Claudin-5

DOE PAGES

Huang, Li -Yun; Stuart, Christine; Takeda, Kazuyo; ...

2016-08-09

Viral infections are often accompanied by pulmonary microvascular leakage and vascular endothelial dysfunction via mechanisms that are not completely defined. Here, we investigated the effect of the Toll-like receptor 3 (TLR3) ligand polyinosinic-polycytidylic acid [Poly(I:C)], a synthetic analog of viral double-stranded RNA (dsRNA) commonly used to simulate viral infections, on the barrier function and tight junction integrity of primary human lung microvascular endothelial cells. Poly(I:C) stimulated IL-6, IL-8, TNFα, and IFNβ production in conjunction with the activation of NF-κB and IRF3 confirming the Poly(I:C)-responsiveness of these cells. Poly(I:C) increased endothelialmonolayer permeability with a corresponding dose- and time-dependent decrease in themore » expression of claudin-5, a transmembrane tight junction protein and reduction of CLDN5 mRNA levels. Immunofluorescence experiments revealed disappearance of membrane-associated claudin-5 and co-localization of cytoplasmic claudin-5 with lysosomal-associated membrane protein 1. Chloroquine and Bay11-7082, inhibitors of TLR3 and NF-κB signaling, respectively, protected against the loss of claudin-5. Altogether, these findings provide new insight on how dsRNA-activated signaling pathways may disrupt vascular endothelial function and contribute to vascular leakage pathologies.« less

Localization and quantification of carbonic anhydrase activity in the symbiotic Scyphozoan Cassiopea xamachana.

PubMed

Estes, Anne M; Kempf, Stephen C; Henry, Raymond P

2003-06-01

The relationship between density and location of zooxanthellae and levels of carbonic anhydrase (CA) activity was examined in Cassiopea xamachana. In freshly collected symbiotic animals, high densities of zooxanthellae corresponded with high levels of CA activity in host bell and oral arm tissues. Bleaching resulted in a significant loss of zooxanthellae and CA activity. Recolonization resulted in full restoration of zooxanthellar densities but only partial restoration of CA activity. High levels of CA activity were also seen in structures with inherently higher zooxanthellar densities, such as oral arm tissues. Similarly, the oral epidermal layer of bell tissue had significantly higher zooxanthellar densities and levels of CA activity than did aboral bell tissues. Fluorescent labeling, using 5-dimethylaminonapthalene-1-sulfonamide (DNSA) also reflected this tight-knit relationship between the presence and density of zooxanthellae, as DNSA-CA fluorescence intensity was greatest in host oral epithelial cells directly overlying zooxanthellae. However, the presence and density of zooxanthellae did not always correspond with enzyme activity levels. A transect of bell tissue from the margin to the manubrium revealed a gradient of CA activity, with the highest values at the bell margin and the lowest at the manubrium, despite an even distribution of zooxanthellae. Thus, abiotic factors may also influence the distribution of CA and the levels of CA activity.

Bandstructure modulation for Si-h and Si-g nanotubes in a transverse electric field: Tight binding approach

NASA Astrophysics Data System (ADS)

Chegel, Raad; Behzad, Somayeh

2013-11-01

We have investigated the electronic properties of SiNTs, under the external electric field, using Tight Binding (TB) approximation. It was found that the energy levels, energy gaps, and density of states (DOS) strongly depend on the electric field strength. The large electric strength leads to coupling the neighbor subbands and induce destruction of subband degeneracy, increase of low-energy states, and strong modulation of energy gap which these effects reflect in the DOS spectrum. It has been shown that, the band gap reduction of Si g-NTs is linearly proportional to the electric field strength. The band gap variation for Si h-NTs increases first and later decreases (Metallic) or first remains constant and then decreases (semiconductor). Also we show that the larger diameter tubes are more sensitive to the field strength than smaller ones. The semiconducting metallic transition or vice versa can be achieved through an increasing of applied fields. Number and position of peaks in DOS spectrum are dependent on electric field strength.

Band structure and orbital character of monolayer MoS2 with eleven-band tight-binding model

NASA Astrophysics Data System (ADS)

Shahriari, Majid; Ghalambor Dezfuli, Abdolmohammad; Sabaeian, Mohammad

2018-02-01

In this paper, based on a tight-binding (TB) model, first we present the calculations of eigenvalues as band structure and then present the eigenvectors as probability amplitude for finding electron in atomic orbitals for monolayer MoS2 in the first Brillouin zone. In these calculations we are considering hopping processes between the nearest-neighbor Mo-S, the next nearest-neighbor in-plan Mo-Mo, and the next nearest-neighbor in-plan and out-of-plan S-S atoms in a three-atom based unit cell of two-dimensional rhombic MoS2. The hopping integrals have been solved in terms of Slater-Koster and crystal field parameters. These parameters are calculated by comparing TB model with the density function theory (DFT) in the high-symmetry k-points (i.e. the K- and Γ-points). In our TB model all the 4d Mo orbitals and the 3p S orbitals are considered and detailed analysis of the orbital character of each energy level at the main high-symmetry points of the Brillouin zone is described. In comparison with DFT calculations, our results of TB model show a very good agreement for bands near the Fermi level. However for other bands which are far from the Fermi level, some discrepancies between our TB model and DFT calculations are observed. Upon the accuracy of Slater-Koster and crystal field parameters, on the contrary of DFT, our model provide enough accuracy to calculate all allowed transitions between energy bands that are very crucial for investigating the linear and nonlinear optical properties of monolayer MoS2.

Intestinal Alkaline Phosphatase Regulates Tight Junction Protein Levels

PubMed Central

Liu, Wei; Hu, Dong; Huo, Haizhong; Zhang, Weifeng; Adiliaghdam, Fatemeh; Morrison, Sarah; Ramirez, Juan M; Gul, Sarah S; Hamarneh, Sulaiman R; Hodin, Richard A

2017-01-01

BACKGROUND Intestinal alkaline phosphatase (IAP) plays a pivotal role in maintaining gut health and well-being. Oral supplementation with IAP in mice improves gut barrier function and prevents luminal proinflammatory factors from gaining access to the circulation. In this study, we sought to explore the relationship between IAP and tight junction protein (TJP) expression and function. STUDY DESIGN The effect of IAP deletion on TJP levels was studied in mouse embryonic fibroblasts (MEFs) generated from IAP-knockout and wild type mice. Regulation of TJPs by IAP was assayed in the human colon cancer Caco-2 and T84 cells by overexpressing the human IAP gene. Tight junction protein levels and localization were measured by using RT q-PCR and antibodies targeting the specific TJPs. Finally, the effect of IAP on inflammation-induced intestinal permeability was measured by in vitro trans-well epithelial electrical resistance (TEER). RESULTS Intestinal alkaline phosphatase gene deletion in MEFs resulted in significantly lower levels of ZO-1, ZO-2, and Occludin compared with levels in wild-type control cells; IAP over-expression in Caco-2 and T84 cells resulted in approximate 2-fold increases in the mRNA levels of ZO-1 and ZO-2. The IAP treatment ameliorated lipopolysaccharide-induced increased permeability in the Caco-2 trans-well system. Furthermore, IAP treatment preserved the localization of the ZO-1 and Occludin proteins during inflammation and was also associated with improved epithelial barrier function. CONCLUSIONS Intestinal alkaline phosphatase is a major regulator of gut mucosal permeability and appears to work at least partly through improving TJP levels and localization. These data provide a strong foundation to develop IAP as a novel therapy to maintain gut barrier function. PMID:27106638

Intestinal Alkaline Phosphatase Regulates Tight Junction Protein Levels.

PubMed

Liu, Wei; Hu, Dong; Huo, Haizhong; Zhang, Weifeng; Adiliaghdam, Fatemeh; Morrison, Sarah; Ramirez, Juan M; Gul, Sarah S; Hamarneh, Sulaiman R; Hodin, Richard A

2016-06-01

Intestinal alkaline phosphatase (IAP) plays a pivotal role in maintaining gut health and well-being. Oral supplementation with IAP in mice improves gut barrier function and prevents luminal proinflammatory factors from gaining access to the circulation. In this study, we sought to explore the relationship between IAP and tight junction protein (TJP) expression and function. The effect of IAP deletion on TJP levels was studied in mouse embryonic fibroblasts (MEFs) generated from IAP-knockout and wild type mice. Regulation of TJPs by IAP was assayed in the human colon cancer Caco-2 and T84 cells by overexpressing the human IAP gene. Tight junction protein levels and localization were measured by using RT q-PCR and antibodies targeting the specific TJPs. Finally, the effect of IAP on inflammation-induced intestinal permeability was measured by in vitro trans-well epithelial electrical resistance (TEER). Intestinal alkaline phosphatase gene deletion in MEFs resulted in significantly lower levels of ZO-1, ZO-2, and Occludin compared with levels in wild-type control cells; IAP overexpression in Caco-2 and T84 cells resulted in approximate 2-fold increases in the mRNA levels of ZO-1 and ZO-2. The IAP treatment ameliorated lipopolysaccharide-induced increased permeability in the Caco-2 trans-well system. Furthermore, IAP treatment preserved the localization of the ZO-1 and Occludin proteins during inflammation and was also associated with improved epithelial barrier function. Intestinal alkaline phosphatase is a major regulator of gut mucosal permeability and appears to work at least partly through improving TJP levels and localization. These data provide a strong foundation to develop IAP as a novel therapy to maintain gut barrier function. Copyright © 2016. Published by Elsevier Inc.

Coupling of lipid membrane elasticity and in-plane dynamics

NASA Astrophysics Data System (ADS)

Tsang, Kuan-Yu; Lai, Yei-Chen; Chiang, Yun-Wei; Chen, Yi-Fan

2017-07-01

Biomembranes exhibit liquid and solid features concomitantly with their in-plane fluidity and elasticity tightly regulated by cells. Here, we present experimental evidence supporting the existence of the dynamics-elasticity correlations for lipid membranes and propose a mechanism involving molecular packing densities to explain them. This paper thereby unifies, at the molecular level, the aspects of the continuum mechanics long used to model the two membrane features. This ultimately may elucidate the universal physical principles governing the cellular phenomena involving biomembranes.

Brittle Materials Design, High Temperature Gas Turbine

DTIC Science & Technology

1977-08-01

hubs were inspected radiographi - cally and by fluoresent dye penetrant. The dye penetrant revealed tight cracks on the inner axial faces of hub A... radiography of green parts has proved effective in detecting major flaws. Slip cast Si3N4 test bars having a density of 2.7 gm/cc show four point MOR...this run. Post inspection showed all ceramic parts to be crack free. The rotor failed during a subsequent run at 50,000 rpm and 2300°F T.I.T. (10

Thermography Control of Heat Insulation and Tightness of Buildings,

DTIC Science & Technology

1980-11-01

drawing, top to bottom: 100 + 50 mm mineral wool panels, bulk density 50 kg/m3 Vapor barrier of plastic foil 3/4" tongue and groove 13 mm gypsum panel...Horizontal steel bolts Horisontella Air leakage, in A Ireqlar Corrugated sheet metal 90 mm mineral wool (with sheathing paper) Ko"mir) emd 30 mm mineral ...bolt; Outward leakage of warm air from the room; Steel siding; 90 mm mineral wool (with wind protection); 30 mm mineral wool (with vapor barrier

Complex absorbing potential based Lorentzian fitting scheme and time dependent quantum transport.

PubMed

Xie, Hang; Kwok, Yanho; Jiang, Feng; Zheng, Xiao; Chen, GuanHua

2014-10-28

Based on the complex absorbing potential (CAP) method, a Lorentzian expansion scheme is developed to express the self-energy. The CAP-based Lorentzian expansion of self-energy is employed to solve efficiently the Liouville-von Neumann equation of one-electron density matrix. The resulting method is applicable for both tight-binding and first-principles models and is used to simulate the transient currents through graphene nanoribbons and a benzene molecule sandwiched between two carbon-atom chains.

Water clusters adsorbed on polycyclic aromatic hydrocarbons: Energetics and conformational dynamics

NASA Astrophysics Data System (ADS)

Simon, Aude; Spiegelman, Fernand

2013-05-01

In this work, we present some classical molecular dynamics (MD) simulations and finite temperature infrared (IR) spectra of water clusters adsorbed on coronene (C24H12), a compact polycyclic aromatic hydrocarbon (PAH). The potential energy surface is obtained within the self-consistent-charge density-functional based tight-binding approach with modifications insuring the correct description of water-water and water-PAH interactions. This scheme is benchmarked for the minimal energy structures of (C24H12)(H2O)n (n = 3-10) against density-functional theory (DFT) calculations and for the low-energy isomers of (H2O)6 and (C6H6)(H2O)3 against correlated wavefunction and DFT calculations. A detailed study of the low energy isomers of (C24H12)(H2O)3, 6 complexes is then provided. On-the-fly Born-Oppenheimer MD simulations are performed in the temperature T range 10-350 K for (C24H12)(H2O)n (n = 3-7) complexes. The description of the evolution of the systems with T is provided with emphasis on (C24H12)(H2O)n (n = 3,6). For T in the range 50-150 K, isomerisation processes are observed and when T increases, a solid-to-liquid phase-change like behavior is shown. The desorption of one water molecule is frequently observed at 300 K. The isomerisation processes are evidenced on the finite temperature IR spectra and the results are presented for (C24H12)(H2O)n (n = 3,6). A signature for the edge-coordination of the water cluster on the PAH is also proposed.

Differential roles of breakfast and supper in rats of a daily three-meal schedule upon circadian regulation and physiology.

PubMed

Wu, Tao; Sun, Lu; ZhuGe, Fen; Guo, Xichao; Zhao, Zhining; Tang, Ruiqi; Chen, Qinping; Chen, Lin; Kato, Hisanori; Fu, Zhengwei

2011-12-01

The timing of meals has been suggested to play an important role in circadian regulation and metabolic health. Three meals a day is a well-established human feeding habit, which in today's lifestyle may or may not be followed. The aim of this study was to test whether the absence of breakfast or supper significantly affects the circadian system and physiological function. The authors developed a rat model for their daily three meals study, whereby animals were divided into three groups (three meals, TM; no first meal, NF; no last meal, NL) all fed with the same amount of food every day. Rats in the NF group displayed significantly decreased levels of plasma triglyceride (TG), total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and glucose in the activity phase, accompanied by delayed circadian phases of hepatic peripheral clock and downstream metabolic genes. Rats in the NL group showed lower concentration of plasma TC, HDL-C, and glucose in the rest phase, plus reduced adipose tissue accumulation and body weight gain. Real-time polymerase chain reaction (PCR) analysis indicated an attenuated rhythm in the food-entraining pathway, including down-regulated expression of the clock genes Per2, Bmal1, and Rev-erbα, which may further contribute to the delayed and decreased expression of FAS in lipogenesis in this group. Our findings are consistent with the conclusion that the daily first meal determines the circadian phasing of peripheral clocks, such as in the liver, whereas the daily last meal tightly couples to lipid metabolism and adipose tissue accumulation, which suggests differential physiological effects and function of the respective meal timings.

Phase transition, thermodynamics properties and IR spectrum of α- and γ-RDX: First principles and MD studies

NASA Astrophysics Data System (ADS)

Yuan, Jiaonan; Ji, Guangfu; Chen, Xiangrong; Wei, Dongqing; Zhao, Feng; Wu, Qiang

2016-01-01

In present letter, based on density functional theory plus dispersion (DFT-D) and a self-consistent charge density-functional tight-binding (SCC-DFTB) method, the structural and electronic properties are reported, and the phase transition are investigated by analyzing its thermodynamics properties and IR spectrum of RDX. The anisotropy of α- and γ-RDX were discussed at 0⿿10 GPa. By fitting the third-order Birch⿿Murnaghan equation of states, the bulk modulus and its pressure derivative of RDX were determined. The α-RDX phase is found stable at ambient condition, however, under pressures, both the values of lattice constants a, b, c and the οEvdw at around 4 GPa show abrupt changes which indicate a structural transition occurred. By analyzing the linear compressibility of a, b, c axes at 0⿿8 GPa, one clearly see that the molecules in α-RDX phase underwent rotations and translational motion to their position in the γ-RDX phase at about 4 GPa, which validates the α⿿γ phase transition. The IR spectra of α-form and γ-form RDX was calculated by analyzing the trajectory of molecules motion, which also show the phase transition from the spectra changes. Employing the quasi-harmonic Debye model, the enthalpy and specific heat were investigated at various pressures of both phases. The condition of equal enthalpies in both phases also indicates the phase transition of α-form to γ-form at around 4 GPa. The variation of specific heat with temperature approaches to the classical Dulong⿿Petit's law at high temperature, while at low-temperature it obeys the Debye's T3 law.

Formulation and validation of a reduced order model of 2D materials exhibiting a two-phase microstructure as applied to graphene oxide

NASA Astrophysics Data System (ADS)

Benedetti, Ivano; Nguyen, Hoang; Soler-Crespo, Rafael A.; Gao, Wei; Mao, Lily; Ghasemi, Arman; Wen, Jianguo; Nguyen, SonBinh; Espinosa, Horacio D.

2018-03-01

Novel 2D materials, e.g., graphene oxide (GO), are attractive building blocks in the design of advanced materials due to their reactive chemistry, which can enhance interfacial interactions while providing good in-plane mechanical properties. Recent studies have hypothesized that the randomly distributed two-phase microstructure of GO, which arises due to its oxidized chemistry, leads to differences in nano- vs meso-scale mechanical responses. However, this effect has not been carefully studied using molecular dynamics due to computational limitations. Herein, a continuum mechanics model, formulated based on density functional based tight binding (DFTB) constitutive results for GO nano-flakes, is establish for capturing the effect of oxidation patterns on the material mechanical properties. GO is idealized as a continuum heterogeneous two-phase material, where the mechanical response of each phase, graphitic and oxidized, is informed from DFTB simulations. A finite element implementation of the model is validated via MD simulations and then used to investigate the existence of GO representative volume elements (RVE). We find that for the studied GO, an RVE behavior arises for monolayer sizes in excess to 40 nm. Moreover, we reveal that the response of monolayers with two main different functional chemistries, epoxide-rich and hydroxyl-rich, present distinct differences in mechanical behavior. In addition, we explored the role of defect density in GO, and validate the applicability of the model to larger length scales by predicting membrane deflection behavior, in close agreement with previous experimental and theoretical observations. As such the work presents a reduced order modeling framework applicable in the study of mechanical properties and deformation mechanisms in 2D multiphase materials.

Transmission eigenchannels from nonequilibrium Green's functions

NASA Astrophysics Data System (ADS)

Paulsson, Magnus; Brandbyge, Mads

2007-09-01

The concept of transmission eigenchannels is described in a tight-binding nonequilibrium Green’s function (NEGF) framework. A simple procedure for calculating the eigenchannels is derived using only the properties of the device subspace and quantities normally available in a NEGF calculation. The method is exemplified by visualization in real space of the eigenchannels for three different molecular and atomic wires.

Enhanced vibronic interaction caused by local lattice symmetry lowering in the (Fe, Mg)As2 ternary system

NASA Astrophysics Data System (ADS)

Pishtshev, A.; Rubin, P.

2018-04-01

By means of periodic density functional theory (DFT) electronic structure calculations, we investigate iron-site doping effects in a structural model of bulk FeAs2. Simulations performed within the projector augmented-wave method-Perdew-Burke-Ernzerhof (PBE) generalized gradient approximation (GGA) functional scheme reveal that the impacts of the two stoichiometric substitutions Fe → Mg and Fe → Ni are radically different with respect to the structural and electronic behavior of the dopants. In particular, unlike the Ni dopant, the Mg dopant incorporated in FeAs2 occupies a noncentral equilibrium position characterized by an off-center displacement from the reference higher-symmetry position. Analysis of the respective electron and vibrational factors allows us to explain this result in terms of the local pseudo Jahn-Teller effect (pJTE). On the basis of DFT calculations, we deduce which electron orbitals and lattice vibrational modes are appropriate for promoting the local instability at the origin of the pJTE. Quantitative evaluations of the pJTE parameters performed within the polyatomic formalism of an effective tight-binding model show that it is just the enhanced vibronic interaction in the Mg-[FeAs6] cluster that is responsible for the local lattice symmetry breaking.

Effect of amylose, particle size & morphology on the functionality of starches of traditional rice cultivars.

PubMed

Bhat, Farhan Mohiuddin; Riar, Charanjit Singh

2016-11-01

The research was carried out to investigate the effect of starch powder particle size, morphology, amylose content and varietal effect on physicochemical, X-ray diffraction pattern, thermal and pasting characteristics. The results indicated that starches isolated from seven traditional rice cultivars of temperate region of India have possessed higher yield (82.47-86.83%) with lower degree of granule damage and higher level of starch crystallinity (36.55-39.15%). The water and oil binding capacities were observed to correlate positively with amylose content. The bulk density and color parameters of starches were found to have linked with starch powder particle size coupled with arrangement and morphology of the starch granules. The rice cultivars having smaller starch powder particle size indicated lowest degree of crystallinity. Morphological studies revealed that the starches with tightly packed granules had greater mean granular width, while granules with openly spaced granular morphology depicted the higher values for mean granular length. The peak height index (PHI) among different starches ranged from 1.01 to 2.57 whereas the gelatinization range varied from 10.66 to 10.88. Concluding, the differences in distributional pattern of starch granule size and shape and powder particle size indicated a significant effect on the functional properties of starch. Copyright © 2016 Elsevier B.V. All rights reserved.

An Applied Physicist Does Econometrics

NASA Astrophysics Data System (ADS)

Taff, L. G.

2010-02-01

The biggest problem those attempting to understand econometric data, via modeling, have is that economics has no F = ma. Without a theoretical underpinning, econometricians have no way to build a good model to fit observations to. Physicists do, and when F = ma failed, we knew it. Still desiring to comprehend econometric data, applied economists turn to mis-applying probability theory---especially with regard to the assumptions concerning random errors---and choosing extremely simplistic analytical formulations of inter-relationships. This introduces model bias to an unknown degree. An applied physicist, used to having to match observations to a numerical or analytical model with a firm theoretical basis, modify the model, re-perform the analysis, and then know why, and when, to delete ``outliers'', is at a considerable advantage when quantitatively analyzing econometric data. I treat two cases. One is to determine the household density distribution of total assets, annual income, age, level of education, race, and marital status. Each of these ``independent'' variables is highly correlated with every other but only current annual income and level of education follow a linear relationship. The other is to discover the functional dependence of total assets on the distribution of assets: total assets has an amazingly tight power law dependence on a quadratic function of portfolio composition. Who knew? )

Quantum transport and nanoplasmonics with carbon nanorings - using HPC in computational nanoscience

NASA Astrophysics Data System (ADS)

Jack, Mark A.

2011-10-01

Central theme of this talk is the theoretical study of toroidal carbon nanostructures as a new form of metamaterial. The interference of ring-generated electromagnetic radiation in a regular array of nanorings driven by an incoming polarized wave front may lead to fascinating new optoelectronics applications. The tight-binding method is used to model charge transport in a carbon nanotorus: All transport observables can be derived from the Green's function of the device region in a non-equilibrium Green's function algorithm. We have calculated density-of-states D(E) and transmissivities T(E) between two metallic leads under a small voltage bias. Electron-phonon coupling is included for low-energy phonon modes of armchair and zigzag nanorings with atomic displacements determined by a collaborator's finite-element based code. A numerically fast and stable algorithm has been developed via parallel linear algebra matrix routines (PETSc) with MPI parallelism to reach significant speed-up. Production runs are planned on the NSF XSEDE network. This project was supported in parts by a 2010 NSF TeraGrid Fellowship and the Sunshine State Education and Research Computing Alliance (SSERCA). Two summer students were supported as 2010 and 2011 NCSI/Shodor Petascale Computing undergraduate interns.[4pt] In collaboration with Leon W. Durivage, Adam Byrd, and Mario Encinosa.

Non-equilibrium STLS approach to transport properties of single impurity Anderson model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rezai, Raheleh, E-mail: R_Rezai@sbu.ac.ir; Ebrahimi, Farshad, E-mail: Ebrahimi@sbu.ac.ir

In this work, using the non-equilibrium Keldysh formalism, we study the effects of the electron–electron interaction and the electron-spin correlation on the non-equilibrium Kondo effect and the transport properties of the symmetric single impurity Anderson model (SIAM) at zero temperature by generalizing the self-consistent method of Singwi, Tosi, Land, and Sjolander (STLS) for a single-band tight-binding model with Hubbard type interaction to out of equilibrium steady-states. We at first determine in a self-consistent manner the non-equilibrium spin correlation function, the effective Hubbard interaction, and the double-occupancy at the impurity site. Then, using the non-equilibrium STLS spin polarization function in themore » non-equilibrium formalism of the iterative perturbation theory (IPT) of Yosida and Yamada, and Horvatic and Zlatic, we compute the spectral density, the current–voltage characteristics and the differential conductance as functions of the applied bias and the strength of on-site Hubbard interaction. We compare our spectral densities at zero bias with the results of numerical renormalization group (NRG) and depict the effects of the electron–electron interaction and electron-spin correlation at the impurity site on the aforementioned properties by comparing our numerical result with the order U{sup 2} IPT. Finally, we show that the obtained numerical results on the differential conductance have a quadratic universal scaling behavior and the resulting Kondo temperature shows an exponential behavior. -- Highlights: •We introduce for the first time the non-equilibrium method of STLS for Hubbard type models. •We determine the transport properties of SIAM using the non-equilibrium STLS method. •We compare our results with order-U2 IPT and NRG. •We show that non-equilibrium STLS, contrary to the GW and self-consistent RPA, produces the two Hubbard peaks in DOS. •We show that the method keeps the universal scaling behavior and correct exponential behavior of Kondo temperature.« less

Electro-optical properties of zigzag and armchair boron nitride nanotubes under a transverse electric field: Tight binding calculations

NASA Astrophysics Data System (ADS)

Chegel, Raad; Behzad, Somayeh

2012-02-01

The electro-optical properties of zigzag and armchair BNNTs in a uniform transverse electric field are investigated within tight binding approximation. It is found that the electric field modifies the band structure and splits band degeneracy where these effects reflect in the DOS and JDOS spectra. A decrease in the band gap, as a function of the electric field, is observed. This gap reduction increases with the diameter and it is independent of chirality. An analytic function to estimate the electric field needed for band gap closing is proposed which is in good agreement with DFT results. In additional, we show that the larger diameter tubes are more sensitive than small ones. Number and position of peaks in DOS and JDOS spectra for armchair and zigzag tubes with similar radius are dependent on electric field strength.

Genome Engineering of the 2,3-Butanediol Biosynthetic Pathway for Tight Regulation in Cyanobacteria.

PubMed

Nozzi, Nicole E; Atsumi, Shota

2015-11-20

Cyanobacteria have gained popularity among the metabolic engineering community as a tractable photosynthetic host for renewable chemical production. However, though a number of successfully engineered production systems have been reported, long-term genetic stability remains an issue for cyanobacterial systems. The genetic engineering toolbox for cyanobacteria is largely lacking inducible systems for expression control. The characterization of tight regulation systems for use in cyanobacteria may help to alleviate this problem. In this work we explore the function of the IPTG inducible promoter P(L)lacO1 in the model cyanobacterium Synechococcus elongatus PCC 7942 as well as the effect of gene order within an operon on pathway expression. According to our experiments, P(L)lacO1 functions well as an inducible promoter in S. elongatus. Additionally, we found that gene order within an operon can strongly influence control of expression of each gene.

Epithelial Integrity Is Maintained by a Matriptase-Dependent Proteolytic Pathway

PubMed Central

List, Karin; Kosa, Peter; Szabo, Roman; Bey, Alexandra L.; Wang, Chao Becky; Molinolo, Alfredo; Bugge, Thomas H.

2009-01-01

A pericellular proteolytic pathway initiated by the transmembrane serine protease matriptase plays a critical role in the terminal differentiation of epidermal tissues. Matriptase is constitutively expressed in multiple other epithelia, suggesting a putative role of this membrane serine protease in general epithelial homeostasis. Here we generated mice with conditional deletion of the St14 gene, encoding matriptase, and show that matriptase indeed is essential for the maintenance of multiple types of epithelia in the mouse. Thus, embryonic or postnatal ablation of St14 in epithelial tissues of diverse origin and function caused severe organ dysfunction, which was often associated with increased permeability, loss of tight junction function, mislocation of tight junction-associated proteins, and generalized epithelial demise. The study reveals that the homeostasis of multiple simple and stratified epithelia is matriptase-dependent, and provides an important animal model for the exploration of this membrane serine protease in a range of physiological and pathological processes. PMID:19717635

Phenomenological QCD equation of state for massive neutron stars

DOE PAGES

Kojo, Toru; Powell, Philip D.; Song, Yifan; ...

2015-02-03

Here, we construct an equation of state for massive neutron stars based on quantum chromodynamics phenomenology. Our primary purpose is to delineate the relevant ingredients of equations of state that simultaneously have the required stiffness and satisfy constraints from thermodynamics and causality. These ingredients are (i) a repulsive density-density interaction, universal for all flavors, (ii) the color-magnetic interaction active from low to high densities, (iii) confining effects, which become increasingly important as the baryon density decreases, and (iv) nonperturbative gluons, which are not very sensitive to changes of the quark density. We use the following “3-window” description: At baryon densitiesmore » below about twice normal nuclear density, 2n 0, we use the Akmal-Pandharipande-Ravenhall (APR) equation of state, and at high densities, ≥(4–7)n 0, we use the three-flavor Nambu-Jona-Lasinio (NJL) model supplemented by vector and diquark interactions. In the transition density region, we smoothly interpolate the hadronic and quark equations of state in the chemical potential-pressure plane. Requiring that the equation of state approach APR at low densities, we find that the quark pressure in nonconfining models can be larger than the hadronic pressure, unlike in conventional equations of state. We show that consistent equations of state of stiffness sufficient to allow massive neutron stars are reasonably tightly constrained, suggesting that gluon dynamics remains nonperturbative even at baryon densities ~10n 0.« less

Overview of exocrine pancreatic pathobiology.

PubMed

Pandiri, Arun R

2014-01-01

Exocrine pancreas is a source of several enzymes that are essential for the digestive process. The exocrine pancreatic secretion is tightly regulated by the neuroendocrine system. The endocrine pancreas is tightly integrated anatomically and physiologically with the exocrine pancreas and modulates its function. Compound-induced pancreatitis is not a common event in toxicology or drug development, but it becomes a significant liability when encountered. Understanding the species-specific differences in physiology is essential to understand the underlying pathobiology of pancreatic disease in animal models and its relevance to human disease. This review will mainly focus on understanding the morphology and physiology of the pancreas, unique islet-exocrine interactions, and pancreatitis.

Prediction and analysis of beta-turns in proteins by support vector machine.

PubMed

Pham, Tho Hoan; Satou, Kenji; Ho, Tu Bao

2003-01-01

Tight turn has long been recognized as one of the three important features of proteins after the alpha-helix and beta-sheet. Tight turns play an important role in globular proteins from both the structural and functional points of view. More than 90% tight turns are beta-turns. Analysis and prediction of beta-turns in particular and tight turns in general are very useful for the design of new molecules such as drugs, pesticides, and antigens. In this paper, we introduce a support vector machine (SVM) approach to prediction and analysis of beta-turns. We have investigated two aspects of applying SVM to the prediction and analysis of beta-turns. First, we developed a new SVM method, called BTSVM, which predicts beta-turns of a protein from its sequence. The prediction results on the dataset of 426 non-homologous protein chains by sevenfold cross-validation technique showed that our method is superior to the other previous methods. Second, we analyzed how amino acid positions support (or prevent) the formation of beta-turns based on the "multivariable" classification model of a linear SVM. This model is more general than the other ones of previous statistical methods. Our analysis results are more comprehensive and easier to use than previously published analysis results.

Thermodynamic studies of a series of homologous HIV-1 TAR RNA ligands reveal that loose binders are stronger Tat competitors than tight ones

PubMed Central

Pascale, Lise; Azoulay, Stéphane; Di Giorgio, Audrey; Zenacker, Laura; Gaysinski, Marc; Clayette, Pascal; Patino, Nadia

2013-01-01

RNA is a major drug target, but the design of small molecules that modulate RNA function remains a great challenge. In this context, a series of structurally homologous ‘polyamide amino acids’ (PAA) was studied as HIV-1 trans-activating response (TAR) RNA ligands. An extensive thermodynamic study revealed the occurence of an enthalpy–entropy compensation phenomenon resulting in very close TAR affinities for all PAA. However, their binding modes and their ability to compete with the Tat fragment strongly differ according to their structure. Surprisingly, PAA that form loose complexes with TAR were shown to be stronger Tat competitors than those forming tight ones, and thermal denaturation studies demonstrated that loose complexes are more stable than tight ones. This could be correlated to the fact that loose and tight ligands induce distinct RNA conformational changes as revealed by circular dichroism experiments, although nuclear magnetic resonance (NMR) experiments showed that the TAR binding site is the same in all cases. Finally, some loose PAA also display promising inhibitory activities on HIV-infected cells. Altogether, these results lead to a better understanding of RNA interaction modes that could be very useful for devising new ligands of relevant RNA targets. PMID:23605042