Efficient self-consistency for magnetic tight binding

Science.gov (United States)

Soin, Preetma; Horsfield, A. P.; Nguyen-Manh, D.

2011-06-01

Tight binding can be extended to magnetic systems by including an exchange interaction on an atomic site that favours net spin polarisation. We have used a published model, extended to include long-ranged Coulomb interactions, to study defects in iron. We have found that achieving self-consistency using conventional techniques was either unstable or very slow. By formulating the problem of achieving charge and spin self-consistency as a search for stationary points of a Harris-Foulkes functional, extended to include spin, we have derived a much more efficient scheme based on a Newton-Raphson procedure. We demonstrate the capabilities of our method by looking at vacancies and self-interstitials in iron. Self-consistency can indeed be achieved in a more efficient and stable manner, but care needs to be taken to manage this. The algorithm is implemented in the code PLATO. Program summaryProgram title:PLATO Catalogue identifier: AEFC_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFC_v2_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.: 228 747 No. of bytes in distributed program, including test data, etc.: 1 880 369 Distribution format: tar.gz Programming language: C and PERL Computer: Apple Macintosh, PC, Unix machines Operating system: Unix, Linux, Mac OS X, Windows XP 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 Catalogue identifier of previous version: AEFC_v1_0 Journal reference of previous version: Comput. Phys. Comm. 180 (2009) 2616 Does the new version supersede the previous version?: Yes Nature of problem: Achieving charge and spin self-consistency in magnetic tight binding can be very

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

Science.gov (United States)

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.

Some Effective Tight-Binding Models for Electrons in DNA Conduction: A Review

International Nuclear Information System (INIS)

Yamada, H.; Iguchi, K.

2010-01-01

Quantum transport for DNA conduction has been widely studied with interest in application as a candidate in making nanowires as well as interest in the scientific mechanism. In this paper, we review recent works concerning the electronic states and the conduction/transfer in DNA polymers. We have mainly investigated the energy-band structure and the correlation effects of localization property in the two- and three-chain systems (ladder model) with long-range correlation as a simple model for electronic property in a double strand of DNA by using the tight-bindingmodel. In addition, we investigated the localization properties of electronic states in several actual DNA sequences such as bacteriophages of Escherichia coli, human-chromosome 22, compared with those of the artificial disordered sequences with correlation. The charge-transfer properties for poly(dA)-poly(dT) and poly(dG)-poly(dC) DNA polymers are also presented in terms of localization lengths within the frameworks of the polaron models due to the coupling between the charge carriers and the lattice vibrations of the double strand of DNA

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

Energy Technology Data Exchange (ETDEWEB)

Majidi, Muhammad Aziz [Departemen Fisika, FMIPA, Universitas Indonesia, Kampus UI Depok (Indonesia); NUSNNI-NanoCore, Department of Physics, National University of Singapore (NUS), Singapore 117576 (Singapore); Singapore Synchrotron Light Source (SSLS), National University of Singapore (NUS), 5 Research Link, Singapore 117603 (Singapore); Naradipa, Muhammad Avicenna, E-mail: muhammad.avicenna11@ui.ac.id; Phan, Wileam Yonatan; Syahroni, Ahmad [Departemen Fisika, FMIPA, Universitas Indonesia, Kampus UI Depok (Indonesia); Rusydi, Andrivo [NUSNNI-NanoCore, Department of Physics, National University of Singapore (NUS), Singapore 117576 (Singapore); Singapore Synchrotron Light Source (SSLS), National University of Singapore (NUS), 5 Research Link, Singapore 117603 (Singapore)

2016-04-19

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 is 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.

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

International Nuclear Information System (INIS)

Majidi, Muhammad Aziz; Naradipa, Muhammad Avicenna; Phan, Wileam Yonatan; Syahroni, Ahmad; Rusydi, Andrivo

2016-01-01

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 is 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.

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

Science.gov (United States)

Tan, Yaohua; Povolotskyi, Micheal; Kubis, Tillmann; Boykin, Timothy; Klimeck, Gerhard

Modern semiconductor devices have reached critical device dimensions in the range of several nanometers. For reliable prediction of device performance, it is critical to have a numerical efficient model that are transferable to material interfaces. In this work, we present an empirical tight binding (ETB) model with transferable parameters for strained IV and III-V group semiconductors. The ETB model is numerically highly efficient as it make use of an orthogonal sp3d5s* basis set with nearest neighbor inter-atomic interactions. The ETB parameters are generated from HSE06 hybrid functional calculations. Band structures of strained group IV and III-V materials by ETB model are in good agreement with corresponding HSE06 calculations. Furthermore, the ETB model is applied to strained superlattices which consist of group IV and III-V elements. The ETB model turns out to be transferable to nano-scale hetero-structure. The ETB band structures agree with the corresponding HSE06 results in the whole Brillouin zone. The ETB band gaps of superlattices with common cations or common anions have discrepancies within 0.05eV.

MANAGING TIGHT BINDING RECEPTORS FOR NEW SPEARATIONS TECHNOLOGIES

Energy Technology Data Exchange (ETDEWEB)

DARYLE H BUSCH RICHARD S GIVENS

2004-12-10

Much of the earth's pollution involves compounds of the metallic elements, including actinides, strontium, cesium, technetium, and RCRA metals. Metal ions bind to molecules called ligands, which are the molecular tools that can manipulate the metal ions under most conditions. This DOE-EMSP sponsored program strives (1) to provide the foundations for using the most powerful ligands in transformational separations technologies and (2) to produce seminal examples of their applications to separations appropriate to the DOE EM mission. These ultra tight-binding ligands can capture metal ions in the most competitive of circumstances (from mineralized sites, lesser ligands, and even extremely dilute solutions), but they react so slowly that they are useless in traditional separations methodologies. Two attacks on this problem are underway. The first accommodates to the challenging molecular lethargy by developing a seminal slow separations methodology termed the soil poultice. The second designs ligands that are only tight-binding while wrapped around the targeted metal ion, but can be put in place by switch-binding and removed by switch-release. We envision a kind of molecular switching process to accelerate the union between metal ion and tight-binding ligand. Molecular switching processes are suggested for overcoming the slow natural equilibration rate with which ultra tight-binding ligands combine with metal ions. Ligands that bind relatively weakly combine with metal ions rapidly, so the trick is to convert a ligand from a weak, rapidly binding species to a powerful, slow releasing ligand--during the binding of the ligand to the metal ion. Such switch-binding ligands must react with themselves, and the reaction must take place under the influence of the metal ion. For example, our generation 1 ligands showed that a well-designed linear ligand with ends that readily combine, forms a cyclic molecule when it wraps around a metal ion. Our generation 2 ligands are

Emergent gravity in the cubic tight-binding model of Weyl semimetal in the presence of elastic deformations

Energy Technology Data Exchange (ETDEWEB)

Cortijo, Alberto [Instituto de Ciencia de Materiales de Madrid, CSIC, Cantoblanco, 28049 Madrid (Spain); Zubkov, M.A., E-mail: zubkov@itep.ru [ITEP, B. Cheremushkinskaya 25, Moscow, 117259 (Russian Federation); Moscow Institute of Physics and Technology, 9, Institutskii per., Dolgoprudny, Moscow Region, 141700 (Russian Federation); Far Eastern Federal University, School of Biomedicine, 690950 Vladivostok (Russian Federation); National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), Kashirskoe highway 31, 115409 Moscow (Russian Federation)

2016-03-15

We consider the tight-binding model with cubic symmetry that may be relevant for the description of a certain class of Weyl semimetals. We take into account elastic deformations of the semimetal through the modification of hopping parameters. This modification results in the appearance of emergent gauge field and the coordinate dependent anisotropic Fermi velocity. The latter may be interpreted as emergent gravitational field.

Tight binding electronic band structure calculation of achiral boron nitride single wall nanotubes

International Nuclear Information System (INIS)

Saxena, Prapti; Sanyal, Sankar P

2006-01-01

In this paper we report the Tight-Binding method, for the electronic structure calculations of achiral single wall Boron Nitride nanotubes. We have used the contribution of π electron only to define the electronic band structure for the solid. The Zone-folding method is used for the Brillouin Zone definition. Calculation of tight binding model parameters is done by fitting them to available experimental results of two-dimensional hexagonal monolayers of Boron Nitride. It has been found that all the boron nitride nanotubes (both zigzag and armchair) are constant gap semiconductors with a band gap of 5.27eV. All zigzag BNNTs are found to be direct gap semiconductors while all armchair nanotubes are indirect gap semiconductors. (author)

Tight-binding model of the photosystem II reaction center: application to two-dimensional electronic spectroscopy

International Nuclear Information System (INIS)

Gelzinis, Andrius; Valkunas, Leonas; Abramavicius, Darius; Fuller, Franklin D; Ogilvie, Jennifer P; Mukamel, Shaul

2013-01-01

We propose an optimized tight-binding electron–hole model of the photosystem II (PSII) reaction center (RC). Our model incorporates two charge separation pathways and spatial correlations of both static disorder and fast fluctuations of energy levels. It captures the main experimental features observed in time-resolved two-dimensional (2D) optical spectra at 77 K: peak pattern, lineshapes and time traces. Analysis of 2D spectra kinetics reveals that specific regions of the 2D spectra of the PSII RC are sensitive to the charge transfer states. We find that the energy disorder of two peripheral chlorophylls is four times larger than the other RC pigments. (paper)

Tight-binding model of the photosystem II reaction center: application to two-dimensional electronic spectroscopy

Science.gov (United States)

Gelzinis, Andrius; Valkunas, Leonas; Fuller, Franklin D.; Ogilvie, Jennifer P.; Mukamel, Shaul; Abramavicius, Darius

2013-07-01

We propose an optimized tight-binding electron-hole model of the photosystem II (PSII) reaction center (RC). Our model incorporates two charge separation pathways and spatial correlations of both static disorder and fast fluctuations of energy levels. It captures the main experimental features observed in time-resolved two-dimensional (2D) optical spectra at 77 K: peak pattern, lineshapes and time traces. Analysis of 2D spectra kinetics reveals that specific regions of the 2D spectra of the PSII RC are sensitive to the charge transfer states. We find that the energy disorder of two peripheral chlorophylls is four times larger than the other RC pigments.

Surface Passivation in Empirical Tight Binding

OpenAIRE

He, Yu; Tan, Yaohua; Jiang, Zhengping; Povolotskyi, Michael; Klimeck, Gerhard; Kubis, Tillmann

2015-01-01

Empirical Tight Binding (TB) methods are widely used in atomistic device simulations. Existing TB methods to passivate dangling bonds fall into two categories: 1) Method that explicitly includes passivation atoms is limited to passivation with atoms and small molecules only. 2) Method that implicitly incorporates passivation does not distinguish passivation atom types. This work introduces an implicit passivation method that is applicable to any passivation scenario with appropriate parameter...

Perspectives from ab-initio and tight-binding: Applications to transition metal compounds and superlattices

Science.gov (United States)

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

Tight-Binding Parametrization for Photonic Band Gap Materials

International Nuclear Information System (INIS)

Lidorikis, E.; Sigalas, M.M.; Soukoulis, C.M.; Economou, E.N.; Soukoulis, C.M.

1998-01-01

The idea of the linear combination of atomic orbitals method, well known from the study of electrons, is extended to the classical wave case. The Mie resonances of the isolated scatterer in the classical wave case are analogous to the atomic orbitals in the electronic case. The matrix elements of the two-dimensional tight-binding (TB) Hamiltonian are obtained by fitting to ab initio results. The transferability of the TB model is tested by reproducing accurately the band structure of different 2D lattices, with and without defects, and at two different dielectric contrasts. copyright 1998 The American Physical Society

LDA+U and tight-binding electronic structure of InN nanowires

Science.gov (United States)

Molina-Sánchez, A.; García-Cristóbal, A.; Cantarero, A.; Terentjevs, A.; Cicero, G.

2010-10-01

In this paper we employ a combined ab initio and tight-binding approach to obtain the electronic and optical properties of hydrogenated Indium nitride (InN) nanowires. We first discuss InN band structure for the wurtzite structure calculated at the LDA+U level and use this information to extract the parameters needed for an empirical tight-binging implementation. These parameters are then employed to calculate the electronic and optical properties of InN nanowires in a diameter range that would not be affordable by ab initio techniques. The reliability of the large nanowires results is assessed by explicitly comparing the electronic structure of a small diameter wire studied both at LDA+U and tight-binding level.

OLIFE: Tight Binding Code for Transmission Coefficient Calculation

Science.gov (United States)

Mijbil, Zainelabideen Yousif

2018-05-01

A new and human friendly transport calculation code has been developed. It requires a simple tight binding Hamiltonian as the only input file and uses a convenient graphical user interface to control calculations. The effect of magnetic field on junction has also been included. Furthermore the transmission coefficient can be calculated between any two points on the scatterer which ensures high flexibility to check the system. Therefore Olife can highly be recommended as an essential tool for pretesting studying and teaching electron transport in molecular devices that saves a lot of time and effort.

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Quantum tight-binding chains with dissipative coupling

International Nuclear Information System (INIS)

Mogilevtsev, D; Slepyan, G Ya; Garusov, E; Kilin, S Ya; Korolkova, N

2015-01-01

We present a one-dimensional tight-binding chain of two-level systems coupled only through common dissipative Markovian reservoirs. This quantum chain can demonstrate anomalous thermodynamic behavior contradicting Fourier law. Population dynamics of individual systems of the chain is polynomial with the order determined by the initial state of the chain. The chain can simulate classically hard problems, such as multi-dimensional random walks. (paper)

Self-consistent tight-binding model of B and N doping in graphene

DEFF Research Database (Denmark)

Pedersen, Thomas Garm; Pedersen, Jesper Goor

2013-01-01

. The impurity potential depends sensitively on the impurity occupancy, leading to a self-consistency requirement. We solve this problem using the impurity Green's function and determine the self-consistent local density of states at the impurity site and, thereby, identify acceptor and donor energy resonances.......Boron and nitrogen substitutional impurities in graphene are analyzed using a self-consistent tight-binding approach. An analytical result for the impurity Green's function is derived taking broken electron-hole symmetry into account and validated by comparison to numerical diagonalization...

The adsorption effect of C6H5 on density of states for double wall carbon nanotubes by tight binding model

International Nuclear Information System (INIS)

Fathalian, A.

2012-01-01

A theoretical approach based on a tight-binding model is developed to study the effects of the adsorption of finite concentrations of C 6 H 5 gas molecules on double-walled carbon nanotube (DWCNT) electronic properties. To obtain proper hopping integrals and random on-site energies for the case of one molecule adsorption, the local density of states for various hopping integrals and random on-site energies are calculated. Since C 6 H 5 molecule is a donor with respect to the carbon nanotubes and their states should appear near the conduction band of the system, effects of various hopping integral deviations and on-site energies for one molecule adsorption are considered to find proper hopping and on-site energies consistent with expected n-type semiconductor. We found that adsorption of C 6 H 5 gas molecules could lead to a (8.0)-(20.0) DWCNT n-type semiconductor. The width of impurity adsorbed gas states in the density of states could be controlled by adsorbed gas concentration.

The tight binding model study of the role of band filling on the charge gap in graphene-on-substrate in paramagnetic state

Science.gov (United States)

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 [ - ] is calculated and computed numerically. The results are reported.

Incipient localization and tight-binding superconductivity: Tsub(c) calculation

International Nuclear Information System (INIS)

Kolley, E.; Kolley, W.

1984-01-01

Localization effects on the superconducting transition temperature Tsub(c) are examined in strongly disordered three-dimensional systems. A tight-binding formulation of strong-coupling superconductivity is combined, after configuration averaging, with the self-consistent treatment of Anderson localization developed by Vollhardt and Woelfle. The Coulomb interaction becomes retarded via the joint local local density of states, giving rise to an enhancement of the pseudopotential. Numerical Tsub(c) results as a function of disorder are compared with another theoretical work and experimental values for some high-Tsub(c) materials. (orig.)

Atomistic modeling of zirconium hydride precipitation: methodology for deriving a tight-binding potential

International Nuclear Information System (INIS)

Dufresne, Alice

2014-01-01

The zirconium-hydrogen system is of nuclear safety interest, as the hydride precipitation leads to the cladding embrittlement, which is made of zirconium-based alloys. The cladding is the first safety barrier confining the radioactive products: its integrity shall be kept during the entire fuel-assemblies life, in reactor, including accidental situation, and post-operation (transport and storage). Many uncertainties remain regarding the hydrides precipitation kinetics and the local stress impact on their precipitation. The atomic scale modeling of this system would bring clarifications on the relevant mechanisms. The usual atomistic modeling methods are based on thermo-statistic approaches, whose precision and reliability depend on the interatomic potential used. However, there was no potential allowing a rigorous study of the Zr-H system. The present work has indeed addressed this issue: a new tight-binding potential for zirconium hydrides modeling is now available. Moreover, this thesis provides a detailed manual for deriving such potentials accounting for spd hybridization, and fitted here on DFT results. This guidebook has be written in light of modeling a pure transition metal followed by a metal-covalent coupling (metallic carbides, nitrides and silicides). (author)

Substrate-Triggered Exosite Binding: Synergistic Dendrimer/Folic Acid Action for Achieving Specific, Tight-Binding to Folate Binding Protein.

Science.gov (United States)

Chen, Junjie; van Dongen, Mallory A; Merzel, Rachel L; Dougherty, Casey A; Orr, Bradford G; Kanduluru, Ananda Kumar; Low, Philip S; Marsh, E Neil G; Banaszak Holl, Mark M

2016-03-14

Polymer-ligand conjugates are designed to bind proteins for applications as drugs, imaging agents, and transport scaffolds. In this work, we demonstrate a folic acid (FA)-triggered exosite binding of a generation five poly(amidoamine) (G5 PAMAM) dendrimer scaffold to bovine folate binding protein (bFBP). The protein exosite is a secondary binding site on the protein surface, separate from the FA binding pocket, to which the dendrimer binds. Exosite binding is required to achieve the greatly enhanced binding constants and protein structural change observed in this study. The G5Ac-COG-FA1.0 conjugate bound tightly to bFBP, was not displaced by a 28-fold excess of FA, and quenched roughly 80% of the initial fluorescence. Two-step binding kinetics were measured using the intrinsic fluorescence of the FBP tryptophan residues to give a KD in the low nanomolar range for formation of the initial G5Ac-COG-FA1.0/FBP* complex, and a slow conversion to the tight complex formed between the dendrimer and the FBP exosite. The extent of quenching was sensitive to the choice of FA-dendrimer linker chemistry. Direct amide conjugation of FA to G5-PAMAM resulted in roughly 50% fluorescence quenching of the FBP. The G5Ac-COG-FA, which has a longer linker containing a 1,2,3-triazole ring, exhibited an ∼80% fluorescence quenching. The binding of the G5Ac-COG-FA1.0 conjugate was compared to poly(ethylene glycol) (PEG) conjugates of FA (PEGn-FA). PEG2k-FA had a binding strength similar to that of FA, whereas other PEG conjugates with higher molecular weight showed weaker binding. However, no PEG conjugates gave an increased degree of total fluorescence quenching.

Finite temperature magnon spectra in yttrium iron garnet from a mean field approach in a tight-binding model

Science.gov (United States)

Shen, Ka

2018-04-01

We study magnon spectra at finite temperature in yttrium iron garnet using a tight-binding model with nearest-neighbor exchange interaction. The spin reduction due to thermal magnon excitation is taken into account via the mean field approximation to the local spin and is found to be different at two sets of iron atoms. The resulting temperature dependence of the spin wave gap shows good agreement with experiment. We find that only two magnon modes are relevant to the ferromagnetic resonance.

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

Science.gov (United States)

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.

Tight-binding tunneling amplitude of an optical lattice

Science.gov (United States)

Arzamasovs, Maksims; Liu, Bo

2017-11-01

The particle in a periodic potential is an important topic in an undergraduate quantum mechanics curriculum and a stepping stone on the way to more advanced topics, such as courses on interacting electrons in crystalline solids, and graduate-level research in solid-state and condensed matter physics. The interacting many-body phenomena are usually described in terms of the second quantized lattice Hamiltonians which treat single-particle physics on the level of tight-binding approximation and add interactions on top of it. The aim of this paper is to show how the tight-binding tunneling amplitude can be related to the strength of the periodic potential for the case of a cosine potential used in the burgeoning field of ultracold atoms. We show how to approach the problem of computing the tunneling amplitude of a deep lattice using the JWKB (Jeffreys-Wentzel-Kramers-Brillouin, also known as semiclassical) approximation. We also point out that care should be taken when applying the method of the linear combination of atomic orbitals (LCAO) in an optical lattice context. A summary of the exact solution in terms of Mathieu functions is also given.

Tight-binding tunneling amplitude of an optical lattice

International Nuclear Information System (INIS)

Arzamasovs, Maksims; Liu, Bo

2017-01-01

The particle in a periodic potential is an important topic in an undergraduate quantum mechanics curriculum and a stepping stone on the way to more advanced topics, such as courses on interacting electrons in crystalline solids, and graduate-level research in solid-state and condensed matter physics. The interacting many-body phenomena are usually described in terms of the second quantized lattice Hamiltonians which treat single-particle physics on the level of tight-binding approximation and add interactions on top of it. The aim of this paper is to show how the tight-binding tunneling amplitude can be related to the strength of the periodic potential for the case of a cosine potential used in the burgeoning field of ultracold atoms. We show how to approach the problem of computing the tunneling amplitude of a deep lattice using the JWKB (Jeffreys–Wentzel–Kramers–Brillouin, also known as semiclassical) approximation. We also point out that care should be taken when applying the method of the linear combination of atomic orbitals (LCAO) in an optical lattice context. A summary of the exact solution in terms of Mathieu functions is also given. (paper)

Electronic and Magnetic Properties of Transition-Metal Oxide Nanocomposites: A Tight-Binding Modeling at Mesoscale

Science.gov (United States)

Tai, Yuan-Yen; Zhu, Jian-Xin

Transition metal oxides (TMOs) exhibit many emergent phenomena ranging from high-temperature superconductivity and giant magnetoresistance to magnetism and ferroelectricity. In addition, when TMOs are interfaced with each other, new functionalities can arise, which are absent in individual components. In this talk, I will present an overview on our recent efforts in theoretical understanding of the electronic and magnetic properties TMO nanocomposites. In particular, I will introduce our recently developed tight-binding modeling of these properties arising from the interplay of competing interactions at the interfaces of planar and pillar nanocomposites. Our theoretical tool package will provide a unique capability to address the emergent phenomena in TMO nanocomposites and their mesoscale response to such effects like strain and microstructures at the interfaces, and ultimately help establish design principles of new multifunctionality with TMOs. This work was carried out under the auspices of the National Nuclear Security Administration of the U.S. Department of Energy at LANL under Contract No. DE-AC52-06NA25396, and was supported by the LANL LDRD Program.

Empirical tight-binding modeling of ordered and disordered semiconductor structures; Empirische Tight-Binding-Modellierung geordneter und ungeordneter Halbleiterstrukturen

Energy Technology Data Exchange (ETDEWEB)

Mourad, Daniel

2010-11-30

In this thesis, we investigate the electronic and optical properties of pure as well as of substitutionally alloyed II-VI and III-V bulk semiconductors and corresponding semiconductor quantum dots by means of an empirical tight-binding (TB) model. In the case of the alloyed systems of the type A{sub x}B{sub 1-x}, where A and B are the pure compound semiconductor materials, we study the influence of the disorder by means of several extensions of the TB model with different levels of sophistication. Our methods range from rather simple mean-field approaches (virtual crystal approximation, VCA) over a dynamical mean-field approach (coherent potential approximation, CPA) up to calculations where substitutional disorder is incorporated on a finite ensemble of microscopically distinct configurations. In the first part of this thesis, we cover the necessary fundamentals in order to properly introduce the TB model of our choice, the effective bond-orbital model (EBOM). In this model, one s- and three p-orbitals per spin direction are localized on the sites of the underlying Bravais lattice. The matrix elements between these orbitals are treated as free parameters in order to reproduce the properties of one conduction and three valence bands per spin direction and can then be used in supercell calculations in order to model mixed bulk materials or pure as well as mixed quantum dots. Part II of this thesis deals with unalloyed systems. Here, we use the EBOM in combination with configuration interaction calculations for the investigation of the electronic and optical properties of truncated pyramidal GaN quantum dots embedded in AlN with an underlying zincblende structure. Furthermore, we develop a parametrization of the EBOM for materials with a wurtzite structure, which allows for a fit of one conduction and three valence bands per spin direction throughout the whole Brillouin zone of the hexagonal system. In Part III, we focus on the influence of alloying on the electronic

Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids

International Nuclear Information System (INIS)

Aradi, Balint; Frauenheim, Thomas

2015-01-01

A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born-Oppenheimer molecular dynamics. Furthermore, for systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can also be applied to a broad range of problems in materials science, chemistry, and biology

Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids.

Science.gov (United States)

Aradi, Bálint; Niklasson, Anders M N; Frauenheim, Thomas

2015-07-14

A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born-Oppenheimer molecular dynamics. For systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can be applied to a broad range of problems in materials science, chemistry, and biology.

Tight-binding calculation of Ti-Rh--type phase diagram

International Nuclear Information System (INIS)

Sluiter, M.; Turchi, P.; Fu Zezhong; de Fontaine, D.

1988-01-01

Tight-binding electronic band-structure calculations were combined with a free-energy expression from a statistical mechanical method called the cluster-variation method. The effective pair interactions used in the cluster-variation calculation were evaluated by the generalized perturbation method. Only d orbitals were included and the numbers of d electrons per atom were taken to be three for the pure A element and eight for the pure B. A phase diagram was constructed incorporating, for the first time, both fcc and bcc lattices and their simple-ordered superstructures. The calculated diagram agreed reasonably well with those determined empirically for Ti-Rh or Ti-Ir

Tight-binding study of the structural and magnetic properties of vanadium clusters

International Nuclear Information System (INIS)

Zhao Jijun; Lain, K.D.

1995-01-01

The structural and magnetic properties of small vanadium clusters are studied in the framework of tight-binding theory. According to parameters of the cluster dimer and bulk solid, we developed a tight-binding interatomic potential and calculated the bonding energies for the different possible structures to determine the ground state atomic configurations of the small vanadium clusters. The theoretical bonding energies for the vanadium clusters agree with the experiment much better than the simple droplet model. However, the calculated values for the clusters of odd atomic number are somewhat higher than the measured ones, corresponding to the pair occupation of delocalized 4s 1 electrons. Based on the optimized geometries, we study the magnetic properties of these clusters through a parametrized Hubbard Hamiltonian. We find the small V clusters of ground-state structures exhibit antiferromagnetic behavior while the alignment of local moments in the clusters with the unoptimized structures may show either ferromagnetic or antiferromagnetic characteristics. The average magnetic moments of the clusters decrease nonmonotonically as cluster size increases and the theoretical results are consistent with the upper limits obtained from a recent experiment. (orig.)

Photocatalytic oxidation dynamics of acetone on TiO2: tight-binding quantum chemical molecular dynamics study

International Nuclear Information System (INIS)

Lv Chen; Wang Xiaojing; Agalya, Govindasamy; Koyama, Michihisa; Kubo, Momoji; Miyamoto, Akira

2005-01-01

The clarification of the excited states dynamics on TiO 2 surface is important subject for the design of the highly active photocatalysts. In the present study, we applied our novel tight-binding quantum chemical molecular dynamics method to the investigation on the photocatalytic oxidation dynamics of acetone by photogenerated OH radicals on the hydrated anatase TiO 2 surface. The elucidated photocatalytic reaction mechanism strongly supports the previous experimental proposal and finally the effectiveness of our new approach for the clarification of the photocatalytic reaction dynamics employing the large simulation model was confirmed

Multi-band tight-binding calculation of electronic transport in Fe/trans-polyacetylene/Fe tunnel junctions

International Nuclear Information System (INIS)

Abedi Ravan, B

2012-01-01

In this paper, the electronic transport characteristics of Fe/trans-polyacetylene/Fe magnetic tunnel junctions (MTJs) are investigated using multi-band tight-binding calculations within the framework of nonequilibrium Green function theory. A CH 2 radical is added to different positions on the polymer chain and its effects on the tunnelling magnetoresistance of the MTJ are studied. The ferromagnetic electrodes are assumed to be single-band and their tight-binding parameters are chosen in such a way as to simulate the ab initio density functional calculations of the band structure of bcc-Fe along its [001] crystallographic direction. In building the Hamiltonian of the trans-polyacetylene (t-PA) chain, we have assumed an s orbital on the H atoms and one s and three p(p x ,p y ,p z ) orbitals on the C atoms, and the dimerization effects are taken into account. It is found that moving the radical out of the centre of the polymer chain enhances the tunnelling magnetoresistance of the MTJ.

Binding Forces and Teachers' School Life: A Recursive Model.

Science.gov (United States)

Pang, Nicolas Sun-Keung

2003-01-01

Formulates theoretical model of four binding forces in school organizations--bureaucratic linkage, cultural linkage, tight coupling, and loose coupling--and examines their effects on teachers' feelings about school life. Finds, for example, that loose coupling had a positive effect on teachers' sense of community, job satisfaction, and commitment.…

Theoretical study of the structure, energetics, and dynamics of silicon and carbon systems using tight-binding approaches

International Nuclear Information System (INIS)

Xu, Chunhui.

1991-01-01

Semiempirical interatomic potentials are developed for silicon and carbon by modeling the total energy of the system using tight-binding approaches. The parameters of the models were obtained by fitting to results from accurate first-principles Local Density Functional calculations. Applications to the computation of phonons as a function of volume for diamond-structured silicon and carbon and the thermal expansions for silicon and diamond yields results which agree well with experiment. The physical origin of the negative thermal expansion observed in silicon is explained. A tight-binding total energy model is generated capable of describing carbon systems with a variety of atomic coordinations and topologies. The model reproduces the total energy versus volume curves of various carbon polytypes as well as phonons and elastic constants of diamond and graphite. The model has also been used in the molecular-dynamics simulation of the properties of carbon clusters. The calculated ground-state geometries of small clusters (C 2 --C 10 ) correlates well with results from accurate quantum chemical calculations, and the structural trend of clusters from C 2 to C 60 are investigated. 67 refs., 19 figs

Surface Passivation in Empirical Tight Binding

Science.gov (United States)

He, Yu; Tan, Yaohua; Jiang, Zhengping; Povolotskyi, Michael; Klimeck, Gerhard; Kubis, Tillmann

2016-03-01

Empirical Tight Binding (TB) methods are widely used in atomistic device simulations. Existing TB methods to passivate dangling bonds fall into two categories: 1) Method that explicitly includes passivation atoms is limited to passivation with atoms and small molecules only. 2) Method that implicitly incorporates passivation does not distinguish passivation atom types. This work introduces an implicit passivation method that is applicable to any passivation scenario with appropriate parameters. This method is applied to a Si quantum well and a Si ultra-thin body transistor oxidized with SiO2 in several oxidation configurations. Comparison with ab-initio results and experiments verifies the presented method. Oxidation configurations that severely hamper the transistor performance are identified. It is also shown that the commonly used implicit H atom passivation overestimates the transistor performance.

Empirical tight-binding modeling of ordered and disordered semiconductor structures

International Nuclear Information System (INIS)

Mourad, Daniel

2010-01-01

In this thesis, we investigate the electronic and optical properties of pure as well as of substitutionally alloyed II-VI and III-V bulk semiconductors and corresponding semiconductor quantum dots by means of an empirical tight-binding (TB) model. In the case of the alloyed systems of the type A x B 1-x , where A and B are the pure compound semiconductor materials, we study the influence of the disorder by means of several extensions of the TB model with different levels of sophistication. Our methods range from rather simple mean-field approaches (virtual crystal approximation, VCA) over a dynamical mean-field approach (coherent potential approximation, CPA) up to calculations where substitutional disorder is incorporated on a finite ensemble of microscopically distinct configurations. In the first part of this thesis, we cover the necessary fundamentals in order to properly introduce the TB model of our choice, the effective bond-orbital model (EBOM). In this model, one s- and three p-orbitals per spin direction are localized on the sites of the underlying Bravais lattice. The matrix elements between these orbitals are treated as free parameters in order to reproduce the properties of one conduction and three valence bands per spin direction and can then be used in supercell calculations in order to model mixed bulk materials or pure as well as mixed quantum dots. Part II of this thesis deals with unalloyed systems. Here, we use the EBOM in combination with configuration interaction calculations for the investigation of the electronic and optical properties of truncated pyramidal GaN quantum dots embedded in AlN with an underlying zincblende structure. Furthermore, we develop a parametrization of the EBOM for materials with a wurtzite structure, which allows for a fit of one conduction and three valence bands per spin direction throughout the whole Brillouin zone of the hexagonal system. In Part III, we focus on the influence of alloying on the electronic and

From structure to spectra. Tight-binding theory of InGaAs quantum dots

International Nuclear Information System (INIS)

Goldmann, Elias

2014-01-01

demonstrates the applicability of InGaAs quantum dots for quantum telecommunication at the desired telecom wavelengths, offering good growth controllability. For the application in lasers, quantum based active media are known to offer superior properties to common quantum well lasers such as low threshold currents or temperature stability. For device design, the knowledge about the saturation behaviour of optical gain with excitation density is of major importance. In the present work we combine quantum-kinetic models for the calculation of the optical gain of quantum dot active media with our atomistic tight-binding model for the calculation of single-particle energies and wave functions. We investigate the interplay between structural properties of the quantum dots and many-body effects in the optical gain spectra and identify different regimes of saturation behaviour. Either phase-space filling dominates the excitation dependence of the optical gain, leading to saturation, or excitation-induced dephasing dominates the excitation dependence of the optical gain, resulting in a negative differential gain.

From structure to spectra. Tight-binding theory of InGaAs quantum dots

Energy Technology Data Exchange (ETDEWEB)

Goldmann, Elias

2014-07-23

counterintuitively. Our result demonstrates the applicability of InGaAs quantum dots for quantum telecommunication at the desired telecom wavelengths, offering good growth controllability. For the application in lasers, quantum based active media are known to offer superior properties to common quantum well lasers such as low threshold currents or temperature stability. For device design, the knowledge about the saturation behaviour of optical gain with excitation density is of major importance. In the present work we combine quantum-kinetic models for the calculation of the optical gain of quantum dot active media with our atomistic tight-binding model for the calculation of single-particle energies and wave functions. We investigate the interplay between structural properties of the quantum dots and many-body effects in the optical gain spectra and identify different regimes of saturation behaviour. Either phase-space filling dominates the excitation dependence of the optical gain, leading to saturation, or excitation-induced dephasing dominates the excitation dependence of the optical gain, resulting in a negative differential gain.

Analysis of the tight-binding description of the structure of metallic 2D systems

International Nuclear Information System (INIS)

Baquero, R.

1990-12-01

Bidimensional metallic systems as interfaces, quantum wells and superlattices with sharp interfaces became recently available and their properties can now be experimentally studied in detail. To calculate the Local Density of States (LDOS) for surfaces, interfaces, quantum wells and superlattices we use empirical tight-binding Hamiltonians together with the Green function matching method (GFM). In this paper we show some examples of our results employing the method just outlined to describe metallic 2D systems. In particular, we refer briefly to the effect on the LDOS of the very recently established contraction of the first interatomic layer distance in the Ta(001) surface. We then discuss the Nb-V ideal (100) interface and conclude that under certain conditions the V-side of an interface can show magnetism as the V(001) surface does. As a last example, we present a calculation that relates the changes with gold coverage of the reaction rate of the catalytic reaction of cyclohexene into benzene on a Pt(001) surface to the changes on the LDOS of the outermost Pt atomic layer. We show that the behavior of the LDOS around the Fermi level is an important factor to the explanation of the behavior of this catalytic reaction. We conclude by stating that the empirical tight-binding method is a very simple and useful tool for the description of 2D metallic systems. The advantage is that the computational demands are low and all the ingredients to take full profit of this method are available (reliable tight-binding parameters and suitable methods for the calculation of the Green function). (author). 14 refs, 3 figs

Consideration of relativistic effects in band structure calculations based on the empirical tight-binding method

International Nuclear Information System (INIS)

Hanke, M.; Hennig, D.; Kaschte, A.; Koeppen, M.

1988-01-01

The energy band structure of cadmium telluride and mercury telluride materials is investigated by means of the tight-binding (TB) method considering relativistic effects and the spin-orbit interaction. Taking into account relativistic effects in the method is rather simple though the size of the Hamilton matrix doubles. Such considerations are necessary for the interesting small-interstice semiconductors, and the experimental results are reflected correctly in the band structures. The transformation behaviour of the eigenvectors within the Brillouin zone gets more complicated, but is, nevertheless, theoretically controllable. If, however, the matrix elements of the Green operator are to be calculated, one has to use formula manipulation programmes in particular for non-diagonal elements. For defect calculations by the Koster-Slater theory of scattering it is necessary to know these matrix elements. Knowledge of the transformation behaviour of eigenfunctions saves frequent diagonalization of the Hamilton matrix and thus permits a numerical solution of the problem. Corresponding results for the sp 3 basis are available

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

Energy Technology Data Exchange (ETDEWEB)

Rout, G. C., E-mail: siva1987@iopb.res.in, E-mail: skp@iopb.res.in, E-mail: gcr@iopb.res.in [Physics Enclave, Plot No-664/4825, Lane-4A, Shree Vihar, Bhubaneswar-751031, Odisha (India); Sahu, Sivabrata [School of Applied Sciences (Physics), KIIT University, Bhubaneswar-751024, Odisha (India); Panda, S. K. [K.D. Science College, Pochilima, Hinjilicut,Pin-761101 Ganjam, Orissa (India)

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 of 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).

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

International Nuclear Information System (INIS)

Rout, G. C.; Sahu, Sivabrata; Panda, S. K.

2016-01-01

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 of 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).

Atomic and electronic structures of a-SiC:H from tight-binding molecular dynamics

CERN Document Server

Ivashchenko, V I; Shevchenko, V I; Ivashchenko, L A; Rusakov, G V

2003-01-01

The atomic and electronic properties of amorphous unhydrogenated (a-SiC) and hydrogenated (a-SiC:H) silicon carbides are studied using an sp sup 3 s sup * tight-binding force model with molecular dynamics simulations. The parameters of a repulsive pairwise potential are determined from ab initio pseudopotential calculations. Both carbides are generated from dilute vapours condensed from high temperature, with post-annealing at low temperature for a-SiC:H. A plausible model for the inter-atomic correlations and electronic states in a-SiC:H is suggested. According to this model, the formation of the amorphous network is weakly sensitive to the presence of hydrogen. Hydrogen passivates effectively only the weak bonds of threefold-coordinated atoms. Chemical ordering is very much affected by the cooling rate and the structure of the high-temperature vapour. The as-computed characteristics are in rather good agreement with the results for a-SiC and a-Si:H from ab initio calculations.

Dispersion relation and self-collimation frequency of spoof surface plasmon using tight binding model

International Nuclear Information System (INIS)

Bhattacharya, Sayak; Shah, Kushal

2015-01-01

The analytical dispersion relation of spoof surface plasmon (SSP) is known only in the low-frequency limit and thus cannot be used to describe various practically important characteristics of SSP in the high-frequency limit (such as multimodal nature, anisotropic propagation, self-collimation). In this article, we consider a square lattice of holes made on a perfect electric conductor and derive a closed form expression of the SSP dispersion relation in the high-frequency limit using a tight binding model. Instead of using prior knowledge of the band diagram along the entire first Brillouin zone (BZ) edge, we analytically determine the hopping parameters by using the eigenfrequencies only at the three high-symmetry points of the square lattice. Using this dispersion relation, we derive an expression for the self-collimation frequency of SSP. We show that this analytical formulation is also applicable to dielectric photonic crystals and can be used to predict the frequencies corresponding to centimetre-scale supercollimation and second band self-collimation in these structures. Finally, we show that our analytical results are in agreement with the simulation results for both SSP and photonic crystals. (paper)

The tightly bound nuclei in the liquid drop model

Science.gov (United States)

Sree Harsha, N. R.

2018-05-01

In this paper, we shall maximise the binding energy per nucleon function in the semi-empirical mass formula of the liquid drop model of the atomic nuclei to analytically prove that the mean binding energy per nucleon curve has local extrema at A ≈ 58.6960, Z ≈ 26.3908 and at A ≈ 62.0178, Z ≈ 27.7506. The Lagrange method of multipliers is used to arrive at these results, while we have let the values of A and Z take continuous fractional values. The shell model that shows why 62Ni is the most tightly bound nucleus is outlined. A brief account on stellar nucleosynthesis is presented to show why 56Fe is more abundant than 62Ni and 58Fe. We believe that the analytical proof presented in this paper can be a useful tool to the instructors to introduce the nucleus with the highest mean binding energy per nucleon.

Vibrationally resolved UV/Vis spectroscopy with time-dependent density functional based tight binding

NARCIS (Netherlands)

Ruger, R.; Niehaus, T.; van Lenthe, E.; Heine, T.; Visscher, L.

2016-01-01

We report a time-dependent density functional based tight-binding (TD-DFTB) scheme for the calculation of UV/Vis spectra, explicitly taking into account the excitation of nuclear vibrations via the adiabatic Hessian Franck-Condon method with a harmonic approximation for the nu- clear wavefunction.

Surface passivation for tight-binding calculations of covalent solids

International Nuclear Information System (INIS)

Bernstein, N

2007-01-01

Simulation of a cluster representing a finite portion of a larger covalently bonded system requires the passivation of the cluster surface. We compute the effects of an explicit hybrid orbital passivation (EHOP) on the atomic structure in a model bulk, three-dimensional, narrow gap semiconductor, which is very different from the wide gap, quasi-one-dimensional organic molecules where most passivation schemes have been studied in detail. The EHOP approach is directly applicable to minimal atomic orbital basis methods such as tight-binding. Each broken bond is passivated by a hybrid created from an explicitly expressed linear combination of basis orbitals, chosen to represent the contribution of the missing neighbour, e.g. a sp 3 hybrid for a single bond. The method is tested by computing the forces on atoms near a point defect as a function of cluster geometry. We show that, compared to alternatives such as pseudo-hydrogen passivation, the force on an atom converges to the correct bulk limit more quickly as a function of cluster radius, and that the force is more stable with respect to perturbations in the position of the cluster centre. The EHOP method also obviates the need for parameterizing the interactions between the system atoms and the passivating atoms. The method is useful for cluster calculations of non-periodic defects in large systems and for hybrid schemes that simulate large systems by treating finite regions with a quantum-mechanical model, coupled to an interatomic potential description of the rest of the system

DFTBaby: A software package for non-adiabatic molecular dynamics simulations based on long-range corrected tight-binding TD-DFT(B)

Science.gov (United States)

Humeniuk, Alexander; Mitrić, Roland

2017-12-01

A software package, called DFTBaby, is published, which provides the electronic structure needed for running non-adiabatic molecular dynamics simulations at the level of tight-binding DFT. A long-range correction is incorporated to avoid spurious charge transfer states. Excited state energies, their analytic gradients and scalar non-adiabatic couplings are computed using tight-binding TD-DFT. These quantities are fed into a molecular dynamics code, which integrates Newton's equations of motion for the nuclei together with the electronic Schrödinger equation. Non-adiabatic effects are included by surface hopping. As an example, the program is applied to the optimization of excited states and non-adiabatic dynamics of polyfluorene. The python and Fortran source code is available at http://www.dftbaby.chemie.uni-wuerzburg.de.

Combinatorial computational chemistry approach of tight-binding quantum chemical molecular dynamics method to the design of the automotive catalysts

International Nuclear Information System (INIS)

Ito, Yuki; Jung, Changho; Luo, Yi; Koyama, Michihisa; Endou, Akira; Kubo, Momoji; Imamura, Akira; Miyamoto, Akira

2006-01-01

Recently, we have developed a new tight-binding quantum chemical molecular dynamics program 'Colors' for combinatorial computational chemistry approach. This methodology is based on our original tight-binding approximation and realized over 5000 times acceleration compared to the conventional first-principles molecular dynamics method. In the present study, we applied our new program to the simulations on various realistic large-scale models of the automotive three-way catalysts, ultrafine Pt particle/CeO 2 (111) support. Significant electron transfer from the Pt particle to the CeO 2 (111) surface was observed and it was found to strongly depend on the size of the Pt particle. Furthermore, our simulation results suggest that the reduction of the Ce atom due to the electron transfer from the Pt particle to the CeO 2 surface is a main reason for the strong interaction of the Pt particle and CeO 2 (111) support

Phononic crystals of spherical particles: A tight binding approach

Energy Technology Data Exchange (ETDEWEB)

Mattarelli, M., E-mail: maurizio.mattarelli@fisica.unipg.it [NiPS Laboratory, Dipartimento di Fisica, Università di Perugia, Via Pascoli, 06100 Perugia (Italy); Secchi, M. [CMM - Fondazione Bruno Kessler, Via Sommarive 18, 38123 Trento (Italy); Dipartimento di Fisica, Università di Trento, Via Sommarive 14, 38123 Trento (Italy); Montagna, M. [Dipartimento di Fisica, Università di Trento, Via Sommarive 14, 38123 Trento (Italy)

2013-11-07

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.

Tight-binding calculation of radiation loss in photonic crystal CROW.

Science.gov (United States)

Ma, Jing; Martínez, Luis Javier; Fan, Shanhui; Povinelli, Michelle L

2013-01-28

The tight binding approximation (TBA) is used to relate the intrinsic, radiation loss of a coupled resonator optical waveguide (CROW) to that of a single constituent resonator within a light cone picture. We verify the validity of the TBA via direct, full-field simulation of CROWs based on the L2 photonic crystal cavity. The TBA predicts that the quality factor of the CROW increases with that of the isolated cavity. Moreover, our results provide a method to design CROWs with low intrinsic loss across the entire waveguide band.

Physics Colloquium - Tight-binding in a new light: Photons in optical lattices

CERN Multimedia

Ecole de Physique - Université de Genève

2011-01-01

Geneva University Physics Department 24, Quai Ernest Ansermet CH-1211 Geneva 4   Lundi 21 mars 2011, 17h00 Ecole de Physique, Auditoire Stueckelberg Tight-binding in a new light: Photons in optical lattices Dr. Niels Madsen Department of Physics, Swansea University, Singleton Park, Swansea, United Kingdom   Antihydrogen, the bound state of an antiproton and a positron, has been produced at low energies at CERN (the European Organization for Nuclear Research) since 2002. Antihydrogen is of interest for use in a precision test of nature's fundamental symmetries. The charge conjugation/parity/time reversal (CPT) theorem, a crucial part of the foundation of the standard model of elementary particles and interactions, demands that hydrogen and antihydrogen have the same spectrum. Given the current experimental precision of measurements on the hydrogen atom, subjecting antihydrogen to rigorous spectroscopic examination would constitute a compelling, model-independent test of CPT. Antihydrogen co...

Tight-binding electrons on triangular and kagome lattices under staggered modulated magnetic fields: quantum Hall effects and Hofstadter butterflies

International Nuclear Information System (INIS)

Li Juan; Wang Yifei; Gong Changde

2011-01-01

We consider the tight-binding models of electrons on a two-dimensional triangular lattice and kagome lattice under staggered modulated magnetic fields. Such fields have two components: a uniform-flux part with strength φ, and a staggered-flux part with strength Δφ. Various properties of the Hall conductances and Hofstadter butterflies are studied. When φ is fixed, variation of Δφ leads to the quantum Hall transitions and Chern numbers of Landau subbands being redistributed between neighboring pairs. The energy spectra with nonzero Δφs have similar fractal structures but quite different energy gaps compared with the original Hofstadter butterflies of Δφ = 0. Moreover, the fan-like structure of Landau levels in the low magnetic field region is also modified appreciably by Δφ.

Tight-binding electrons on triangular and kagome lattices under staggered modulated magnetic fields: quantum Hall effects and Hofstadter butterflies

Energy Technology Data Exchange (ETDEWEB)

Li Juan; Wang Yifei; Gong Changde, E-mail: yfwang_nju@hotmail.com [Center for Statistical and Theoretical Condensed Matter Physics, and Department of Physics, Zhejiang Normal University, Jinhua 321004 (China)

2011-04-20

We consider the tight-binding models of electrons on a two-dimensional triangular lattice and kagome lattice under staggered modulated magnetic fields. Such fields have two components: a uniform-flux part with strength {phi}, and a staggered-flux part with strength {Delta}{phi}. Various properties of the Hall conductances and Hofstadter butterflies are studied. When {phi} is fixed, variation of {Delta}{phi} leads to the quantum Hall transitions and Chern numbers of Landau subbands being redistributed between neighboring pairs. The energy spectra with nonzero {Delta}{phi}s have similar fractal structures but quite different energy gaps compared with the original Hofstadter butterflies of {Delta}{phi} = 0. Moreover, the fan-like structure of Landau levels in the low magnetic field region is also modified appreciably by {Delta}{phi}.

Total-energy Assisted Tight-binding Method Based on Local Density Approximation of Density Functional Theory

Science.gov (United States)

Fujiwara, Takeo; Nishino, Shinya; Yamamoto, Susumu; Suzuki, Takashi; Ikeda, Minoru; Ohtani, Yasuaki

2018-06-01

A novel tight-binding method is developed, based on the extended Hückel approximation and charge self-consistency, with referring the band structure and the total energy of the local density approximation of the density functional theory. The parameters are so adjusted by computer that the result reproduces the band structure and the total energy, and the algorithm for determining parameters is established. The set of determined parameters is applicable to a variety of crystalline compounds and change of lattice constants, and, in other words, it is transferable. Examples are demonstrated for Si crystals of several crystalline structures varying lattice constants. Since the set of parameters is transferable, the present tight-binding method may be applicable also to molecular dynamics simulations of large-scale systems and long-time dynamical processes.

Low-order moment expansions to tight binding for interatomic potentials: Successes and failures

International Nuclear Information System (INIS)

Kress, J.D.; Voter, A.F.

1995-01-01

We discuss the use of moment-based approximations to tight binding. Using a maximum entropy form for the electronic density of states, we show that a general interatomic potential can be defined that is suitable for molecular-dynamics simulations and has several other desirable features. For covalent materials (C and Si), properties where the atoms are in equivalent environments are well converged at low-order moments. For defect environments, which offer a more critical (and relevant) test, the method is found to give less satisfactory results. For example, the vacancy formation energy for Si is too low by ∼2 eV at 10 moments relative to exact tight binding. Attempts to improve the accuracy were unsuccessful, leading to the conclusion that potentials based on this approach are inadequate for covalent materials. We speculate that this may be a deficiency of low-order moment methods in general. For metals, in contrast to the covalent systems, we find that the low-order moment approach is better behaved. This finding is consistent with the success of existing empirical fourth-moment potentials for metals

Free energy of RNA-counterion interactions in a tight-binding model computed by a discrete space mapping

International Nuclear Information System (INIS)

Henke, Paul S.; Mak, Chi H.

2014-01-01

The thermodynamic stability of a folded RNA is intricately tied to the counterions and the free energy of this interaction must be accounted for in any realistic RNA simulations. Extending a tight-binding model published previously, in this paper we investigate the fundamental structure of charges arising from the interaction between small functional RNA molecules and divalent ions such as Mg 2+ that are especially conducive to stabilizing folded conformations. The characteristic nature of these charges is utilized to construct a discretely connected energy landscape that is then traversed via a novel application of a deterministic graph search technique. This search method can be incorporated into larger simulations of small RNA molecules and provides a fast and accurate way to calculate the free energy arising from the interactions between an RNA and divalent counterions. The utility of this algorithm is demonstrated within a fully atomistic Monte Carlo simulation of the P4-P6 domain of the Tetrahymena group I intron, in which it is shown that the counterion-mediated free energy conclusively directs folding into a compact structure

Free energy of RNA-counterion interactions in a tight-binding model computed by a discrete space mapping

Energy Technology Data Exchange (ETDEWEB)

Henke, Paul S. [Department of Chemistry, University of Southern California, Los Angeles, California 90089 (United States); Mak, Chi H., E-mail: cmak@usc.edu [Department of Chemistry, University of Southern California, Los Angeles, California 90089 (United States); Center of Applied Mathematical Sciences, University of Southern California, Los Angeles, California 90089 (United States)

2014-08-14

The thermodynamic stability of a folded RNA is intricately tied to the counterions and the free energy of this interaction must be accounted for in any realistic RNA simulations. Extending a tight-binding model published previously, in this paper we investigate the fundamental structure of charges arising from the interaction between small functional RNA molecules and divalent ions such as Mg{sup 2+} that are especially conducive to stabilizing folded conformations. The characteristic nature of these charges is utilized to construct a discretely connected energy landscape that is then traversed via a novel application of a deterministic graph search technique. This search method can be incorporated into larger simulations of small RNA molecules and provides a fast and accurate way to calculate the free energy arising from the interactions between an RNA and divalent counterions. The utility of this algorithm is demonstrated within a fully atomistic Monte Carlo simulation of the P4-P6 domain of the Tetrahymena group I intron, in which it is shown that the counterion-mediated free energy conclusively directs folding into a compact structure.

Gate dielectric strength dependent performance of CNT MOSFET and CNT TFET: A tight binding study

Directory of Open Access Journals (Sweden)

Md. Shamim Sarker

Full Text Available This paper presents a comparative study between CNT MOSFET and CNT TFET taking into account of different dielectric strength of gate oxide materials. Here we have studied the transfer characteristics, on/off current (ION/IOFF ratio and subthreshold slope of the device using Non Equilibrium Greens Function (NEGF formalism in tight binding frameworks. The results are obtained by solving the NEGF and Poisson’s equation self-consistently in NanoTCADViDES environment and found that the ON state performance of CNT MOSFET and CNT TFET have significant dependency on the dielectric strength of the gate oxide materials. The figure of merits of the devices also demonstrates that the CNT TFET is promising for high-speed and low-power logic applications. Keywords: CNT TFET, Subthreshold slop, Barrier width, Conduction band (C.B and Valance band (V.B, Oxide dielectric strength, Tight binding approach

Effective-medium tight-binding model for silicon

DEFF Research Database (Denmark)

Stokbro, Kurt; Chetty, N.; Jacobsen, Karsten Wedel

1994-01-01

A method for calculating the total energy of Si systems, which is based on the effective-medium-theory concept of a reference system, is presented. Instead of calculating the energy of an atom in the system of interest, a reference system is introduced where the local surroundings are similar. Th...

The band gap of II-Vi ternary alloys in a tight-binding description

Energy Technology Data Exchange (ETDEWEB)

Olguin, Daniel; Blanquero, Rafael [Instituto Politecnico Nacional, Mexico, D.F (Mexico); De Coss, Romeo [Instituto Politecnico Nacional, Yucatan (Mexico)

2001-02-01

We present tight-binding calculations for the band gap of II-Vi pseudobinary ternary alloys. We use an sp{sup 3} s* tight-binding Hamiltonian which include spin-orbit coupling. The band gap composition dependence is calculated using a extended version of the virtual crystal approximation, which introduce an empirical correction factor that takes into account the non-linear dependence of the band gap with the composition. The results compare quite well with the experimental data, both for the ternary alloys with wide band gap and for the narrow band gap ones. [Spanish] Presentamos el calculo de la banda de energia prohibida de aleaciones ternarias de compuestos II-VI. El calculo, que incluye interaccion espin-orbita, se hace con el metodo de enlace fuerte, utilizando una base ortogonal de cinco orbitales atomicos por atomo (sp{sup 3} s*), en conjunto con la aproximacion del cristal virtual. En la aproximacion del cristal virtual, incluimos un factor de correccion que toma en cuenta la no linealidad de la banda de energia prohibida como funcion de la concentracion. Con esta correccion nuestros resultados reproducen aceptablemente los datos experimentales hallados en la literatura.

Band structure and orbital character of monolayer MoS2 with eleven-band tight-binding model

Science.gov (United States)

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.

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

Science.gov (United States)

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.

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

International Nuclear Information System (INIS)

Hegde, Ganesh; Povolotskyi, Michael; Kubis, Tillmann; Charles, James; Klimeck, Gerhard

2014-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

Hegde, Ganesh, E-mail: ghegde@purdue.edu; Povolotskyi, Michael; Kubis, Tillmann; Charles, James; Klimeck, Gerhard, E-mail: gekco@purdue.edu [Network for Computational Nanotechnology (NCN), Department of Electrical and Computer Engineering, Purdue University, West Lafayette, Indiana 47907 (United States)

2014-03-28

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.

Energy spectrum of two-dimensional tight-binding electrons in a spatially varying magnetic field

International Nuclear Information System (INIS)

Oh, G.Y.; Lee, M.H.

1996-01-01

The electronic energy spectrum of a two-dimensional lattice in a spatially varying magnetic field is studied within the framework of the tight-binding model by using the scheme of the transfer matrix. It is found that, in comparison with the case of a uniform magnetic field, the energy spectrum exhibits more complicated behavior; band broadening (or gap closing) and band splitting (or gap opening) occur depending on characteristic parameters of the lattice. The origin of these phenomena lies in the existence of direct touching and indirect overlapping between neighboring subbands. Dependence of direct touching and indirect overlapping, and thus the electronic band structure together with the density of states, on characteristic parameters of the lattice is elucidated in detail. copyright 1996 The American Physical Society

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Time-efficient simulations of tight-binding electronic structures with Intel Xeon PhiTM many-core processors

Science.gov (United States)

Ryu, Hoon; Jeong, Yosang; Kang, Ji-Hoon; Cho, Kyu Nam

2016-12-01

Modelling of multi-million atomic semiconductor structures is important as it not only predicts properties of physically realizable novel materials, but can accelerate advanced device designs. This work elaborates a new Technology-Computer-Aided-Design (TCAD) tool for nanoelectronics modelling, which uses a sp3d5s∗ tight-binding approach to describe multi-million atomic structures, and simulate electronic structures with high performance computing (HPC), including atomic effects such as alloy and dopant disorders. Being named as Quantum simulation tool for Advanced Nanoscale Devices (Q-AND), the tool shows nice scalability on traditional multi-core HPC clusters implying the strong capability of large-scale electronic structure simulations, particularly with remarkable performance enhancement on latest clusters of Intel Xeon PhiTM coprocessors. A review of the recent modelling study conducted to understand an experimental work of highly phosphorus-doped silicon nanowires, is presented to demonstrate the utility of Q-AND. Having been developed via Intel Parallel Computing Center project, Q-AND will be open to public to establish a sound framework of nanoelectronics modelling with advanced HPC clusters of a many-core base. With details of the development methodology and exemplary study of dopant electronics, this work will present a practical guideline for TCAD development to researchers in the field of computational nanoelectronics.

Development of tight-binding, chemical-reaction-dynamics simulator for combinatorial computational chemistry

International Nuclear Information System (INIS)

Kubo, Momoji; Ando, Minako; Sakahara, Satoshi; Jung, Changho; Seki, Kotaro; Kusagaya, Tomonori; Endou, Akira; Takami, Seiichi; Imamura, Akira; Miyamoto, Akira

2004-01-01

Recently, we have proposed a new concept called 'combinatorial computational chemistry' to realize a theoretical, high-throughput screening of catalysts and materials. We have already applied our combinatorial, computational-chemistry approach, mainly based on static first-principles calculations, to various catalysts and materials systems and its applicability to the catalysts and materials design was strongly confirmed. In order to realize more effective and efficient combinatorial, computational-chemistry screening, a high-speed, chemical-reaction-dynamics simulator based on quantum-chemical, molecular-dynamics method is essential. However, to the best of our knowledge, there is no chemical-reaction-dynamics simulator, which has an enough high-speed ability to perform a high-throughput screening. In the present study, we have succeeded in the development of a chemical-reaction-dynamics simulator based on our original, tight-binding, quantum-chemical, molecular-dynamics method, which is more than 5000 times faster than the regular first-principles, molecular-dynamics method. Moreover, its applicability and effectiveness to the atomistic clarification of the methanol-synthesis dynamics at reaction temperature were demonstrated

Tight-Binding simulations of InAs/GaAs quantum dots; Tight-Binding Simulationen von InAs/GaAs Quantenpunkten

Energy Technology Data Exchange (ETDEWEB)

Kleinsorge, Alexander

2008-06-23

For several years, the technological potential of self-organized grown quantum dots (QD) has been known. Their usage as an effective light source or memory requires the precise prediction of their electronic properties. Hence, this report will study InAs quantum dots at GaAs substrate. After relaxing the atomic positions with a many body potential of Abell-Tersoff type, I calculated the electronic structure using the Tight-Binding method which is reasonable for large systems. During the investigation of wavefunctions depend on the shape, size and temperature, the impact of strain showed up as the main reason for the p-splitting. Typically flat QDs (relative to lateral dimensions) are grown, therefore the energy of bound states depends mostly on their height. The crystal's orientation had a strong impact on the wavefunctions. Moreover, the understanding of STS experiments, which inspected the connection between shape and wavefunction, is better now. Because of the possible simultaneous occupation of semiconductor quantum dots with an electron and a hole, there is a dipole moment of the exciton (due to their different behaviour inside the QD). This is a further experimental access to inner details of the QD. I ascertained the interplay of composition profile and dipole moment. The force caused by additional potentials (piezoelectricity, outer homogeneous and inhomogeneous electrical fields) was also an subject of my inquiries. To conclude, I executed kMC simulations, to better apprehend the annealing experiments. I was able to explain the narrowing of the PL peak width better. Furthermore I showed a ramification of the strain field to the diffusion development (and the following electronic properties). (orig.)

Zonula occludens toxin structure-function analysis. Identification of the fragment biologically active on tight junctions and of the zonulin receptor binding domain.

Science.gov (United States)

Di Pierro, M; Lu, R; Uzzau, S; Wang, W; Margaretten, K; Pazzani, C; Maimone, F; Fasano, A

2001-06-01

Zonula occludens toxin (Zot) is an enterotoxin elaborated by Vibrio cholerae that increases intestinal permeability by interacting with a mammalian cell receptor with subsequent activation of intracellular signaling leading to the disassembly of the intercellular tight junctions. Zot localizes in the bacterial outer membrane of V. cholerae with subsequent cleavage and secretion of a carboxyl-terminal fragment in the host intestinal milieu. To identify the Zot domain(s) directly involved in the protein permeating effect, several zot gene deletion mutants were constructed and tested for their biological activity in the Ussing chamber assay and their ability to bind to the target receptor on intestinal epithelial cell cultures. The Zot biologically active domain was localized toward the carboxyl terminus of the protein and coincided with the predicted cleavage product generated by V. cholerae. This domain shared a putative receptor-binding motif with zonulin, the Zot mammalian analogue involved in tight junction modulation. Amino acid comparison between the Zot active fragment and zonulin, combined with site-directed mutagenesis experiments, confirmed the presence of an octapeptide receptor-binding domain toward the amino terminus of the processed Zot.

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

Energy Technology Data Exchange (ETDEWEB)

Hegde, Ganesh, E-mail: ghegde@purdue.edu; Povolotskyi, Michael; Kubis, Tillmann; Klimeck, Gerhard, E-mail: gekco@purdue.edu [Network for Computational Nanotechnology (NCN), Department of Electrical and Computer Engineering, Purdue University, West Lafayette, Indiana 47907 (United States); Boykin, Timothy [Department of Electrical and Computer Engineering, University of Alabama, Huntsville, Alabama (United States)

2014-03-28

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.

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

International Nuclear Information System (INIS)

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

2014-01-01

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

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

Science.gov (United States)

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.

Theory of the electronic structure of dilute bismide and bismide-nitride alloys of GaAs: Tight-binding and k.p models

International Nuclear Information System (INIS)

Usman, Muhammad; Broderick, Christopher A.; O'Reilly, Eoin P.

2013-01-01

The addition of dilute concentrations of bismuth (Bi) into GaAs to form GaBi x As 1−x alloys results in a large reduction of the band gap energy (E g ) accompanied by a significant increase of the spin-orbit-splitting energy (Δ SO ), leading to an E g SO regime for x ∼ 10% which is technologically relevant for the design of highly efficient photonic devices. The quaternary alloy GaBi x N y As 1−x−y offers further flexibility for band gap tuning, because both nitrogen and bismuth can independently induce band gap reduction. This work reports sp 3 s* tight binding and 14-band k⋅p models for the study of the electronic structure of GaBi x As 1−x and GaBi x N y As 1−x−y alloys. Our results are in good agreement with the available experimental data

Mechanical Control of ATP Synthase Function: Activation Energy Difference between Tight and Loose Binding Sites

KAUST Repository

Beke-Somfai, Tamás

2010-01-26

Despite exhaustive chemical and crystal structure studies, the mechanistic details of how FoF1-ATP synthase can convert mechanical energy to chemical, producing ATP, are still not fully understood. On the basis of quantum mechanical calculations using a recent highresolution X-ray structure, we conclude that formation of the P-O bond may be achieved through a transition state (TS) with a planar PO3 - ion. Surprisingly, there is a more than 40 kJ/mol difference between barrier heights of the loose and tight binding sites of the enzyme. This indicates that even a relatively small change in active site conformation, induced by the γ-subunit rotation, may effectively block the back reaction in βTP and, thus, promote ATP. © 2009 American Chemical Society.

Atomic scale simulations of pyrochlore oxides with a tight-binding variable-charge model: implications for radiation tolerance

International Nuclear Information System (INIS)

Sattonnay, G; Tétot, R

2014-01-01

Atomistic simulations with new interatomic potentials derived from a tight-binding variable-charge model were performed in order to investigate the lattice properties and the defect formation energies in Gd 2 Ti 2 O 7 and Gd 2 Zr 2 O 7 pyrochlores. The main objective was to determine the role played by the defect stability on the radiation tolerance of these compounds. Calculations show that the titanate has a more covalent character than the zirconate. Moreover, the properties of oxygen Frenkel pairs, cation antisite defects and cation Frenkel pairs were studied. In Gd 2 Ti 2 O 7 the cation antisite defect and the Ti-Frenkel pair are not stable: they evolve towards more stable defect configurations during the atomic relaxation process. This phenomenon is driven by a decrease of the Ti coordination number down to five which leads to a local atomic reorganization and strong structural distortions around the defects. These kinds of atomic rearrangements are not observed around defects in Gd 2 Zr 2 O 7 . Therefore, the defect stability in A 2 B 2 O 7 depends on the ability of B atoms to accommodate high coordination number (higher than six seems impossible for Ti). The accumulation of structural distortions around Ti-defects due to this phenomenon could drive the Gd 2 Ti 2 O 7 amorphization induced by irradiation. (paper)

Time-dependent density-functional tight-binding method with the third-order expansion of electron density.

Science.gov (United States)

Nishimoto, Yoshio

2015-09-07

We develop a formalism for the calculation of excitation energies and excited state gradients for the self-consistent-charge density-functional tight-binding method with the third-order contributions of a Taylor series of the density functional theory energy with respect to the fluctuation of electron density (time-dependent density-functional tight-binding (TD-DFTB3)). The formulation of the excitation energy is based on the existing time-dependent density functional theory and the older TD-DFTB2 formulae. The analytical gradient is computed by solving Z-vector equations, and it requires one to calculate the third-order derivative of the total energy with respect to density matrix elements due to the inclusion of the third-order contributions. The comparison of adiabatic excitation energies for selected small and medium-size molecules using the TD-DFTB2 and TD-DFTB3 methods shows that the inclusion of the third-order contributions does not affect excitation energies significantly. A different set of parameters, which are optimized for DFTB3, slightly improves the prediction of adiabatic excitation energies statistically. The application of TD-DFTB for the prediction of absorption and fluorescence energies of cresyl violet demonstrates that TD-DFTB3 reproduced the experimental fluorescence energy quite well.

Identification of Tight-Binding Plasmepsin II and Falcipain 2 Inhibitors in Aqueous Extracts of Marine Invertebrates by the Combination of Enzymatic and Interaction-Based Assays

Science.gov (United States)

Salas-Sarduy, Emir; Guerra, Yasel; Covaleda Cortés, Giovanni; Avilés, Francesc Xavier; Chávez Planes, María A.

2017-01-01

Natural products from marine origin constitute a very promising and underexplored source of interesting compounds for modern biotechnological and pharmaceutical industries. However, their evaluation is quite challenging and requires specifically designed assays to reliably identify the compounds of interest in a highly heterogeneous and interfering context. In the present study, we describe a general strategy for the confident identification of tight-binding protease inhibitors in the aqueous extracts of 62 Cuban marine invertebrates, using Plasmodium falciparum hemoglobinases Plasmepsin II and Falcipain 2 as model enzymes. To this end, we first developed a screening strategy that combined enzymatic with interaction-based assays and then validated screening conditions using five reference extracts. Interferences were evaluated and minimized. The results from the massive screening of such extracts, the validation of several hits by a variety of interaction-based assays and the purification and functional characterization of PhPI, a multifunctional and reversible tight-binding inhibitor for Plasmepsin II and Falcipain 2 from the gorgonian Plexaura homomalla, are presented. PMID:28430158

Influence of chemical disorder on the electronic level spacing distribution of the Ag{sub 5083} nanoparticle: A tight-binding study

Energy Technology Data Exchange (ETDEWEB)

Medrano, L.R., E-mail: leonardoms20@gmail.com [Faculty of Physical Sciences, National University of San Marcos, P.O. Box 14-0149, Lima 14 (Peru); Landauro, C.V., E-mail: clandauros@unmsm.edu.pe [Faculty of Physical Sciences, National University of San Marcos, P.O. Box 14-0149, Lima 14 (Peru)

2013-03-01

In the present work we study, employing a tight-binding Hamiltonian, the influence of chemical disorder on the electronic level spacing distribution of a silver nanoparticle containing 5083 atoms (∼ 5.5 nm). This nanoparticle was obtained by molecular dynamics simulations with a tight-binding atomic potential. The results indicate that in the absence of disorder the level spacing distributions are similar to those expected for systems belonging to the Gaussian Orthogonal Ensemble. Whereas, after increasing the chemical disorder, the electronic level spacing distribution and the Σ{sub 2} statistics tend to the corresponding form for the Poisson Ensemble, i.e., the silver nanoparticle acquires an insulating character which is expected for strongly disordered systems. Hence, this kind of disorder produces the localization of the electronic states of the nanoparticle.

Assessment of the Density Functional Tight Binding Method for Protic Ionic Liquids.

Science.gov (United States)

Addicoat, Matthew A; Stefanovic, Ryan; Webber, Grant B; Atkin, Rob; Page, Alister J

2014-10-14

Density functional tight binding (DFTB), which is ∼100-1000 times faster than full density functional theory (DFT), has been used to simulate the structure and properties of protic ionic liquid (IL) ions, clusters of ions and the bulk liquid. Proton affinities for a wide range of IL cations and anions determined using DFTB generally reproduce G3B3 values to within 5-10 kcal/mol. The structures and thermodynamic stabilities of n -alkyl ammonium nitrate clusters (up to 450 quantum chemical atoms) predicted with DFTB are in excellent agreement with those determined using DFT. The IL bulk structure simulated using DFTB with periodic boundary conditions is in excellent agreement with published neutron diffraction data.

Tightness of voter model interfaces

Czech Academy of Sciences Publication Activity Database

Sturm, A.; Swart, Jan M.

2008-01-01

Roč. 13, - (2008), s. 165-174 ISSN 1083-589X R&D Projects: GA ČR GA201/06/1323; GA ČR GA201/07/0237 Institutional research plan: CEZ:AV0Z10750506 Keywords : long range voter model * swapping voter model * interface tightness * exclusion process Subject RIV: BD - Theory of Information Impact factor: 0.392, year: 2008 http://www.emis.de/journals/EJP-ECP/_ejpecp/index.html

Environment-dependent crystal-field tight-binding based on density-functional theory

International Nuclear Information System (INIS)

Urban, Alexander

2012-01-01

Electronic structure calculations based on Kohn-Sham density-functional theory (DFT) allow the accurate prediction of chemical bonding and materials properties. Due to the high computational demand DFT calculations are, however, restricted to structures containing at most several hundreds of atoms, i.e., to length scales of a few nanometers. Though, many processes of technological relevance, for example in the field of nanoelectronics, are governed by phenomena that occur on a slightly larger length scale of up to 100 nanometers, which corresponds to tens of thousands of atoms. The semiempirical Slater-Koster tight-binding (TB) method makes it feasible to calculate the electronic structure of such large systems. In contrast to first-principles-based DFT, which is universally applicable to almost all chemical species, the TB method is based on parametrized models that are usually specialized for a particular application or for one certain class of compounds. Usually the model parameters (Slater-Koster tables) are empirically adjusted to reproduce either experimental reference data (e.g., geometries, elastic constants) or data from first-principles methods such as DFT. The construction of a new TB model is therefore connected with a considerable effort that is often contrasted by a low transferability of the parametrization. In this thesis we develop a systematic methodology for the derivation of accurate and transferable TB models from DFT calculations. Our procedure exploits the formal relationship between the two methods, according to which the TB total energy can be understood as a direct approximation of the Kohn--Sham energy functional. The concept of our method is different to previous approaches such as the DFTB method, since it allows to extract TB parameters from converged DFT wave functions and Hamiltonians of arbitrary reference structures. In the following the different subjects of this thesis are briefly summarized. We introduce a new technique for the

Coxibs interfere with the action of aspirin by binding tightly to one monomer of cyclooxygenase-1

Energy Technology Data Exchange (ETDEWEB)

Rimon, Gilad; Sidhu, Ranjinder S.; Lauver, D. Adam; Lee, Jullia Y.; Sharma, Narayan P.; Yuan, Chong; Frieler, Ryan A.; Trievel, Raymond C.; Lucchesi, Benedict R.; Smith, William L. (Michigan)

2010-02-11

Pain associated with inflammation involves prostaglandins synthesized from arachidonic acid (AA) through cyclooxygenase-2 (COX-2) pathways while thromboxane A{sub 2} formed by platelets from AA via cyclooxygenase-1 (COX-1) mediates thrombosis. COX-1 and COX-2 are both targets of nonselective nonsteroidal antiinflammatory drugs (nsNSAIDs) including aspirin whereas COX-2 activity is preferentially blocked by COX-2 inhibitors called coxibs. COXs are homodimers composed of identical subunits, but we have shown that only one subunit is active at a time during catalysis; moreover, many nsNSAIDS bind to a single subunit of a COX dimer to inhibit the COX activity of the entire dimer. Here, we report the surprising observation that celecoxib and other coxibs bind tightly to a subunit of COX-1. Although celecoxib binding to one monomer of COX-1 does not affect the normal catalytic processing of AA by the second, partner subunit, celecoxib does interfere with the inhibition of COX-1 by aspirin in vitro. X-ray crystallographic results obtained with a celecoxib/COX-1 complex show how celecoxib can bind to one of the two available COX sites of the COX-1 dimer. Finally, we find that administration of celecoxib to dogs interferes with the ability of a low dose of aspirin to inhibit AA-induced ex vivo platelet aggregation. COX-2 inhibitors such as celecoxib are widely used for pain relief. Because coxibs exhibit cardiovascular side effects, they are often prescribed in combination with low-dose aspirin to prevent thrombosis. Our studies predict that the cardioprotective effect of low-dose aspirin on COX-1 may be blunted when taken with coxibs.

Tight-binding analysis of Si and GaAs ultrathin bodies with subatomic wave-function resolution

Science.gov (United States)

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.

Effective Medium Tight-Binding Theory

OpenAIRE

Stokbro, Kurt

1994-01-01

In this thesis a new model for calculating the total energy of atomic and solid systems is presented. The model is used to study the properties of the Si(100) surface and dislocation dynamics in the diamond structure. For the Si(100) surface the main result is the finding of an incomplete melted state at $1550^0 K$. The studied dislocation is the $90^0$ partial and it is found that the barriers for kink formation and migration are in good accordance with experimental observations. The general...

DFTB3: Extension of the self-consistent-charge density-functional tight-binding method (SCC-DFTB).

Science.gov (United States)

Gaus, Michael; Cui, Qiang; Elstner, Marcus

2012-04-10

The self-consistent-charge density-functional tight-binding method (SCC-DFTB) is an approximate quantum chemical method derived from density functional theory (DFT) based on a second-order expansion of the DFT total energy around a reference density. In the present study we combine earlier extensions and improve them consistently with, first, an improved Coulomb interaction between atomic partial charges, and second, the complete third-order expansion of the DFT total energy. These modifications lead us to the next generation of the DFTB methodology called DFTB3, which substantially improves the description of charged systems containing elements C, H, N, O, and P, especially regarding hydrogen binding energies and proton affinities. As a result, DFTB3 is particularly applicable to biomolecular systems. Remaining challenges and possible solutions are also briefly discussed.

Modelling the delay between pharmacokinetics and EEG effects of morphine in rats: binding kinetic versus effect compartment models.

Science.gov (United States)

de Witte, Wilhelmus E A; Rottschäfer, Vivi; Danhof, Meindert; van der Graaf, Piet H; Peletier, Lambertus A; de Lange, Elizabeth C M

2018-05-18

Drug-target binding kinetics (as determined by association and dissociation rate constants, k on and k off ) can be an important determinant of the kinetics of drug action. However, the effect compartment model is used most frequently instead of a target binding model to describe hysteresis. Here we investigate when the drug-target binding model should be used in lieu of the effect compartment model. The utility of the effect compartment (EC), the target binding kinetics (TB) and the combined effect compartment-target binding kinetics (EC-TB) model were tested on either plasma (EC PL , TB PL and EC-TB PL ) or brain extracellular fluid (ECF) (EC ECF , TB ECF and EC-TB ECF ) morphine concentrations and EEG amplitude in rats. It was also analyzed when a significant shift in the time to maximal target occupancy (Tmax TO ) with increasing dose, the discriminating feature between the TB and EC model, occurs in the TB model. All TB models assumed a linear relationship between target occupancy and drug effect on the EEG amplitude. All three model types performed similarly in describing the morphine pharmacodynamics data, although the EC model provided the best statistical result. The analysis of the shift in Tmax TO (∆Tmax TO ) as a result of increasing dose revealed that ∆Tmax TO is decreasing towards zero if the k off is much smaller than the elimination rate constant or if the target concentration is larger than the initial morphine concentration. The results for the morphine PKPD modelling and the analysis of ∆Tmax TO indicate that the EC and TB models do not necessarily lead to different drug effect versus time curves for different doses if a delay between drug concentrations and drug effect (hysteresis) is described. Drawing mechanistic conclusions from successfully fitting one of these two models should therefore be avoided. Since the TB model can be informed by in vitro measurements of k on and k off , a target binding model should be considered more often

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

Science.gov (United States)

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.

Dielectric constant of graphene-on-polarized substrate: A tight ...

Indian Academy of Sciences (India)

2017-06-24

Jun 24, 2017 ... We report here a microscopic tight-binding theoretical study of the dynamic dielectric response of graphene-on-polarizable substrate with impurity. The Hamiltonian consists of first, second and third nearest neighbour electron hopping interactions besides doping and substrate-induced effects on graphene.

Tight-binding study of the hole subband structure properties of p-type delta-doped quantum wells in Si by using a Thomas-Fermi-Dirac potential

International Nuclear Information System (INIS)

Rodriguez-Vargas, I; Madrigal-Melchor, J; Vlaev, S J

2009-01-01

We present the hole subband structure of p-type delta-doped single, double, multiple and superlattice quantum wells in Si. We use the first neighbors sp 3 s' tight-binding approximation including spin for the hole level structure analysis. The parameters of the tight-binding hamiltonian were taken from Klimeck et al. [Klimeck G, Bowen R C, Boykin T B, Salazar-Lazaro C, Cwik T A and Stoica A 2000 Superlattice. Microst. 27 77], first neighbors parameters that give realiable results for the valence band of Si. The calculations are based on a scheme previously proposed and applied to delta-doped quantum well systems [Vlaev S J and Gaggero-Sager L M 1998 Phys. Rev. B 58 1142]. The scheme relies on the incorporation of the delta-doped quantum well potential in the diagonal terms of the tight-binding hamiltonian. We give a detail description of the delta-doped quantum well structures, this is, we study the hole subband structure behavior as a function of the impurity density, the interwell distance of the doped planes and the superlattice period. We also compare our results with the available theoretical and experimental data, obtaining a reasonable agreement.

Tight-binding study of the hole subband structure properties of p-type delta-doped quantum wells in Si by using a Thomas-Fermi-Dirac potential

Energy Technology Data Exchange (ETDEWEB)

Rodriguez-Vargas, I; Madrigal-Melchor, J; Vlaev, S J, E-mail: isaac@planck.reduaz.m [Unidad Academica de Fisica, Universidad Autonoma de Zacatecas, Calzada Solidaridad Esquina Con Paseo La Bufa S/N, 98060 Zacatecas, ZAC. (Mexico)

2009-05-01

We present the hole subband structure of p-type delta-doped single, double, multiple and superlattice quantum wells in Si. We use the first neighbors sp{sup 3}s' tight-binding approximation including spin for the hole level structure analysis. The parameters of the tight-binding hamiltonian were taken from Klimeck et al. [Klimeck G, Bowen R C, Boykin T B, Salazar-Lazaro C, Cwik T A and Stoica A 2000 Superlattice. Microst. 27 77], first neighbors parameters that give realiable results for the valence band of Si. The calculations are based on a scheme previously proposed and applied to delta-doped quantum well systems [Vlaev S J and Gaggero-Sager L M 1998 Phys. Rev. B 58 1142]. The scheme relies on the incorporation of the delta-doped quantum well potential in the diagonal terms of the tight-binding hamiltonian. We give a detail description of the delta-doped quantum well structures, this is, we study the hole subband structure behavior as a function of the impurity density, the interwell distance of the doped planes and the superlattice period. We also compare our results with the available theoretical and experimental data, obtaining a reasonable agreement.

Calculation of elastic constants of BCC transition metals: tight-binding recursion method

International Nuclear Information System (INIS)

Masuda, K.; Hamada, N.; Terakura, K.

1984-01-01

The elastic constants of BCC transition metals (Fe, Nb, Mo and W) are calculated by using the tight-binding d band and the Born-Mayer repulsive potential. Introducing a small distortion characteristic to C 44 (or C') elastic deformation and calculating the energy change up to second order in the atomic displacement, the shear elastic constants C 44 and C' are determined. The elastic constants C 11 and C 12 are then calculated by using the relations B=1/3(C 11 + 2C 12 ) and C'=1/2(C 11 -C 12 ), where B is the bulk modulus. In general, the agreement between the present results and the experimental values is satisfactory. The characteristic elasticity behaviour, i.e. the strong Nsub(d) (number of d electrons) dependence of the observed anisotropy factor A=C 44 /C', will also be discussed. (author)

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

Science.gov (United States)

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.

Large-scale calculations of solid oxide fuel cell cermet anode by tight-binding quantum chemistry method

International Nuclear Information System (INIS)

Koyama, Michihisa; Kubo, Momoji; Miyamoto, Akira

2005-01-01

Improvement of anode characteristics of solid oxide fuel cells is important for the better cell performance and especially the direct use of hydrocarbons. A mixture of ceramics and metal is generally used as anode, and different combinations of ceramics and metals lead to different electrode characteristics. We performed large-scale calculations to investigate the characteristics of Ni/CeO 2 and Cu/CeO 2 anodes at the electronic level using our tight-binding quantum chemical molecular dynamics program. Charge distribution analysis clarified the electron transfer from metal to oxide in both anodes. The calculations of density of states clarified different contributions of Ni and Cu orbitals to the energy levels at around Fermi level in each cermet. Based on the obtained results, we made considerations to explain different characteristics of both cermet anodes. The effectiveness of our approach for the investigation of complex cermet system was proved

Slater-Koster Tight-Binding parametrization of single and few-layer Black-Phosphorus from first-principles calculations

Science.gov (United States)

Menezes, Marcos; Capaz, Rodrigo

Black Phosphorus (BP) is a promising material for applications in electronics, especially due to the tuning of its band gap by increasing the number of layers. In single-layer BP, also called Phosphorene, the P atoms form two staggered chains bonded by sp3 hybridization, while neighboring layers are bonded by Van-der-Waals interactions. In this work, we present a Tight-Binding (TB) parametrization of the electronic structure of single and few-layer BP, based on the Slater-Koster model within the two-center approximation. Our model includes all 3s and 3p orbitals, which makes this problem more complex than that of graphene, where only 2pz orbitals are needed for most purposes. The TB parameters are obtained from a least-squares fit of DFT calculations carried on the SIESTA code. We compare the results for different basis-sets used to expand the ab-initio wavefunctions and discuss their applicability. Our model can fit a larger number of bands than previously reported calculations based on Wannier functions. Moreover, our parameters have a clear physical interpretation based on chemical bonding. As such, we expect our results to be useful in a further understanding of multilayer BP and other 2D-materials characterized by strong sp3 hybridization. CNPq, FAPERJ, INCT-Nanomateriais de Carbono.

Tight-Binding simulations of InAs/GaAs quantum dots

International Nuclear Information System (INIS)

Kleinsorge, Alexander

2008-01-01

For several years, the technological potential of self-organized grown quantum dots (QD) has been known. Their usage as an effective light source or memory requires the precise prediction of their electronic properties. Hence, this report will study InAs quantum dots at GaAs substrate. After relaxing the atomic positions with a many body potential of Abell-Tersoff type, I calculated the electronic structure using the Tight-Binding method which is reasonable for large systems. During the investigation of wavefunctions depend on the shape, size and temperature, the impact of strain showed up as the main reason for the p-splitting. Typically flat QDs (relative to lateral dimensions) are grown, therefore the energy of bound states depends mostly on their height. The crystal's orientation had a strong impact on the wavefunctions. Moreover, the understanding of STS experiments, which inspected the connection between shape and wavefunction, is better now. Because of the possible simultaneous occupation of semiconductor quantum dots with an electron and a hole, there is a dipole moment of the exciton (due to their different behaviour inside the QD). This is a further experimental access to inner details of the QD. I ascertained the interplay of composition profile and dipole moment. The force caused by additional potentials (piezoelectricity, outer homogeneous and inhomogeneous electrical fields) was also an subject of my inquiries. To conclude, I executed kMC simulations, to better apprehend the annealing experiments. I was able to explain the narrowing of the PL peak width better. Furthermore I showed a ramification of the strain field to the diffusion development (and the following electronic properties). (orig.)

Chirality dependence of dipole matrix element of carbon nanotubes in axial magnetic field: A third neighbor tight binding approach

Science.gov (United States)

Chegel, Raad; Behzad, Somayeh

2014-02-01

We have studied the electronic structure and dipole matrix element, D, of carbon nanotubes (CNTs) under magnetic field, using the third nearest neighbor tight binding model. It is shown that the 1NN and 3NN-TB band structures show differences such as the spacing and mixing of neighbor subbands. Applying the magnetic field leads to breaking the degeneracy behavior in the D transitions and creates new allowed transitions corresponding to the band modifications. It is found that |D| is proportional to the inverse tube radius and chiral angle. Our numerical results show that amount of filed induced splitting for the first optical peak is proportional to the magnetic field by the splitting rate ν11. It is shown that ν11 changes linearly and parabolicly with the chiral angle and radius, respectively.

A Density Functional Tight Binding Study of Acetic Acid Adsorption on Crystalline and Amorphous Surfaces of Titania

Directory of Open Access Journals (Sweden)

Sergei Manzhos

2015-02-01

Full Text Available We present a comparative density functional tight binding study of an organic molecule attachment to TiO2 via a carboxylic group, with the example of acetic acid. For the first time, binding to low-energy surfaces of crystalline anatase (101, rutile (110 and (B-TiO2 (001, as well as to the surface of amorphous (a- TiO2 is compared with the same computational setup. On all surfaces, bidentate configurations are identified as providing the strongest adsorption energy, Eads = −1.93, −2.49 and −1.09 eV for anatase, rutile and (B-TiO2, respectively. For monodentate configurations, the strongest Eads = −1.06, −1.11 and −0.86 eV for anatase, rutile and (B-TiO2, respectively. Multiple monodentate and bidentate configurations are identified on a-TiO2 with a distribution of adsorption energies and with the lowest energy configuration having stronger bonding than that of the crystalline counterparts, with Eads up to −4.92 eV for bidentate and −1.83 eV for monodentate adsorption. Amorphous TiO2 can therefore be used to achieve strong anchoring of organic molecules, such as dyes, that bind via a -COOH group. While the presence of the surface leads to a contraction of the band gap vs. the bulk, molecular adsorption caused no appreciable effect on the band structure around the gap in any of the systems.

First-principles real-space tight-binding LMTO calculation of electronic structures for atomic clusters

International Nuclear Information System (INIS)

Xie, Z.L.; Dy, K.S.; Wu, S.Y.

1997-01-01

A real-space scheme has been developed for a first-principles calculation of electronic structures and total energies of atomic clusters. The scheme is based on the combination of the tight-binding linear muffin-tin orbital (TBLMTO) method and the method of real-space Green close-quote s function. With this approach, the local electronic density of states can be conveniently determined from the real-space Green close-quote s function. Furthermore, the full electron density of a cluster can be directly calculated in real space. The scheme has been shown to be very efficient due to the incorporation of the method of real-space Green close-quote s function and Delley close-quote s method of evaluating multicenter integrals. copyright 1996 The American Physical Society

Human zonulin, a potential modulator of intestinal tight junctions.

Science.gov (United States)

Wang, W; Uzzau, S; Goldblum, S E; Fasano, A

2000-12-01

Intercellular tight junctions are dynamic structures involved in vectorial transport of water and electrolytes across the intestinal epithelium. Zonula occludens toxin derived from Vibrio cholerae interacts with a specific intestinal epithelial surface receptor, with subsequent activation of a complex intracellular cascade of events that regulate tight junction permeability. We postulated that this toxin may mimic the effect of a functionally and immunologically related endogenous modulator of intestinal tight junctions. Affinity-purified anti-zonula occludens toxin antibodies and the Ussing chamber assay were used to screen for one or more mammalian zonula occludens toxin analogues in both fetal and adult human intestine. A novel protein, zonulin, was identified that induces tight junction disassembly in non-human primate intestinal epithelia mounted in Ussing chambers. Comparison of amino acids in the active zonula occludens toxin fragment and zonulin permitted the identification of the putative receptor binding domain within the N-terminal region of the two proteins. Zonulin likely plays a pivotal role in tight junction regulation during developmental, physiological, and pathological processes, including tissue morphogenesis, movement of fluid, macromolecules and leukocytes between the intestinal lumen and the interstitium, and inflammatory/autoimmune disorders.

Electro-optical properties of zigzag and armchair boron nitride nanotubes under a transverse electric field: Tight binding calculations

Science.gov (United States)

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.

Prime tight frames

DEFF Research Database (Denmark)

Lemvig, Jakob; Miller, Christopher; Okoudjou, Kasso A.

2014-01-01

to suggest effective analysis and synthesis computation strategies for such frames. Finally, we describe all prime frames constructed from the spectral tetris method, and, as a byproduct, we obtain a characterization of when the spectral tetris construction works for redundancies below two.......We introduce a class of finite tight frames called prime tight frames and prove some of their elementary properties. In particular, we show that any finite tight frame can be written as a union of prime tight frames. We then characterize all prime harmonic tight frames and use thischaracterization...

Bandstructure modulation for Si-h and Si-g nanotubes in a transverse electric field: Tight binding approach

Science.gov (United States)

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.

Chromate Binding and Removal by the Molybdate-Binding Protein ModA.

Science.gov (United States)

Karpus, Jason; Bosscher, Michael; Ajiboye, Ifedayo; Zhang, Liang; He, Chuan

2017-04-04

Effective and cheap methods and techniques for the safe removal of hexavalent chromate from the environment are in increasingly high demand. High concentrations of hexavalent chromate have been shown to have numerous harmful effects on human biology. We show that the E. coli molybdate-binding protein ModA is a genetically encoded tool capable of removing chromate from aqueous solutions. Although previously reported to not bind chromate, we show that ModA binds chromate tightly and is capable of removing chromate to levels well below current US federal standards. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

Science.gov (United States)

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 (Contract DE-AC52-07NA27344.

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

Science.gov (United States)

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 (Contract DE-AC52-07NA27344.

Experimental study and theoretical interpretation of saturation effect on ultrasonic velocity in tight sandstones under different pressure conditions

Science.gov (United States)

Li, Dongqing; Wei, Jianxin; Di, Bangrang; Ding, Pinbo; Huang, Shiqi; Shuai, Da

2018-03-01

Understanding the influence of lithology, porosity, permeability, pore structure, fluid content and fluid distribution on the elastic wave properties of porous rocks is of great significance for seismic exploration. However, unlike conventional sandstones, the petrophysical characteristics of tight sandstones are more complex and less understood. To address this problem, we measured ultrasonic velocity in partially saturated tight sandstones under different effective pressures. A new model is proposed, combining the Mavko-Jizba-Gurevich relations and the White model. The proposed model can satisfactorily simulate and explain the saturation dependence and pressure dependence of velocity in tight sandstones. Under low effective pressure, the relationship of P-wave velocity to saturation is pre-dominantly attributed to local (pore scale) fluid flow and inhomogeneous pore-fluid distribution (large scale). At higher effective pressure, local fluid flow gradually decreases, and P-wave velocity gradually shifts from uniform saturation towards patchy saturation. We also find that shear modulus is more sensitive to saturation at low effective pressures. The new model includes wetting ratio, an adjustable parameter that is closely related to the relationship between shear modulus and saturation.

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

Science.gov (United States)

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.

Less-Tight versus Tight Control of Hypertension in Pregnancy

NARCIS (Netherlands)

Magee, Laura A.; von Dadelszen, Peter; Rey, Evelyne; Ross, Susan; Asztalos, Elizabeth; Murphy, Kellie E.; Menzies, Jennifer; Sanchez, Johanna; Singer, Joel; Gafni, Amiram; Gruslin, Andrée; Helewa, Michael; Hutton, Eileen; Lee, Shoo K.; Lee, Terry; Logan, Alexander G.; Ganzevoort, Wessel; Welch, Ross; Thornton, Jim G.; Moutquin, Jean-Marie

2015-01-01

BACKGROUND The effects of less-tight versus tight control of hypertension on pregnancy complications are unclear. METHODS We performed an open, international, multicenter trial involving women at 14 weeks 0 days to 33 weeks 6 days of gestation who had nonproteinuric preexisting or gestational

Well test mathematical model for fractures network in tight oil reservoirs

Science.gov (United States)

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.

Productivity Analysis of Volume Fractured Vertical Well Model in Tight Oil Reservoirs

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Jiahang Wang

2017-01-01

Full Text Available This paper presents a semianalytical model to simulate the productivity of a volume fractured vertical well in tight oil reservoirs. In the proposed model, the reservoir is a composite system which contains two regions. The inner region is described as formation with finite conductivity hydraulic fracture network and the flow in fracture is assumed to be linear, while the outer region is simulated by the classical Warren-Root model where radial flow is applied. The transient rate is calculated, and flow patterns and characteristic flowing periods caused by volume fractured vertical well are analyzed. Combining the calculated results with actual production data at the decline stage shows a good fitting performance. Finally, the effects of some sensitive parameters on the type curves are also analyzed extensively. The results demonstrate that the effect of fracture length is more obvious than that of fracture conductivity on improving production in tight oil reservoirs. When the length and conductivity of main fracture are constant, the contribution of stimulated reservoir volume (SRV to the cumulative oil production is not obvious. When the SRV is constant, the length of fracture should also be increased so as to improve the fracture penetration and well production.

Dynamics of the HCP/BCC phase transition and of the diffusion in zirconium: a model based on a tight-binding potential

International Nuclear Information System (INIS)

Willaime, F.

1991-09-01

We have developed an N-body interatomic potential, based on the second moment approximation of the tight-binding scheme, by fitting its four adjustable parameters to the cohesive energy, atomic volume, and elastic constants of hcp-Zr. We then showed that various properties of this potential compare favorably with those of zirconium in both the low temperatures hcp phase and the high temperature bcc phase. Such is the case in particular for the elastic constants, the phonon dispersion curves, the thermal expansion, and the melting temperature. We reproduced by molecular dynamics (MD) simulations on this potential the hcp/bcc phase transformation in both ways. It indeed occurs following the mechanism predicted by Burgers. We find a vibrational entropy of transformation equal to 0.13 k B . Our calculations suggest that in real zirconium the electronic contribution to the transformation entropy is important. We show that some interatomic potential lead to a higher value of the vibrational entropy in the hcp phase than in the bcc phase. We specified the dynamics of the vacancy migration in the bcc phase. The atomic jumps are almost exclusively nearest neighbour ones. The walk of the vacancy becomes strongly correlated at high temperatures. The vacancy jump frequency is very large and has a perfectly arrhenian behaviour. There is no evicence of a dynamical lowering of the vacancy migration barrier: the static and dynamic values of the vacancy migration energy are almost equal, both being unusually small (0.3 eV). The self diffusion coefficent of our model for the vacancy mechanism reproduces an anomalous fast diffusion close to that measured experimentally in bcc-Zr. In our model at high temperatures the time interval between successive jumps is almost equal to the time of flight. The migration events will therefore influence the formation of the vacancies [fr

Physics and performances of III-V nanowire broken-gap heterojunction TFETs using an efficient tight-binding mode-space NEGF model enabling million-atom nanowire simulations.

Science.gov (United States)

Afzalian, A; Vasen, T; Ramvall, P; Shen, T-M; Wu, J; Passlack, M

2018-06-27

We report the capability to simulate in a quantum-mechanical atomistic fashion record-large nanowire devices, featuring several hundred to millions of atoms and a diameter up to 18.2 nm. We have employed a tight-binding mode-space NEGF technique demonstrating by far the fastest (up to 10 000  ×  faster) but accurate (error  <  1%) atomistic simulations to date. Such technique and capability opens new avenues to explore and understand the physics of nanoscale and mesoscopic devices dominated by quantum effects. In particular, our method addresses in an unprecedented way the technologically-relevant case of band-to-band tunneling (BTBT) in III-V nanowire broken-gap heterojunction tunnel-FETs (HTFETs). We demonstrate an accurate match of simulated BTBT currents to experimental measurements in a 12 nm diameter InAs NW and in an InAs/GaSb Esaki tunneling diode. We apply our TB MS simulations and report the first in-depth atomistic study of the scaling potential of III-V GAA nanowire HTFETs including the effect of electron-phonon scattering and discrete dopant impurity band tails, quantifying the benefits of this technology for low-power low-voltage CMOS applications.

Structural properties of metal-organic frameworks within the density-functional based tight-binding method

Energy Technology Data Exchange (ETDEWEB)

Lukose, Binit; Supronowicz, Barbara; Kuc, Agnieszka B.; Heine, Thomas [School of Engineering and Science, Jacobs University Bremen (Germany); Petkov, Petko S.; Vayssilov, Georgi N. [Faculty of Chemistry, University of Sofia (Bulgaria); Frenzel, Johannes [Lehrstuhl fuer Theoretische Chemie, Ruhr-Universitaet Bochum (Germany); Seifert, Gotthard [Physikalische Chemie, Technische Universitaet Dresden (Germany)

2012-02-15

Density-functional based tight-binding (DFTB) is a powerful method to describe large molecules and materials. Metal-organic frameworks (MOFs), materials with interesting catalytic properties and with very large surface areas, have been developed and have become commercially available. Unit cells of MOFs typically include hundreds of atoms, which make the application of standard density-functional methods computationally very expensive, sometimes even unfeasible. The aim of this paper is to prepare and to validate the self-consistent charge-DFTB (SCC-DFTB) method for MOFs containing Cu, Zn, and Al metal centers. The method has been validated against full hybrid density-functional calculations for model clusters, against gradient corrected density-functional calculations for supercells, and against experiment. Moreover, the modular concept of MOF chemistry has been discussed on the basis of their electronic properties. We concentrate on MOFs comprising three common connector units: copper paddlewheels (HKUST-1), zinc oxide Zn{sub 4}O tetrahedron (MOF-5, MOF-177, DUT-6 (MOF-205)), and aluminum oxide AlO{sub 4}(OH){sub 2} octahedron (MIL-53). We show that SCC-DFTB predicts structural parameters with a very good accuracy (with less than 5% deviation, even for adsorbed CO and H{sub 2}O on HKUST-1), while adsorption energies differ by 12 kJ mol{sup -1} or less for CO and water compared to DFT benchmark calculations. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

Less-tight versus tight control of hypertension in pregnancy.

Science.gov (United States)

Magee, Laura A; von Dadelszen, Peter; Rey, Evelyne; Ross, Susan; Asztalos, Elizabeth; Murphy, Kellie E; Menzies, Jennifer; Sanchez, Johanna; Singer, Joel; Gafni, Amiram; Gruslin, Andrée; Helewa, Michael; Hutton, Eileen; Lee, Shoo K; Lee, Terry; Logan, Alexander G; Ganzevoort, Wessel; Welch, Ross; Thornton, Jim G; Moutquin, Jean-Marie

2015-01-29

The effects of less-tight versus tight control of hypertension on pregnancy complications are unclear. We performed an open, international, multicenter trial involving women at 14 weeks 0 days to 33 weeks 6 days of gestation who had nonproteinuric preexisting or gestational hypertension, office diastolic blood pressure of 90 to 105 mm Hg (or 85 to 105 mm Hg if the woman was taking antihypertensive medications), and a live fetus. Women were randomly assigned to less-tight control (target diastolic blood pressure, 100 mm Hg) or tight control (target diastolic blood pressure, 85 mm Hg). The composite primary outcome was pregnancy loss or high-level neonatal care for more than 48 hours during the first 28 postnatal days. The secondary outcome was serious maternal complications occurring up to 6 weeks post partum or until hospital discharge, whichever was later. Included in the analysis were 987 women; 74.6% had preexisting hypertension. The primary-outcome rates were similar among 493 women assigned to less-tight control and 488 women assigned to tight control (31.4% and 30.7%, respectively; adjusted odds ratio, 1.02; 95% confidence interval [CI], 0.77 to 1.35), as were the rates of serious maternal complications (3.7% and 2.0%, respectively; adjusted odds ratio, 1.74; 95% CI, 0.79 to 3.84), despite a mean diastolic blood pressure that was higher in the less-tight-control group by 4.6 mm Hg (95% CI, 3.7 to 5.4). Severe hypertension (≥160/110 mm Hg) developed in 40.6% of the women in the less-tight-control group and 27.5% of the women in the tight-control group (Phypertension. (Funded by the Canadian Institutes of Health Research; CHIPS Current Controlled Trials number, ISRCTN71416914; ClinicalTrials.gov number, NCT01192412.).

Atomistic Tight-Binding Theory of Electron-Hole Exchange Interaction in Morphological Evolution of CdSe/ZnS Core/Shell Nanodisk to CdSe/ZnS Core/Shell Nanorod

Directory of Open Access Journals (Sweden)

Worasak Sukkabot

2016-01-01

Full Text Available Based on the atomistic tight-binding theory (TB and a configuration interaction (CI description, the electron-hole exchange interaction in the morphological transformation of CdSe/ZnS core/shell nanodisk to CdSe/ZnS core/shell nanorod is described with the aim of understanding the impact of the structural shapes on the change of the electron-hole exchange interaction. Normally, the ground hole states confined in typical CdSe/ZnS core/shell nanocrystals are of heavy hole-like character. However, the atomistic tight-binding theory shows that a transition of the ground hole states from heavy hole-like to light hole-like contribution with the increasing aspect ratios of the CdSe/ZnS core/shell nanostructures is recognized. According to the change in the ground-state hole characters, the electron-hole exchange interaction is also significantly altered. To do so, optical band gaps, ground-state electron character, ground-state hole character, oscillation strengths, ground-state coulomb energies, ground-state exchange energies, and dark-bright (DB excitonic splitting (stoke shift are numerically demonstrated. These atomistic computations obviously show the sensitivity with the aspect ratios. Finally, the alteration in the hole character has a prominent effect on dark-bright (DB excitonic splitting.

Electronic Properties of SiNTs Under External Electric and Magnetic Fields Using the Tight-Binding Method

Science.gov (United States)

Chegel, Raad; Behzad, Somayeh

2014-02-01

We investigated the electronic properties of silicon nanotubes (SiNTs) under external transverse electric fields and axial magnetic fields using the tight-binding approximation. It was found that, after switching on the electric and magnetic fields, band modifications such as distortion of degeneracy, change in energy dispersion and subband spacing, and bandgap size reduction occur. The bandgap of silicon gear-like nanotubes (Si g-NTs) decreases linearly with increasing electric field strength, but the bandgap for silicon hexagonal nanotubes (Si h-NTs) first increases and then decreases (metallic) or first remains constant and then decreases (semiconducting). Our results show that the bandgap of Si h-NTs is very sensitive to both electric and magnetic fields, unlike Si g-NTs, which are more sensitive to electric than magnetic fields.

A Tightly Coupled Non-Equilibrium Magneto-Hydrodynamic Model for Inductively Coupled RF Plasmas

Science.gov (United States)

2016-02-29

development a tightly coupled magneto-hydrodynamic model for Inductively Coupled Radio- Frequency (RF) Plasmas. Non Local Thermodynamic Equilibrium (NLTE...for Inductively Coupled Radio-Frequency (RF) Plasmas. Non Local Thermodynamic Equilibrium (NLTE) effects are described based on a hybrid State-to-State...Inductively Coupled Plasma (ICP) torches have wide range of possible applications which include deposition of metal coatings, synthesis of ultra-fine powders

Effect of cAMP derivates on assembly and maintenance of tight junctions in human umbilical vein endothelial cells

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Beese Michaela

2010-09-01

Full Text Available Abstract Background Endothelial tight and adherens junctions control a variety of physiological processes like adhesion, paracellular transport of solutes or trafficking of activated leukocytes. Formation and maintenance of endothelial junctions largely depend on the microenvironment of the specific vascular bed and on interactions of the endothelium with adjacent cell types. Consequently, primary cultures of endothelial cells often lose their specific junctional pattern and fail to establish tight monolayer in vitro. This is also true for endothelial cells isolated from the vein of human umbilical cords (HUVEC which are widely used as model for endothelial cell-related studies. Results We here compared the effect of cyclic 3'-5'-adenosine monophosphate (cAMP and its derivates on formation and stabilization of tight junctions and on alterations in paracellular permeability in HUVEC. We demonstrated by light and confocal laser microscopy that for shorter time periods the sodium salt of 8-bromoadenosine-cAMP (8-Br-cAMP/Na and for longer incubation periods 8-(4-chlorophenylthio-cAMP (pCPT-cAMP exerted the greatest effects of all compounds tested here on formation of continuous tight junction strands in HUVEC. We further demonstrated that although all compounds induced protein kinase A-dependent expression of the tight junction proteins claudin-5 and occludin only pCPT-cAMP slightly enhanced paracellular barrier functions. Moreover, we showed that pCPT-cAMP and 8-Br-cAMP/Na induced expression and membrane translocation of tricellulin. Conclusions pCPT-cAMP and, to a lesser extend, 8-Br-cAMP/Na improved formation of continuous tight junction strands and decreased paracellular permeability in primary HUVEC. We concluded that under these conditions HUVEC represent a feasible in vitro model to study formation and disassembly of endothelial tight junctions and to characterize tight junction-associated proteins

Identification of Critical Residues for the Tight Binding of Both Correct and Incorrect Nucleotides to Human DNA Polymerase λ

Science.gov (United States)

Brown, Jessica A.; Pack, Lindsey R.; Sherrer, Shanen M.; Kshetry, Ajay K.; Newmister, Sean A.; Fowler, Jason D.; Taylor, John-Stephen; Suo, Zucai

2010-01-01

DNA polymerase λ (Pol λ) is a novel X-family DNA polymerase that shares 34% sequence identity with DNA polymerase β (Pol β). Pre-steady state kinetic studies have shown that the Pol λ•DNA complex binds both correct and incorrect nucleotides 130-fold tighter on average than the Pol β•DNA complex, although, the base substitution fidelity of both polymerases is 10−4 to 10−5. To better understand Pol λ’s tight nucleotide binding affinity, we created single- and double-substitution mutants of Pol λ to disrupt interactions between active site residues and an incoming nucleotide or a template base. Single-turnover kinetic assays showed that Pol λ binds to an incoming nucleotide via cooperative interactions with active site residues (R386, R420, K422, Y505, F506, A510, and R514). Disrupting protein interactions with an incoming correct or incorrect nucleotide impacted binding with each of the common structural moieties in the following order: triphosphate ≫ base > ribose. In addition, the loss of Watson-Crick hydrogen bonding between the nucleotide and template base led to a moderate increase in the Kd. The fidelity of Pol λ was maintained predominantly by a single residue, R517, which has minor groove interactions with the DNA template. PMID:20851705

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

Science.gov (United States)

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.

Production of Natural Gas and Fluid Flow in Tight Sand Reservoirs

Energy Technology Data Exchange (ETDEWEB)

Maria Cecilia Bravo

2006-06-30

This document reports progress of this research effort in identifying relationships and defining dependencies between macroscopic reservoir parameters strongly affected by microscopic flow dynamics and production well performance in tight gas sand reservoirs. These dependencies are investigated by identifying the main transport mechanisms at the pore scale that should affect fluids flow at the reservoir scale. A critical review of commercial reservoir simulators, used to predict tight sand gas reservoir, revealed that many are poor when used to model fluid flow through tight reservoirs. Conventional simulators ignore altogether or model incorrectly certain phenomena such as, Knudsen diffusion, electro-kinetic effects, ordinary diffusion mechanisms and water vaporization. We studied the effect of Knudsen's number in Klinkenberg's equation and evaluated the effect of different flow regimes on Klinkenberg's parameter b. We developed a model capable of explaining the pressure dependence of this parameter that has been experimentally observed, but not explained in the conventional formalisms. We demonstrated the relevance of this, so far ignored effect, in tight sands reservoir modeling. A 2-D numerical simulator based on equations that capture the above mentioned phenomena was developed. Dynamic implications of new equations are comprehensively discussed in our work and their relative contribution to the flow rate is evaluated. We performed several simulation sensitivity studies that evidenced that, in general terms, our formalism should be implemented in order to get more reliable tight sands gas reservoirs' predictions.

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.

Science.gov (United States)

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.

Determinants for Tight and Selective Binding of a Medicinal Dicarbene Gold(I) Complex to a Telomeric DNA G-Quadruplex: a Joint ESI MS and XRD Investigation.

Science.gov (United States)

Bazzicalupi, Carla; Ferraroni, Marta; Papi, Francesco; Massai, Lara; Bertrand, Benoît; Messori, Luigi; Gratteri, Paola; Casini, Angela

2016-03-18

The dicarbene gold(I) complex [Au(9-methylcaffein-8-ylidene)2 ]BF4 is an exceptional organometallic compound of profound interest as a prospective anticancer agent. This gold(I) complex was previously reported to be highly cytotoxic toward various cancer cell lines in vitro and behaves as a selective G-quadruplex stabilizer. Interactions of the gold complex with various telomeric DNA models have been analyzed by a combined ESI MS and X-ray diffraction (XRD) approach. ESI MS measurements confirmed formation of stable adducts between the intact gold(I) complex and Tel 23 DNA sequence. The crystal structure of the adduct formed between [Au(9-methylcaffein-8-ylidene)2 ](+) and Tel 23 DNA G-quadruplex was solved. Tel 23 maintains a characteristic propeller conformation while binding three gold(I) dicarbene moieties at two distinct sites. Stacking interactions appear to drive noncovalent binding of the gold(I) complex. The structural basis for tight gold(I) complex/G-quadruplex recognition and its selectivity are described. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effects of ethanol and acetaldehyde on tight junction integrity: in vitro study in a three dimensional intestinal epithelial cell culture model.

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Elhaseen Elamin

Full Text Available BACKGROUND: Intestinal barrier dysfunction and translocation of endotoxins are involved in the pathogenesis of alcoholic liver disease. Exposure to ethanol and its metabolite, acetaldehyde at relatively high concentrations have been shown to disrupt intestinal epithelial tight junctions in the conventional two dimensional cell culture models. The present study investigated quantitatively and qualitatively the effects of ethanol at concentrations detected in the blood after moderate ethanol consumption, of its metabolite acetaldehyde and of the combination of both compounds on intestinal barrier function in a three-dimensional cell culture model. METHODS AND FINDINGS: Caco-2 cells were grown in a basement membrane matrix (Matrigel™ to induce spheroid formation and were then exposed to the compounds at the basolateral side. Morphological differentiation of the spheroids was assessed by immunocytochemistry and transmission electron microscopy. The barrier function was assessed by the flux of FITC-labeled dextran from the basal side into the spheroids' luminal compartment using confocal microscopy. Caco-2 cells grown on Matrigel assembled into fully differentiated and polarized spheroids with a central lumen, closely resembling enterocytes in vivo and provide an excellent model to study epithelial barrier functionality. Exposure to ethanol (10-40 mM or acetaldehyde (25-200 µM for 3 h, dose-dependently and additively increased the paracellular permeability and induced redistribution of ZO-1 and occludin without affecting cell viability or tight junction-encoding gene expression. Furthermore, ethanol and acetaldehyde induced lysine residue and microtubules hyperacetylation. CONCLUSIONS: These results indicate that ethanol at concentrations found in the blood after moderate drinking and acetaldehyde, alone and in combination, can increase the intestinal epithelial permeability. The data also point to the involvement of protein hyperacetylation in

Tight-binding approximations to time-dependent density functional theory — A fast approach for the calculation of electronically excited states

Energy Technology Data Exchange (ETDEWEB)

Rüger, Robert, E-mail: rueger@scm.com [Scientific Computing & Modelling NV, De Boelelaan 1083, 1081 HV Amsterdam (Netherlands); Department of Theoretical Chemistry, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam (Netherlands); Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Linnéstr. 2, 04103 Leipzig (Germany); Lenthe, Erik van [Scientific Computing & Modelling NV, De Boelelaan 1083, 1081 HV Amsterdam (Netherlands); Heine, Thomas [Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Linnéstr. 2, 04103 Leipzig (Germany); Visscher, Lucas [Department of Theoretical Chemistry, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam (Netherlands)

2016-05-14

We propose a new method of calculating electronically excited states that combines a density functional theory based ground state calculation with a linear response treatment that employs approximations used in the time-dependent density functional based tight binding (TD-DFTB) approach. The new method termed time-dependent density functional theory TD-DFT+TB does not rely on the DFTB parametrization and is therefore applicable to systems involving all combinations of elements. We show that the new method yields UV/Vis absorption spectra that are in excellent agreement with computationally much more expensive TD-DFT calculations. Errors in vertical excitation energies are reduced by a factor of two compared to TD-DFTB.

A Comparative Density Functional Theory and Density Functional Tight Binding Study of Phases of Nitrogen Including a High Energy Density Material N8

Directory of Open Access Journals (Sweden)

Nicholas Capel

2015-11-01

Full Text Available We present a comparative dispersion-corrected Density Functional Theory (DFT and Density Functional Tight Binding (DFTB-D study of several phases of nitrogen, including the well-known alpha, beta, and gamma phases as well as recently discovered highly energetic phases: covalently bound cubic gauche (cg nitrogen and molecular (vdW-bound N8 crystals. Among several tested parametrizations of N–N interactions for DFTB, we identify only one that is suitable for modeling of all these phases. This work therefore establishes the applicability of DFTB-D to studies of phases, including highly metastable phases, of nitrogen, which will be of great use for modelling of dynamics of reactions involving these phases, which may not be practical with DFT due to large required space and time scales. We also derive a dispersion-corrected DFT (DFT-D setup (atom-centered basis parameters and Grimme dispersion parameters tuned for accurate description simultaneously of several nitrogen allotropes including covalently and vdW-bound crystals and including high-energy phases.

A comparative study of density functional and density functional tight binding calculations of defects in graphene

Energy Technology Data Exchange (ETDEWEB)

Zobelli, Alberto [Laboratoire de Physique des Solides, Univ. Paris Sud, CNRS UMR, Orsay (France); Ivanovskaya, Viktoria; Wagner, Philipp; Yaya, Abu; Ewels, Chris P. [Institut des Materiaux Jean Rouxel (IMN), CNRS UMR, University of Nantes (France); Suarez-Martinez, Irene [Nanochemistry Research Institute, Curtin University of Technology, Perth, Western Australia (Australia)

2012-02-15

The density functional tight binding approach (DFTB) is well adapted for the study of point and line defects in graphene based systems. After briefly reviewing the use of DFTB in this area, we present a comparative study of defect structures, energies, and dynamics between DFTB results obtained using the dftb+ code, and density functional results using the localized Gaussian orbital code, AIMPRO. DFTB accurately reproduces structures and energies for a range of point defect structures such as vacancies and Stone-Wales defects in graphene, as well as various unfunctionalized and hydroxylated graphene sheet edges. Migration barriers for the vacancy and Stone-Wales defect formation barriers are accurately reproduced using a nudged elastic band approach. Finally we explore the potential for dynamic defect simulations using DFTB, taking as an example electron irradiation damage in graphene. DFTB-MD derived sputtering energy threshold map for a carbon atom in a graphene plane. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

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

Science.gov (United States)

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.

Mechanism-based population pharmacokinetic modelling in diabetes: vildagliptin as a tight binding inhibitor and substrate of dipeptidyl peptidase IV

Science.gov (United States)

Landersdorfer, Cornelia B; He, Yan-Ling; Jusko, William J

2012-01-01

AIMS To assess the pharmacokinetics of vildagliptin at different doses and build a mechanism-based population model that simultaneously describes vildagliptin pharmacokinetics and its effects on DPP-4 activity based on underlying physiology and biology. METHODS Vildagliptin concentrations and DPP-4 activity vs. time from 13 type 2 diabetic patients after oral vildagliptin 10, 25 or 100 mg and placebo twice daily for 28 days were co-modelled. NONMEM VI and S-ADAPT were utilized for population modelling. RESULTS A target-mediated drug disposition (TMDD) model accounting for capacity-limited high affinity binding of vildagliptin to DPP-4 in plasma and tissues had good predictive performance. Modelling the full time course of the vildagliptin-DPP-4 interaction suggested parallel vildagliptin dissociation from DPP-4 by a slow first-order process and hydrolysis by DPP-4 to an inactive metabolite as a disposition mechanism. Due to limited amounts of DPP-4, vildagliptin concentrations increased slightly more than dose proportionally. This newly proposed model and the parameter estimates are supported by published in vitro studies. Mean parameter estimates (inter-individual coefficient of variation) were: non-saturable clearance 36 l h−1 (25%), central volume of distribution 22 l (37%), half-life of dissociation from DPP-4 1.1 h (94%) and half-life of hydrolysis 6.3 h (81%). CONCLUSIONS Vildagliptin is both an inhibitor and substrate for DPP-4. By utilizing the TMDD approach, slow dissociation of vildagliptin from DPP-4 was found in patients and the half-life of hydrolysis by DPP-4 estimated. This model can be used to predict DPP-4 inhibition effects of other dosage regimens and be modified for other DPP-4 inhibitors to differentiate their properties. PMID:22442826

Dielectric constant of graphene-on-polarized substrate: A tight ...

Indian Academy of Sciences (India)

Sivabrata Sahu

Corresponding author. E-mail: gcr@iopb.res.in. Published online 24 June 2017. Abstract. We report here a microscopic tight-binding theoretical study of the dynamic dielectric response of graphene-on-polarizable substrate with impurity. The Hamiltonian consists of first, second and third nearest- neighbour electron hopping ...

Extension of the self-consistent-charge density-functional tight-binding method: third-order expansion of the density functional theory total energy and introduction of a modified effective coulomb interaction.

Science.gov (United States)

Yang, Yang; Yu, Haibo; York, Darrin; Cui, Qiang; Elstner, Marcus

2007-10-25

The standard self-consistent-charge density-functional-tight-binding (SCC-DFTB) method (Phys. Rev. B 1998, 58, 7260) is derived by a second-order expansion of the density functional theory total energy expression, followed by an approximation of the charge density fluctuations by charge monopoles and an effective damped Coulomb interaction between the atomic net charges. The central assumptions behind this effective charge-charge interaction are the inverse relation of atomic size and chemical hardness and the use of a fixed chemical hardness parameter independent of the atomic charge state. While these approximations seem to be unproblematic for many covalently bound systems, they are quantitatively insufficient for hydrogen-bonding interactions and (anionic) molecules with localized net charges. Here, we present an extension of the SCC-DFTB method to incorporate third-order terms in the charge density fluctuations, leading to chemical hardness parameters that are dependent on the atomic charge state and a modification of the Coulomb scaling to improve the electrostatic treatment within the second-order terms. These modifications lead to a significant improvement in the description of hydrogen-bonding interactions and proton affinities of biologically relevant molecules.

Relativistic band-structure calculations for CeTIn sub 5 (T=Ir and Co) and analysis of the energy bands by using tight-binding method

CERN Document Server

Maehira, T; Ueda, K; Hasegawa, A

2003-01-01

In order to investigate electronic properties of recently discovered heavy fermion superconductors CeTIn sub 5 (T=Ir and Co), we employ the relativistic linear augmented-plane-wave (RLAPW) method to clarify the energy band structures and Fermi surfaces of those materials. The obtained energy bands mainly due to the large hybridization between Ce 4 f and In 5 p states well reproduce the Fermi surfaces consistent with the de Haas-van Alphen experimental results. However, when we attempt to understand magnetism and superconductively in CeTIn sub 5 from the microscopic viewpoint, the energy bands obtained in the RLAPW method are too complicated to analyze the system by further including electron correlations. Thus, it is necessary to prepare a more simplified model, keeping correctly the essential characters of the energy bands obtained in the band-structure calculation. For the purpose, we construct a tight-binding model for CeTIn sub 5 by including f-f and p-p hoppings as well as f-p hybridization, which are ex...

Fluctuations of cytoskeleton-bound microbeads-the effect of bead-receptor binding dynamics

International Nuclear Information System (INIS)

Metzner, C; Raupach, C; Mierke, C T; Fabry, B

2010-01-01

The cytoskeleton (CSK) of living cells is a crosslinked fiber network, subject to ongoing biochemical remodeling processes that can be visualized by tracking the spontaneous motion of CSK-bound microbeads. The bead motion is characterized by anomalous diffusion with a power-law time evolution of the mean square displacement (MSD), and can be described as a stochastic transport process with apparent diffusivity D and power-law exponent β: MSD ∼ D (t/t 0 ) β . Here we studied whether D and β change with the time that has passed after the initial bead-cell contact, and whether they are sensitive to bead coating (fibronectin, integrin antibodies, poly-L-lysine, albumin) and bead size (0.5-4.5 μm). The measurements are interpreted in the framework of a simple model that describes the bead as an overdamped particle coupled to the fluctuating CSK network by an elastic spring. The viscous damping coefficient characterizes the degree of bead internalization into the cell, and the spring constant characterizes the strength of the binding of the bead to the CSK. The model predicts distinctive signatures of the MSD that change with time as the bead couples more tightly to the CSK and becomes internalized. Experimental data show that the transition from the unbound to the tightly bound state occurs in an all-or-nothing manner. The time point of this transition shows considerable variability between individual cells (2-30 min) and depends on the bead size and bead coating. On average, this transition occurs later for smaller beads and beads coated with ligands that trigger the formation of adhesion complexes (fibronectin, integrin antibodies). Once the bead is linked to the CSK, however, the ligand type and bead size have little effect on the MSD. On longer timescales of several hours after bead addition, smaller beads are internalized into the cell more readily, leading to characteristic changes in the MSD that are consistent with increased viscous damping by the

Tight closure and vanishing theorems

International Nuclear Information System (INIS)

Smith, K.E.

2001-01-01

applications of tight closure include Frobenius characterizations of certain singularities arising in the minimal model program and uniform bounds for global generation of adjoint linear series. Both of these applications are closely tied to vanishing theorems, and indeed, the Kodaira vanishing theorem itself has an equivalent formulation in terms of tight closure

A business process model as a starting point for tight cooperation among organizations

Directory of Open Access Journals (Sweden)

O. Mysliveček

2006-01-01

Full Text Available Outsourcing and other kinds of tight cooperation among organizations are more and more necessary for success on all markets (markets of high technology products are particularly influenced. Thus it is important for companies to be able to effectively set up all kinds of cooperation. A business process model (BPM is a suitable starting point for this future cooperation. In this paper the process of setting up such cooperation is outlined, as well as why it is important for business success. 

Investigation of hydraulic fracture re-orientation effects in tight gas reservoirs

Energy Technology Data Exchange (ETDEWEB)

Hagemann, B.; Wegner, J.; Ganzer, L. [Technische Univ. Clausthal, Clausthal-Zellerfeld (Germany). ITE

2013-08-01

In tight gas formations where the low matrix permeability prevents successful and economic production rates, hydraulic fracturing is required to produce a well at economic rates. The initial fracture opens in the direction of minimum stress and propagates into the direction of maximum stress. As production from the well and its initial fracture declines, re-fracturing treatments are required to accelerate recovery. The orientation of the following hydraulic fracture depends on the actual stress-state of the formation in the vicinity of the wellbore. Previous investigations by Elbel and Mack (1993) demonstrated that the stress alters during depletion and a stress reversal region appears. This behavior causes a different fracture orientation of the re-fracturing operation. For the investigation of re-fracture orientation a two-dimensional reservoir model has been designed using COMSOL Multiphysics. The model represents a fractured vertical well in a tight gas reservoir of infinite thickness. A time dependent study was set up to simulate the reservoir depletion by the production from the fractured well. The theory of poroelasticity was used to couple the fluid flow and geo-mechanical behavior. The stress state is initially defined as uniform and the attention is concentrated to the alteration of stress due to the lowered pore pressure. Different cases with anisotropic and heterogeneous permeability are set up to determine its significance. The simulation shows that an elliptical shaped drainage area appears around the fracture. The poroelastic behavior effects that the stress re-orientates and a stress reversal region originates, if the difference between minimum and maximum horizontal stresses is small. The consideration of time indicates that the dimension of the region initially extends fast until it reaches its maximum. Subsequently, the stress reversal region's extent shrinks slowly until it finally disappears. The reservoir characteristics, e.g. the

Ti(IV) and the Siderophore Desferrioxamine B: A Tight Complex Has Biological and Environmental Implications.

Science.gov (United States)

Jones, Kayleigh E; Batchler, Kathleen L; Zalouk, Célia; Valentine, Ann M

2017-02-06

The siderophore desferrioxamine B (DFOB) binds Ti(IV) tightly and precludes its hydrolytic precipitation under biologically and environmentally relevant conditions. This interaction of DFOB with Ti(IV) is investigated by using spectro-potentiometric and spectro-photometric titrations, mass spectrometry, isothermal titration calorimetry (ITC), and computational modeling. The data from pH 2-10 suggest two one-proton equilibria among three species, with one species predominating below pH 3.5, a second from pH 3.5 to 8, and a third above pH 8. The latter species is prone to slow hydrolytic precipitation. Electrospray mass spectrometry allowed the detection of [Ti(IV) (HDFOB)] 2+ and [Ti(DFOB)] + ; these species were assigned as the pH UV/vis-monitored competition with ethylenediaminetetraacetic acid (EDTA). Taking into consideration the available binding constant of Ti(IV) and EDTA, the data reveal values of log β 111 = 41.7, log β 110 = 38.1, and log β 11-1 = 30.1. The former value was supported by ITC, with the transfer of Ti(IV) from EDTA to DFOB determined to be both enthalpically and entropically favorable. Computational methods yielded a model of Ti-DFOB. The physiological and environmental implications of this tight interaction and the potential role of DFOB in solubilizing Ti(IV) are discussed.

Petri Net-Based Model of Helicobacter pylori Mediated Disruption of Tight Junction Proteins in Stomach Lining during Gastric Carcinoma

Directory of Open Access Journals (Sweden)

Anam Naz

2017-09-01

Full Text Available Tight junctions help prevent the passage of digestive enzymes and microorganisms through the space between adjacent epithelial cells lining. However, Helicobacter pylori encoded virulence factors negatively regulate these tight junctions and contribute to dysfunction of gastric mucosa. Here, we have predicted the regulation of important tight junction proteins, such as Zonula occludens-1, Claudin-2 and Connexin32 in the presence of pathogenic proteins. Molecular events such as post translational modifications and crosstalk between phosphorylation, O-glycosylation, palmitoylation and methylation are explored which may compromise the integrity of these tight junction proteins. Furthermore, the signaling pathways disrupted by dysregulated kinases, proteins and post-translational modifications are reviewed to design an abstracted computational model showing the situation-dependent dynamic behaviors of these biological processes and entities. A qualitative hybrid Petri Net model is therefore constructed showing the altered host pathways in the presence of virulence factor cytotoxin-associated gene A, leading to the disruption of tight junction proteins. The model is qualitative logic-based, which does not depend on any kinetic parameter and quantitative data and depends on knowledge derived from experiments. The designed model provides insights into the tight junction disruption and disease progression. Model is then verified by the available experimental data, nevertheless formal in vitro experimentation is a promising way to ensure its validation. The major findings propose that H. pylori activated kinases are responsible to trigger specific post translational modifications within tight junction proteins, at specific sites. These modifications may favor alterations in gastric barrier and provide a route to bacterial invasion into host cells.

To bind or not to bind? Different temporal binding effects from voluntary pressing and releasing actions.

Science.gov (United States)

Zhao, Ke; Chen, Yu-Hsin; Yan, Wen-Jing; Fu, Xiaolan

2013-01-01

Binding effect refers to the perceptual attraction between an action and an outcome leading to a subjective compression of time. Most studies investigating binding effects exclusively employ the "pressing" action without exploring other types of actions. The present study addresses this issue by introducing another action, releasing action or the voluntary lifting of the finger/wrist, to investigate the differences between voluntary pressing and releasing actions. Results reveal that releasing actions led to robust yet short-lived temporal binding effects, whereas pressing condition had steady temporal binding effects up to super-seconds. The two actions also differ in sensitivity to changes in temporal contiguity and contingency, which could be attributed to the difference in awareness of action. Extending upon current models of "willed action," our results provide insights from a temporal point of view and support the concept of a dual system consisting of predictive motor control and top-down mechanisms.

Parallel decomposition of the tight-binding fictitious Lagrangian algorithm for molecular dynamics simulations of semiconductors

International Nuclear Information System (INIS)

Yeh, M.; Kim, J.; Khan, F.S.

1995-01-01

We present a parallel decomposition of the tight-binding fictitious Lagrangian algorithm for the Intel iPSC/860 and the Intel Paragon parallel computers. We show that it is possible to perform long simulations, of the order of 10 000 time steps, on semiconducting clusters consisting of as many as 512 atoms, on a time scale of the order of 20 h or less. We have made a very careful timing analysis of all parts of our code, and have identified the bottlenecks. We have also derived formulas which can predict the timing of our code, based on the number of processors, message passing bandwidth, floating point performance of each node, and the set up time for message passing, appropriate to the machine being used. The time of the simulation scales as the square of the number of particles, if the number of processors is made to scale linearly with the number of particles. We show that for a system as large as 512 atoms, the main bottleneck of the computation is the orthogonalization of the wave functions, which consumes about 90% of the total time of the simulation

Valence band states in Si-based p-type delta-doped field effect transistors

International Nuclear Information System (INIS)

Martinez-Orozco, J C; Vlaev, Stoyan J

2009-01-01

We present tight-binding calculations of the hole level structure of δ-doped Field Effect Transistor in a Si matrix within the first neighbors sp 3 s* semi-empirical tight-binding model including spin. We employ analytical expressions for Schottky barrier potential and the p-type δ-doped well based on a Thomas-Fermi approximation, we consider these potentials as external ones, so in the computations they are added to the diagonal terms of the tight-binding Hamiltonian, by this way we have the possibility to study the energy levels behavior as we vary the backbone parameters in the system: the two-dimensional impurity density (p 2d ) of the p-type δ-doped well and the contact voltage (V c ). The aim of this calculation is to demonstrate that the tight-binding approximation is suitable for device characterization that permits us to propose optimal values for the input parameters involved in the device design.

Valence band states in Si-based p-type delta-doped field effect transistors

Energy Technology Data Exchange (ETDEWEB)

Martinez-Orozco, J C; Vlaev, Stoyan J, E-mail: jcmover@correo.unam.m [Unidad Academica de Fisica, Universidad Autonoma de Zacatecas, Calzada Solidaridad esquina con Paseo la Bufa S/N, C.P. 98060, Zacatecas, Zac. (Mexico)

2009-05-01

We present tight-binding calculations of the hole level structure of delta-doped Field Effect Transistor in a Si matrix within the first neighbors sp{sup 3}s* semi-empirical tight-binding model including spin. We employ analytical expressions for Schottky barrier potential and the p-type delta-doped well based on a Thomas-Fermi approximation, we consider these potentials as external ones, so in the computations they are added to the diagonal terms of the tight-binding Hamiltonian, by this way we have the possibility to study the energy levels behavior as we vary the backbone parameters in the system: the two-dimensional impurity density (p{sub 2d}) of the p-type delta-doped well and the contact voltage (V{sub c}). The aim of this calculation is to demonstrate that the tight-binding approximation is suitable for device characterization that permits us to propose optimal values for the input parameters involved in the device design.

Reformulated tight binding calculation for band discontinuity at CdTe/Hg xCd1-xTe heterointerfaces and their type I-type III transitions

International Nuclear Information System (INIS)

Ekpunobi, A.J.

2005-01-01

A recently reformulated tight binding method is used to calculate the valence band discontinuity at the CdTe/Hg x Cd 1-x Te interface in the s 2 p 2 configuration. The calculated valence band discontinuity of 0.31 eV at CdTe/HgTe interface is in good agreement with self-consistent calculation and accepted experimental value. Calculations were extended to alloy interfaces, which enabled the investigation of the band-offset problem at the transition point. Both valence band discontinuity ratio and conduction band discontinuity ratio show inflexions at the transition point

A tight-binding model of the transmission probability through a molecular junction; a single molecule vs. a molecular layer

International Nuclear Information System (INIS)

Landau, A.; Nitzan, A.

2006-01-01

Full Text: Molecular electronics, one of the major fields of the current effort in nano-science, may be de ed as the study of electronic behaviors, devices and applications that depend on the properties of matter at the molecular scale. If the miniaturization trend of microelectronic devices is to continue, elements such as transistors and contacts will soon shrink to single molecules. The promise of these new technological breakthroughs has been major driving force in this ld. Moreover, the consideration of molecular systems as electronic devices has raised new fundamental questions. In particular, while traditional quantum chemistry deals with electronically closed systems, we now face problems involving molecular systems that are open to their electronic environment, moreover, function in far from equilibrium situations. A generic molecular junction is made of two electrodes connected by a molecular spacer that takes the form of a molecular chain of varying length or a molecular layer of varying thickness. We use a simple nearest-neighbors tight-biding model with the non-equilibrium Green's function (NEGF) method to investigate and compare between a self-assembled monolayer (SAM), finite molecular layer (FML), and single molecule (SM) chemisorption to a surface of a metal substrate. In addition, we examine the difference in the transmission probability through a SAM, FML and SM sandwiched between two metallic electrodes. Dramatic differences are observed between the SM, FML and SAM density of electronic states and transmission functions. In addition, we analyze the effects of changing different physical parameters such as molecule-substrate interaction, molecule-molecule interactions, etc; interesting effects that pertain to the conduction properties of single molecules and molecular layers are observed. Intriguing results are attained when we investigate the commensurability of the SAM with the metallic surface

Band gap engineering for poly(p-phenylene) and poly(p-phenylene vinylene) copolymers using the tight-binding approach

Science.gov (United States)

Giro, R.; Caldas, M. J.; Galvão, D. S.

The interest in poly(p-phenylene) (PPP) and poly(p-phenylene vinylene) (PPV) copolymers stems from the fact that these homopolymers present interesting optical and electronic properties that allow a great variety of technological applications. Combining different numbers of PPP and PPV units it is possible, in principle, to obtain new structures presenting intermediate gap values (2.8 eV and 2.4 eV for PPP and PPV, respectively). For this study we used a Hückel Hamiltonian tight-binding coupled to the negative factor counting (NFC) technique. We carried out a systematic search to determine optimum relative concentrations for disordered binary polymeric alloys with predefined gap values. Once these structures were obtained, we used the semiempirical methods AM1/PM3 and ZINDO/S-CI for geometrical and optical studies, respectively. Our theoretical results show that it is possible to obtain copolymers of PPP and PPV with intermediate gap values of their parent structures.

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

Science.gov (United States)

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.

Simulations and measurements of adiabatic annular flows in triangular, tight lattice nuclear fuel bundle model

Energy Technology Data Exchange (ETDEWEB)

Saxena, Abhishek, E-mail: asaxena@lke.mavt.ethz.ch [ETH Zurich, Laboratory for Nuclear Energy Systems, Department of Mechanical and Process Engineering, Sonneggstrasse 3, 8092 Zürich (Switzerland); Zboray, Robert [Laboratory for Thermal-hydraulics, Nuclear Energy and Safety Department, Paul Scherrer Institute, 5232 Villigen PSI (Switzerland); Prasser, Horst-Michael [ETH Zurich, Laboratory for Nuclear Energy Systems, Department of Mechanical and Process Engineering, Sonneggstrasse 3, 8092 Zürich (Switzerland); Laboratory for Thermal-hydraulics, Nuclear Energy and Safety Department, Paul Scherrer Institute, 5232 Villigen PSI (Switzerland)

2016-04-01

High conversion light water reactors (HCLWR) having triangular, tight-lattice fuels bundles could enable improved fuel utilization compared to present day LWRs. However, the efficient cooling of a tight lattice bundle has to be still proven. Major concern is the avoidance of high-quality boiling crisis (film dry-out) by the use of efficient functional spacers. For this reason, we have carried out experiments on adiabatic, air-water annular two-phase flows in a tight-lattice, triangular fuel bundle model using generic spacers. A high-spatial-resolution, non-intrusive measurement technology, cold neutron tomography, has been utilized to resolve the distribution of the liquid film thickness on the virtual fuel pin surfaces. Unsteady CFD simulations have also been performed to replicate and compare with the experiments using the commercial code STAR-CCM+. Large eddies have been resolved on the grid level to capture the dominant unsteady flow features expected to drive the liquid film thickness distribution downstream of a spacer while the subgrid scales have been modeled using the Wall Adapting Local Eddy (WALE) subgrid model. A Volume of Fluid (VOF) method, which directly tracks the interface and does away with closure relationship models for interfacial exchange terms, has also been employed. The present paper shows first comparison of the measurement with the simulation results.

A Simplified Baseband Prefilter Model with Adaptive Kalman Filter for Ultra-Tight COMPASS/INS Integration

Science.gov (United States)

Luo, Yong; Wu, Wenqi; Babu, Ravindra; Tang, Kanghua; Luo, Bing

2012-01-01

COMPASS is an indigenously developed Chinese global navigation satellite system and will share many features in common with GPS (Global Positioning System). Since the ultra-tight GPS/INS (Inertial Navigation System) integration shows its advantage over independent GPS receivers in many scenarios, the federated ultra-tight COMPASS/INS integration has been investigated in this paper, particularly, by proposing a simplified prefilter model. Compared with a traditional prefilter model, the state space of this simplified system contains only carrier phase, carrier frequency and carrier frequency rate tracking errors. A two-quadrant arctangent discriminator output is used as a measurement. Since the code tracking error related parameters were excluded from the state space of traditional prefilter models, the code/carrier divergence would destroy the carrier tracking process, and therefore an adaptive Kalman filter algorithm tuning process noise covariance matrix based on state correction sequence was incorporated to compensate for the divergence. The federated ultra-tight COMPASS/INS integration was implemented with a hardware COMPASS intermediate frequency (IF), and INS's accelerometers and gyroscopes signal sampling system. Field and simulation test results showed almost similar tracking and navigation performances for both the traditional prefilter model and the proposed system; however, the latter largely decreased the computational load. PMID:23012564

A Simplified Baseband Prefilter Model with Adaptive Kalman Filter for Ultra-Tight COMPASS/INS Integration

Directory of Open Access Journals (Sweden)

Bing Luo

2012-07-01

Full Text Available COMPASS is an indigenously developed Chinese global navigation satellite system and will share many features in common with GPS (Global Positioning System. Since the ultra-tight GPS/INS (Inertial Navigation System integration shows its advantage over independent GPS receivers in many scenarios, the federated ultra-tight COMPASS/INS integration has been investigated in this paper, particularly, by proposing a simplified prefilter model. Compared with a traditional prefilter model, the state space of this simplified system contains only carrier phase, carrier frequency and carrier frequency rate tracking errors. A two-quadrant arctangent discriminator output is used as a measurement. Since the code tracking error related parameters were excluded from the state space of traditional prefilter models, the code/carrier divergence would destroy the carrier tracking process, and therefore an adaptive Kalman filter algorithm tuning process noise covariance matrix based on state correction sequence was incorporated to compensate for the divergence. The federated ultra-tight COMPASS/INS integration was implemented with a hardware COMPASS intermediate frequency (IF, and INS’s accelerometers and gyroscopes signal sampling system. Field and simulation test results showed almost similar tracking and navigation performances for both the traditional prefilter model and the proposed system; however, the latter largely decreased the computational load.

Grain-Boundary Resistance in Copper Interconnects: From an Atomistic Model to a Neural Network

Science.gov (United States)

Valencia, Daniel; Wilson, Evan; Jiang, Zhengping; Valencia-Zapata, Gustavo A.; Wang, Kuang-Chung; Klimeck, Gerhard; Povolotskyi, Michael

2018-04-01

Orientation effects on the specific resistance of copper grain boundaries are studied systematically with two different atomistic tight-binding methods. A methodology is developed to model the specific resistance of grain boundaries in the ballistic limit using the embedded atom model, tight- binding methods, and nonequilibrium Green's functions. The methodology is validated against first-principles calculations for thin films with a single coincident grain boundary, with 6.4% deviation in the specific resistance. A statistical ensemble of 600 large, random structures with grains is studied. For structures with three grains, it is found that the distribution of specific resistances is close to normal. Finally, a compact model for grain-boundary-specific resistance is constructed based on a neural network.

Additive Effects of Rebamipide Plus Proton Pump Inhibitors on the Expression of Tight Junction Proteins in a Rat Model of Gastro-Esophageal Reflux Disease.

Science.gov (United States)

Gweon, Tae-Geun; Park, Jong-Hyung; Kim, Byung-Wook; Choi, Yang Kyu; Kim, Joon Sung; Park, Sung Min; Kim, Chang Whan; Kim, Hyung-Gil; Chung, Jun-Won

2018-01-15

The aim of this study was to investigate the effects of rebamipide on tight junction proteins in the esophageal mucosa in a rat model of gastroesophageal reflux disease (GERD). GERD was created in rats by tying the proximal stomach. The rats were divided into a control group, a proton pump inhibitor (PPI) group, and a PPI plus rebamipide (PPI+R) group. Pantoprazole (5 mg/kg) was administered intraperitoneally to the PPI and PPI+R groups. An additional dose of rebamipide (100 mg/kg) was administered orally to the PPI+R group. Mucosal erosions, epithelial thickness, and leukocyte infiltration into the esophageal mucosa were measured in isolated esophagi 14 days after the procedure. A Western blot analysis was conducted to measure the expression of claudin-1, -3, and -4. The mean surface area of mucosal erosions, epithelial thickness, and leukocyte infiltration were lower in the PPI group and the PPI+R group than in the control group. Western blot analysis revealed that the expression of claudin-3 and -4 was significantly higher in the PPI+R group than in the control group. Rebamipide may exert an additive effect in combination with PPI to modify the tight junction proteins of the esophageal mucosa in a rat model of GERD. This treatment might be associated with the relief of GERD symptoms.

Effect of two novel CGRP-binding compounds in a closed cranial window rat model

DEFF Research Database (Denmark)

Juhl, Louise Kathrine; Edvinsson, Lars; Olesen, Jes

2007-01-01

We investigated the in vivo effects of two novel calcitonin gene-related peptide (CGRP) binding molecules in the genuine closed cranial window model in the rat. The RNA-Spiegelmer (NOX-C89) and the monoclonal CGRP antibody are CGRP scavengers and might be used as an alternative to CGRP-receptor a......We investigated the in vivo effects of two novel calcitonin gene-related peptide (CGRP) binding molecules in the genuine closed cranial window model in the rat. The RNA-Spiegelmer (NOX-C89) and the monoclonal CGRP antibody are CGRP scavengers and might be used as an alternative to CGRP......-receptor antagonists in the treatment of migraine. Rats were anaesthetized and a closed cranial window established. Changes in dural and pial artery diameter and mean arterial blood pressure were measured simultaneously. Infusion of the RNA-Spiegelmer or the CGRP antibody alone had no effect on the arteries...... and the consequent liberation of CGRP from perivascular sensory nerve fibres....

Tightly Secure Signatures From Lossy Identification Schemes

OpenAIRE

Abdalla , Michel; Fouque , Pierre-Alain; Lyubashevsky , Vadim; Tibouchi , Mehdi

2015-01-01

International audience; In this paper, we present three digital signature schemes with tight security reductions in the random oracle model. Our first signature scheme is a particularly efficient version of the short exponent discrete log-based scheme of Girault et al. (J Cryptol 19(4):463–487, 2006). Our scheme has a tight reduction to the decisional short discrete logarithm problem, while still maintaining the non-tight reduction to the computational version of the problem upon which the or...

Stokes shift and fine structure splitting in composition-tunable Zn{sub x}Cd{sub 1−x}Se nanocrystals: Atomistic tight-binding theory

Energy Technology Data Exchange (ETDEWEB)

Sukkabot, Worasak, E-mail: w.sukkabot@gmail.com

2017-02-01

I report on the atomistic correlation of the structural properties and excitonic splitting of ternary alloy Zn{sub x}Cd{sub 1−x}Se wurtzite nanocrystals using the sp{sup 3}s* empirical tight-binding method with the description of the first nearest neighbouring interaction and bowing effect. Based on a successful model, the computations are presented under various Zn compositions (x) and diameters of alloy Zn{sub x}Cd{sub 1−x}Se nanocrystals with the experimentally synthesized compositions and sizes. With increasing Zn contents (x), the optical band gaps and electron-hole coulomb energies are improved, while ground electron-hole wave function overlaps, electron-hole exchange energies, stokes shift and fine structure splitting are reduced. A composition-tunable emission from blue to yellow wavelength is obviously demonstrated. The optical band gaps, ground electron-hole wave function overlaps, electron-hole interactions, stokes shift and fine structure splitting are progressively decreased with the increasing diameters. Alloy Zn{sub x}Cd{sub 1−x}Se nanocrystal with Zn rich and large diameter is the best candidate to optimistically be used as a source of entangled photon pairs. The agreement with the experimental data is remarkable. Finally, the present systematic study on the structural properties and excitonic splitting predominantly opens a new perspective to understand the size- and composition-dependent properties of Zn{sub x}Cd{sub 1−x}Se nanocrystals with a comprehensive strategy to design the optoelectronic devices.

Expression patterns of tight junction components induced by CD24 in an oral epithelial cell-culture model correlated to affected periodontal tissues.

Science.gov (United States)

Ye, P; Yu, H; Simonian, M; Hunter, N

2014-04-01

Previously we demonstrated uniformly strong expression of CD24 in the epithelial attachment to the tooth and in the migrating epithelium of the periodontitis lesion. Titers of serum antibodies autoreactive with CD24 peptide correlated with reduced severity of periodontal disease. Ligation of CD24 expressed by oral epithelial cells induced formation of tight junctions that limited paracellular diffusion. In this study, we aimed to reveal that the lack of uniform expression of tight junction components in the pocket epithelium of periodontitis lesions is likely to contribute to increased paracellular permeability to bacterial products. This is proposed as a potential driver of the immunopathology of periodontitis. An epithelial culture model with close correspondence for expression patterns for tight junction components in periodontal epithelia was used. Immunohistochemical staining and confocal laser scanning microscopy were used to analyse patterns of expression of gingival epithelial tight junction components. The minimally inflamed gingival attachment was characterized by uniformly strong staining at cell contacts for the tight junction components zona occludens-1, zona occludens-2, occludin, junction adhesion molecule-A, claudin-4 and claudin-15. In contrast, the pocket epithelium of the periodontal lesion showed scattered, uneven staining for these components. This pattern correlated closely with that of unstimulated oral epithelial cells in culture. Following ligation of CD24 expressed by these cells, the pattern of tight junction component expression of the minimally inflamed gingival attachment developed rapidly. There was evidence for non-uniform and focal expression only of tight junction components in the pocket epithelium. In the cell-culture model, ligation of CD24 induced a tight junction expression profile equivalent to that observed for the minimally inflamed gingival attachment. Ligation of CD24 expressed by gingival epithelial cells by lectin

No Change in Bicarbonate Transport but Tight-Junction Formation Is Delayed by Fluoride in a Novel Ameloblast Model

Directory of Open Access Journals (Sweden)

Róbert Rácz

2017-12-01

Full Text Available We have recently developed a novel in vitro model using HAT-7 rat ameloblast cells to functionally study epithelial ion transport during amelogenesis. Our present aims were to identify key transporters of bicarbonate in HAT-7 cells and also to examine the effects of fluoride exposure on vectorial bicarbonate transport, cell viability, and the development of transepithelial resistance. To obtain monolayers, the HAT-7 cells were cultured on Transwell permeable filters. We monitored transepithelial resistance (TER as an indicator of tight junction formation and polarization. We evaluated intracellular pH changes by microfluorometry using the fluorescent indicator BCECF. Activities of ion transporters were tested by withdrawal of various ions from the bathing medium, by using transporter specific inhibitors, and by activation of transporters with forskolin and ATP. Cell survival was estimated by alamarBlue assay. Changes in gene expression were monitored by qPCR. We identified the activity of several ion transporters, NBCe1, NHE1, NKCC1, and AE2, which are involved in intracellular pH regulation and vectorial bicarbonate and chloride transport. Bicarbonate secretion by HAT-7 cells was not affected by acute fluoride exposure over a wide range of concentrations. However, tight-junction formation was inhibited by 1 mM fluoride, a concentration which did not substantially reduce cell viability, suggesting an effect of fluoride on paracellular permeability and tight-junction formation. Cell viability was only reduced by prolonged exposure to fluoride concentrations greater than 1 mM. In conclusion, cultured HAT-7 cells are functionally polarized and are able to transport bicarbonate ions from the basolateral to the apical fluid spaces. Exposure to 1 mM fluoride has little effect on bicarbonate secretion or cell viability but delays tight-junction formation, suggesting a novel mechanism that may contribute to dental fluorosis.

Evolving Transcription Factor Binding Site Models From Protein Binding Microarray Data

KAUST Repository

Wong, Ka-Chun; Peng, Chengbin; Li, Yue

2016-01-01

Protein binding microarray (PBM) is a high-throughput platform that can measure the DNA binding preference of a protein in a comprehensive and unbiased manner. In this paper, we describe the PBM motif model building problem. We apply several evolutionary computation methods and compare their performance with the interior point method, demonstrating their performance advantages. In addition, given the PBM domain knowledge, we propose and describe a novel method called kmerGA which makes domain-specific assumptions to exploit PBM data properties to build more accurate models than the other models built. The effectiveness and robustness of kmerGA is supported by comprehensive performance benchmarking on more than 200 datasets, time complexity analysis, convergence analysis, parameter analysis, and case studies. To demonstrate its utility further, kmerGA is applied to two real world applications: 1) PBM rotation testing and 2) ChIP-Seq peak sequence prediction. The results support the biological relevance of the models learned by kmerGA, and thus its real world applicability.

Evolving Transcription Factor Binding Site Models From Protein Binding Microarray Data

KAUST Repository

Wong, Ka-Chun

2016-02-02

Protein binding microarray (PBM) is a high-throughput platform that can measure the DNA binding preference of a protein in a comprehensive and unbiased manner. In this paper, we describe the PBM motif model building problem. We apply several evolutionary computation methods and compare their performance with the interior point method, demonstrating their performance advantages. In addition, given the PBM domain knowledge, we propose and describe a novel method called kmerGA which makes domain-specific assumptions to exploit PBM data properties to build more accurate models than the other models built. The effectiveness and robustness of kmerGA is supported by comprehensive performance benchmarking on more than 200 datasets, time complexity analysis, convergence analysis, parameter analysis, and case studies. To demonstrate its utility further, kmerGA is applied to two real world applications: 1) PBM rotation testing and 2) ChIP-Seq peak sequence prediction. The results support the biological relevance of the models learned by kmerGA, and thus its real world applicability.

Triazole biotin: a tight-binding biotinidase-resistant conjugate.

Science.gov (United States)

Germeroth, Anne I; Hanna, Jill R; Karim, Rehana; Kundel, Franziska; Lowther, Jonathan; Neate, Peter G N; Blackburn, Elizabeth A; Wear, Martin A; Campopiano, Dominic J; Hulme, Alison N

2013-11-28

The natural amide bond found in all biotinylated proteins has been replaced with a triazole through CuAAC reaction of an alkynyl biotin derivative. The resultant triazole-linked adducts are shown to be highly resistant to the ubiquitous hydrolytic enzyme biotinidase and to bind avidin with dissociation constants in the low pM range. Application of this strategy to the production of a series of biotinidase-resistant biotin-Gd-DOTA contrast agents is demonstrated.

Coupling of Hubbard fermions with phonons in La{sub 2} CuO{sub 4}: A combined study using density-functional theory and the generalized tight-binding method

Energy Technology Data Exchange (ETDEWEB)

Shneyder, E.I., E-mail: shneyder@iph.krasn.ru [Kirensky Institute of Physics SB RAS, Krasnoyarsk 660036 (Russian Federation); Reshetnev Siberian State Aerospace University, Krasnoyarsk 660014 (Russian Federation); Spitaler, J. [Materials Center Leoben Forschung GmbH, Rosegger-Straße 18, A-8700 Leoben (Austria); Kokorina, E.E.; Nekrasov, I.A. [Institute of Electrophysics UB RAS, Amundsena Str. 106, 620016 Yekaterinburg (Russian Federation); Gavrichkov, V.A. [Kirensky Institute of Physics SB RAS, Krasnoyarsk 660036 (Russian Federation); Draxl, C. [Physics Department and IRIS Adlershof, Humboldt-Universität zu Berlin, Zum Großen Windkanal 6, 12489 Berlin (Germany); Ovchinnikov, S.G. [Kirensky Institute of Physics SB RAS, Krasnoyarsk 660036 (Russian Federation)

2015-11-05

We present results for the electron-phonon interaction of the Γ-point phonons in the tetragonal high-temperature phase of La{sub 2} CuO{sub 4} obtained from a hybrid scheme, combining density-functional theory (DFT) with the generalized tight-binding approach. As a starting point, eigenfrequencies and eigenvectors for the Γ-point phonons are determined from DFT within the frozen phonon approach utilizing the augmented plane wave + local orbitals method. The so obtained characteristics of electron-phonon coupling are converted into parameters of the generalized tight-binding method. This approach is a version of cluster perturbation theory and takes the strong on-site electron correlations into account. The obtained parameters describe the interaction of phonons with Hubbard fermions which form quasiparticle bands in strongly correlated electron systems. As a result, it is found that the Γ-point phonons with the strongest electron-phonon interaction are the A{sub 2u} modes (236 cm{sup −1}, 131 cm{sup −1} and 476 cm{sup −1}). Finally it is shown, that the single-electron spectral-weight redistribution between different Hubbard fermion quasiparticles results in a suppression of electron-phonon interaction which is strongest for the triplet Hubbard band with z oriented copper and oxygen electrons. - Highlights: • Electron-phonon interaction in strongly correlated electron systems is analyzed. • Interaction parameters between strongly correlated electrons and phonons are obtained. • The suppression of these parameters by strong electron correlations is demonstrated.

Nonlinear Filtering with IMM Algorithm for Ultra-Tight GPS/INS Integration

Directory of Open Access Journals (Sweden)

Dah-Jing Jwo

2013-05-01

Full Text Available Abstract This paper conducts a performance evaluation for the ultra-tight integration of a Global positioning system (GPS and an inertial navigation system (INS, using nonlinear filtering approaches with an interacting multiple model (IMM algorithm. An ultra-tight GPS/INS architecture involves the integration of in-phase and quadrature components from the correlator of a GPS receiver with INS data. An unscented Kalman filter (UKF, which employs a set of sigma points by deterministic sampling, avoids the error caused by linearization as in an extended Kalman filter (EKF. Based on the filter structural adaptation for describing various dynamic behaviours, the IMM nonlinear filtering provides an alternative for designing the adaptive filter in the ultra-tight GPS/INS integration. The use of IMM enables tuning of an appropriate value for the process of noise covariance so as to maintain good estimation accuracy and tracking capability. Two examples are provided to illustrate the effectiveness of the design and demonstrate the effective improvement in navigation estimation accuracy. A performance comparison among various filtering methods for ultra-tight integration of GPS and INS is also presented. The IMM based nonlinear filtering approach demonstrates the effectiveness of the algorithm for improved positioning performance.

Tightness Entropic Uncertainty Relation in Quantum Markovian-Davies Environment

Science.gov (United States)

Zhang, Jun; Liu, Liang; Han, Yan

2018-05-01

In this paper, we investigate the tightness of entropic uncertainty relation in the absence (presence) of the quantum memory which the memory particle being weakly coupled to a decohering Davies-type Markovian environment. The results show that the tightness of the quantum uncertainty relation can be controlled by the energy relaxation time F, the dephasing time G and the rescaled temperature p, the perfect tightness can be arrived by dephasing and energy relaxation satisfying F = 2G and p = 1/2. In addition, the tightness of the memory-assisted entropic uncertainty relation and the entropic uncertainty relation can be influenced mainly by the purity. While in memory-assisted model, the purity and quantum correlation can also influence the tightness actively while the quantum entanglement can influence the tightness slightly.

The experimental modeling of gas percolation mechanisms in a coal-measure tight sandstone reservoir: A case study on the coal-measure tight sandstone gas in the Upper Triassic Xujiahe Formation, Sichuan Basin, China

Directory of Open Access Journals (Sweden)

Shizhen Tao

2016-12-01

Full Text Available Tight sandstone gas from coal-measure source rock is widespread in China, and it is represented by the Xujiahe Formation of the Sichuan Basin and the Upper Paleozoic of the Ordos Basin. It is affected by planar evaporative hydrocarbon expulsion of coal-measure source rock and the gentle structural background; hydrodynamics and buoyancy play a limited role in the gas migration-accumulation in tight sandstone. Under the conditions of low permeability and speed, non-Darcy flow is quite apparent, it gives rise to gas-water mixed gas zone. In the gas displacing water experiment, the shape of percolation flow curve is mainly influenced by core permeability. The lower the permeability, the higher the starting pressure gradient as well as the more evident the non-Darcy phenomenon will be. In the gas displacing water experiment of tight sandstone, the maximum gas saturation of the core is generally less than 50% (ranging from 30% to 40% and averaging at 38%; it is similar to the actual gas saturation of the gas zone in the subsurface core. The gas saturation and permeability of the core have a logarithm correlation with a correlation coefficient of 0.8915. In the single-phase flow of tight sandstone gas, low-velocity non-Darcy percolation is apparent; the initial flow velocity (Vd exists due to the slippage effect of gas flow. The shape of percolation flow curve of a single-phase gas is primarily controlled by core permeability and confining pressure; the lower the permeability or the higher the confining pressure, the higher the starting pressure (0.02–0.08 MPa/cm, whereas, the higher the quasi-initial flow speed, the longer the nonlinear section and the more obvious the non-Darcy flow will be. The tight sandstone gas seepage mechanism study shows that the lower the reservoir permeability, the higher the starting pressure and the slower the flow velocity will be, this results in the low efficiency of natural gas migration and accumulation as well as

A Comparison Study for DNA Motif Modeling on Protein Binding Microarray

KAUST Repository

Wong, Ka-Chun; Li, Yue; Peng, Chengbin; Wong, Hau-San

2015-01-01

Transcription Factor Binding Sites (TFBSs) are relatively short (5-15 bp) and degenerate. Identifying them is a computationally challenging task. In particular, Protein Binding Microarray (PBM) is a high-throughput platform that can measure the DNA binding preference of a protein in a comprehensive and unbiased manner; for instance, a typical PBM experiment can measure binding signal intensities of a protein to all possible DNA k-mers (k=810). Since proteins can often bind to DNA with different binding intensities, one of the major challenges is to build motif models which can fully capture the quantitative binding affinity data. To learn DNA motif models from the non-convex objective function landscape, several optimization methods are compared and applied to the PBM motif model building problem. In particular, representative methods from different optimization paradigms have been chosen for modeling performance comparison on hundreds of PBM datasets. The results suggest that the multimodal optimization methods are very effective for capturing the binding preference information from PBM data. In particular, we observe a general performance improvement using di-nucleotide modeling over mono-nucleotide modeling. In addition, the models learned by the best-performing method are applied to two independent applications: PBM probe rotation testing and ChIP-Seq peak sequence prediction, demonstrating its biological applicability.

A Comparison Study for DNA Motif Modeling on Protein Binding Microarray

KAUST Repository

Wong, Ka-Chun

2015-06-11

Transcription Factor Binding Sites (TFBSs) are relatively short (5-15 bp) and degenerate. Identifying them is a computationally challenging task. In particular, Protein Binding Microarray (PBM) is a high-throughput platform that can measure the DNA binding preference of a protein in a comprehensive and unbiased manner; for instance, a typical PBM experiment can measure binding signal intensities of a protein to all possible DNA k-mers (k=810). Since proteins can often bind to DNA with different binding intensities, one of the major challenges is to build motif models which can fully capture the quantitative binding affinity data. To learn DNA motif models from the non-convex objective function landscape, several optimization methods are compared and applied to the PBM motif model building problem. In particular, representative methods from different optimization paradigms have been chosen for modeling performance comparison on hundreds of PBM datasets. The results suggest that the multimodal optimization methods are very effective for capturing the binding preference information from PBM data. In particular, we observe a general performance improvement using di-nucleotide modeling over mono-nucleotide modeling. In addition, the models learned by the best-performing method are applied to two independent applications: PBM probe rotation testing and ChIP-Seq peak sequence prediction, demonstrating its biological applicability.

Reformulated tight binding calculation for band discontinuity at CdTe/Hg {sub x}Cd{sub 1-x}Te heterointerfaces and their type I-type III transitions

Energy Technology Data Exchange (ETDEWEB)

Ekpunobi, A.J. [Department of Physics and Industrial Physics, Nnamdi Azikiwe University, P.M.B. 5025, Awka, Anambra State (Nigeria)

2005-02-25

A recently reformulated tight binding method is used to calculate the valence band discontinuity at the CdTe/Hg {sub x}Cd{sub 1-x}Te interface in the s{sup 2}p{sup 2} configuration. The calculated valence band discontinuity of 0.31 eV at CdTe/HgTe interface is in good agreement with self-consistent calculation and accepted experimental value. Calculations were extended to alloy interfaces, which enabled the investigation of the band-offset problem at the transition point. Both valence band discontinuity ratio and conduction band discontinuity ratio show inflexions at the transition point.

Tight Temporal Bounds for Dataflow Applications Mapped onto Shared Resources

NARCIS (Netherlands)

Alizadeh Ara, H.; Geilen, M.; Basten, T.; Behrouzian, A.R.B.; Hendriks, M.; Goswami, D.

2016-01-01

We present an analysis method that provides tight temporal bounds for applications modeled by Synchronous Dataflow Graphs and mapped to shared resources. We consider the resource sharing effects on the temporal behaviour of the application by embedding worst case resource availability curves in the

Steam and electroheating remediation of tight soils

Energy Technology Data Exchange (ETDEWEB)

Balshaw-Biddle, K.; Oubre, C.L.; Ward, C.H. [eds.; Dablow, J.F. III; Pearce, J.A.; Johnson, P.C.

2000-07-01

In the past few decades the need for soil remediation has become urgent, even more necessary--innovative, cost effective methods. Steam and Electroheating Remediation of Tight Soils presents the results of a field study testing the cleanup of semi-volatile fuels from tight soils using combination of hydraulic fracturing and soil heating technologies.

Charge superlattice effects on the electronic structure of a model acceptor graphite intercalation compound

International Nuclear Information System (INIS)

Campagnoli, G.; Tosatti, E.

1981-08-01

In the present attempt we have considered a model ordered situation (a super-superlattice) where starting from a basic stoichiometry C 8 X, a fraction 1/3 of the molecules acquire one electron, the remaining 2/3 being left neutral. We have performed an electronic structure calculation using tight-binding plus electrostatic (Hartree) self-consistency

Unconventional Tight Reservoirs Characterization with Nuclear Magnetic Resonance

Science.gov (United States)

Santiago, C. J. S.; Solatpour, R.; Kantzas, A.

2017-12-01

The increase in tight reservoir exploitation projects causes producing many papers each year on new, modern, and modified methods and techniques on estimating characteristics of these reservoirs. The most ambiguous of all basic reservoir property estimations deals with permeability. One of the logging methods that is advertised to predict permeability but is always met by skepticism is Nuclear Magnetic Resonance (NMR). The ability of NMR to differentiate between bound and movable fluids and providing porosity increased the capability of NMR as a permeability prediction technique. This leads to a multitude of publications and the motivation of a review paper on this subject by Babadagli et al. (2002). The first part of this presentation is dedicated to an extensive review of the existing correlation models for NMR based estimates of tight reservoir permeability to update this topic. On the second part, the collected literature information is used to analyze new experimental data. The data are collected from tight reservoirs from Canada, the Middle East, and China. A case study is created to apply NMR measurement in the prediction of reservoir characterization parameters such as porosity, permeability, cut-offs, irreducible saturations etc. Moreover, permeability correlations are utilized to predict permeability. NMR experiments were conducted on water saturated cores. NMR T2 relaxation times were measured. NMR porosity, the geometric mean relaxation time (T2gm), Irreducible Bulk Volume (BVI), and Movable Bulk Volume (BVM) were calculated. The correlation coefficients were computed based on multiple regression analysis. Results are cross plots of NMR permeability versus the independently measured Klinkenberg corrected permeability. More complicated equations are discussed. Error analysis of models is presented and compared. This presentation is beneficial in understanding existing tight reservoir permeability models. The results can be used as a guide for choosing

Tight Money, Real Interest Rates, and Inflation in Sub-Saharan Africa

OpenAIRE

Edward F. Buffie

2003-01-01

The consequences of tight monetary policy are analyzed in an optimizing currency-substitution model of a small, open economy that operates under an open capital account and a flexible exchange rate. There is a reasonably good fit between the dynamics generated by the model and the stylized facts in the tight-money episodes that occurred in Kenya in 1993 and Nigeria in 1989-91. The study's results shed light on two issues: why tight money has provoked stupendous increases in inflation and the ...

US production of natural gas from tight reservoirs

International Nuclear Information System (INIS)

1993-01-01

For the purposes of this report, tight gas reservoirs are defined as those that meet the Federal Energy Regulatory Commission's (FERC) definition of tight. They are generally characterized by an average reservoir rock permeability to gas of 0.1 millidarcy or less and, absent artificial stimulation of production, by production rates that do not exceed 5 barrels of oil per day and certain specified daily volumes of gas which increase with the depth of the reservoir. All of the statistics presented in this report pertain to wells that have been classified, from 1978 through 1991, as tight according to the FERC; i.e., they are ''legally tight'' reservoirs. Additional production from ''geologically tight'' reservoirs that have not been classified tight according to the FERC rules has been excluded. This category includes all producing wells drilled into legally designated tight gas reservoirs prior to 1978 and all producing wells drilled into physically tight gas reservoirs that have not been designated legally tight. Therefore, all gas production referenced herein is eligible for the Section 29 tax credit. Although the qualification period for the credit expired at the end of 1992, wells that were spudded (began to be drilled) between 1978 and May 1988, and from November 5, 1990, through year end 1992, are eligible for the tax credit for a subsequent period of 10 years. This report updates the EIA's tight gas production information through 1991 and considers further the history and effect on tight gas production of the Federal Government's regulatory and tax policy actions. It also provides some high points of the geologic background needed to understand the nature and location of low-permeability reservoirs

Improving horizontal completions on heterogeneous tight shales

Energy Technology Data Exchange (ETDEWEB)

Suarez-Rivera, Roberto; Deenadayalu, Chaitanya; Chertov, Maxim; Novalo Hartanto, Ricardo; Gathogo, Patrick [Schlumberger (United States); Kunjir, Rahul [University of Utah (United States)

2011-07-01

Evaluation of the two formation characteristics conducive to economic well production is important when tight shale formation characterization and completion design are being considered. This paper presents the basic understanding required to improve the efficiency of horizontal completions in oil and gas producing shales. Guidelines are defined for effective perforation and fracturing to improve the efficiency and sustainability of horizontal completions using extensive laboratory characterization of mechanical properties on core, core/log integration and continuous mapping of these properties by logging-while-drilling (LWD) methods. The objective is to improve completion design efficiency. This is accomplished by suitable selection of perforation intervals based on an understanding of the relevant physical processes and rock characterization. Conditions at two reservoir regions, the near-wellbore and the far-wellbore, are outlined and are essential to completion design. From the study, it can be concluded that tight shales are strongly anisotropic and cannot be approximated using isotropic models.

Pore Structure and Limit Pressure of Gas Slippage Effect in Tight Sandstone

Science.gov (United States)

You, Lijun; Xue, Kunlin; Kang, Yili; Liao, Yi

2013-01-01

Gas slip effect is an important mechanism that the gas flow is different from liquid flow in porous media. It is generally considered that the lower the permeability in porous media is, the more severe slip effect of gas flow will be. We design and then carry out experiments with the increase of backpressure at the outlet of the core samples based on the definition of gas slip effect and in view of different levels of permeability of tight sandstone reservoir. This study inspects a limit pressure of the gas slip effect in tight sandstones and analyzes the characteristic parameter of capillary pressure curves. The experimental results indicate that gas slip effect can be eliminated when the backpressure reaches a limit pressure. When the backpressure exceeds the limit pressure, the measured gas permeability is a relatively stable value whose range is less than 3% for a given core sample. It is also found that the limit pressure increases with the decreasing in permeability and has close relation with pore structure of the core samples. The results have an important influence on correlation study on gas flow in porous medium, and are beneficial to reduce the workload of laboratory experiment. PMID:24379747

Vector fields in a tight laser focus: comparison of models.

Science.gov (United States)

Peatross, Justin; Berrondo, Manuel; Smith, Dallas; Ware, Michael

2017-06-26

We assess several widely used vector models of a Gaussian laser beam in the context of more accurate vector diffraction integration. For the analysis, we present a streamlined derivation of the vector fields of a uniformly polarized beam reflected from an ideal parabolic mirror, both inside and outside of the resulting focus. This exact solution to Maxwell's equations, first developed in 1920 by V. S. Ignatovsky, is highly relevant to high-intensity laser experiments since the boundary conditions at a focusing optic dictate the form of the focus in a manner analogous to a physical experiment. In contrast, many models simply assume a field profile near the focus and develop the surrounding vector fields consistent with Maxwell's equations. In comparing the Ignatovsky result with popular closed-form analytic vector models of a Gaussian beam, we find that the relatively simple model developed by Erikson and Singh in 1994 provides good agreement in the paraxial limit. Models involving a Lax expansion introduce a divergences outside of the focus while providing little if any improvement in the focal region. Extremely tight focusing produces a somewhat complicated structure in the focus, and requires the Ignatovsky model for accurate representation.

On the mechanism of sulfite activation of chloroplast thylakoid ATPase and the relation of ADP tightly bound at a catalytic site to the binding change mechanism

International Nuclear Information System (INIS)

Du, Z.; Boyer, P.D.

1990-01-01

Washed chloroplast thylakoid membranes upon exposure to [ 3 H]ADP retain in tightly bound [ 3 H]ADP on a catalytic site of the ATP synthase. The presence of sufficient endogenous or added Mg 2+ results in an enzyme with essentially no ATPase activity. Sulfite activates the ATPase, and many molecules of ATP per synthase can be hydrolyzed before most of the bound [ 3 H]ADP is released, a result interpreted as indicating that the ADP is not bound at a site participating in catalysis by the sulfite-activated enzyme. The authors present evidence that this is not the case. The Mg 2+ - and ADP-inhibited enzyme when exposed to MgATP and 20-100 mM sulfite shows a lag of about 1 min at 22 degree C and of about 15 s at 37 degree C before reaching the same steady-state rate as attained with light-activated ATPase that has not been inhibited by Mg 2+ and ADP. The lag is not eliminated if the enzyme is exposed to sulfite prior to MgATP addition, indicating that ATPase turnover is necessary for the activation. The release of most of the bound [ 3 H]ADP parallels the onset of ATPase activity, although some [ 3 H]ADP is not released even with prolonged catalytic turnover and may be on poorly active or inactive enzyme or at noncatalytic sites. The results are consistent with most of the tightly bound [ 3 H]ADP being at a catalytic site and being replaced as this Mg 2+ - and ADP-inhibited site regains equivalent participation with other catalytic sites on the activated enzyme. The sulfite activation can be explained by sulfite combination at a P i binding site of the enzyme-ADP-Mg 2+ complex to give a form more readily activated by ATP binding at an alternative site

Integration of seismic data and a triple porosity model for interpretation of tight gas formations in the Western Canada sedimentary basin

Energy Technology Data Exchange (ETDEWEB)

Castillo, Fernando; Aguilera, Roberto; Lawton, Don [University of Calgary (Canada)

2011-07-01

Due to the increased global demand for oil and gas, companies are looking to unconventional methods for exploring, drilling and refining these products. Unconventional reservoirs are found in the form of shale gas, coal bed methane and tight gas. This paper presents a model for evaluating various tight gas reservoirs in the Western Canada sedimentary basin (WCSB) by developing an equation. The proposed method integrates a triple porosity model with sonic, density and resistivity logs. The model uses petrographic data from work in the WCSB to determine the types of pores that are present in the tight rocks. The process also provides information on inter-well formation resistivity, porosity and water saturation to allow estimation of the amount of original gas in place. The results calculated from this study agreed with the actual deep resistivities of the WCSB Nikanassin group. This model can also be applied to other regions of the world that have similar characteristics to those of the WCSB.

Effects of Kaixin Powder on melatonin receptor expression and (125)I-Mel binding affinity in a rat model of depression.

Science.gov (United States)

Huang, Yan-li; Liang, Xue-bing; Qian, Li-qi; Cai, Chuan; Guo, Jun; Gao, Chao; Guan, Jian-hua; Zhao, Guo-ping

2015-07-01

To explore the effects of Kaixin Powder (, KXP) on melatonin receptor (MR) expression and (125)I-Mel binding affinity in a depression rat model. Seventy-two male Wistar rats were divided into six groups: a blank control group, model group, ramelteon group, KXP high-dosage group (HKXP), medium-dosage group (MKXP) and low-dosage group (LKXP). To establish the depression model, all groups except the blank control group were singly housed and exposed to chronic unpredictable mild stress. Weight gain, sucrose consumption and the open-field test were used to evaluate induction of depression. KXP at 260, 130 and 65 mg/(kg•d) was also respectively administered to the rats in the HKXP, MKXP and LKXP groups for 21 days. Ramelteon [0.83 mg/(kg•d)] was given to the positive drug control group. An equivalent volume of physiological saline was given to the blank and model groups. The liquid chip method was used to measure the concentration of plasma melatonin (MT). Mel1a (MT1) and Mel1b (MT2) expression levels were determined by Western blotting. In addition, a radioactive ligand-binding assay was used to analyze the specific binding properties and dynamic characteristics between MR and (125)I-Mel. The results of weight gain, sucrose consumption and the open-field test showed that our model successfully produced depressive symptoms and depressive-like behavior. The concentration of plasma MT in the model group decreased significantly at night but increased in the MKXP group (P0.05). The maximum binding capacity (B(max)) for specific binding between MR and 125I-Mel in the MKXP group was significantly higher than that in the model group (P0.05). KXP may have a similar effect as ramelteon. KXP improved depressive-like behavior by increasing the concentration of plasma MT and MT1 expression, thereby increasing three B(max) of MR to achieve the desired antidepressant effect.

Effective mass approximation versus full atomistic model to calculate the output characteristics of a gate-all-around germanium nanowire field effect transistor (GAA-GeNW-FET)

Science.gov (United States)

Bayani, Amir Hossein; Voves, Jan; Dideban, Daryoosh

2018-01-01

Here, we compare the output characteristics of a gate-all-around germanium nanowire field effect transistor (GAA-GeNW-FET) with 2.36 nm2 square cross-section area using tight-binding (TB) sp3d5s∗ model (full atomistic model (FAM)) and effective mass approximation (EMA). Synopsys/QuantumWise Atomistix ToolKit (ATK) and Silvaco Atlas3D are used to consider the TB model and EMA, respectively. Results show that EMA predicted only one quantum state (QS) for quantum transport, whereas FAM predicted three QSs. A cosine function behavior is obtained by both methods for the first quantum state. The calculated bandgap value by EMA is almost twice smaller than that of the FAM. Also, a fluctuating current is predicted by both methods but in different oscillation values.

Tight junctions and human diseases.

Science.gov (United States)

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.

A statistical model for investigating binding probabilities of DNA nucleotide sequences using microarrays.

Science.gov (United States)

Lee, Mei-Ling Ting; Bulyk, Martha L; Whitmore, G A; Church, George M

2002-12-01

There is considerable scientific interest in knowing the probability that a site-specific transcription factor will bind to a given DNA sequence. Microarray methods provide an effective means for assessing the binding affinities of a large number of DNA sequences as demonstrated by Bulyk et al. (2001, Proceedings of the National Academy of Sciences, USA 98, 7158-7163) in their study of the DNA-binding specificities of Zif268 zinc fingers using microarray technology. In a follow-up investigation, Bulyk, Johnson, and Church (2002, Nucleic Acid Research 30, 1255-1261) studied the interdependence of nucleotides on the binding affinities of transcription proteins. Our article is motivated by this pair of studies. We present a general statistical methodology for analyzing microarray intensity measurements reflecting DNA-protein interactions. The log probability of a protein binding to a DNA sequence on an array is modeled using a linear ANOVA model. This model is convenient because it employs familiar statistical concepts and procedures and also because it is effective for investigating the probability structure of the binding mechanism.

Quantification of Cooperativity in Heterodimer-DNA Binding Improves the Accuracy of Binding Specificity Models*

Science.gov (United States)

Isakova, Alina; Berset, Yves; Hatzimanikatis, Vassily; Deplancke, Bart

2016-01-01

Many transcription factors (TFs) have the ability to cooperate on DNA elements as heterodimers. Despite the significance of TF heterodimerization for gene regulation, a quantitative understanding of cooperativity between various TF dimer partners and its impact on heterodimer DNA binding specificity models is still lacking. Here, we used a novel integrative approach, combining microfluidics-steered measurements of dimer-DNA assembly with mechanistic modeling of the implicated protein-protein-DNA interactions to quantitatively interrogate the cooperative DNA binding behavior of the adipogenic peroxisome proliferator-activated receptor γ (PPARγ):retinoid X receptor α (RXRα) heterodimer. Using the high throughput MITOMI (mechanically induced trapping of molecular interactions) platform, we derived equilibrium DNA binding data for PPARγ, RXRα, as well as the PPARγ:RXRα heterodimer to more than 300 target DNA sites and variants thereof. We then quantified cooperativity underlying heterodimer-DNA binding and derived an integrative heterodimer DNA binding constant. Using this cooperativity-inclusive constant, we were able to build a heterodimer-DNA binding specificity model that has superior predictive power than the one based on a regular one-site equilibrium. Our data further revealed that individual nucleotide substitutions within the target site affect the extent of cooperativity in PPARγ:RXRα-DNA binding. Our study therefore emphasizes the importance of assessing cooperativity when generating DNA binding specificity models for heterodimers. PMID:26912662

Quantification of Cooperativity in Heterodimer-DNA Binding Improves the Accuracy of Binding Specificity Models.

Science.gov (United States)

Isakova, Alina; Berset, Yves; Hatzimanikatis, Vassily; Deplancke, Bart

2016-05-06

Many transcription factors (TFs) have the ability to cooperate on DNA elements as heterodimers. Despite the significance of TF heterodimerization for gene regulation, a quantitative understanding of cooperativity between various TF dimer partners and its impact on heterodimer DNA binding specificity models is still lacking. Here, we used a novel integrative approach, combining microfluidics-steered measurements of dimer-DNA assembly with mechanistic modeling of the implicated protein-protein-DNA interactions to quantitatively interrogate the cooperative DNA binding behavior of the adipogenic peroxisome proliferator-activated receptor γ (PPARγ):retinoid X receptor α (RXRα) heterodimer. Using the high throughput MITOMI (mechanically induced trapping of molecular interactions) platform, we derived equilibrium DNA binding data for PPARγ, RXRα, as well as the PPARγ:RXRα heterodimer to more than 300 target DNA sites and variants thereof. We then quantified cooperativity underlying heterodimer-DNA binding and derived an integrative heterodimer DNA binding constant. Using this cooperativity-inclusive constant, we were able to build a heterodimer-DNA binding specificity model that has superior predictive power than the one based on a regular one-site equilibrium. Our data further revealed that individual nucleotide substitutions within the target site affect the extent of cooperativity in PPARγ:RXRα-DNA binding. Our study therefore emphasizes the importance of assessing cooperativity when generating DNA binding specificity models for heterodimers. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Development of a transverse mixing model for large scale impulsion phenomenon in tight lattice

International Nuclear Information System (INIS)

Liu, Xiaojing; Ren, Shuo; Cheng, Xu

2017-01-01

Highlights: • Experiment data of Krauss is used to validate the feasibility of CFD simulation method. • CFD simulation is performed to simulate the large scale impulsion phenomenon for tight-lattice bundle. • A mixing model to simulate the large scale impulsion phenomenon is proposed based on CFD result fitting. • The new developed mixing model has been added in the subchannel code. - Abstract: Tight-lattice is widely adopted in the innovative reactor fuel bundles design since it can increase the conversion ratio and improve the heat transfer between fuel bundles and coolant. It has been noticed that a large scale impulsion of cross-velocity exists in the gap region, which plays an important role on the transverse mixing flow and heat transfer. Although many experiments and numerical simulation have been carried out to study the impulsion of velocity, a model to describe the wave length, amplitude and frequency of mixing coefficient is still missing. This research work takes advantage of the CFD method to simulate the experiment of Krauss and to compare experiment data and simulation result in order to demonstrate the feasibility of simulation method and turbulence model. Then, based on this verified method and model, several simulations are performed with different Reynolds number and different Pitch-to-Diameter ratio. By fitting the CFD results achieved, a mixing model to simulate the large scale impulsion phenomenon is proposed and adopted in the current subchannel code. The new mixing model is applied to some fuel assembly analysis by subchannel calculation, it can be noticed that the new developed mixing model can reduce the hot channel factor and contribute to a uniform distribution of outlet temperature.

Microscopic theory of substrate-induced gap effect on real AFM ...

Indian Academy of Sciences (India)

2017-06-24

Jun 24, 2017 ... We address here a tight-binding model study of frequency-dependent real part of antiferromagnetic susceptibility for the graphene systems. TheHamiltonian consists of electron hopping upto third nearest-neighbours,substrate and impurity effects in the presence of electron–electron interactions at A and B ...

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

Science.gov (United States)

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.

Effect of dipole polarizability on positron binding by strongly polar molecules

International Nuclear Information System (INIS)

Gribakin, G F; Swann, A R

2015-01-01

A model for positron binding to polar molecules is considered by combining the dipole potential outside the molecule with a strongly repulsive core of a given radius. Using existing experimental data on binding energies leads to unphysically small core radii for all of the molecules studied. This suggests that electron–positron correlations neglected in the simple model play a large role in determining the binding energy. We account for these by including the polarization potential via perturbation theory and non-perturbatively. The perturbative model makes reliable predictions of binding energies for a range of polar organic molecules and hydrogen cyanide. The model also agrees with the linear dependence of the binding energies on the polarizability inferred from the experimental data (Danielson et al 2009 J. Phys. B: At. Mol. Opt. Phys. 42 235203). The effective core radii, however, remain unphysically small for most molecules. Treating molecular polarization non-perturbatively leads to physically meaningful core radii for all of the molecules studied and enables even more accurate predictions of binding energies to be made for nearly all of the molecules considered. (paper)

Effects of reduced surface tension on two-phase diversion cross-flow between subchannels simplifying triangle tight lattice rod bundle

International Nuclear Information System (INIS)

Kawahara, Akimaro; Sadatomi, Michio; Higuchi, Tatsuya

2009-01-01

Two-phase diversion cross-flow between tight lattice subchannels has been investigated experimentally and analytically. For hydraulically non-equilibrium flows with the pressure difference between the subchannels, experiments were conducted using a vertical multiple-channel with two subchannels simplifying a triangle tight lattice rod bundle. To know the effects of the reduced surface tension on the diversion cross-flow, water and water with a surfactant were used as the test liquids. Data were obtained on the axial variations in the pressure difference between the subchannels, gas and liquid flow rates and void fraction in each subchannel for slug-churn and annular flows. In the analysis, flow redistribution processes due to the diversion cross-flow have been calculated by our subchannel analysis code based on a two-fluid model. From a comparison between the experiment and the code calculation, the code was found to be valid against the present data if the improved constitutive equations of wall and interfacial friction reported in our previous paper were incorporated to account for the reduced surface tension effects. (author)

Numerical prediction of pressure loss in tight-lattice rod bundle by use of 3-dimensional two-fluid model simulation code ACE-3D

International Nuclear Information System (INIS)

Yoshida, Hiroyuki; Takase, Kazuyuki; Suzuki, Takayuki

2009-01-01

Two-fluid model can simulate two-phase flow by computational cost less than detailed two-phase flow simulation method such as interface tracking method or particle interaction method. Therefore, two-fluid model is useful for thermal hydraulic analysis in large-scale domain such as a rod bundle. Japan Atomic Energy Agency (JAEA) develops three dimensional two-fluid model analysis code ACE-3D that adopts boundary fitted coordinate system in order to simulate complex shape flow channel. In this paper, boiling two-phase flow analysis in a tight-lattice rod bundle was performed by the ACE-3D. In the results, the void fraction, which distributes in outermost region of rod bundle, is lower than that in center region of rod bundle. The tendency of void fraction distribution agreed with the measurement results by neutron radiography qualitatively. To evaluate effects of two-phase flow model used in the ACE-3D, numerical simulation of boiling two-phase in tight-lattice rod bundle with no lift force model was also performed. In the results, the lift force model has direct effects on void fraction concentration in gap region, and pressure distribution in horizontal plane induced by void fraction distribution cause of bubble movement from the gap region to the subchannel region. The predicted pressure loss in the section that includes no spacer accorded with experimental results with around 10% of differences. The predicted friction pressure loss was underestimated around 20% of measured values, and the effect of the turbulence model is considered as one of the causes of this underestimation. (author)

Cobalt uptake and binding in human red blood cells

DEFF Research Database (Denmark)

Simonsen, Lars Ole; Brown, Anthony M; Harbak, Henrik

2011-01-01

of cobalt, and also from the initial slope of the cobalt buffering curve. The cobalt accumulation is similar in fed and ATP-depleted cells. The buffering curve for [Co(T)](c) can be fitted by a Michaelis type function with B(max)=24 mmol (l cells)(-1) and half-saturation at 240 µM [Co(2+)](c). The tracer...... reversibly bound, being releasable by excess extracellular EGTA in the presence of A23187, and partly tightly bound, remaining in the cells even at high ionophore concentrations. The tightly bound fraction builds up over time, and is larger and develops earlier in fed cells compared to ATP-depleted cells......-migrate with hemoglobin in Sephadex column chromatography of a lysate of (57)Co-loaded cells. (57)Co also co-migrates with hemoglobin when added to a lysate of unlabeled cells or to a solution of purified hemoglobin, in both cases with a time-dependent development of tight binding. Cobalt is known to bind to the globin...

An improved method for predicting brittleness of rocks via well logs in tight oil reservoirs

Science.gov (United States)

Wang, Zhenlin; Sun, Ting; Feng, Cheng; Wang, Wei; Han, Chuang

2018-06-01

There can be no industrial oil production in tight oil reservoirs until fracturing is undertaken. Under such conditions, the brittleness of the rocks is a very important factor. However, it has so far been difficult to predict. In this paper, the selected study area is the tight oil reservoirs in Lucaogou formation, Permian, Jimusaer sag, Junggar basin. According to the transformation of dynamic and static rock mechanics parameters and the correction of confining pressure, an improved method is proposed for quantitatively predicting the brittleness of rocks via well logs in tight oil reservoirs. First, 19 typical tight oil core samples are selected in the study area. Their static Young’s modulus, static Poisson’s ratio and petrophysical parameters are measured. In addition, the static brittleness indices of four other tight oil cores are measured under different confining pressure conditions. Second, the dynamic Young’s modulus, Poisson’s ratio and brittleness index are calculated using the compressional and shear wave velocity. With combination of the measured and calculated results, the transformation model of dynamic and static brittleness index is built based on the influence of porosity and clay content. The comparison of the predicted brittleness indices and measured results shows that the model has high accuracy. Third, on the basis of the experimental data under different confining pressure conditions, the amplifying factor of brittleness index is proposed to correct for the influence of confining pressure on the brittleness index. Finally, the above improved models are applied to formation evaluation via well logs. Compared with the results before correction, the results of the improved models agree better with the experimental data, which indicates that the improved models have better application effects. The brittleness index prediction method of tight oil reservoirs is improved in this research. It is of great importance in the optimization of

Effect of binding in cyclic phosphorylation-dephosphorylation process and in energy transformation.

Science.gov (United States)

Sarkar, A; Beard, D A; Franza, B R

2006-07-01

The effects of binding on the phosphorylation-dephosphorylation cycle (PDPC) - one of the key components of the signal transduction processes - is analyzed based on a mathematical model. The model shows that binding of proteins, forming a complex, diminishes the ultrasensitivity of the PDPC to the differences in activity between kinase and phosphatase in the cycle. It is also found that signal amplification depends upon the strength of the binding affinity of the protein (phosphorylated or dephosphorylated) to other proteins . It is also observed that the amplification of signal is not only dependent on phosphorylation potential but also on binding properties and resulting adjustments in binding energies.

Numerical simulation of flow behavior in tight lattice rod bundle

International Nuclear Information System (INIS)

Yu Yiqi; Yang Yanhua; Gu Hanyang; Cheng Xu; Song Xiaoming; Wang Xiaojun

2009-01-01

The Numerical investigation is performed on the air turbulent flow in triangular rod bundle array. Based on the experimental data, the eddy viscosity turbulent model and the Reynold stress turbulent model are evaluated to simulate the flow behavior in the tight lattice. The results show that SSG Reynolds Stress Model has shown superior predictive performance than other Reynolds-stress models, which indicates that the simulation of the anisotropy of the turbulence is significant in the tight lattice. The result with different Reynolds number and geometry shows that the magnitude of the secondary flow is almost independent of the Reynolds number, but it increases with the decrease of the P/D. (authors)

Performance Improvement of Receivers Based on Ultra-Tight Integration in GNSS-Challenged Environments

Directory of Open Access Journals (Sweden)

Feng Qin

2013-12-01

Full Text Available Ultra-tight integration was first proposed by Abbott in 2003 with the purpose of integrating a global navigation satellite system (GNSS and an inertial navigation system (INS. This technology can improve the tracking performances of a receiver by reconfiguring the tracking loops in GNSS-challenged environments. In this paper, the models of all error sources known to date in the phase lock loops (PLLs of a standard receiver and an ultra-tightly integrated GNSS/INS receiver are built, respectively. Based on these models, the tracking performances of the two receivers are compared to verify the improvement due to the ultra-tight integration. Meanwhile, the PLL error distributions of the two receivers are also depicted to analyze the error changes of the tracking loops. These results show that the tracking error is significantly reduced in the ultra-tightly integrated GNSS/INS receiver since the receiver’s dynamics are estimated and compensated by an INS. Moreover, the mathematical relationship between the tracking performances of the ultra-tightly integrated GNSS/INS receiver and the quality of the selected inertial measurement unit (IMU is derived from the error models and proved by the error comparisons of four ultra-tightly integrated GNSS/INS receivers aided by different grade IMUs.

Strength and water-tightness of the closure head and valves of a model cask under high external pressure

International Nuclear Information System (INIS)

Terada, O.; Kumada, M.; Hayakawa, T.; Mochizuki, S.; Ohrui, K.

1978-01-01

This paper describes experimental research on the strength and water-tightness of the closure head and attached valves of a model cask under high external pressure, in simulation of its having been accidentally lost in the deep sea. Both the external pressure tests and the corrosion tests were carried out using scale models of the closure head of an 80-ton spent-fuel shipping cask, and the full size pressure relief valves and drain valves which were to be attached to the actual cask. Based on the results of the above tests, evaluations were made, and new information was obtained on the pressure-proof strength and water-tightness of the closure head of the cask and the valves. Lastly, research which is being carried on in Japan on the pressure equalizer is also introduced

Tightness of the Ising-Kac Model on the Two-Dimensional Torus

Science.gov (United States)

Hairer, Martin; Iberti, Massimo

2018-05-01

We consider the sequence of Gibbs measures of Ising models with Kac interaction defined on a periodic two-dimensional discrete torus near criticality. Using the convergence of the Glauber dynamic proven by Mourrat and Weber (Commun Pure Appl Math 70:717-812, 2017) and a method by Tsatsoulis and Weber employed in (arXiv:1609.08447 2016), we show tightness for the sequence of Gibbs measures of the Ising-Kac model near criticality and characterise the law of the limit as the Φ ^4_2 measure on the torus. Our result is very similar to the one obtained by Cassandro et al. (J Stat Phys 78(3):1131-1138, 1995) on Z^2, but our strategy takes advantage of the dynamic, instead of correlation inequalities. In particular, our result covers the whole critical regime and does not require the large temperature/large mass/small coupling assumption present in earlier results.

On the mechanism of sulfite activation of chloroplast thylakoid ATPase and the relation of ADP tightly bound at a catalytic site to the binding change mechanism

Energy Technology Data Exchange (ETDEWEB)

Du, Z.; Boyer, P.D. (Univ. of California, Los Angeles (USA))

1990-01-16

Washed chloroplast thylakoid membranes upon exposure to ({sup 3}H)ADP retain in tightly bound ({sup 3}H)ADP on a catalytic site of the ATP synthase. The presence of sufficient endogenous or added Mg{sup 2+} results in an enzyme with essentially no ATPase activity. Sulfite activates the ATPase, and many molecules of ATP per synthase can be hydrolyzed before most of the bound ({sup 3}H)ADP is released, a result interpreted as indicating that the ADP is not bound at a site participating in catalysis by the sulfite-activated enzyme. The authors present evidence that this is not the case. The Mg{sup 2+}- and ADP-inhibited enzyme when exposed to MgATP and 20-100 mM sulfite shows a lag of about 1 min at 22{degree}C and of about 15 s at 37{degree}C before reaching the same steady-state rate as attained with light-activated ATPase that has not been inhibited by Mg{sup 2+} and ADP. The lag is not eliminated if the enzyme is exposed to sulfite prior to MgATP addition, indicating that ATPase turnover is necessary for the activation. The release of most of the bound ({sup 3}H)ADP parallels the onset of ATPase activity, although some ({sup 3}H)ADP is not released even with prolonged catalytic turnover and may be on poorly active or inactive enzyme or at noncatalytic sites. The results are consistent with most of the tightly bound ({sup 3}H)ADP being at a catalytic site and being replaced as this Mg{sup 2+}- and ADP-inhibited site regains equivalent participation with other catalytic sites on the activated enzyme. The sulfite activation can be explained by sulfite combination at a P{sub i} binding site of the enzyme-ADP-Mg{sup 2+} complex to give a form more readily activated by ATP binding at an alternative site.

A tightly coupled non-equilibrium model for inductively coupled radio-frequency plasmas

International Nuclear Information System (INIS)

Munafò, A.; Alfuhaid, S. A.; Panesi, M.; Cambier, J.-L.

2015-01-01

The objective of the present work is the development of a tightly coupled magneto-hydrodynamic model for inductively coupled radio-frequency plasmas. Non Local Thermodynamic Equilibrium (NLTE) effects are described based on a hybrid State-to-State approach. A multi-temperature formulation is used to account for thermal non-equilibrium between translation of heavy-particles and vibration of molecules. Excited electronic states of atoms are instead treated as separate pseudo-species, allowing for non-Boltzmann distributions of their populations. Free-electrons are assumed Maxwellian at their own temperature. The governing equations for the electro-magnetic field and the gas properties (e.g., chemical composition and temperatures) are written as a coupled system of time-dependent conservation laws. Steady-state solutions are obtained by means of an implicit Finite Volume method. The results obtained in both LTE and NLTE conditions over a broad spectrum of operating conditions demonstrate the robustness of the proposed coupled numerical method. The analysis of chemical composition and temperature distributions along the torch radius shows that: (i) the use of the LTE assumption may lead to an inaccurate prediction of the thermo-chemical state of the gas, and (ii) non-equilibrium phenomena play a significant role close the walls, due to the combined effects of Ohmic heating and macroscopic gradients

Comparative testing of women's tights, which are realized in the Ukrainian market

OpenAIRE

Мартосенко, Марина Григорьевна; Браилко, Анна Сергеевна

2015-01-01

Assortment of women's tights represented on the Ukrainian market is diverse: medical and corrective tights, classic thin and warm, simple and exclusive, ornamental and sports, for pregnant women and moisturizing effect. The size, density, pattern, material composition, visual appearance, matching fashion trends, colors, pricing policy – all these are criteria for the selection of women's tights.With such huge and diverse range of women's tights in the Ukrainian market, the problem of quality ...

Tight turns

CERN Multimedia

Anaïs Schaeffer

2012-01-01

The Italian National Institute for Nuclear Physics (INFN) has successfully tested the first model of a new fast-ramping curved dipole magnet. This is great news for CERN, which sees the advance as holding potential for the future of the SPS.   The first model of a new fast-ramping curved dipole magnet being prepared for cryogenic testing at the LASA laboratory (INFN Milano, Italy). On 16 July INFN introduced an innovative dipole magnet. With a length of some 4 metres, it can produce a 4.5 Tesla magnetic field and achieve a tighter bend than ever before (the bending radius has been squeezed to a remarkable 66.7 metres). This new magnet was designed in the first instance for GSI’s SIS300 synchrotron (in Germany), which will require 60 dipoles of this type. "Achieving such a tight bend demanded a major R&D effort," stressed Pasquale Fabbricatore, the spokesman of the INFN collaboration responsible for the magnet’s development. "We had to not o...

Modeling Shear Induced Von Willebrand Factor Binding to Collagen

Science.gov (United States)

Dong, Chuqiao; Wei, Wei; Morabito, Michael; Webb, Edmund; Oztekin, Alparslan; Zhang, Xiaohui; Cheng, Xuanhong

2017-11-01

Von Willebrand factor (vWF) is a blood glycoprotein that binds with platelets and collagen on injured vessel surfaces to form clots. VWF bioactivity is shear flow induced: at low shear, binding between VWF and other biological entities is suppressed; for high shear rate conditions - as are found near arterial injury sites - VWF elongates, activating its binding with platelets and collagen. Based on parameters derived from single molecule force spectroscopy experiments, we developed a coarse-grain molecular model to simulate bond formation probability as a function of shear rate. By introducing a binding criterion that depends on the conformation of a sub-monomer molecular feature of our model, the model predicts shear-induced binding, even for conditions where binding is highly energetically favorable. We further investigate the influence of various model parameters on the ability to predict shear-induced binding (vWF length, collagen site density and distribution, binding energy landscape, and slip/catch bond length) and demonstrate parameter ranges where the model provides good agreement with existing experimental data. Our results may be important for understanding vWF activity and also for achieving targeted drug therapy via biomimetic synthetic molecules. National Science Foundation (NSF),Division of Mathematical Sciences (DMS).

Device-Level Models Using Multi-Valley Effective Mass

Science.gov (United States)

Baczewski, Andrew D.; Frees, Adam; Gamble, John King; Gao, Xujiao; Jacobson, N. Tobias; Mitchell, John A.; Montaño, Inès; Muller, Richard P.; Nielsen, Erik

2015-03-01

Continued progress in quantum electronics depends critically on the availability of robust device-level modeling tools that capture a wide range of physics and effective mass theory (EMT) is one means of building such models. Recent developments in multi-valley EMT show quantitative agreement with more detailed atomistic tight-binding calculations of phosphorus donors in silicon (Gamble, et. al., arXiv:1408.3159). Leveraging existing PDE solvers, we are developing a framework in which this multi-valley EMT is coupled to an integrated device-level description of several experimentally active qubit technologies. Device-level simulations of quantum operations will be discussed, as well as the extraction of process matrices at this level of theory. The authors gratefully acknowledge support from the Sandia National Laboratories Truman Fellowship Program, which is funded by the Laboratory Directed Research and Development (LDRD) Program. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Security Administration under contract DE-AC04-94AL85000.

The necessity of connection structures in neural models of variable binding.

Science.gov (United States)

van der Velde, Frank; de Kamps, Marc

2015-08-01

In his review of neural binding problems, Feldman (Cogn Neurodyn 7:1-11, 2013) addressed two types of models as solutions of (novel) variable binding. The one type uses labels such as phase synchrony of activation. The other ('connectivity based') type uses dedicated connections structures to achieve novel variable binding. Feldman argued that label (synchrony) based models are the only possible candidates to handle novel variable binding, whereas connectivity based models lack the flexibility required for that. We argue and illustrate that Feldman's analysis is incorrect. Contrary to his conclusion, connectivity based models are the only viable candidates for models of novel variable binding because they are the only type of models that can produce behavior. We will show that the label (synchrony) based models analyzed by Feldman are in fact examples of connectivity based models. Feldman's analysis that novel variable binding can be achieved without existing connection structures seems to result from analyzing the binding problem in a wrong frame of reference, in particular in an outside instead of the required inside frame of reference. Connectivity based models can be models of novel variable binding when they possess a connection structure that resembles a small-world network, as found in the brain. We will illustrate binding with this type of model with episode binding and the binding of words, including novel words, in sentence structures.

Nanofiltration and Tight Ultrafiltration Membranes for Natural Organic Matter Removal-Contribution of Fouling and Concentration Polarization to Filtration Resistance.

Science.gov (United States)

Winter, Joerg; Barbeau, Benoit; Bérubé, Pierre

2017-07-02

Nanofiltration (NF) and tight ultrafiltration (tight UF) membranes are a viable treatment option for high quality drinking water production from sources with high concentrations of contaminants. To date, there is limited knowledge regarding the contribution of concentration polarization (CP) and fouling to the increase in resistance during filtration of natural organic matter (NOM) with NF and tight UF. Filtration tests were conducted with NF and tight UF membranes with molecular weight cut offs (MWCOs) of 300, 2000 and 8000 Da, and model raw waters containing different constituents of NOM. When filtering model raw waters containing high concentrations of polysaccharides (i.e., higher molecular weight NOM), the increase in resistance was dominated by fouling. When filtering model raw waters containing humic substances (i.e., lower molecular weight NOM), the increase in filtration resistance was dominated by CP. The results indicate that low MWCO membranes are better suited for NOM removal, because most of the NOM in surface waters consist mainly of humic substances, which were only effectively rejected by the lower MWCO membranes. However, when humic substances are effectively rejected, CP can become extensive, leading to a significant increase in filtration resistance by the formation of a cake/gel layer at the membrane surface. For this reason, cross-flow operation, which reduces CP, is recommended.

The Effects of Tight Budgetary Control on Managerial Bahaviour in the Swedish Public Sector : Emphasizing Motivation, Commitment, Satisfaction and Stress

OpenAIRE

Hemsing, Malte; Baker, Fadi

2013-01-01

This thesis study is about the effects of tight budgetary control on managerial behaviour in the Swedish public sector. Managerial behaviour represents the four variables; motivation, organizational commitment, stress, and satisfaction. As previous research mostly investigated the effects of tight budgetary control on organizational performance in the private sector, this study can be seen as one of the first that focus on managerial behaviour and is based on the public sector. For the data c...

Development of constraint algorithm for the number of electrons in molecular orbitals consisting mainly 4f atomic orbitals of rare-earth elements and its introduction to tight-binding quantum chemical molecular dynamics method

International Nuclear Information System (INIS)

Endou, Akira; Onuma, Hiroaki; Jung, Sun-ho

2007-01-01

Our original tight-binding quantum chemical molecular dynamics code, Colors', has been successfully applied to the theoretical investigation of complex materials including rare-earth elements, e.g., metal catalysts supported on a CeO 2 surface. To expand our code so as to obtain a good convergence for the electronic structure of a calculation system including a rare-earth element, we developed a novel algorithm to provide a constraint condition for the number of electrons occupying the selected molecular orbitals that mainly consist of 4f atomic orbitals of the rare-earth element. This novel algorithm was introduced in Colors. Using Colors, we succeeded in obtaining the classified electronic configurations of the 4f atomic orbitals of Ce 4+ and reduced Ce ions in a CeO 2 bulk model with one oxygen defect, which makes it difficult to obtain a good convergence using a conventional first-principles quantum chemical calculation code. (author)

Model many-body Stoner Hamiltonian for binary FeCr alloys

Science.gov (United States)

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.

Unified Drain Current Model of Armchair Graphene Nanoribbons with Uniaxial Strain and Quantum Effect

Directory of Open Access Journals (Sweden)

EngSiew Kang

2014-01-01

Full Text Available A unified current-voltage I-V model of uniaxial strained armchair graphene nanoribbons (AGNRs incorporating quantum confinement effects is presented in this paper. The I-V model is enhanced by integrating both linear and saturation regions into a unified and precise model of AGNRs. The derivation originates from energy dispersion throughout the entire Brillouin zone of uniaxial strained AGNRs based on the tight-binding approximation. Our results reveal the modification of the energy band gap, carrier density, and drain current upon strain. The effects of quantum confinement were investigated in terms of the quantum capacitance calculated from the broadening density of states. The results show that quantum effect is greatly dependent on the magnitude of applied strain, gate voltage, channel length, and oxide thickness. The discrepancies between the classical calculation and quantum calculation were also measured and it has been found to be as high as 19% drive current loss due to the quantum confinement. Our finding which is in good agreement with the published data provides significant insight into the device performance of uniaxial strained AGNRs in nanoelectronic applications.

Are tight gas resources overstated?

Energy Technology Data Exchange (ETDEWEB)

Roche, P.

2004-11-01

According to conventional wisdom, North America's tight gas resources are continuous, regional accumulations of water-free methane, trapped in low-permeability rock, and involving very little exploration risk. Backing up conventional wisdom, EnCana Corporation is investing heavily in technology-intensive and capital-intensive tight gas plays in Western Canada and the Rocky Mountain regions of the United States. On the other hand, a recent study in the Greater Green River Basin of southwestern Wyoming says that tight gas resources have been significantly overestimated, by as much as three to five times too high, and the risks of exploration are every bit as high as those for conventional exploration. This study essentially dismisses the whole idea of tight gas, or basin-centred gas as a myth, the authors being firmly convinced that tight gas formations should be viewed as conventional hydrocarbon systems, with the usual risks of exploration. This paper discusses the controversy created by this recent study and the implications for natural gas reserves on a basin and individual company level, and the risks associated with exploration. The views of EnCana Corporation, being the company most heavily involved in tight gas and coalbed methane, and those of John Masters, co-founder of Canadian Hunter Exploration Ltd., and discoverer of the blockbuster Elsmworth tight gas deposit in northeastern Alberta in the mid-1970s, are explained in considerable detail, in an effort to dismiss the doubters. EnCana officials and Masters argue that the points raised by the authors of the Greater Green River study do not hold water: Tight gas or basin gas is a distinct hydrocarbon formation, characterized by low permeability, therefore it is to be expected that the gas will take longer to come out of the ground. Neither is the role of water in basin-centred gas systems the major problem as claimed by the doubters. They also characterize it as imprudent to claim to know what the

Trapping a Knot into Tight Conformations by Intra-Chain Repulsions

Directory of Open Access Journals (Sweden)

Liang Dai

2017-02-01

Full Text Available Knots can occur in biopolymers such as DNA and peptides. In our previous study, we systematically investigated the effects of intra-chain interactions on knots and found that long-range repulsions can surprisingly tighten knots. Here, we use this knowledge to trap a knot into tight conformations in Langevin dynamics simulations. By trapping, we mean that the free energy landscape with respect to the knot size exhibits a potential well around a small knot size in the presence of long-range repulsions, and this potential can well lead to long-lived tight knots when its depth is comparable to or larger than thermal energy. We tune the strength of intra-chain repulsion such that a knot is weakly trapped. Driven by thermal fluctuations, the knot can escape from the trap and is then re-trapped. We find that the knot switches between tight and loose conformations—referred to as “knot breathing”. We use a Yukawa potential to model screened electrostatic interactions to explore the relevance of knot trapping and breathing in charged biopolymers. We determine the minimal screened length and the minimal strength of repulsion for knot trapping. We find that Coulomb-induced knot trapping is possible to occur in single-stranded DNA and peptides for normal ionic strengths.

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

Science.gov (United States)

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.

Microscopic theory of the superconducting gap in the quasi-one-dimensional organic conductor (TMTSF) 2ClO4 : Model derivation and two-particle self-consistent analysis

Science.gov (United States)

Aizawa, Hirohito; Kuroki, Kazuhiko

2018-03-01

We present a first-principles band calculation for the quasi-one-dimensional (Q1D) organic superconductor (TMTSF) 2ClO4 . An effective tight-binding model with the TMTSF molecule to be regarded as the site is derived from a calculation based on maximally localized Wannier orbitals. We apply a two-particle self-consistent (TPSC) analysis by using a four-site Hubbard model, which is composed of the tight-binding model and an onsite (intramolecular) repulsive interaction, which serves as a variable parameter. We assume that the pairing mechanism is mediated by the spin fluctuation, and the sign of the superconducting gap changes between the inner and outer Fermi surfaces, which correspond to a d -wave gap function in a simplified Q1D model. With the parameters we adopt, the critical temperature for superconductivity estimated by the TPSC approach is approximately 1 K, which is consistent with experiment.

Balanced sparse model for tight frames in compressed sensing magnetic resonance imaging.

Directory of Open Access Journals (Sweden)

Yunsong Liu

Full Text Available Compressed sensing has shown to be promising to accelerate magnetic resonance imaging. In this new technology, magnetic resonance images are usually reconstructed by enforcing its sparsity in sparse image reconstruction models, including both synthesis and analysis models. The synthesis model assumes that an image is a sparse combination of atom signals while the analysis model assumes that an image is sparse after the application of an analysis operator. Balanced model is a new sparse model that bridges analysis and synthesis models by introducing a penalty term on the distance of frame coefficients to the range of the analysis operator. In this paper, we study the performance of the balanced model in tight frame based compressed sensing magnetic resonance imaging and propose a new efficient numerical algorithm to solve the optimization problem. By tuning the balancing parameter, the new model achieves solutions of three models. It is found that the balanced model has a comparable performance with the analysis model. Besides, both of them achieve better results than the synthesis model no matter what value the balancing parameter is. Experiment shows that our proposed numerical algorithm constrained split augmented Lagrangian shrinkage algorithm for balanced model (C-SALSA-B converges faster than previously proposed algorithms accelerated proximal algorithm (APG and alternating directional method of multipliers for balanced model (ADMM-B.

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

International Nuclear Information System (INIS)

Grimme, Stefan; Bannwarth, Christoph

2016-01-01

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 well 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

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

Energy Technology Data Exchange (ETDEWEB)

Grimme, Stefan, E-mail: grimme@thch.uni-bonn.de; Bannwarth, Christoph [Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn (Germany)

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 well 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

Improved Characterization and Modeling of Tight Oil Formations for CO₂ Enhanced Oil Recovery Potential and Storage Capacity Estimation

Energy Technology Data Exchange (ETDEWEB)

Sorensen, James [Univ. of North Dakota, Grand Forks, ND (United States). Energy & Environmental Research Center (EERC); Smith, Steven [Univ. of North Dakota, Grand Forks, ND (United States). Energy & Environmental Research Center (EERC); Kurz, Bethany [Univ. of North Dakota, Grand Forks, ND (United States). Energy & Environmental Research Center (EERC); Hawthorne, Steven [Univ. of North Dakota, Grand Forks, ND (United States). Energy & Environmental Research Center (EERC); Jin, Lu [Univ. of North Dakota, Grand Forks, ND (United States). Energy & Environmental Research Center (EERC); Bosshart, Nicholas [Univ. of North Dakota, Grand Forks, ND (United States). Energy & Environmental Research Center (EERC); Torres, Jose [Univ. of North Dakota, Grand Forks, ND (United States). Energy & Environmental Research Center (EERC); Nyberg, Carolyn [Univ. of North Dakota, Grand Forks, ND (United States). Energy & Environmental Research Center (EERC); Heebink, Loreal [Univ. of North Dakota, Grand Forks, ND (United States). Energy & Environmental Research Center (EERC); Hurley, John [Univ. of North Dakota, Grand Forks, ND (United States). Energy & Environmental Research Center (EERC)

2018-03-09

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 CO₂. 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 the 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 CO₂ 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 CO₂ and oil mobility within tight oil formation samples, 2) the determination of CO₂ permeation and oil extraction rates in tight reservoir rocks and organic-rich shales of the Bakken, and 3) the integration of the laboratory-based CO₂ permeation and oil extraction data and the characterization data into geologic models and dynamic simulations to develop predictions of CO₂ 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

Prediction of new tightly bound-states of H2+(d2+) and ''cold fusion''-experiments

International Nuclear Information System (INIS)

Barut, A.O.

1989-06-01

It is suggested that in the ''cold-fusion'' experiments of Fleischmann and Pons new tightly-bound molecular states of D 2 + are formed with binding energies predicted to be of the order of 50 keV accounting for the heat released without appreciable fusion. Other tests of the suggested mechanism are proposed and the derivation of the new energy levels is given. (author). 3 refs

Nanofiltration and Tight Ultrafiltration Membranes for Natural Organic Matter Removal—Contribution of Fouling and Concentration Polarization to Filtration Resistance

Directory of Open Access Journals (Sweden)

Joerg Winter

2017-07-01

Full Text Available Nanofiltration (NF and tight ultrafiltration (tight UF membranes are a viable treatment option for high quality drinking water production from sources with high concentrations of contaminants. To date, there is limited knowledge regarding the contribution of concentration polarization (CP and fouling to the increase in resistance during filtration of natural organic matter (NOM with NF and tight UF. Filtration tests were conducted with NF and tight UF membranes with molecular weight cut offs (MWCOs of 300, 2000 and 8000 Da, and model raw waters containing different constituents of NOM. When filtering model raw waters containing high concentrations of polysaccharides (i.e., higher molecular weight NOM, the increase in resistance was dominated by fouling. When filtering model raw waters containing humic substances (i.e., lower molecular weight NOM, the increase in filtration resistance was dominated by CP. The results indicate that low MWCO membranes are better suited for NOM removal, because most of the NOM in surface waters consist mainly of humic substances, which were only effectively rejected by the lower MWCO membranes. However, when humic substances are effectively rejected, CP can become extensive, leading to a significant increase in filtration resistance by the formation of a cake/gel layer at the membrane surface. For this reason, cross-flow operation, which reduces CP, is recommended.

Does the low hole transport mass in and Si nanowires lead to mobility enhancements at high field and stress: A self-consistent tight-binding study

Science.gov (United States)

Kotlyar, R.; Linton, T. D.; Rios, R.; Giles, M. D.; Cea, S. M.; Kuhn, K. J.; Povolotskyi, Michael; Kubis, Tillmann; Klimeck, Gerhard

2012-06-01

The hole surface roughness and phonon limited mobility in the silicon , , and square nanowires under the technologically important conditions of applied gate bias and stress are studied with the self-consistent Poisson-sp3d5s*-SO tight-binding bandstructure method. Under an applied gate field, the hole carriers in a wire undergo a volume to surface inversion transition diminishing the positive effects of the high and valence band nonparabolicities, which are known to lead to the large gains of the phonon limited mobility at a zero field in narrow wires. Nonetheless, the hole mobility in the unstressed wires down to the 5 nm size remains competitive or shows an enhancement at high gate field over the large wire limit. Down to the studied 3 nm sizes, the hole mobility is degraded by strong surface roughness scattering in and wires. The channels are shown to experience less surface scattering degradation. The physics of the surface roughness scattering dependence on wafer and channel orientations in a wire is discussed. The calculated uniaxial compressive channel stress gains of the hole mobility are found to reduce in the narrow wires and at the high field. This exacerbates the stressed mobility degradation with size. Nonetheless, stress gains of a factor of 2 are obtained for wires down to 3 nm size at a 5×1012 cm-2 hole inversion density per gate area.

A 3D regression surface for the room temperature tightness gasket data reduction and bolt load design

International Nuclear Information System (INIS)

Jolly, Pascal; Marchand, Luc

2008-01-01

The purpose of the present work is to propose a new approach for modelling the tightness behaviour of the gaskets used in bolted flange joints. This new approach consists of developing a mathematical model for a three-dimensional (3D) representation of the gasket tightness performance. Rather than considering a 2D graph for characterizing the complete gasket behaviour, a third axis is added to the S g vs. Tp plot to dissociate the unloading cycles from initial gasket tightening. This leads to the definition of a surface that is represented by a simple polynomial equation that contains six coefficients that are determined by a simple regression calculation. In the first part of the paper, the new approach is tested through a database of 406 room temperature tightness (ROTT) tests performed on different gasket styles. Then, a statistical analysis of the predictions made with the new model demonstrates its ability to predict gasket leak rates much more accurately than it was previously possible with the gasket constants derived from the ROTT Draft 9 or 10 methods. It is also demonstrated that the new approach can be used to model successfully complex gasket behaviours such as the tightness hardening phenomenon. Secondly, the effect of gas pressure change on the leak rate is analysed. It turns out that at high gasket stresses, the actual scheme of the ROTT tests may not allow enough time for reaching a stabilized leak rate value because of a transitory time effect in the porous structure of gaskets. Then, in order to evaluate the characteristic waiting period (dwell time) before a stabilized flow rate is achieved following a change in the gas pressure level, a simple phenomenological analysis of the flow is performed

Effective field theory of interactions on the lattice

DEFF Research Database (Denmark)

Valiente, Manuel; Zinner, Nikolaj T.

2015-01-01

We consider renormalization of effective field theory interactions by discretizing the continuum on a tight-binding lattice. After studying the one-dimensional problem, we address s-wave collisions in three dimensions and relate the bare lattice coupling constants to the continuum coupling consta...... constants. Our method constitutes a very simple avenue for the systematic renormalization in effective field theory, and is especially useful as the number of interaction parameters increases.......We consider renormalization of effective field theory interactions by discretizing the continuum on a tight-binding lattice. After studying the one-dimensional problem, we address s-wave collisions in three dimensions and relate the bare lattice coupling constants to the continuum coupling...

Thermodynamic studies of a series of homologous HIV-1 TAR RNA ligands reveal that loose binders are stronger Tat competitors than tight ones.

Science.gov (United States)

Pascale, Lise; Azoulay, Stéphane; Di Giorgio, Audrey; Zenacker, Laura; Gaysinski, Marc; Clayette, Pascal; Patino, Nadia

2013-06-01

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.

Appraisal of the tight sands potential of the Sand Wash and Great Divide Basins

International Nuclear Information System (INIS)

1993-08-01

The volume of future tight gas reserve additions is difficult to estimate because of uncertainties in the characterization and extent of the resource and the performance and cost-effectiveness of stimulation and production technologies. Ongoing R ampersand D by industry and government aims to reduce the risks and costs of producing these tight resources, increase the certainty of knowledge of their geologic characteristics and extent, and increase the efficiency of production technologies. Some basins expected to contain large volumes of tight gas are being evaluated as to their potential contribution to domestic gas supplies. This report describes the results of one such appraisal. This analysis addresses the tight portions of the Eastern Greater Green River Basin (Sand Wash and Great Divide Subbasins in Northwestern Colorado and Southwestern Wyoming, respectively), with respect to estimated gas-in-place, technical recovery, and potential reserves. Geological data were compiled from public and proprietary sources. The study estimated gas-in-place in significant (greater than 10 feet net sand thickness) tight sand intervals for six distinct vertical and 21 areal units of analysis. These units of analysis represent tight gas potential outside current areas of development. For each unit of analysis, a ''typical'' well was modeled to represent the costs, recovery and economics of near-term drilling prospects in that unit. Technically recoverable gas was calculated using reservoir properties and assumptions about current formation evaluation and extraction technology performance. Basin-specific capital and operating costs were incorporated along with taxes, royalties and current regulations to estimate the minimum required wellhead gas price required to make the typical well in each of unit of analysis economic

Hermetic compartments leak-tightness enhancement

International Nuclear Information System (INIS)

Murani, J.

2000-01-01

In connection with the enhancement of the nuclear safety of the Jaslovske Bohunice V-1 NPP actions for the increase of the leak tightness are performed. The reconstruction has been done in the following directions: hermetic compartments leak tightness enhancement; air lock installation; installation of air lock in SP 4 vent system; integrated leakage rate test to hermetic compartments with leak detection. After 'major' leaks on the hermetic boundary components had been eliminated, since 1994 works on a higher qualitative level began. The essence of the works consists in the detection and identification of leaks in the structural component of the hermetic boundary during the planned refueling outages. The results of the Small Reconstruction and gradual enhancement of leak tightness are presented

Faradaic Impedance Spectroscopy for Detection of Small Molecules Binding using the Avidin-Biotin Model

International Nuclear Information System (INIS)

Yoetz-Kopelman, Tal; Ram, Yaron; Freeman, Amihay; Shacham-Diamand, Yosi

2015-01-01

The changes in the Faradaic impedance of gold/biomolecules system due to specific binding of small molecule to a significantly larger binding protein molecule were investigated. The biotin (244.31 Da) - avidin (66000 Da) couple was used as a model for small ligand - binding protein biorecognition. The study was carried out under open circuit potential in the presence of [Fe(CN) 6 ] −3/−4 redox couple. An equivalent electrical circuit was proposed and used for the interpretation of the recorded impedance spectra. Adsorption of thiolated avidin increased the electron transfer resistance, R ct , by a factor of about 7.5 while subsequent addition of biotin within the concentration range of 4.1-40.9 nM reduced the value of R ct by amount proportional to the biotin concentration. The addition of biotin did not affect, however, the equivalent double layer capacitance or other equivalent circuit parameters. A simple model based on effective surface coverage by the avidin molecules and the effect of the added biotin on electron transfer through the coated surface is proposed. A model for the minimum detection limit based on the random distribution of the binding protein and its dimensions is proposed

Interaction between the C-terminal domains of measles virus nucleoprotein and phosphoprotein: a tight complex implying one binding site.

Science.gov (United States)

Blocquel, David; Habchi, Johnny; Costanzo, Stéphanie; Doizy, Anthony; Oglesbee, Michael; Longhi, Sonia

2012-10-01

The intrinsically disordered C-terminal domain (N(TAIL) ) of the measles virus (MeV) nucleoprotein undergoes α-helical folding upon binding to the C-terminal X domain (XD) of the phosphoprotein. The N(TAIL) region involved in binding coupled to folding has been mapped to a conserved region (Box2) encompassing residues 489-506. In the previous studies published in this journal, we obtained experimental evidence supporting a K(D) for the N(TAIL) -XD binding reaction in the nM range and also showed that an additional N(TAIL) region (Box3, aa 517-525) plays a role in binding to XD. In striking contrast with these data, studies published in this journal by Kingston and coworkers pointed out a much less stable complex (K(D) in the μM range) and supported lack of involvement of Box3 in complex formation. The objective of this study was to critically re-evaluate the role of Box3 in N(TAIL) -XD binding. Since our previous studies relied on N(TAIL) -truncated forms possessing an irrelevant Flag sequence appended at their C-terminus, we, herein, generated an N(TAIL) devoid of Box3 and any additional C-terminal residues, as well as a form encompassing only residues 482-525. We then used isothermal titration calorimetry to characterize the binding reactions between XD and these N(TAIL) forms. Results effectively argue for the presence of a single XD-binding site located within Box2, in agreement with the results by Kingston et al., while providing clear experimental support for a high-affinity complex. Altogether, the present data provide mechanistic insights into the replicative machinery of MeV and clarify a hitherto highly debated point. Copyright © 2012 The Protein Society.

Effect of cobratoxin binding on the normal mode vibration within acetylcholine binding protein.

Science.gov (United States)

Bertaccini, Edward J; Lindahl, Erik; Sixma, Titia; Trudell, James R

2008-04-01

Recent crystal structures of the acetylcholine binding protein (AChBP) have revealed surprisingly small structural alterations upon ligand binding. Here we investigate the extent to which ligand binding may affect receptor dynamics. AChBP is a homologue of the extracellular component of ligand-gated ion channels (LGICs). We have previously used an elastic network normal-mode analysis to propose a gating mechanism for the LGICs and to suggest the effects of various ligands on such motions. However, the difficulties with elastic network methods lie in their inability to account for the modest effects of a small ligand or mutation on ion channel motion. Here, we report the successful application of an elastic network normal mode technique to measure the effects of large ligand binding on receptor dynamics. The present calculations demonstrate a clear alteration in the native symmetric motions of a protein due to the presence of large protein cobratoxin ligands. In particular, normal-mode analysis revealed that cobratoxin binding to this protein significantly dampened the axially symmetric motion of the AChBP that may be associated with channel gating in the full nAChR. The results suggest that alterations in receptor dynamics could be a general feature of ligand binding.

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.

Science.gov (United States)

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.

Revisiting interaction specificity reveals neuronal and adipocyte Munc18 membrane fusion regulatory proteins differ in their binding interactions with partner SNARE Syntaxins.

Directory of Open Access Journals (Sweden)

Michelle P Christie

Full Text Available The efficient delivery of cellular cargo relies on the fusion of cargo-carrying vesicles with the correct membrane at the correct time. These spatiotemporal fusion events occur when SNARE proteins on the vesicle interact with cognate SNARE proteins on the target membrane. Regulatory Munc18 proteins are thought to contribute to SNARE interaction specificity through interaction with the SNARE protein Syntaxin. Neuronal Munc18a interacts with Syntaxin1 but not Syntaxin4, and adipocyte Munc18c interacts with Syntaxin4 but not Syntaxin1. Here we show that this accepted view of specificity needs revision. We find that Munc18c interacts with both Syntaxin4 and Syntaxin1, and appears to bind "non-cognate" Syntaxin1 a little more tightly than Syntaxin4. Munc18a binds Syntaxin1 and Syntaxin4, though it interacts with its cognate Syntaxin1 much more tightly. We also observed that when bound to non-cognate Munc18c, Syntaxin1 captures its neuronal SNARE partners SNAP25 and VAMP2, and Munc18c can bind to pre-formed neuronal SNARE ternary complex. These findings reveal that Munc18a and Munc18c bind Syntaxins differently. Munc18c relies principally on the Syntaxin N-peptide interaction for binding Syntaxin4 or Syntaxin1, whereas Munc18a can bind Syntaxin1 tightly whether or not the Syntaxin1 N-peptide is present. We conclude that Munc18a and Munc18c differ in their binding interactions with Syntaxins: Munc18a has two tight binding modes/sites for Syntaxins as defined previously but Munc18c has just one that requires the N-peptide. These results indicate that the interactions between Munc18 and Syntaxin proteins, and the consequences for in vivo function, are more complex than can be accounted for by binding specificity alone.

Mechanistic models enable the rational use of in vitro drug-target binding kinetics for better drug effects in patients.

Science.gov (United States)

de Witte, Wilhelmus E A; Wong, Yin Cheong; Nederpelt, Indira; Heitman, Laura H; Danhof, Meindert; van der Graaf, Piet H; Gilissen, Ron A H J; de Lange, Elizabeth C M

2016-01-01

Drug-target binding kinetics are major determinants of the time course of drug action for several drugs, as clearly described for the irreversible binders omeprazole and aspirin. This supports the increasing interest to incorporate newly developed high-throughput assays for drug-target binding kinetics in drug discovery. A meaningful application of in vitro drug-target binding kinetics in drug discovery requires insight into the relation between in vivo drug effect and in vitro measured drug-target binding kinetics. In this review, the authors discuss both the relation between in vitro and in vivo measured binding kinetics and the relation between in vivo binding kinetics, target occupancy and effect profiles. More scientific evidence is required for the rational selection and development of drug-candidates on the basis of in vitro estimates of drug-target binding kinetics. To elucidate the value of in vitro binding kinetics measurements, it is necessary to obtain information on system-specific properties which influence the kinetics of target occupancy and drug effect. Mathematical integration of this information enables the identification of drug-specific properties which lead to optimal target occupancy and drug effect in patients.

Predicting nucleic acid binding interfaces from structural models of proteins.

Science.gov (United States)

Dror, Iris; Shazman, Shula; Mukherjee, Srayanta; Zhang, Yang; Glaser, Fabian; Mandel-Gutfreund, Yael

2012-02-01

The function of DNA- and RNA-binding proteins can be inferred from the characterization and accurate prediction of their binding interfaces. However, the main pitfall of various structure-based methods for predicting nucleic acid binding function is that they are all limited to a relatively small number of proteins for which high-resolution three-dimensional structures are available. In this study, we developed a pipeline for extracting functional electrostatic patches from surfaces of protein structural models, obtained using the I-TASSER protein structure predictor. The largest positive patches are extracted from the protein surface using the patchfinder algorithm. We show that functional electrostatic patches extracted from an ensemble of structural models highly overlap the patches extracted from high-resolution structures. Furthermore, by testing our pipeline on a set of 55 known nucleic acid binding proteins for which I-TASSER produces high-quality models, we show that the method accurately identifies the nucleic acids binding interface on structural models of proteins. Employing a combined patch approach we show that patches extracted from an ensemble of models better predicts the real nucleic acid binding interfaces compared with patches extracted from independent models. Overall, these results suggest that combining information from a collection of low-resolution structural models could be a valuable approach for functional annotation. We suggest that our method will be further applicable for predicting other functional surfaces of proteins with unknown structure. Copyright © 2011 Wiley Periodicals, Inc.

Thermodynamics of cooperative binding of FAD to human NQO1: Implications to understanding cofactor-dependent function and stability of the flavoproteome.

Science.gov (United States)

Clavería-Gimeno, Rafael; Velazquez-Campoy, Adrian; Pey, Angel Luis

2017-12-15

The stability of human flavoproteins strongly depends on flavin levels, although the structural and energetic basis of this relationship is poorly understood. Here, we report an in-depth analysis on the thermodynamics of FAD binding to one of the most representative examples of such relationship, NAD(P)H:quinone oxidoreductase 1 (NQO1). NQO1 is a dimeric enzyme that tightly binds FAD, which triggers large structural changes upon binding. A common cancer-associated polymorphism (P187S) severely compromises FAD binding. We show that FAD binding is described well by a thermodynamic model explicitly incorporating binding cooperativity when applied to different sets of calorimetric analyses and NQO1 variants, thus providing insight on the effects in vitro and in cells of cancer-associated P187S, its suppressor mutation H80R and the role of NQO1 C-terminal domain to modulate binding cooperativity and energetics. Furthermore, we show that FAD binding to NQO1 is very sensitive to physiologically relevant environmental conditions, such as the presence of phosphate buffer and salts. Overall, our results contribute to understanding at the molecular level the link between NQO1 stability and fluctuations of FAD levels intracellularly, and supports the notion that FAD binding energetics and cooperativity are fundamentally linked with the dynamic nature of apo-NQO1 conformational ensemble. Copyright © 2017 Elsevier Inc. All rights reserved.

Electronic Properties of III-V Semiconductors under [111] Uniaxial Strain; a Tight-Binding Approach: I. Arsenides and Gallium Phosphide

Directory of Open Access Journals (Sweden)

Miguel E. Mora-Ramos

2009-01-01

Full Text Available Empleando un esquema de cálculo tight-binding que usa una base de orbitales sp3s*d5, se estudian propiedades de la estructura electrónica de un grupo de materiales semiconductores IIIV los cuales son de notable interés para la tecnología de dispositivos electrónicos y optoelectrónicos. En específico, se analiza la influencia sobre estas propiedades de una tensión aplicada según la dirección cristalográfica [111], haciendo uso de una formulación basada en la teoría de la elasticidad para establecer las posiciones relativas de los iones vecinos más próximos. Especial atención se presta a la inclusión del efecto de deformación interna de la red cristalina. Para cada material de los estudiados presentamos las dependencias de las brechas energéticas asociadas a los puntos L, X y L de la zona de Brillouin como funciones de la tensión uniaxial en AlAs, GaAs, InAs y GaP. Asimismo, reportamos expresiones de ajuste para los valores de las masas efectivas de conducción en esos cuatro materiales. La comparación de la variación de la brecha de energía en X para el GaP, calculada con nuestro modelo, y recientes resultados experimentales para la transición indirecta entre la banda de huecos pesados y la banda X de conducción arroja una muy buena concordancia.

Binding free energy analysis of protein-protein docking model structures by evERdock.

Science.gov (United States)

Takemura, Kazuhiro; Matubayasi, Nobuyuki; Kitao, Akio

2018-03-14

To aid the evaluation of protein-protein complex model structures generated by protein docking prediction (decoys), we previously developed a method to calculate the binding free energies for complexes. The method combines a short (2 ns) all-atom molecular dynamics simulation with explicit solvent and solution theory in the energy representation (ER). We showed that this method successfully selected structures similar to the native complex structure (near-native decoys) as the lowest binding free energy structures. In our current work, we applied this method (evERdock) to 100 or 300 model structures of four protein-protein complexes. The crystal structures and the near-native decoys showed the lowest binding free energy of all the examined structures, indicating that evERdock can successfully evaluate decoys. Several decoys that show low interface root-mean-square distance but relatively high binding free energy were also identified. Analysis of the fraction of native contacts, hydrogen bonds, and salt bridges at the protein-protein interface indicated that these decoys were insufficiently optimized at the interface. After optimizing the interactions around the interface by including interfacial water molecules, the binding free energies of these decoys were improved. We also investigated the effect of solute entropy on binding free energy and found that consideration of the entropy term does not necessarily improve the evaluations of decoys using the normal model analysis for entropy calculation.

An Enhanced Error Model for EKF-Based Tightly-Coupled Integration of GPS and Land Vehicle's Motion Sensors.

Science.gov (United States)

Karamat, Tashfeen B; Atia, Mohamed M; Noureldin, Aboelmagd

2015-09-22

Reduced inertial sensor systems (RISS) have been introduced by many researchers as a low-cost, low-complexity sensor assembly that can be integrated with GPS to provide a robust integrated navigation system for land vehicles. In earlier works, the developed error models were simplified based on the assumption that the vehicle is mostly moving on a flat horizontal plane. Another limitation is the simplified estimation of the horizontal tilt angles, which is based on simple averaging of the accelerometers' measurements without modelling their errors or tilt angle errors. In this paper, a new error model is developed for RISS that accounts for the effect of tilt angle errors and the accelerometer's errors. Additionally, it also includes important terms in the system dynamic error model, which were ignored during the linearization process in earlier works. An augmented extended Kalman filter (EKF) is designed to incorporate tilt angle errors and transversal accelerometer errors. The new error model and the augmented EKF design are developed in a tightly-coupled RISS/GPS integrated navigation system. The proposed system was tested on real trajectories' data under degraded GPS environments, and the results were compared to earlier works on RISS/GPS systems. The findings demonstrated that the proposed enhanced system introduced significant improvements in navigational performance.

Comparison of Transcription Factor Binding Site Models

KAUST Repository

Bhuyan, Sharifulislam

2012-05-01

Modeling of transcription factor binding sites (TFBSs) and TFBS prediction on genomic sequences are important steps to elucidate transcription regulatory mechanism. Dependency of transcription regulation on a great number of factors such as chemical specificity, molecular structure, genomic and epigenetic characteristics, long distance interaction, makes this a challenging problem. Different experimental procedures generate evidence that DNA-binding domains of transcription factors show considerable DNA sequence specificity. Probabilistic modeling of TFBSs has been moderately successful in identifying patterns from a family of sequences. In this study, we compare performances of different probabilistic models and try to estimate their efficacy over experimental TFBSs data. We build a pipeline to calculate sensitivity and specificity from aligned TFBS sequences for several probabilistic models, such as Markov chains, hidden Markov models, Bayesian networks. Our work, containing relevant statistics and evaluation for the models, can help researchers to choose the most appropriate model for the problem at hand.

Target-mediated drug disposition model for drugs with two binding sites that bind to a target with one binding site.

Science.gov (United States)

Gibiansky, Leonid; Gibiansky, Ekaterina

2017-10-01

The paper extended the TMDD model to drugs with two identical binding sites (2-1 TMDD). The quasi-steady-state (2-1 QSS), quasi-equilibrium (2-1 QE), irreversible binding (2-1 IB), and Michaelis-Menten (2-1 MM) approximations of the model were derived. Using simulations, the 2-1 QSS approximation was compared with the full 2-1 TMDD model. As expected and similarly to the standard TMDD for monoclonal antibodies (mAb), 2-1 QSS predictions were nearly identical to 2-1 TMDD predictions, except for times of fast changes following initiation of dosing, when equilibrium has not yet been reached. To illustrate properties of new equations and approximations, several variations of population PK data for mAbs with soluble (slow elimination of the complex) or membrane-bound (fast elimination of the complex) targets were simulated from a full 2-1 TMDD model and fitted to 2-1 TMDD models, to its approximations, and to the standard (1-1) QSS model. For a mAb with a soluble target, it was demonstrated that the 2-1 QSS model provided nearly identical description of the observed (simulated) free drug and total target concentrations, although there was some minor bias in predictions of unobserved free target concentrations. The standard QSS approximation also provided a good description of the observed data, but was not able to distinguish between free drug concentrations (with no target attached and both binding site free) and partially bound drug concentrations (with one of the binding sites occupied by the target). For a mAb with a membrane-bound target, the 2-1 MM approximation adequately described the data. The 2-1 QSS approximation converged 10 times faster than the full 2-1 TMDD, and its run time was comparable with the standard QSS model.

21-Benzylidene Digoxin: A Proapoptotic Cardenolide of Cancer Cells That Up-Regulates Na,K-ATPase and Epithelial Tight Junctions

Science.gov (United States)

Rocha, Sayonarah C.; Pessoa, Marco T. C.; Neves, Luiza D. R.; Alves, Silmara L. G.; Silva, Luciana M.; Santos, Herica L.; Oliveira, Soraya M. F.; Taranto, Alex G.; Comar, Moacyr; Gomes, Isabella V.; Santos, Fabio V.; Paixão, Natasha; Quintas, Luis E. M.; Noël, François; Pereira, Antonio F.; Tessis, Ana C. S. C.; Gomes, Natalia L. S.; Moreira, Otacilio C.; Rincon-Heredia, Ruth; Varotti, Fernando P.; Blanco, Gustavo; Villar, Jose A. F. P.; Contreras, Rubén G.; Barbosa, Leandro A.

2014-01-01

Cardiotonic steroids are used to treat heart failure and arrhythmia and have promising anticancer effects. The prototypic cardiotonic steroid ouabain may also be a hormone that modulates epithelial cell adhesion. Cardiotonic steroids consist of a steroid nucleus and a lactone ring, and their biological effects depend on the binding to their receptor, Na,K-ATPase, through which, they inhibit Na+ and K+ ion transport and activate of several intracellular signaling pathways. In this study, we added a styrene group to the lactone ring of the cardiotonic steroid digoxin, to obtain 21-benzylidene digoxin (21-BD), and investigated the effects of this synthetic cardiotonic steroid in different cell models. Molecular modeling indicates that 21-BD binds to its target Na,K-ATPase with low affinity, adopting a different pharmacophoric conformation when bound to its receptor than digoxin. Accordingly, 21-DB, at relatively high µM amounts inhibits the activity of Na,K-ATPase α1, but not α2 and α3 isoforms. In addition, 21-BD targets other proteins outside the Na,K-ATPase, inhibiting the multidrug exporter Pdr5p. When used on whole cells at low µM concentrations, 21-BD produces several effects, including: 1) up-regulation of Na,K-ATPase expression and activity in HeLa and RKO cancer cells, which is not found for digoxin, 2) cell specific changes in cell viability, reducing it in HeLa and RKO cancer cells, but increasing it in normal epithelial MDCK cells, which is different from the response to digoxin, and 3) changes in cell-cell interaction, altering the molecular composition of tight junctions and elevating transepithelial electrical resistance of MDCK monolayers, an effect previously found for ouabain. These results indicate that modification of the lactone ring of digoxin provides new properties to the compound, and shows that the structural change introduced could be used for the design of cardiotonic steroid with novel functions. PMID:25290152

A strategy for increasing the brain uptake of a radioligand in animals: use of a drug that inhibits plasma protein binding

International Nuclear Information System (INIS)

Haradahira, Terushi; Zhang, Ming-Rong; Maeda, Jun; Okauchi, Takashi; Kawabe, Kouichi; Kida, Takayo; Suzuki, Kazutoshi; Suhara, Tetsuya

2000-01-01

A positron-emitter labeled radioligand for the glycine-binding site of the N-methyl-D-aspartate (NMDA) receptor, [ 11 C]L-703,717, was examined for its ability to penetrate the brain in animals by simultaneous use with drugs having high-affinity separate binding sites on human serum albumin. [ 11 C]L-703,717 has poor blood-brain barrier (BBB) permeability because it binds tightly to plasma proteins. Co-injection of warfarin (50-200 mg/kg), a drug that binds to albumin and resembles L-703,717 in structure, dose-dependently enhanced the penetration by [ 11 C]L-703,717 in mice, resulting in a five-fold increase in the brain radioactivity at 1 min after the injection. Drugs structurally unrelated to L-703,717, salicylate, phenol red, and L-tryptophan, were less effective or ineffective in increasing the uptake of [ 11 C]L-703,717. These results suggest that the simultaneous use of a drug that inhibits the binding of a radioligand to plasma proteins is a useful way to overcome the poor BBB permeability of the radioligand triggered by its tight binding to plasma proteins. In brain distribution studies in rodents, it was found that, after the increase in brain uptake with warfarin, much of the glycine site antagonist accumulates in the cerebellum but its pharmacological specificity did not match the glycine site of NMDA receptors

Effects of adenine nucleotide and sterol depletion on tight junction structure and function in MDCK cells

International Nuclear Information System (INIS)

Ladino, C.A.

1988-01-01

The antitumor agent Hadacidin (H), N-formyl-hydroxyamino-acetic acid, reversibly inhibited the multiplication of clone 4 Madin-Darby canine kidney (MDCK) cells at a 4 mM concentration within 24-48 hours. Treated cells were arrested in the S phase of the cell cycle. Accompanying this action was a 16-fold increase in the area occupied b the cells and a refractoriness to trypsin treatment. To test whether this effect was due to an increase in tight junction integrity, electrical resistance (TER) was measured across H-treated monolayers. Addition of H at the onset of junction formation reversibly prevented the development of TER. ATP and cAMP levels were decreased by H, as well as the rate of [ 3 H]-leucine incorporation into protein. When 1 mM dibutyryl-cAMP (d.cAMP) and theophylline were added, H had no effect on cell division or protein synthesis, and TER was partially restored. The addition of 1 mM d.cAMP and 1 mM theophylline to control cultures decreased TER, indicating a biphasic effect on TER development/maintenance. In a separate study, the effect of sterol depletion on tight junctions formation/maintenance in wild-type MDCK cells was investigated

Superconducting characteristics of the Penson-Kolb model

International Nuclear Information System (INIS)

Czart, W.R.; Robaszkiewicz, S.

2000-01-01

We study superconducting properties of the Penson-Kolb model, i. e. the tight-binding model with the pair-hopping (intersite charge exchange) interaction J. The evolution of the critical fields, the coherence length, the Ginzburg ratio, and London penetration depth with particle concentration n and pairing strength are determined. The results are compared with those found earlier for the attractive Hubbard model. (author)

Anion-induced reconstitution of a self-assembling system to express a chloride-binding Co10L15 pentagonal prism.

Science.gov (United States)

Riddell, Imogen A; Smulders, Maarten M J; Clegg, Jack K; Hristova, Yana R; Breiner, Boris; Thoburn, John D; Nitschke, Jonathan R

2012-09-01

Biochemical systems are adaptable, capable of reconstitution at all levels to achieve the functions associated with life. Synthetic chemical systems are more limited in their ability to reorganize to achieve new functions; they can reconfigure to bind an added substrate (template effect) or one binding event may modulate a receptor's affinity for a second substrate (allosteric effect). Here we describe a synthetic chemical system that is capable of structural reconstitution on receipt of one anionic signal (perchlorate) to create a tight binding pocket for another anion (chloride). The complex, barrel-like structure of the chloride receptor is templated by five perchlorate anions. This second-order templation phenomenon allows chemical networks to be envisaged that express more complex responses to chemical signals than is currently feasible.

Effect of film roughness in Fe/MgO/Fe magnetic tunnel junctions: model calculations

Energy Technology Data Exchange (ETDEWEB)

Edalati Boostan, Saeideh; Heiliger, Christian [I. Physikalisches Institut, Justus Liebig University Giessen, D-35392 (Germany); Moradi, Hosein [Department of Physics,Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad (Iran, Islamic Republic of)

2011-07-01

We calculate how interface roughness affects the tunneling magnetoresistance (TMR) in Fe/MgO/Fe (100) junctions. The used method is based on a single-band tight-binding (SBTB) approximation employing the Green's function formalism. We investigate the influence of disorder at the TMR ratio. Thereby, the disorder is modeled by considering different occupation probabilities of Fe and MgO at interface sites. We calculate the current densities for parallel and anti-parallel configurations for different disorders. The results show that the roughness decreases the TMR that match well with experimental observations.

Structural insights into human peroxisome proliferator activated receptor delta (PPAR-delta selective ligand binding.

Directory of Open Access Journals (Sweden)

Fernanda A H Batista

Full Text Available Peroxisome proliferator activated receptors (PPARs δ, α and γ are closely related transcription factors that exert distinct effects on fatty acid and glucose metabolism, cardiac disease, inflammatory response and other processes. Several groups developed PPAR subtype specific modulators to trigger desirable effects of particular PPARs without harmful side effects associated with activation of other subtypes. Presently, however, many compounds that bind to one of the PPARs cross-react with others and rational strategies to obtain highly selective PPAR modulators are far from clear. GW0742 is a synthetic ligand that binds PPARδ more than 300-fold more tightly than PPARα or PPARγ but the structural basis of PPARδ:GW0742 interactions and reasons for strong selectivity are not clear. Here we report the crystal structure of the PPARδ:GW0742 complex. Comparisons of the PPARδ:GW0742 complex with published structures of PPARs in complex with α and γ selective agonists and pan agonists suggests that two residues (Val312 and Ile328 in the buried hormone binding pocket play special roles in PPARδ selective binding and experimental and computational analysis of effects of mutations in these residues confirms this and suggests that bulky substituents that line the PPARα and γ ligand binding pockets as structural barriers for GW0742 binding. This analysis suggests general strategies for selective PPARδ ligand design.

Tight connection between fission gas discharge channels

International Nuclear Information System (INIS)

Jung, W.; Peehs, M.; Rau, P.; Krug, W.; Stechemesser, H.

1978-01-01

The invention is concerned with the tight connection between the fission gas discharge channel, leading away from the support plate of a gas-cooled reactor, and the top of the fuel element suspended from this support plate. The closure is designed to be gas-tight for the suspended as well as for the released fuel element. The tight connection has got an annular body resting on the core support plate in the mouth region of the fission gas discharge channel. This body is connected with the fission gas discharge channel in the fuel element top fitting via a gas-tight part and supported by a compression spring. Care is taken for sealing if the fuel element is removal. (RW) [de

Fatty acids bind tightly to the N-terminal domain of angiopoietin-like protein 4 and modulate its interaction with lipoprotein lipase.

Science.gov (United States)

Robal, Terje; Larsson, Mikael; Martin, Miina; Olivecrona, Gunilla; Lookene, Aivar

2012-08-24

Angiopoietin-like protein 4 (Angptl4), a potent regulator of plasma triglyceride metabolism, binds to lipoprotein lipase (LPL) through its N-terminal coiled-coil domain (ccd-Angptl4) inducing dissociation of the dimeric enzyme to inactive monomers. In this study, we demonstrate that fatty acids reduce the inactivation of LPL by Angptl4. This was the case both with ccd-Angptl4 and full-length Angptl4, and the effect was seen in human plasma or in the presence of albumin. The effect decreased in the sequence oleic acid > palmitic acid > myristic acid > linoleic acid > linolenic acid. Surface plasmon resonance, isothermal titration calorimetry, fluorescence, and chromatography measurements revealed that fatty acids bind with high affinity to ccd-Angptl4. The interactions were characterized by fast association and slow dissociation rates, indicating formation of stable complexes. The highest affinity for ccd-Angptl4 was detected for oleic acid with a subnanomolar equilibrium dissociation constant (K(d)). The K(d) values for palmitic and myristic acid were in the nanomolar range. Linoleic and linolenic acid bound with much lower affinity. On binding of fatty acids, ccd-Angptl4 underwent conformational changes resulting in a decreased helical content, weakened structural stability, dissociation of oligomers, and altered fluorescence properties of the Trp-38 residue that is located close to the putative LPL-binding region. Based on these results, we propose that fatty acids play an important role in modulating the effects of Angptl4.

Economic evaluation on tight sandstone gas development projects in China and recommendation on fiscal and taxation support policies

OpenAIRE

Zhen Yang; Lingfeng Kong; Min Du; Chenhui Zhao

2016-01-01

China is rich in tight sandstone gas resources (“tight gas” for short). For example, the Sulige Gasfield in the Ordos Basin and the Upper Triassic Xujiahe Fm gas reservoir in the Sichuan Basin are typical tight gas reservoirs. In the past decade, tight gas reserve and production both have increased rapidly in China, but tight gas reservoirs are always managed as conventional gas reservoirs without effective fiscal, taxation and policy supports. The potential of sustainable tight gas productio...

Dietary Gluten-Induced Gut Dysbiosis Is Accompanied by Selective Upregulation of microRNAs with Intestinal Tight Junction and Bacteria-Binding Motifs in Rhesus Macaque Model of Celiac Disease

Directory of Open Access Journals (Sweden)

Mahesh Mohan

2016-10-01

Full Text Available The composition of the gut microbiome reflects the overall health status of the host. In this study, stool samples representing the gut microbiomes from 6 gluten-sensitive (GS captive juvenile rhesus macaques were compared with those from 6 healthy, age- and diet-matched peers. A total of 48 samples representing both groups were studied using V4 16S rRNA gene DNA analysis. Samples from GS macaques were further characterized based on type of diet administered: conventional monkey chow, i.e., wheat gluten-containing diet (GD, gluten-free diet (GFD, barley gluten-derived diet (BOMI and reduced gluten barley-derived diet (RGB. It was hypothesized that the GD diet would lower the gut microbial diversity in GS macaques. This is the first report illustrating the reduction of gut microbial alpha-diversity (p < 0.05 following the consumption of dietary gluten in GS macaques. Selected bacterial families (e.g., Streptococcaceae and Lactobacillaceae were enriched in GS macaques while Coriobacteriaceae was enriched in healthy animals. Within several weeks after the replacement of the GD by the GFD diet, the composition (beta-diversity of gut microbiome in GS macaques started to change (p = 0.011 towards that of a normal macaque. Significance for alpha-diversity however, was not reached by the day 70 when the feeding experiment ended. Several inflammation-associated microRNAs (miR-203, -204, -23a, -23b and -29b were upregulated (p < 0.05 in jejunum of 4 biopsied GS macaques fed GD with predicted binding sites on 16S ribosomal RNA of Lactobacillus reuteri (accession number: NR_025911, Prevotella stercorea (NR_041364 and Streptococcus luteciae (AJ297218 that were overrepresented in feces. Additionally, claudin-1, a validated tight junction protein target of miR-29b was significantly downregulated in jejunal epithelium of GS macaques. Taken together, we predict that with the introduction of effective treatments in future studies the diversity of gut microbiomes

Binding of chloroquine to ionic micelles: Effect of pH and micellar surface charge

Energy Technology Data Exchange (ETDEWEB)

Souza Santos, Marcela de, E-mail: marcelafarmausp77@gmail.com [Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Avenida do Café, s/n, Ribeirão Preto, São Paulo 14040-903 (Brazil); Perpétua Freire de Morais Del Lama, Maria, E-mail: mpemdel@fcfrp.usp.br [Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Avenida do Café, s/n, Ribeirão Preto, São Paulo 14040-903 (Brazil); Instituto Nacional de Ciência e Tecnologia de Bioanalítica, Departamento de Química Analítica, Universidade Estadual de Campinas, Cidade Universitária Zeferino Vaz, s/n, Campinas, São Paulo 13083-970 (Brazil); Siuiti Ito, Amando, E-mail: amandosi@ffclrp.usp.br [Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Avenida Bandeirantes, 3900, Ribeirão Preto, São Paulo 14040-901 (Brazil); and others

2014-03-15

The pharmacological action of chloroquine relies on its ability to cross biological membranes in order to accumulate inside lysosomes. The present work aimed at understanding the basis for the interaction between different chloroquine species and ionic micelles of opposite charges, the latter used as a simple membrane model. The sensitivity of absorbance and fluorescence of chloroquine to changes in its local environment was used to probe its interaction with cetyltrimethylammonium micelles presenting bromide (CTAB) and sulfate (CTAS) as counterions, in addition to dodecyl sulfate micelles bearing sodium (SDS) and tetramethylammonium (TMADS) counterions. Counterion exchange was shown to have little effect on drug–micelle interaction. Chloroquine first dissociation constant (pKa{sub 1}) shifted to opposite directions when anionic and cationic micelles were compared. Chloroquine binding constants (K{sub b}) revealed that electrostatic forces mediate charged drug–micelle association, whereas hydrophobic interactions allowed neutral chloroquine to associate with anionic and cationic micelles. Fluorescence quenching studies indicated that monoprotonated chloroquine is inserted deeper into the micelle surface of anionic micelles than its neutral form, the latter being less exposed to the aqueous phase when associated with cationic over anionic assemblies. The findings provide further evidence that chloroquine–micelle interaction is driven by a tight interplay between the drug form and the micellar surface charge, which can have a major effect on the drug biological activity. -- Highlights: • Chloroquine (CQ) pKa{sub 1} increased for SDS micelles and decreased for CTAB micelles. • CQ is solubilized to the surface of both CTAB and SDS micelles. • Monoprotonated CQ is buried deeper into SDS micelles than neutral CQ. • Neutral CQ is less exposed to aqueous phase in CTAB over SDS micelles. • Local pH and micellar surface charge mediate interaction of CQ with

Flow and Transport in Tight and Shale Formations: A Review

KAUST Repository

Salama, Amgad

2017-09-18

A review on the recent advances of the flow and transport phenomena in tight and shale formations is presented in this work. Exploration of oil and gas in resources that were once considered inaccessible opened the door to highlight interesting phenomena that require attention and understanding. The length scales associated with transport phenomena in tight and shale formations are rich. From nanoscale phenomena to field-scale applications, a unified frame that is able to encounter the varieties of phenomena associated with each scale may not be possible. Each scale has its own tools and limitations that may not, probably, be suitable at other scales. Multiscale algorithms that effectively couple simulations among various scales of porous media are therefore important. In this article, a review of the different length scales and the tools associated with each scale is introduced. Highlights on the different phenomena pertinent to each scale are summarized. Furthermore, the governing equations describing flow and transport phenomena at different scales are investigated. In addition, methods to solve these equations using numerical techniques are introduced. Cross-scale analysis and derivation of linear and nonlinear Darcy\\'s scale laws from pore-scale governing equations are described. Phenomena occurring at molecular scales and their thermodynamics are discussed. Flow slippage at the nanosize pores and its upscaling to Darcy\\'s scale are highlighted. Pore network models are discussed as a viable tool to estimate macroscopic parameters that are otherwise difficult to measure. Then, the environmental aspects associated with the different technologies used in stimulating the gas stored in tight and shale formations are briefly discussed.

Flow and Transport in Tight and Shale Formations: A Review

KAUST Repository

Salama, Amgad; El-Amin, Mohamed; Kumar, Kundan; Sun, Shuyu

2017-01-01

A review on the recent advances of the flow and transport phenomena in tight and shale formations is presented in this work. Exploration of oil and gas in resources that were once considered inaccessible opened the door to highlight interesting phenomena that require attention and understanding. The length scales associated with transport phenomena in tight and shale formations are rich. From nanoscale phenomena to field-scale applications, a unified frame that is able to encounter the varieties of phenomena associated with each scale may not be possible. Each scale has its own tools and limitations that may not, probably, be suitable at other scales. Multiscale algorithms that effectively couple simulations among various scales of porous media are therefore important. In this article, a review of the different length scales and the tools associated with each scale is introduced. Highlights on the different phenomena pertinent to each scale are summarized. Furthermore, the governing equations describing flow and transport phenomena at different scales are investigated. In addition, methods to solve these equations using numerical techniques are introduced. Cross-scale analysis and derivation of linear and nonlinear Darcy's scale laws from pore-scale governing equations are described. Phenomena occurring at molecular scales and their thermodynamics are discussed. Flow slippage at the nanosize pores and its upscaling to Darcy's scale are highlighted. Pore network models are discussed as a viable tool to estimate macroscopic parameters that are otherwise difficult to measure. Then, the environmental aspects associated with the different technologies used in stimulating the gas stored in tight and shale formations are briefly discussed.

Three-dimensional stochastic model of actin–myosin binding in the sarcomere lattice

Energy Technology Data Exchange (ETDEWEB)

Mijailovich, Srboljub M.; Kayser-Herold, Oliver; Stojanovic, Boban; Nedic, Djordje; Irving, Thomas C.; Geeves, MA (Harvard); (IIT); (U. Kent); (Kragujevac)

2016-11-18

The effect of molecule tethering in three-dimensional (3-D) space on bimolecular binding kinetics is rarely addressed and only occasionally incorporated into models of cell motility. The simplest system that can quantitatively determine this effect is the 3-D sarcomere lattice of the striated muscle, where tethered myosin in thick filaments can only bind to a relatively small number of available sites on the actin filament, positioned within a limited range of thermal movement of the myosin head. Here we implement spatially explicit actomyosin interactions into the multiscale Monte Carlo platform MUSICO, specifically defining how geometrical constraints on tethered myosins can modulate state transition rates in the actomyosin cycle. The simulations provide the distribution of myosin bound to sites on actin, ensure conservation of the number of interacting myosins and actin monomers, and most importantly, the departure in behavior of tethered myosin molecules from unconstrained myosin interactions with actin. In addition, MUSICO determines the number of cross-bridges in each actomyosin cycle state, the force and number of attached cross-bridges per myosin filament, the range of cross-bridge forces and accounts for energy consumption. At the macroscopic scale, MUSICO simulations show large differences in predicted force-velocity curves and in the response during early force recovery phase after a step change in length comparing to the two simplest mass action kinetic models. The origin of these differences is rooted in the different fluxes of myosin binding and corresponding instantaneous cross-bridge distributions and quantitatively reflects a major flaw of the mathematical description in all mass action kinetic models. Consequently, this new approach shows that accurate recapitulation of experimental data requires significantly different binding rates, number of actomyosin states, and cross-bridge elasticity than typically used in mass action kinetic models to

Effect of tight control management on Crohn's disease (CALM): a multicentre, randomised, controlled phase 3 trial.

Science.gov (United States)

Colombel, Jean-Frederic; Panaccione, Remo; Bossuyt, Peter; Lukas, Milan; Baert, Filip; Vaňásek, Tomas; Danalioglu, Ahmet; Novacek, Gottfried; Armuzzi, Alessandro; Hébuterne, Xavier; Travis, Simon; Danese, Silvio; Reinisch, Walter; Sandborn, William J; Rutgeerts, Paul; Hommes, Daniel; Schreiber, Stefan; Neimark, Ezequiel; Huang, Bidan; Zhou, Qian; Mendez, Paloma; Petersson, Joel; Wallace, Kori; Robinson, Anne M; Thakkar, Roopal B; D'Haens, Geert

2018-12-23

). 29 (24%) patients in the clinical management group and 32 (26%) patients in the tight control group discontinued the study, mostly because of adverse events. A significantly higher proportion of patients in the tight control group achieved the primary endpoint at week 48 (56 [46%] of 122 patients) than in the clinical management group (37 [30%] of 122 patients), with a Cochran-Mantel-Haenszel test-adjusted risk difference of 16·1% (95% CI 3·9-28·3; p=0·010). 105 (86%) of 122 patients in the tight control group and 100 (82%) of 122 patients in the clinical management group reported treatment-emergent adverse events; no treatment-related deaths occurred. The most common adverse events were nausea (21 [17%] of 122 patients), nasopharyngitis (18 [15%]), and headache (18 [15%]) in the tight control group, and worsening Crohn's disease (35 [29%] of 122 patients), arthralgia (19 [16%]), and nasopharyngitis (18 [15%]) in the clinical management group. CALM is the first study to show that timely escalation with an anti-tumour necrosis factor therapy on the basis of clinical symptoms combined with biomarkers in patients with early Crohn's disease results in better clinical and endoscopic outcomes than symptom-driven decisions alone. Future studies should assess the effects of such a strategy on long-term outcomes such as bowel damage, surgeries, hospital admissions, and disability. AbbVie. Copyright © 2017 Elsevier Ltd. All rights reserved.

Measurement of free glucocorticoids: quantifying corticosteroid-binding globulin binding affinity and its variation within and among mammalian species.

Science.gov (United States)

Delehanty, Brendan; Hossain, Sabrina; Jen, Chao Ching; Crawshaw, Graham J; Boonstra, Rudy

2015-01-01

Plasma glucocorticoids (GCs) are commonly used as measures of stress in wildlife. A great deal of evidence indicates that only free GC (GC not bound by the specific binding protein, corticosteroid-binding globulin, CBG) leaves the circulation and exerts biological effects on GC-sensitive tissues. Free hormone concentrations are difficult to measure directly, so researchers estimate free GC using two measures: the binding affinity and the binding capacity in plasma. We provide an inexpensive saturation binding method for calculating the binding affinity (equilibrium dissociation constant, K d) of CBG that can be run without specialized laboratory equipment. Given that other plasma proteins, such as albumin, also bind GCs, the method compensates for this non-specific binding. Separation of bound GC from free GC was achieved with dextran-coated charcoal. The method provides repeatable estimates (12% coefficient of variation in the red squirrel, Tamiasciurus hudsonicus), and there is little evidence of inter-individual variation in K d (range 2.0-7.3 nM for 16 Richardson's ground squirrels, Urocitellus richardsonii). The K d values of 28 mammalian species we assessed were mostly clustered around a median of 4 nM, but five species had values between 13 and 61 nM. This pattern may be distinct from birds, for which published values are more tightly distributed (1.5-5.1 nM). The charcoal separation method provides a reliable and robust method for measuring the K d in a wide range of species. It uses basic laboratory equipment to provide rapid results at very low cost. Given the importance of CBG in regulating the biological activity of GCs, this method is a useful tool for physiological ecologists.

Identification and characterization of riboflavin-binding proteins in human circulation

International Nuclear Information System (INIS)

Innis-Whitehouse, W.S.A.

1988-01-01

Riboflavin binding by plasma proteins from healthy human subjects was examined by equilibrium dialysis and binding was observed to vary over a greater than 10-fold range. Upon fractionation of plasma by gel filtration, the major riboflavin-binding components eluted with albumin and gamma-globulins. Albumin was purified and found to bind riboflavin only very weakly, although FMN and photo-chemical degradation products were more tightly bound. Most of the binding occurred in the gamma-globulin fraction and was attributed to immunoglobulins because the binding proteins and immunoglobulins copurified using various methods, were removed by treatment of plasma with protein A-agarose, and were coincident upon immuno-electrophoresis followed by autoradiography to detect [2- 14 C]-riboflavin. Binding differences among plasma samples were reflected in the binding recovered with the immunoglobulin fractions; however, there was not a direct relationship between the amount of immunoglobulin and the amount of [2- 14 C]riboflavin bound. Hence, it appeared that the binding was due to a subfraction of immunoglobulins

Analysis of Seven NEPTUN-III (Tight-Lattice) Bottom-Flooding Experiments with RELAP5/MOD3.3/BETA

International Nuclear Information System (INIS)

Analytis, G.Th.

2004-01-01

Seven tight-lattice NEPTUN-III bottom-flooding experiments are analyzed by using the frozen version of RELAP5, RELAP5/MOD3.3/BETA. This work is part of the Paul Scherrer Institute (PSI) contribution to the High Performance Light Water Reactor (HPLWR) European Union project and aims at assessing the capabilities of the code to model the reflooding phenomena in a tight hexagonal lattice (which was one of the core geometries considered at the time for an HPLWR) following a hypothetical loss-of-coolant accident scenario. Even though the latest version of the code has as a default the new PSI reflood model developed by the author, which was tested and assessed against reflooding data obtained at standard light water reactor lattices, this work shows that for tight lattices, the code underpredicts the peak clad temperatures measured during a series of reflooding experiments performed at the NEPTUN-III tight-lattice heater rod bundle facility. The reasons for these differences are discussed, and the (possible) changes needed in the framework of RELAP5/MOD3.3 for improving the modeling of reflooding in tight lattices are investigated

Equiangular tight frames and unistochastic matrices

Czech Academy of Sciences Publication Activity Database

Goyeneche, D.; Turek, Ondřej

2017-01-01

Roč. 50, č. 24 (2017), č. článku 245304. ISSN 1751-8113 R&D Projects: GA ČR GA17-01706S Institutional support: RVO:61389005 Keywords : equiangular tight frames * unistochastic matrices * SIC POVM Subject RIV: BE - Theoretical Physics OBOR OECD: Atomic, molecular and chemical physics (physics of atoms and molecules including collision, interaction with radiation, magnetic resonances, Mössbauer effect) Impact factor: 1.857, year: 2016

House Dust Mite Der p 1 Effects on Sinonasal Epithelial Tight Junctions

Science.gov (United States)

Henriquez, Oswaldo A.; Beste, Kyle Den; Hoddeson, Elizabeth K.; Parkos, Charles A.; Nusrat, Asma; Wise, Sarah K.

2013-01-01

Background Epithelial permeability is highly dependent upon the integrity of tight junctions, cell-cell adhesion complexes located at the apical aspect of the lateral membrane of polarized epithelial cells. We hypothesize that sinonasal epithelial exposure to Der p 1 house dust mite antigen decreases expression of tight junction proteins (TJPs), representing a potential mechanism for increased permeability and presentation of antigens across the sinonasal epithelial layer. Methods Confluent cultured primary human sinonasal epithelial cells were exposed to recombinant Der p 1 antigen versus control, and transepithelial resistance measurements were performed over 24 hours. Antibody staining for a panel of tight junction proteins was examined with immunofluorescence/confocal microscopy and Western blotting. Tissue for these experiments was obtained from 4 patients total. Results Der p 1 exposed sinonasal cells showed a marked decrease in transepithelial resistance when compared to control cells. In addition, results of Western immunoblot and immunofluorescent labeling demonstrated decreased expression of TJPs claudin-1 and junction adhesion molecule-A (JAM-A) in Der p 1 exposed cultured sinonasal cells versus controls. Conclusion Der p 1 antigen exposure decreases sinonasal epithelium TJP expression, most notably seen in JAM-A and claudin-1 in these preliminary experiments. This decreased TJP expression likely contributes to increased epithelial permeability and represents a potential mechanism for transepithelial antigen exposure in allergic rhinitis. PMID:23592402

Thermodynamic model of binding of flexible bivalent haptens to antibody

Energy Technology Data Exchange (ETDEWEB)

Dembo, M; Goldstein, B

1978-01-01

Studies by Wilder et al. of the binding of Fab' fragments to small haptens have shown that the cross-linking constant (the equilibrium constant for binding an additional Fab' fragment to a hapten-Fab' complex) is strongly dependent on the length of the hapten. We present a simple model for predicting the relationship between the intermolecular cross-linking constant and the monovalent hapten-antibody binding constant. In particular we used the model to obtain the dependence of the cross-linking constant on the length of th hapten, the depth to which the hapten fills th Fab' binding site, and the size of the Fab' fragment. To test the model, we devised expressions which allowed us to analyze the data of Wilder et al. From their data we determined the values of two parameters which we took to be unknown in the theory, the size of the Fab' fragment and the depth to which the hapten fills the Fab' binding site. The values arrived at in this way agreed well with published measurements of these parameters.

Modeling of the atomic and electronic structures of interfaces

International Nuclear Information System (INIS)

Sutton, A.P.

1988-01-01

Recent tight binding and Car-Parrinello simulations of grain boundaries in semiconductors are reviewed. A critique is given of some models of embrittlement that are based on electronic structure considerations. The structural unit model of grain boundary structure is critically assessed using some results for mixed tilt and twist grain boundaries. A new method of characterizing interfacial structure in terms of bond angle distribution functions is described. A new formulation of thermodynamic properties of interfaces is presented which focusses on the local atomic environment. Effective, temperature dependent N-body atomic interactions are derived for studying grain boundary structure at elevated temperature

An Enhanced Error Model for EKF-Based Tightly-Coupled Integration of GPS and Land Vehicle’s Motion Sensors

Science.gov (United States)

Karamat, Tashfeen B.; Atia, Mohamed M.; Noureldin, Aboelmagd

2015-01-01

Reduced inertial sensor systems (RISS) have been introduced by many researchers as a low-cost, low-complexity sensor assembly that can be integrated with GPS to provide a robust integrated navigation system for land vehicles. In earlier works, the developed error models were simplified based on the assumption that the vehicle is mostly moving on a flat horizontal plane. Another limitation is the simplified estimation of the horizontal tilt angles, which is based on simple averaging of the accelerometers’ measurements without modelling their errors or tilt angle errors. In this paper, a new error model is developed for RISS that accounts for the effect of tilt angle errors and the accelerometer’s errors. Additionally, it also includes important terms in the system dynamic error model, which were ignored during the linearization process in earlier works. An augmented extended Kalman filter (EKF) is designed to incorporate tilt angle errors and transversal accelerometer errors. The new error model and the augmented EKF design are developed in a tightly-coupled RISS/GPS integrated navigation system. The proposed system was tested on real trajectories’ data under degraded GPS environments, and the results were compared to earlier works on RISS/GPS systems. The findings demonstrated that the proposed enhanced system introduced significant improvements in navigational performance. PMID:26402680

Effects of heparin on insulin binding and biological activity

International Nuclear Information System (INIS)

Kriauciunas, K.M.; Grigorescu, F.; Kahn, C.R.

1987-01-01

The effect of heparin, a polyanionic glycosaminoglycan known to alter the function of many proteins, on insulin binding and bioactivity was studied. Cultured human lymphocytes (IM-9) were incubated with varying concentrations of heparin, then extensively washed, and 125 I-labeled insulin binding was measured. Heparin at concentrations used clinically for anticoagulation (1-50 U/ml) inhibited binding in a dose-dependent manner; 50% inhibition of binding occurred with 5-10 U/ml. Scatchard analysis indicated that the decrease in binding was due to a decrease in both the affinity and the apparent number of available insulin receptors. The effect occurred within 10 min at 22 degrees C and persisted even after the cells were extensively washed. Inhibition of insulin binding also occurred when cells were preincubated with heparinized plasma or heparinized serum but not when cells were incubated with normal serum or plasma from blood anticoagulated with EDTA. By contrast, other polyanions and polycations, e.g., poly-L-glutamic acid, poly-L-lysine, succinylated poly-L-lysine, and histone, did not inhibit binding. Heparin also inhibited insulin binding in Epstein-Barr (EB) virus-transformed lymphocytes but had no effect on insulin binding to isolated adipocytes, human erythrocytes, or intact hepatoma cells. When isolated adipocytes were incubated with heparin, there was a dose-dependent inhibition of insulin-stimulated glucose oxidation and, to a lesser extent, of basal glucose oxidation. Although heparin has no effect on insulin binding to intact hepatoma cells, heparin inhibited both insulin binding and insulin-stimulated autophosphorylation in receptors solubilized from these cells

Tight-Binding Description of Impurity States in Semiconductors

Science.gov (United States)

Dominguez-Adame, F.

2012-01-01

Introductory textbooks in solid state physics usually present the hydrogenic impurity model to calculate the energy of carriers bound to donors or acceptors in semiconductors. This model treats the pure semiconductor as a homogeneous medium and the impurity is represented as a fixed point charge. This approach is only valid for shallow impurities…

A strategy for increasing the brain uptake of a radioligand in animals: use of a drug that inhibits plasma protein binding

Energy Technology Data Exchange (ETDEWEB)

Haradahira, Terushi E-mail: terushi@nirs.go.jp; Zhang, Ming-Rong; Maeda, Jun; Okauchi, Takashi; Kawabe, Kouichi; Kida, Takayo; Suzuki, Kazutoshi; Suhara, Tetsuya

2000-05-01

A positron-emitter labeled radioligand for the glycine-binding site of the N-methyl-D-aspartate (NMDA) receptor, [{sup 11}C]L-703,717, was examined for its ability to penetrate the brain in animals by simultaneous use with drugs having high-affinity separate binding sites on human serum albumin. [{sup 11}C]L-703,717 has poor blood-brain barrier (BBB) permeability because it binds tightly to plasma proteins. Co-injection of warfarin (50-200 mg/kg), a drug that binds to albumin and resembles L-703,717 in structure, dose-dependently enhanced the penetration by [{sup 11}C]L-703,717 in mice, resulting in a five-fold increase in the brain radioactivity at 1 min after the injection. Drugs structurally unrelated to L-703,717, salicylate, phenol red, and L-tryptophan, were less effective or ineffective in increasing the uptake of [{sup 11}C]L-703,717. These results suggest that the simultaneous use of a drug that inhibits the binding of a radioligand to plasma proteins is a useful way to overcome the poor BBB permeability of the radioligand triggered by its tight binding to plasma proteins. In brain distribution studies in rodents, it was found that, after the increase in brain uptake with warfarin, much of the glycine site antagonist accumulates in the cerebellum but its pharmacological specificity did not match the glycine site of NMDA receptors.

Development of estrogen receptor beta binding prediction model using large sets of chemicals.

Science.gov (United States)

Sakkiah, Sugunadevi; Selvaraj, Chandrabose; Gong, Ping; Zhang, Chaoyang; Tong, Weida; Hong, Huixiao

2017-11-03

We developed an ER β binding prediction model to facilitate identification of chemicals specifically bind ER β or ER α together with our previously developed ER α binding model. Decision Forest was used to train ER β binding prediction model based on a large set of compounds obtained from EADB. Model performance was estimated through 1000 iterations of 5-fold cross validations. Prediction confidence was analyzed using predictions from the cross validations. Informative chemical features for ER β binding were identified through analysis of the frequency data of chemical descriptors used in the models in the 5-fold cross validations. 1000 permutations were conducted to assess the chance correlation. The average accuracy of 5-fold cross validations was 93.14% with a standard deviation of 0.64%. Prediction confidence analysis indicated that the higher the prediction confidence the more accurate the predictions. Permutation testing results revealed that the prediction model is unlikely generated by chance. Eighteen informative descriptors were identified to be important to ER β binding prediction. Application of the prediction model to the data from ToxCast project yielded very high sensitivity of 90-92%. Our results demonstrated ER β binding of chemicals could be accurately predicted using the developed model. Coupling with our previously developed ER α prediction model, this model could be expected to facilitate drug development through identification of chemicals that specifically bind ER β or ER α .

Effects of Tight Versus Non Tight Control of Metabolic Acidosis on Early Renal Function After Kidney Transplantation

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Farhad Etezadi

2012-09-01

Full Text Available Background Recently, several studies have been conducted to determine the optimal strategy for intraoperative fluid replacement therapy in renal transplantation surgery. Since infusion of sodium bicarbonate as a buffer seems to be safer than other buffer compounds (lactate, gluconate, acetatethat indirectly convert into it within the liver, We hypothesized tight control of metabolic acidosis by infusion of sodium bicarbonate may improve early post-operative renal function in renal transplant recipients. Methods:120 patients were randomly divided into two equal groups. In group A, bicarbonate was infused intra-operatively according to Base Excess (BE measurements to achieve the normal values of BE (5 to +5 mEq/L. In group B, infusion of bicarbonate was allowed only in case of severe metabolic acidosis (BE [less than or equal to] 15 mEq/L or bicarbonate [less than or equal to] 10 mEq/L or PH [less than or equal to] 7.15. Minute ventilation was adjusted to keep PaCO2 within the normal range. Primary end-point was sampling of serum creatinine level in first, second, third and seventh post-operative days for statistical comparison between groups. Secondary objectives were comparison of cumulative urine volumes in the first 24 h of post-operative period and serum BUN levels which were obtained in first, second, third and seventh post-operative days. Results:In group A, all of consecutive serum creatinine levels were significantly lower in comparison with group B. With regard to secondary outcomes, no significant difference between groups was observed. Conclusion:Intra-operative tight control of metabolic acidosis by infusion of Sodium Bicarbonate in renal transplant recipients may improve early post-operative renal function.

Effects of tight versus non tight control of metabolic acidosis on early renal function after kidney transplantation

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Etezadi Farhad

2012-09-01

Full Text Available Abstract Background Recently, several studies have been conducted to determine the optimal strategy for intra-operative fluid replacement therapy in renal transplantation surgery. Since infusion of sodium bicarbonate as a buffer seems to be safer than other buffer compounds (lactate, gluconate, acetatethat indirectly convert into it within the liver, We hypothesized tight control of metabolic acidosis by infusion of sodium bicarbonate may improve early post-operative renal function in renal transplant recipients. Methods 120 patients were randomly divided into two equal groups. In group A, bicarbonate was infused intra-operatively according to Base Excess (BE measurements to achieve the normal values of BE (−5 to +5 mEq/L. In group B, infusion of bicarbonate was allowed only in case of severe metabolic acidosis (BE ≤ −15 mEq/L or bicarbonate ≤ 10 mEq/L or PH ≤ 7.15. Minute ventilation was adjusted to keep PaCO2 within the normal range. Primary end-point was sampling of serum creatinine level in first, second, third and seventh post-operative days for statistical comparison between groups. Secondary objectives were comparison of cumulative urine volumes in the first 24 h of post-operative period and serum BUN levels which were obtained in first, second, third and seventh post-operative days. Results In group A, all of consecutive serum creatinine levels were significantly lower in comparison with group B. With regard to secondary outcomes, no significant difference between groups was observed. Conclusion Intra-operative tight control of metabolic acidosis by infusion of Sodium Bicarbonate in renal transplant recipients may improve early post-operative renal function.

Theoretical study on the perpendicular anisotropic magnetoresistance using Rashba-type ferromagnetic model

Science.gov (United States)

Yahagi, Y.; Miura, D.; Sakuma, A.

2018-05-01

We investigated the anisotropic magnetoresistance (AMR) effects in ferromagnetic-metal multi-layers stacked on non-magnetic insulators in the context of microscopic theory. We represented this situation with tight-binding models that included the exchange and Rashba fields, where the Rashba field was assumed to originate from spin-orbit interactions as junction effects with the insulator. To describe the AMR ratios, the DC conductivity was calculated based on the Kubo formula. As a result, we showed that the Rashba field induced both perpendicular and in-plane AMR effects and that the perpendicular AMR effect rapidly decayed with increasing film thickness.

Dominant Alcohol-Protein Interaction via Hydration-Enabled Enthalpy-Driven Binding Mechanism

Science.gov (United States)

Chong, Yuan; Kleinhammes, Alfred; Tang, Pei; Xu, Yan; Wu, Yue

2015-01-01

Water plays an important role in weak associations of small drug molecules with proteins. Intense focus has been on binding-induced structural changes in the water network surrounding protein binding sites, especially their contributions to binding thermodynamics. However, water is also tightly coupled to protein conformations and dynamics, and so far little is known about the influence of water-protein interactions on ligand binding. Alcohols are a type of low-affinity drugs, and it remains unclear how water affects alcohol-protein interactions. Here, we present alcohol adsorption isotherms under controlled protein hydration using in-situ NMR detection. As functions of hydration level, Gibbs free energy, enthalpy, and entropy of binding were determined from the temperature dependence of isotherms. Two types of alcohol binding were found. The dominant type is low-affinity nonspecific binding, which is strongly dependent on temperature and the level of hydration. At low hydration levels, this nonspecific binding only occurs above a threshold of alcohol vapor pressure. An increased hydration level reduces this threshold, with it finally disappearing at a hydration level of h~0.2 (g water/g protein), gradually shifting alcohol binding from an entropy-driven to an enthalpy-driven process. Water at charged and polar groups on the protein surface was found to be particularly important in enabling this binding. Although further increase in hydration has smaller effects on the changes of binding enthalpy and entropy, it results in significant negative change in Gibbs free energy due to unmatched enthalpy-entropy compensation. These results show the crucial role of water-protein interplay in alcohol binding. PMID:25856773

Application of Reservoir Flow Simulation Integrated with Geomechanics in Unconventional Tight Play

Science.gov (United States)

Lin, Menglu; Chen, Shengnan; Mbia, Ernest; Chen, Zhangxing

2018-01-01

Multistage hydraulic fracturing techniques, combined with horizontal drilling, have enabled commercial production from the vast reserves of unconventional tight formations. During hydraulic fracturing, fracturing fluid and proppants are pumped into the reservoir matrix to create the hydraulic fractures. Understanding the propagation mechanism of hydraulic fractures is essential to estimate their properties, such as half-length. In addition, natural fractures are often present in tight formations, which might be activated during the fracturing process and contribute to the post-stimulation well production rates. In this study, reservoir simulation is integrated with rock geomechanics to predict the well post-stimulation productivities. Firstly, a reservoir geological model is built based on the field data collected from the Montney formation in the Western Canadian Sedimentary Basin. The hydraulic fracturing process is then simulated through an integrated approach of fracturing fluid injection, rock geomechanics, and tensile failure criteria. In such a process, the reservoir pore pressure increases with a continuous injection of the fracturing fluid and proppants, decreasing the effective stress exerted on the rock matrix accordingly as the overburden pressure remains constant. Once the effective stress drops to a threshold value, tensile failure of the reservoir rock occurs, creating hydraulic fractures in the formation. The early production history of the stimulated well is history-matched to validate the predicted fracture geometries (e.g., half-length) generated from the fracturing simulation process. The effects of the natural fracture properties and well bottom-hole pressures on well productivity are also studied. It has been found that nearly 40% of hydraulic fractures propagate in the beginning stage (the pad step) of the fracturing schedule. In addition, well post-stimulation productivity will increase significantly if the natural fractures are propped or

Advanced Hydraulic Fracturing Technology for Unconventional Tight Gas Reservoirs

Energy Technology Data Exchange (ETDEWEB)

Stephen Holditch; A. Daniel Hill; D. Zhu

2007-06-19

The objectives of this project are to develop and test new techniques for creating extensive, conductive hydraulic fractures in unconventional tight gas reservoirs by statistically assessing the productivity achieved in hundreds of field treatments with a variety of current fracturing practices ranging from 'water fracs' to conventional gel fracture treatments; by laboratory measurements of the conductivity created with high rate proppant fracturing using an entirely new conductivity test - the 'dynamic fracture conductivity test'; and by developing design models to implement the optimal fracture treatments determined from the field assessment and the laboratory measurements. One of the tasks of this project is to create an 'advisor' or expert system for completion, production and stimulation of tight gas reservoirs. A central part of this study is an extensive survey of the productivity of hundreds of tight gas wells that have been hydraulically fractured. We have been doing an extensive literature search of the SPE eLibrary, DOE, Gas Technology Institute (GTI), Bureau of Economic Geology and IHS Energy, for publicly available technical reports about procedures of drilling, completion and production of the tight gas wells. We have downloaded numerous papers and read and summarized the information to build a database that will contain field treatment data, organized by geographic location, and hydraulic fracture treatment design data, organized by the treatment type. We have conducted experimental study on 'dynamic fracture conductivity' created when proppant slurries are pumped into hydraulic fractures in tight gas sands. Unlike conventional fracture conductivity tests in which proppant is loaded into the fracture artificially; we pump proppant/frac fluid slurries into a fracture cell, dynamically placing the proppant just as it occurs in the field. From such tests, we expect to gain new insights into some of the critical

Pore-scale mechanisms of gas flow in tight sand reservoirs

Energy Technology Data Exchange (ETDEWEB)

Silin, D.; Kneafsey, T.J.; Ajo-Franklin, J.B.; Nico, P.

2010-11-30

Tight gas sands are unconventional hydrocarbon energy resource storing large volume of natural gas. Microscopy and 3D imaging of reservoir samples at different scales and resolutions provide insights into the coaredo not significantly smaller in size than conventional sandstones, the extremely dense grain packing makes the pore space tortuous, and the porosity is small. In some cases the inter-granular void space is presented by micron-scale slits, whose geometry requires imaging at submicron resolutions. Maximal Inscribed Spheres computations simulate different scenarios of capillary-equilibrium two-phase fluid displacement. For tight sands, the simulations predict an unusually low wetting fluid saturation threshold, at which the non-wetting phase becomes disconnected. Flow simulations in combination with Maximal Inscribed Spheres computations evaluate relative permeability curves. The computations show that at the threshold saturation, when the nonwetting fluid becomes disconnected, the flow of both fluids is practically blocked. The nonwetting phase is immobile due to the disconnectedness, while the permeability to the wetting phase remains essentially equal to zero due to the pore space geometry. This observation explains the Permeability Jail, which was defined earlier by others. The gas is trapped by capillarity, and the brine is immobile due to the dynamic effects. At the same time, in drainage, simulations predict that the mobility of at least one of the fluids is greater than zero at all saturations. A pore-scale model of gas condensate dropout predicts the rate to be proportional to the scalar product of the fluid velocity and pressure gradient. The narrowest constriction in the flow path is subject to the highest rate of condensation. The pore-scale model naturally upscales to the Panfilov's Darcy-scale model, which implies that the condensate dropout rate is proportional to the pressure gradient squared. Pressure gradient is the greatest near the

Conformational dynamics and ligand binding in the multi-domain protein PDC109.

Directory of Open Access Journals (Sweden)

Hyun Jin Kim

2010-02-01

Full Text Available PDC109 is a modular multi-domain protein with two fibronectin type II (Fn2 repeats joined by a linker. It plays a major role in bull sperm binding to the oviductal epithelium through its interactions with phosphorylcholines (PhCs, a head group of sperm cell membrane lipids. The crystal structure of the PDC109-PhC complex shows that each PhC binds to the corresponding Fn2 domain, while the two domains are on the same face of the protein. Long timescale explicit solvent molecular dynamics (MD simulations of PDC109, in the presence and absence of PhC, suggest that PhC binding strongly correlates with the relative orientation of choline-phospholipid binding sites of the two Fn2 domains; unless the two domains tightly bind PhCs, they tend to change their relative orientation by deforming the flexible linker. The effective PDC109-PhC association constant of 28 M(-1, estimated from their potential of mean force is consistent with the experimental result. Principal component analysis of the long timescale MD simulations was compared to the significantly less expensive normal mode analysis of minimized structures. The comparison indicates that difference between relative domain motions of PDC109 with bound and unbound PhC is captured by the first principal component in the principal component analysis as well as the three lowest normal modes in the normal mode analysis. The present study illustrates the use of detailed MD simulations to clarify the energetics of specific ligand-domain interactions revealed by a static crystallographic model, as well as their influence on relative domain motions in a multi-domain protein.

Bifunctional avidin with covalently modifiable ligand binding site.

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Jenni Leppiniemi

Full Text Available The extensive use of avidin and streptavidin in life sciences originates from the extraordinary tight biotin-binding affinity of these tetrameric proteins. Numerous studies have been performed to modify the biotin-binding affinity of (streptavidin to improve the existing applications. Even so, (streptavidin greatly favours its natural ligand, biotin. Here we engineered the biotin-binding pocket of avidin with a single point mutation S16C and thus introduced a chemically active thiol group, which could be covalently coupled with thiol-reactive molecules. This approach was applied to the previously reported bivalent dual chain avidin by modifying one binding site while preserving the other one intact. Maleimide was then coupled to the modified binding site resulting in a decrease in biotin affinity. Furthermore, we showed that this thiol could be covalently coupled to other maleimide derivatives, for instance fluorescent labels, allowing intratetrameric FRET. The bifunctional avidins described here provide improved and novel tools for applications such as the biofunctionalization of surfaces.

The effect of macromolecular crowding on the electrostatic component of barnase-barstar binding: a computational, implicit solvent-based study.

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Helena W Qi

Full Text Available Macromolecular crowding within the cell can impact both protein folding and binding. Earlier models of cellular crowding focused on the excluded volume, entropic effect of crowding agents, which generally favors compact protein states. Recently, other effects of crowding have been explored, including enthalpically-related crowder-protein interactions and changes in solvation properties. In this work, we explore the effects of macromolecular crowding on the electrostatic desolvation and solvent-screened interaction components of protein-protein binding. Our simple model enables us to focus exclusively on the electrostatic effects of water depletion on protein binding due to crowding, providing us with the ability to systematically analyze and quantify these potentially intuitive effects. We use the barnase-barstar complex as a model system and randomly placed, uncharged spheres within implicit solvent to model crowding in an aqueous environment. On average, we find that the desolvation free energy penalties incurred by partners upon binding are lowered in a crowded environment and solvent-screened interactions are amplified. At a constant crowder density (fraction of total available volume occupied by crowders, this effect generally increases as the radius of model crowders decreases, but the strength and nature of this trend can depend on the water probe radius used to generate the molecular surface in the continuum model. In general, there is huge variation in desolvation penalties as a function of the random crowder positions. Results with explicit model crowders can be qualitatively similar to those using a lowered "effective" solvent dielectric to account for crowding, although the "best" effective dielectric constant will likely depend on multiple system properties. Taken together, this work systematically demonstrates, quantifies, and analyzes qualitative intuition-based insights into the effects of water depletion due to crowding on the

Regulation of Tight Junctions in Upper Airway Epithelium

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Takashi Kojima

2013-01-01

Full Text Available The mucosal barrier of the upper respiratory tract including the nasal cavity, which is the first site of exposure to inhaled antigens, plays an important role in host defense in terms of innate immunity and is regulated in large part by tight junctions of epithelial cells. Tight junction molecules are expressed in both M cells and dendritic cells as well as epithelial cells of upper airway. Various antigens are sampled, transported, and released to lymphocytes through the cells in nasal mucosa while they maintain the integrity of the barrier. Expression of tight junction molecules and the barrier function in normal human nasal epithelial cells (HNECs are affected by various stimuli including growth factor, TLR ligand, and cytokine. In addition, epithelial-derived thymic stromal lymphopoietin (TSLP, which is a master switch for allergic inflammatory diseases including allergic rhinitis, enhances the barrier function together with an increase of tight junction molecules in HNECs. Furthermore, respiratory syncytial virus infection in HNECs in vitro induces expression of tight junction molecules and the barrier function together with proinflammatory cytokine release. This paper summarizes the recent progress in our understanding of the regulation of tight junctions in the upper airway epithelium under normal, allergic, and RSV-infected conditions.

Feasibility study on thermal-hydraulic performance in tight-lattice rod bundles for reduced-moderation water reactors

International Nuclear Information System (INIS)

Ohnuki, A.; Kureta, M.; Liu, W.; Tamai, H.; Akimoto, H.

2004-01-01

Research and development project for investigating thermal-hydraulic performance in tight-lattice rod bundles for Reduced-Moderation Water Reactor (RMWR) started at Japan Atomic Energy Research Institute (JAERI) in 2002. The RMWR can attain the favorable characteristics such as effective utilization of uranium resources, multiple recycling of plutonium, high burn-up and long operation cycle, based on matured light-water reactor technologies. MOX fuel assemblies with tight lattice arrangement are used to increase the conversion ratio by reducing the moderation of neutron. Increasing the in-core void fraction also contributes to the reduction of neutron moderation. The confirmation of thermal-hydraulic feasibility is one of the most important issues for the RMWR because of the tight-lattice configuration. The project has mainly consisted of a large-scale thermal-hydraulic test and development of analytical methods named modeling engineering. In the large-scale test, 37-rod bundle experiments can be performed. Steady-state critical power experiments have been achieved in the test facility and the experimental data reveal the feasibility of RMWR

Discrete persistent-chain model for protein binding on DNA.

Science.gov (United States)

Lam, Pui-Man; Zhen, Yi

2011-04-01

We describe and solve a discrete persistent-chain model of protein binding on DNA, involving an extra σ(i) at a site i of the DNA. This variable takes the value 1 or 0, depending on whether or not the site is occupied by a protein. In addition, if the site is occupied by a protein, there is an extra energy cost ɛ. For a small force, we obtain analytic expressions for the force-extension curve and the fraction of bound protein on the DNA. For higher forces, the model can be solved numerically to obtain force-extension curves and the average fraction of bound proteins as a function of applied force. Our model can be used to analyze experimental force-extension curves of protein binding on DNA, and hence deduce the number of bound proteins in the case of nonspecific binding. ©2011 American Physical Society

Status of the substrate binding sites of ribulose bisphosphate carboxylase as determined with 2-C-carboxyarabinitol 1,5-bisphosphate. [Spinacia oleracea

Energy Technology Data Exchange (ETDEWEB)

Zhu, Genhai; Jensen, R.G. (Univ. of Arizona, Tucson (USA))

1990-05-01

The properties of the tight and specific binding of 2-C-carboxy-D-arabinitol 1,5-bisphosphate (CABP), which occurs only to reaction sites of ribulose 1,5-bisphosphate carboxylase (Rubisco) that are activated by CO{sub 2} and Mg{sup 2+}, were studied. With fully active purified spinach (Spinacia oleracea) Rubisco the rate of tight binding of ({sup 14}C)CABP fit a multiple exponential rate equation with half of the sites binding with a rate constant of 40 per minute and the second half of the sites binding at 3.2 per minute. This suggests that after CABP binds to one site of a dimer of Rubisco large subunits, binding to the second site is considerably slower, indicating negative cooperativity as previously reported. The rate of CABP binding to partially activated Rubisco was complete within 2 to 5 minutes, with slower binding to inactive sites as they formed the carbamate and bound Mg{sup 2+}. Addition of ({sup 14}C)CABP and EDTA stopped binding of Mg{sup 2+} and allowed tight binding of the radiolabel only to sites which were CO{sub 2}/Mg{sup 2+}-activated at that moment. The rate of CO{sub 2} fixation was proportional to the CO{sub 2}/Mg{sup 2+}-activated sites. During light-dependent CO{sub 2} fixation with isolated spinach chloroplasts, the amount of carbamylation was proportional to Rubisco activity either initially upon lysis of the plastids or following total activation with Mg{sup 2+} and CO{sub 2}. Lysis of chloroplasts in media with ({sup 14}C)CABP plus EDTA estimated those carbamylated sites having Mg{sup 2+}. The loss of Rubisco activation during illumination was partially due to the lack of Mg{sup 2+} to stabilize the carbamylated sites.

EFFECTIVENESS OF PNF STRETCHING AND CYCLIC STRETCHING OF CALF TIGHTNESS ON COLLEGE GOING GIRLS

Directory of Open Access Journals (Sweden)

Ashlesha Sirari

2015-06-01

Full Text Available Background: Flexibility helps with injury prevention, the reduction of soreness following a workout, and a general sense of well-being. There are different stretching techniques and protocols for improvements in calf extensibility and flexibility. The purpose of the study was to investigate the effectiveness of two techniques i.e. CYCLIC and PNF stretching which improves calf flexibility. This study was done to find the effectiveness of calf Cyclic and PNF stretching technique to improve calf flexibility. Methods: 30 subjects with age group 21-22 years were randomly allocated to 2 groups equally. Group 1(n=15 were given CYCLIC and group 2(n=15 were given PNF stretching technique. Plantar flexion was used to measure the calf tightness which was done before and after the treatment. Treatment was given for 7 days and on the 7th day the calf tightness was again measured. Results: The mean difference of the CYCLIC is 4.6 and mean difference of PNF is 4.7 which indicate that CYCLIC and PNF both are effective to improve calf flexibility but PNF is more effective than CYCLIC to improve calf flexibility. Conclusion: The neurophysiological basis of PNF, stating that the excitatory efficient of the neuromuscular spindle or the inhibitory afferent of the Golgi tendon organ (GTO or both are responsible for the effects. During PNF stretch and isometric contraction of stretched agonists for extended period may cause activation of its neuromuscular spindle. The increase in tension created during the isometric contraction of the pre – lengthened agonist contracts concentrically. Both the fascia & the spindle of the agonist adjust to the nearly lengthened position. These impulses travel via causing post synaptic inhibition of the motor neuron to agonist increasing the tension from the GTO. These impulses can override the impulses coming from the neuromuscular spindles arousing the muscle to reflexly resist to the change in length, thus helping in lengthening

Active stretching for lower extremity muscle tightness in pediatric patients with lumbar spondylolysis.

Science.gov (United States)

Sato, Masahiro; Mase, Yasuyoshi; Sairyo, Koichi

2017-01-01

It was reported that hamstring muscle tightness may increase mechanical loading on the lumbar spine. Therefore, we attempt to decrease tightness in the leg muscles in pediatric patients. Forty-six pediatric patients with spondylolysis underwent rehabilitation. We applied active stretching to the hamstrings, quadriceps, and triceps surae. Tightness in each muscle was graded as good, fair, or poor. We educated each patient on how to perform active stretching at home. They were re-evaluated for muscle tightness 2 months later. Tightness at baseline and after 2 months was as follows: for the hamstrings, good in 3 patients, fair in 9, and poor in 34 and significant improved after 2 months (p<0.05), with improvement by least 1 grade seen in 86% of patients with fair or poor at baseline; for the quadriceps, 7, 3, and 30 patients had good, fair and poor, with significant improvements in 72% (p<0.05). For the triceps surae, 6, 3 and 10 patients had good, fair and poor, which improved significantly (p<0.05). Home-based active stretching was effective for relieving muscle tightness in the leg in a pediatric population. Adolescent athletes should perform such exercise to maintain flexibility and prevent lumbar disorders. J. Med. Invest. 64: 136-139, February, 2017.

A binomial truncation function proposed for the second-moment approximation of tight-binding potential and application in the ternary Ni-Hf-Ti system

International Nuclear Information System (INIS)

Li, J H; Dai, X D; Wang, T L; Liu, B X

2007-01-01

We propose a two-parameter binomial truncation function for the second-moment approximation of the tight-binding (TB-SMA) interatomic potential and illustrate in detail the procedure of constructing the potentials for binary and ternary transition metal systems. For the ternary Ni-Hf-Ti system, the lattice constants, cohesion energies, elastic constants and bulk moduli of six binary compounds, i.e. L1 2 Ni 3 Hf, NiHf 3 , Ni 3 Ti, NiTi 3 , Hf 3 Ti and HfTi 3 , are firstly acquired by ab initio calculations and then employed to derive the binomial-truncated TB-SMA Ni-Hf-Ti potential. Applying the ab initio derived Ni-Hf-Ti potential, the lattice constants, cohesive energy, elastic constants and bulk moduli of another six binary compounds, i.e. D0 3 NiHf 3 , NiTi 3 HfTi 3 , and B2 NiHf, NiTi, HfTi, and two ternary compounds, i.e. C1 b NiHfTi, L2 1 Ni 2 HfTi, are calculated, respectively. It is found that, for the eight binary compounds studied, the calculated lattice constants and cohesion energies are in excellent agreement with those directly acquired from ab initio calculations and that the elastic constants and bulk moduli calculated from the potential are also qualitatively consistent with the results from ab initio calculations

Mobbing and sitting tight at the nest as methods of avoiding brood parasitism.

Science.gov (United States)

Rands, Sean A

2012-04-06

The arms race between brood parasites and their hosts has led to many different host behaviours for avoiding parasitism. Some of these behaviours are social, and require the presence of conspecifics to work effectively: in response to alarm calls, some species engage in mobbing behaviour where neighbours join nest tenants in attacking and repelling an invading brood parasite. There are risks involved for the neighbours, but it has been demonstrated that social mobbing allows individuals to learn about the presence of brood parasites in the environment, suggesting that social learning is occurring. Here, I consider whether using social signals to alert naive individuals to the presence of brood parasites is a suitable strategy, compared with sitting tight on the nest in response to the signal (which should reduce the chances of being parasitized). I also compare the efficiency of these strategies with the case where individuals fail to change behaviour in response a brood parasite. Using an individual-based simulation model, I demonstrate that both mobbing and sitting tight are effective strategies in response to a signal, and that mobbing is more effective when the chances of being parasitized increase. These results are discussed and compared with known host-brood parasite relationships.

The effectiveness of ski bindings and their professional adjustment for preventing alpine skiing injuries.

Science.gov (United States)

Finch, C F; Kelsall, H L

1998-06-01

This article presents a critical review of the extent to which alpine ski bindings and their adjustment have been formally demonstrated to prevent injuries. It considers a range of evidence, from anecdotal evidence and informed opinion to biomechanical studies, testing of equipment, epidemiological studies and controlled field evaluations. A total of 15 published studies examining the effectiveness of bindings and their adjustment were identified. All of these included anecdotal or informed opinion, and all but one focused on equipment design. Seven studies involved the testing of bindings or binding prototypes, 2 studies presented biomechanical models of the forces involved in binding operation, 6 reported an epidemiological evaluation of ski bindings and 2 considered skiers' behaviours towards binding adjustment. Some of the reviewed articles relate to the study of the biomechanics of ski bindings and their release in response to various loads and loading patterns. Other studies examined the contribution of bindings and binding-release to lower extremity, equipment-related injuries, the effect of various methods of binding adjustment on injury risk and the determinants of skiers' behaviour relating to professional binding adjustment. Most of the evidence suggests that currently used bindings are insufficient for the multidirectional release required to reduce the risk of injury to the lower limb, especially at the knee. This evidence suggests that further technical developments and innovations are required. The standard of the manufacture of bindings and boots also needs to be considered. The optimal adjustment of bindings using a testing device has been shown to be associated with a reduced risk of lower extremity injury. Generally, however, the adjustment of bindings has been shown to be inadequate, especially for children's bindings. Recommendations for further research, development and implementation with respect to ski binding and their adjustment are given

A model for the direct-to-indirect band-gap transition in monolayer ...

Indian Academy of Sciences (India)

Abstract. A monolayer of MoSe2 is found to be a direct band-gap semiconductor. We show, ... In order to determine appropriate basis for the tight-binding model, the Mo and Se ..... RD thanks the Council of Scientific and Industrial Research.

An introduction to finite tight frames

CERN Document Server

Waldron, Shayne F D

2018-01-01

This textbook is an introduction to the theory and applications of finite tight frames, an area that has developed rapidly in the last decade. Stimulating much of this growth are the applications of finite frames to diverse fields such as signal processing, quantum information theory, multivariate orthogonal polynomials, and remote sensing. Key features and topics: * First book entirely devoted to finite frames * Extensive exercises and MATLAB examples for classroom use * Important examples, such as harmonic and Heisenberg frames, are presented in preliminary chapters, encouraging readers to explore and develop an intuitive feeling for tight frames * Later chapters delve into general theory details and recent research results * Many illustrations showing the special aspects of the geometry of finite frames * Provides an overview of the field of finite tight frames * Discusses future research directions in the field Featuring exercises and MATLAB examples in each chapter, the book is well suited as a textbook ...

Tight or sick building syndrome

Energy Technology Data Exchange (ETDEWEB)

Thirumalaikolundusubramanian, P; Shanmuganadan, S [Madurai Kamaraj Univ. (India). Dept. of Geography; Uma, A [Madurai Medical Coll. (India). Dept. of Medicine and Microbiology

1991-01-01

Modern buildings are designed with the usual heating, air-conditioning and ventilation equipment. In most of these buildings, air is continuously recirculated and, as a result, workers suffer from tight or sick building syndrome. This syndrome is discussed with reference to symptoms of air contamination, ventilation system standards and research needs. The most common symptoms of tight building syndrome are eye, nose and throat irritation, headache, fatigue, sneezing, difficulty in wearing contact lenses, chest tightness, nausea, dizziness and dermatitis. Symptoms experienced by 50 doctors and 50 paramedical personnel working in an air-conditioned intensive care unit and operating theatres of the Government Rajaji Hospital, Madurai in India were studied by means of a questionnaire survey. In the present study, respiratory and ocular symptoms were observed more in those working in operating theatres and were believed to be due to excessive use of formaldehyde used for sterilization. Various suggestions were made to prevent sick building syndrome. Moreover, the physicians treating sick individuals should be aware of the symptoms caused by indoor air pollutants as sufferers invariably require a change of environment rather than drugs. (orig.).

Superconductivity of the two-dimensional Penson-Kolb model

International Nuclear Information System (INIS)

Czart, W.R.; Robaszkiewicz, S.

2001-01-01

Two-dimensional (d = 2) Penson-Kolb model, i.e. the tight-binding model with the pair-hopping (intersite charge exchange) interaction, is considered and the effects of phase fluctuations on the s-wave superconductivity of this system are discussed within Kosterlitz-Thouless scenario. The London penetration depth λ at T = 0, the Kosterlitz Thouless critical temperature T c , and the Hartree-Fock approximation critical temperature T p are determined as a function of particle concentration and interaction. The Uemura type plots (T c vs. λ -2 (0)) are derived. Beyond weak coupling and for low concentrations they show the existence of universal scaling: T c ∼ 1/λ 2 (0), as it previously found for the attractive Hubbard model and for the models intersite electron pairing. (author)

Binding energies of sd-shell nuclei with a realistic effective Hamiltonian

International Nuclear Information System (INIS)

Dalton, B.J.; Vary, J.P.; Baldridge, W.J.

1977-01-01

The nuclear shell model with a second-order effective Hamiltonian derived within Brueckner theory from the free nucleon-nucleon interaction is shown to yield accurate binding energies of nuclei with 16 < A < 40. This agreement is obtained by choosing the spectrum of low-lying unoccupied orbitals in a justified manner and, when necessary, by employing a statistical method to approximate the lowest eigenvalue of very large shell-model diagonalizations

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

Science.gov (United States)

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.

CHARACTERIZATION OF TIGHTLY-ASSOCIATED SMOOTH MUSCLE MYOSIN-MYOSIN LIGHT CHAIN KINASE-CALMODULIN COMPLEXES*

OpenAIRE

Hong, Feng; Haldeman, Brian D.; John, Olivia A.; Brewer, Paul D.; Wu, Yi-Ying; Ni, Shaowei; Wilson, David P.; Walsh, Michael P.; Baker, Jonathan E.; Cremo, Christine R.

2009-01-01

A current popular model to explain phosphorylation of smooth muscle myosin (SMM) by smooth muscle myosin light chain kinase (MLCK) proposes that MLCK is bound tightly to actin but weakly to SMM. We found that MLCK and calmodulin (CaM) co-purify with unphosphorylated SMM (up-SMM) from chicken gizzard, suggesting that they are tightly bound. Although the MLCK:SMM molar ratio in SMM preparations was well below stoichiometric (1:73 ± 9), the ratio was ~ 23–37% of that in gizzard tissue. Fifteen t...

USING MICROSCALE THERMOPHORESIS TO EASILY MEASURE BINDING AFFINITY

Directory of Open Access Journals (Sweden)

Dennis Breitsprecher*

2018-03-01

Full Text Available While it’s very common for biologists and chemists to test whether or not two molecules interact with each other, it’s much more useful to gather information on the nature of that interaction. How strong is it? How long will it last? What does that mean for its biological function? One way to answer these questions is to study affinity. Binding affinity is defined as the strength of the binding interaction between a single biomolecule to its binding partner, or ligand, and it can be quantifiably measured, providing information on whether or not molecules are interacting, as well as assigning a value to the affinity. When measuring binding affinity, there are several parameters to look at, but the dissociation constant (Kd, which defines the likelihood that an interaction between two molecules will break, is a very common measurement. The smaller the dissociation constant, the more tightly bound the ligand is, and the higher the affinity is between the two molecules.

A model of mitochondrial creatine kinase binding to membranes: adsorption constants, essential amino acids and the effect of ionic strength

DEFF Research Database (Denmark)

Fedosov, Sergey; Belousova, Lubov; Plesner, Igor

1993-01-01

The quantitative aspects of mitochondrial creatinekinase (mitCK) binding to mitochondrial membranes were investigated. A simple adsorption and binding model was used for data fitting, taking into account the influence of protein concentration, pH, ionic strength and substrate concentration on the...

Critical heat flux experiments in tight lattice core

Energy Technology Data Exchange (ETDEWEB)

Kureta, Masatoshi [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment

2002-12-01

Fuel rods of the Reduced-Moderation Water Reactor (RMWR) are so designed to be in tight lattices as to reduce moderation and achieve higher conversion ratio. As for the BWR type reactor coolant flow rate is reduced small compared with the existing BWR, so average void fraction comes to be langer. In order to evaluate thermo hydraulic characteristics of designed cores, critical heat flux experiments in tight lattice core have been conducted using simulated high pressure coolant loops for both the PWR and BWR seven fuel rod bundles. Experimental data on critical heat flux for full bundles have been accumulated and applied to assess the critical power of designed cores using existing codes. Evaluated results are conservative enough to satisfy the limiting condition. Further experiments on axial power distribution effects and 37 fuel rod bundle tests will be performed to validate thermohydraulic characteristics of designed cores. (T. Tanaka)

Critical heat flux experiments in tight lattice core

International Nuclear Information System (INIS)

Kureta, Masatoshi

2002-01-01

Fuel rods of the Reduced-Moderation Water Reactor (RMWR) are so designed to be in tight lattices as to reduce moderation and achieve higher conversion ratio. As for the BWR type reactor coolant flow rate is reduced small compared with the existing BWR, so average void fraction comes to be langer. In order to evaluate thermo hydraulic characteristics of designed cores, critical heat flux experiments in tight lattice core have been conducted using simulated high pressure coolant loops for both the PWR and BWR seven fuel rod bundles. Experimental data on critical heat flux for full bundles have been accumulated and applied to assess the critical power of designed cores using existing codes. Evaluated results are conservative enough to satisfy the limiting condition. Further experiments on axial power distribution effects and 37 fuel rod bundle tests will be performed to validate thermohydraulic characteristics of designed cores. (T. Tanaka)

Calcium binding in α-amylases: An X-ray diffraction study at 2.1-angstrom resolution of two enzymes from Aspergillus

International Nuclear Information System (INIS)

Boel, E.; Jensen, V.J.; Petersen, S.B.; Thim, L.; Woldike, H.F.; Brady, L.; Brzozowski, AM.; Derewenda, Z.; Dodson, G.G.; Swift, H.

1990-01-01

X-ray diffraction analysis (at 2.1-angstrom resolution) of an acid alpha-amylase from Aspergillus niger allowed a detailed description of the stereochemistry of the calcium-binding sites. The primary site (which is essential in maintaining proper folding around the active site) contains a tightly bound Ca 2+ with an unusually high number of eight ligands. A secondary binding site was identified at the bottom of the substrate binding cleft; it involves the residues presumed to play a catalytic role (Asp206 and Glu230). This explains the inhibitory effect of calcium observed at higher concentrations. Neutral Aspergillus oryzae (TAKA) α-amylase was also refined in a new crystal at 2.1-angstrom resolution. The structure of this homologous (over 80%) enzyme and addition kinetic studies support all the structural conclusions regarding both calcium-binding sites

Effect of pore structure on the seepage characteristics of tight sandstone reservoirs: A case study of Upper Jurassic Penglaizhen Fm reservoirs in the western Sichuan Basin

Directory of Open Access Journals (Sweden)

Liqiang Sima

2017-01-01

Full Text Available Tight sandstone reservoirs are characterized by complex pore structures and strong heterogeneity, and their seepage characteristics are much different from those of conventional sandstone reservoirs. In this paper, the tight sandstone reservoirs of Upper Jurassic Penglaizhen Fm in western Sichuan Basin were analyzed in terms of their pore structures by using the data about physical property, mercury injection and nuclear magnetic resonance (NMR tests. Then, the seepage characteristics and the gas–water two-phase migration mechanisms and distribution of tight sandstone reservoirs with different types of pore structures in the process of hydrocarbon accumulation and development were simulated by combining the relative permeability experiment with the visual microscopic displacement model. It is shown that crotch-like viscous fingering occurs in the process of gas front advancing in reservoirs with different pore structures. The better the pore structure is, the lower the irreducible water saturation is; the higher the gas-phase relative permeability of irreducible water is, the more easily the gas reservoir can be developed. At the late stage of development, the residual gas is sealed in reservoirs in the forms of bypass, cutoff and dead end. In various reservoirs, the interference between gas and water is stronger, so gas and water tends to be produced simultaneously. The sealed gas may reduce the production rate of gas wells significantly, and the existence of water phase may reduce the gas permeability greatly; consequently, the water-bearing low-permeability tight sandstone gas reservoirs reveal serious water production, highly-difficult development and low-recovery percentage at the late stage, which have adverse impacts on the effective production and development of gas wells.

Interplay of electrostatics and lipid packing determines the binding of charged polymer coated nanoparticles to model membranes.

Science.gov (United States)

Biswas, Nupur; Bhattacharya, Rupak; Saha, Arindam; Jana, Nikhil R; Basu, Jaydeep K

2015-10-07

Understanding of nanoparticle-membrane interactions is useful for various applications of nanoparticles like drug delivery and imaging. Here we report on the studies of interaction between hydrophilic charged polymer coated semiconductor quantum dot nanoparticles with model lipid membranes. Atomic force microscopy and X-ray reflectivity measurements suggest that cationic nanoparticles bind and penetrate bilayers of zwitterionic lipids. Penetration and binding depend on the extent of lipid packing and result in the disruption of the lipid bilayer accompanied by enhanced lipid diffusion. On the other hand, anionic nanoparticles show minimal membrane binding although, curiously, their interaction leads to reduction in lipid diffusivity. It is suggested that the enhanced binding of cationic QDs at higher lipid packing can be understood in terms of the effective surface potential of the bilayers which is tunable through membrane lipid packing. Our results bring forth the subtle interplay of membrane lipid packing and electrostatics which determine nanoparticle binding and penetration of model membranes with further implications for real cell membranes.

Effects of bromocriptine on [3H]estradiol binding in cytosol of anterior pituitary

International Nuclear Information System (INIS)

De Nicola, A.F.; Weisenberg, L.S.; Arakelian, M.C.; Libertun, C.

1981-01-01

The hypothalamus may control hormone receptors in the anterior pituitary either by a direct trophic effect or indirectly by regulation of serum pituitary hormone levels. Rats whose medial basal hypothalamus had been destroyed in order to suppress neural control of the gland showed a reduction in [ 3 H]estradiol binding in the anterior pituitary and high serum PRL levels; both changes were reversed by treatment of the lesioned rats with daily injections of bromocriptine, a dopamine agonist. In nonlesioned animals, the same treatment did not modify significantly those parameters. In another hyperprolactinemic model (rats with anterior pituitaries transplanted under the kidney capsule), [ 3 H]estradiol binding by the in situ pituitaries of the host rats was similar to that in the nongrafted controls. These results suggest that changes due to median eminence lesion are reversible and that bromocriptine is able to act as a substitutive therapy which restores binding of estradiol in glands whose receptors have been decreased by the effect of the lesion. High PRL levels due to pituitary transplant do not account for the observed changes in the pituitary estradiol binding

Analysis of functional importance of binding sites in the Drosophila gap gene network model.

Science.gov (United States)

Kozlov, Konstantin; Gursky, Vitaly V; Kulakovskiy, Ivan V; Dymova, Arina; Samsonova, Maria

2015-01-01

The statistical thermodynamics based approach provides a promising framework for construction of the genotype-phenotype map in many biological systems. Among important aspects of a good model connecting the DNA sequence information with that of a molecular phenotype (gene expression) is the selection of regulatory interactions and relevant transcription factor bindings sites. As the model may predict different levels of the functional importance of specific binding sites in different genomic and regulatory contexts, it is essential to formulate and study such models under different modeling assumptions. We elaborate a two-layer model for the Drosophila gap gene network and include in the model a combined set of transcription factor binding sites and concentration dependent regulatory interaction between gap genes hunchback and Kruppel. We show that the new variants of the model are more consistent in terms of gene expression predictions for various genetic constructs in comparison to previous work. We quantify the functional importance of binding sites by calculating their impact on gene expression in the model and calculate how these impacts correlate across all sites under different modeling assumptions. The assumption about the dual interaction between hb and Kr leads to the most consistent modeling results, but, on the other hand, may obscure existence of indirect interactions between binding sites in regulatory regions of distinct genes. The analysis confirms the previously formulated regulation concept of many weak binding sites working in concert. The model predicts a more or less uniform distribution of functionally important binding sites over the sets of experimentally characterized regulatory modules and other open chromatin domains.

B-spline tight frame based force matching method

Science.gov (United States)

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.

Effect of fullerenol surface chemistry on nanoparticle binding-induced protein misfolding

Science.gov (United States)

Radic, Slaven; Nedumpully-Govindan, Praveen; Chen, Ran; Salonen, Emppu; Brown, Jared M.; Ke, Pu Chun; Ding, Feng

2014-06-01

Fullerene and its derivatives with different surface chemistry have great potential in biomedical applications. Accordingly, it is important to delineate the impact of these carbon-based nanoparticles on protein structure, dynamics, and subsequently function. Here, we focused on the effect of hydroxylation -- a common strategy for solubilizing and functionalizing fullerene -- on protein-nanoparticle interactions using a model protein, ubiquitin. We applied a set of complementary computational modeling methods, including docking and molecular dynamics simulations with both explicit and implicit solvent, to illustrate the impact of hydroxylated fullerenes on the structure and dynamics of ubiquitin. We found that all derivatives bound to the model protein. Specifically, the more hydrophilic nanoparticles with a higher number of hydroxyl groups bound to the surface of the protein via hydrogen bonds, which stabilized the protein without inducing large conformational changes in the protein structure. In contrast, fullerene derivatives with a smaller number of hydroxyl groups buried their hydrophobic surface inside the protein, thereby causing protein denaturation. Overall, our results revealed a distinct role of surface chemistry on nanoparticle-protein binding and binding-induced protein misfolding.Fullerene and its derivatives with different surface chemistry have great potential in biomedical applications. Accordingly, it is important to delineate the impact of these carbon-based nanoparticles on protein structure, dynamics, and subsequently function. Here, we focused on the effect of hydroxylation -- a common strategy for solubilizing and functionalizing fullerene -- on protein-nanoparticle interactions using a model protein, ubiquitin. We applied a set of complementary computational modeling methods, including docking and molecular dynamics simulations with both explicit and implicit solvent, to illustrate the impact of hydroxylated fullerenes on the structure and

Pressure drop characteristics in tight-lattice bundles for reduced-moderation water reactors

International Nuclear Information System (INIS)

Tamai, Hidesada; Kureta, Masatoshi; Yoshida, Hiroyuki; Akimoto, Hajime

2004-01-01

The reduced-moderation water reactor (RMWR) consists of several distinctive structures; a triangular tight-lattice configuration and a double-flat core. In order to design the RMWR core from the point of view of thermal-hydraulics, an evaluation method on pressure drop characteristics in the rod bundles at the tight-lattice configuration is required. In this study, calculated results by the Martinelli-Nelson's and Hancox's correlations were compared with experimental results in 4 x 5 rod bundles and seven-rod bundles. Consequently, the friction loss in two-phase flows becomes smaller at the tight-lattice configuration with the hydraulic diameter less than about 3 mm. This reason is due to the difference of the configuration between the multi-rod bundle and the circular tube and due to the effect of the small hydraulic diameter on the two-phase multiplier. (author)

Loose and Tight GNSS/INS Integrations: Comparison of Performance Assessed in Real Urban Scenarios.

Science.gov (United States)

Falco, Gianluca; Pini, Marco; Marucco, Gianluca

2017-01-29

Global Navigation Satellite Systems (GNSSs) remain the principal mean of positioning in many applications and systems, but in several types of environment, the performance of standalone receivers is degraded. Although many works show the benefits of the integration between GNSS and Inertial Navigation Systems (INSs), tightly-coupled architectures are mainly implemented in professional devices and are based on high-grade Inertial Measurement Units (IMUs). This paper investigates the performance improvements enabled by the tight integration, using low-cost sensors and a mass-market GNSS receiver. Performance is assessed through a series of tests carried out in real urban scenarios and is compared against commercial modules, operating in standalone mode or featuring loosely-coupled integrations. The paper describes the developed tight-integration algorithms with a terse mathematical model and assesses their efficacy from a practical perspective.

Disorder effect on heat capacity, self-diffusion coefficient, and choosing best potential model for melting temperature, in gold–copper bimetallic nanocluster with 55 atoms

International Nuclear Information System (INIS)

Taherkhani, Farid; Akbarzadeh, Hamed; Feyzi, Mostafa; Rafiee, Hamid Reza

2015-01-01

Molecular dynamics simulation has been implemented for doping effect on melting temperature, heat capacity, self-diffusion coefficient of gold–copper bimetallic nanostructure with 55 total gold and copper atom numbers and its bulk alloy. Trend of melting temperature for gold–copper bimetallic nanocluster is not same as melting temperature copper–gold bulk alloy. Molecular dynamics simulation of our result regarding bulk melting temperature is consistence with available experimental data. Molecular dynamics simulation shows that melting temperature of gold–copper bimetallic nanocluster increases with copper atom fraction. Semi-empirical potential model and quantum Sutton–Chen potential models do not change melting temperature trend with copper doping of gold–copper bimetallic nanocluster. Self-diffusion coefficient of copper atom is greater than gold atom in gold–copper bimetallic nanocluster. Semi-empirical potential within the tight-binding second moment approximation as new application potential model for melting temperature of gold–copper bulk structure shows better result in comparison with EAM, Sutton–Chen potential, and quantum Sutton–Chen potential models

Disorder effect on heat capacity, self-diffusion coefficient, and choosing best potential model for melting temperature, in gold–copper bimetallic nanocluster with 55 atoms

Energy Technology Data Exchange (ETDEWEB)

Taherkhani, Farid, E-mail: faridtaherkhani@gmail.com, E-mail: f.taherkhani@razi.ac.ir [Razi University, Department of Physical Chemistry (Iran, Islamic Republic of); Akbarzadeh, Hamed [Hakim Sabzevari University, Department of Chemistry (Iran, Islamic Republic of); Feyzi, Mostafa; Rafiee, Hamid Reza [Razi University, Department of Physical Chemistry (Iran, Islamic Republic of)

2015-01-15

Molecular dynamics simulation has been implemented for doping effect on melting temperature, heat capacity, self-diffusion coefficient of gold–copper bimetallic nanostructure with 55 total gold and copper atom numbers and its bulk alloy. Trend of melting temperature for gold–copper bimetallic nanocluster is not same as melting temperature copper–gold bulk alloy. Molecular dynamics simulation of our result regarding bulk melting temperature is consistence with available experimental data. Molecular dynamics simulation shows that melting temperature of gold–copper bimetallic nanocluster increases with copper atom fraction. Semi-empirical potential model and quantum Sutton–Chen potential models do not change melting temperature trend with copper doping of gold–copper bimetallic nanocluster. Self-diffusion coefficient of copper atom is greater than gold atom in gold–copper bimetallic nanocluster. Semi-empirical potential within the tight-binding second moment approximation as new application potential model for melting temperature of gold–copper bulk structure shows better result in comparison with EAM, Sutton–Chen potential, and quantum Sutton–Chen potential models.

Statistical-mechanical lattice models for protein-DNA binding in chromatin

International Nuclear Information System (INIS)

Teif, Vladimir B; Rippe, Karsten

2010-01-01

Statistical-mechanical lattice models for protein-DNA binding are well established as a method to describe complex ligand binding equilibria measured in vitro with purified DNA and protein components. Recently, a new field of applications has opened up for this approach since it has become possible to experimentally quantify genome-wide protein occupancies in relation to the DNA sequence. In particular, the organization of the eukaryotic genome by histone proteins into a nucleoprotein complex termed chromatin has been recognized as a key parameter that controls the access of transcription factors to the DNA sequence. New approaches have to be developed to derive statistical-mechanical lattice descriptions of chromatin-associated protein-DNA interactions. Here, we present the theoretical framework for lattice models of histone-DNA interactions in chromatin and investigate the (competitive) DNA binding of other chromosomal proteins and transcription factors. The results have a number of applications for quantitative models for the regulation of gene expression.

HOCOMOCO: a comprehensive collection of human transcription factor binding sites models

Science.gov (United States)

Kulakovskiy, Ivan V.; Medvedeva, Yulia A.; Schaefer, Ulf; Kasianov, Artem S.; Vorontsov, Ilya E.; Bajic, Vladimir B.; Makeev, Vsevolod J.

2013-01-01

Transcription factor (TF) binding site (TFBS) models are crucial for computational reconstruction of transcription regulatory networks. In existing repositories, a TF often has several models (also called binding profiles or motifs), obtained from different experimental data. Having a single TFBS model for a TF is more pragmatic for practical applications. We show that integration of TFBS data from various types of experiments into a single model typically results in the improved model quality probably due to partial correction of source specific technique bias. We present the Homo sapiens comprehensive model collection (HOCOMOCO, http://autosome.ru/HOCOMOCO/, http://cbrc.kaust.edu.sa/hocomoco/) containing carefully hand-curated TFBS models constructed by integration of binding sequences obtained by both low- and high-throughput methods. To construct position weight matrices to represent these TFBS models, we used ChIPMunk software in four computational modes, including newly developed periodic positional prior mode associated with DNA helix pitch. We selected only one TFBS model per TF, unless there was a clear experimental evidence for two rather distinct TFBS models. We assigned a quality rating to each model. HOCOMOCO contains 426 systematically curated TFBS models for 401 human TFs, where 172 models are based on more than one data source. PMID:23175603

HOCOMOCO: A comprehensive collection of human transcription factor binding sites models

KAUST Repository

Kulakovskiy, Ivan V.; Medvedeva, Yulia A.; Schaefer, Ulf; Kasianov, Artem S.; Vorontsov, Ilya E.; Bajic, Vladimir B.; Makeev, Vsevolod J.

2012-01-01

Transcription factor (TF) binding site (TFBS) models are crucial for computational reconstruction of transcription regulatory networks. In existing repositories, a TF often has several models (also called binding profiles or motifs), obtained from different experimental data. Having a single TFBS model for a TF is more pragmatic for practical applications. We show that integration of TFBS data from various types of experiments into a single model typically results in the improved model quality probably due to partial correction of source specific technique bias. We present the Homo sapiens comprehensive model collection (HOCOMOCO, http://autosome.ru/HOCOMOCO/, http://cbrc.kaust.edu.sa/ hocomoco/) containing carefully hand-curated TFBS models constructed by integration of binding sequences obtained by both low- and high-throughput methods. To construct position weight matrices to represent these TFBS models, we used ChIPMunk software in four computational modes, including newly developed periodic positional prior mode associated with DNA helix pitch. We selected only one TFBS model per TF, unless there was a clear experimental evidence for two rather distinct TFBS models. We assigned a quality rating to each model. HOCOMOCO contains 426 systematically curated TFBS models for 401 human TFs, where 172 models are based on more than one data source. The Author(s) 2012.

HOCOMOCO: A comprehensive collection of human transcription factor binding sites models

KAUST Repository

Kulakovskiy, Ivan V.

2012-11-21

Transcription factor (TF) binding site (TFBS) models are crucial for computational reconstruction of transcription regulatory networks. In existing repositories, a TF often has several models (also called binding profiles or motifs), obtained from different experimental data. Having a single TFBS model for a TF is more pragmatic for practical applications. We show that integration of TFBS data from various types of experiments into a single model typically results in the improved model quality probably due to partial correction of source specific technique bias. We present the Homo sapiens comprehensive model collection (HOCOMOCO, http://autosome.ru/HOCOMOCO/, http://cbrc.kaust.edu.sa/ hocomoco/) containing carefully hand-curated TFBS models constructed by integration of binding sequences obtained by both low- and high-throughput methods. To construct position weight matrices to represent these TFBS models, we used ChIPMunk software in four computational modes, including newly developed periodic positional prior mode associated with DNA helix pitch. We selected only one TFBS model per TF, unless there was a clear experimental evidence for two rather distinct TFBS models. We assigned a quality rating to each model. HOCOMOCO contains 426 systematically curated TFBS models for 401 human TFs, where 172 models are based on more than one data source. The Author(s) 2012.

Interpretation of Ocular Melanin Drug Binding Assays. Alternatives to the Model of Multiple Classes of Independent Sites.

Science.gov (United States)

Manzanares, José A; Rimpelä, Anna-Kaisa; Urtti, Arto

2016-04-04

Melanin has a high binding affinity for a wide range of drugs. The determination of the melanin binding capacity and its binding affinity are important, e.g., in the determination of the ocular drug distribution, the prediction of drug effects in the eye, and the trans-scleral drug delivery. The binding parameters estimated from a given data set vary significantly when using different isotherms or different nonlinear fitting methods. In this work, the commonly used bi-Langmuir isotherm, which assumes two classes of independent sites, is confronted with the Sips isotherm. Direct, log-log, and Scatchard plots are used, and the interpretation of the binding curves in the latter is critically analyzed. In addition to the goodness of fit, the emphasis is placed on the physical meaning of the binding parameters. The bi-Langmuir model imposes a bimodal distribution of binding energies for the sites on the melanin granules, but the actual distribution is most likely continuous and unimodal, as assumed by the Sips isotherm. Hence, the latter describes more accurately the distribution of binding energies and also the experimental results of melanin binding to drugs and metal ions. Simulations are used to show that the existence of two classes of sites cannot be confirmed on the sole basis of the shape of the binding curve in the Scatchard plot, and that serious doubts may appear on the meaning of the binding parameters of the bi-Langmuir model. Experimental results of melanin binding to chloroquine and metoprolol are used to illustrate the importance of the choice of the binding isotherm and of the method used to evaluate the binding parameters.

ADVANCED FRACTURING TECHNOLOGY FOR TIGHT GAS: AN EAST TEXAS FIELD DEMONSTRATION

Energy Technology Data Exchange (ETDEWEB)

Mukul M. Sharma

2005-03-01

The primary objective of this research was to improve completion and fracturing practices in gas reservoirs in marginal plays in the continental United States. The Bossier Play in East Texas, a very active tight gas play, was chosen as the site to develop and test the new strategies for completion and fracturing. Figure 1 provides a general location map for the Dowdy Ranch Field, where the wells involved in this study are located. The Bossier and other tight gas formations in the continental Unites States are marginal plays in that they become uneconomical at gas prices below $2.00 MCF. It was, therefore, imperative that completion and fracturing practices be optimized so that these gas wells remain economically attractive. The economic viability of this play is strongly dependent on the cost and effectiveness of the hydraulic fracturing used in its well completions. Water-fracs consisting of proppant pumped with un-gelled fluid is the type of stimulation used in many low permeability reservoirs in East Texas and throughout the United States. The use of low viscosity Newtonian fluids allows the creation of long narrow fractures in the reservoir, without the excessive height growth that is often seen with cross-linked fluids. These low viscosity fluids have poor proppant transport properties. Pressure transient tests run on several wells that have been water-fractured indicate a long effective fracture length with very low fracture conductivity even when large amounts of proppant are placed in the formation. A modification to the water-frac stimulation design was needed to transport proppant farther out into the fracture. This requires suspending the proppant until the fracture closes without generating excessive fracture height. A review of fracture diagnostic data collected from various wells in different areas (for conventional gel and water-fracs) suggests that effective propped lengths for the fracture treatments are sometimes significantly shorter than those

Mutational analysis of the high-affinity zinc binding site validates a refined human dopamine transporter homology model.

Directory of Open Access Journals (Sweden)

Thomas Stockner

Full Text Available The high-resolution crystal structure of the leucine transporter (LeuT is frequently used as a template for homology models of the dopamine transporter (DAT. Although similar in structure, DAT differs considerably from LeuT in a number of ways: (i when compared to LeuT, DAT has very long intracellular amino and carboxyl termini; (ii LeuT and DAT share a rather low overall sequence identity (22% and (iii the extracellular loop 2 (EL2 of DAT is substantially longer than that of LeuT. Extracellular zinc binds to DAT and restricts the transporter's movement through the conformational cycle, thereby resulting in a decrease in substrate uptake. Residue H293 in EL2 praticipates in zinc binding and must be modelled correctly to allow for a full understanding of its effects. We exploited the high-affinity zinc binding site endogenously present in DAT to create a model of the complete transmemberane domain of DAT. The zinc binding site provided a DAT-specific molecular ruler for calibration of the model. Our DAT model places EL2 at the transporter lipid interface in the vicinity of the zinc binding site. Based on the model, D206 was predicted to represent a fourth co-ordinating residue, in addition to the three previously described zinc binding residues H193, H375 and E396. This prediction was confirmed by mutagenesis: substitution of D206 by lysine and cysteine affected the inhibitory potency of zinc and the maximum inhibition exerted by zinc, respectively. Conversely, the structural changes observed in the model allowed for rationalizing the zinc-dependent regulation of DAT: upon binding, zinc stabilizes the outward-facing state, because its first coordination shell can only be completed in this conformation. Thus, the model provides a validated solution to the long extracellular loop and may be useful to address other aspects of the transport cycle.

Potential evaluation of CO2 storage and enhanced oil recovery of tight oil reservoir in the Ordos Basin, China.

Science.gov (United States)

Tian, Xiaofeng; Cheng, Linsong; Cao, Renyi; Zhang, Miaoyi; Guo, Qiang; Wang, Yimin; Zhang, Jian; Cui, Yu

2015-07-01

Carbon -di-oxide (CO2) is regarded as the most important greenhouse gas to accelerate climate change and ocean acidification. The Chinese government is seeking methods to reduce anthropogenic CO2 gas emission. CO2 capture and geological storage is one of the main methods. In addition, injecting CO2 is also an effective method to replenish formation energy in developing tight oil reservoirs. However, exiting methods to estimate CO2 storage capacity are all based on the material balance theory. This was absolutely correct for normal reservoirs. However, as natural fractures widely exist in tight oil reservoirs and majority of them are vertical ones, tight oil reservoirs are not close. Therefore, material balance theory is not adaptive. In the present study, a new method to calculate CO2 storage capacity is presented. The CO2 effective storage capacity, in this new method, consisted of free CO2, CO2 dissolved in oil and CO2 dissolved in water. Case studies of tight oil reservoir from Ordos Basin was conducted and it was found that due to far lower viscosity of CO2 and larger solubility in oil, CO2 could flow in tight oil reservoirs more easily. As a result, injecting CO2 in tight oil reservoirs could obviously enhance sweep efficiency by 24.5% and oil recovery efficiency by 7.5%. CO2 effective storage capacity of Chang 7 tight oil reservoir in Longdong area was 1.88 x 10(7) t. The Chang 7 tight oil reservoir in Ordos Basin was estimated to be 6.38 x 10(11) t. As tight oil reservoirs were widely distributed in Songliao Basin, Sichuan Basin and so on, geological storage capacity of CO2 in China is potential.

Gaussian-Based Smooth Dielectric Function: A Surface-Free Approach for Modeling Macromolecular Binding in Solvents

Directory of Open Access Journals (Sweden)

Arghya Chakravorty

2018-03-01

Full Text Available Conventional modeling techniques to model macromolecular solvation and its effect on binding in the framework of Poisson-Boltzmann based implicit solvent models make use of a geometrically defined surface to depict the separation of macromolecular interior (low dielectric constant from the solvent phase (high dielectric constant. Though this simplification saves time and computational resources without significantly compromising the accuracy of free energy calculations, it bypasses some of the key physio-chemical properties of the solute-solvent interface, e.g., the altered flexibility of water molecules and that of side chains at the interface, which results in dielectric properties different from both bulk water and macromolecular interior, respectively. Here we present a Gaussian-based smooth dielectric model, an inhomogeneous dielectric distribution model that mimics the effect of macromolecular flexibility and captures the altered properties of surface bound water molecules. Thus, the model delivers a smooth transition of dielectric properties from the macromolecular interior to the solvent phase, eliminating any unphysical surface separating the two phases. Using various examples of macromolecular binding, we demonstrate its utility and illustrate the comparison with the conventional 2-dielectric model. We also showcase some additional abilities of this model, viz. to account for the effect of electrolytes in the solution and to render the distribution profile of water across a lipid membrane.

Comparison of the effects of local cryotherapy and passive cross-body stretch on extensibility in subjects with posterior shoulder tightness.

Science.gov (United States)

Park, Kyue-Nam; Kwon, Oh-Yun; Weon, Jong-Hyuck; Choung, Sung-Dae; Kim, Si-Hyun

2014-01-01

The objective was to compare the immediate effects of local cryotherapy (LC) and passive cross-body stretch on the extensibility of the posterior shoulder muscle in individuals with posterior shoulder tightness. Eighty-seven healthy subjects with a between-shoulder difference in internal rotation (IR) range of motion (ROM) greater than 10° were randomly divided into three groups: LC group, stretching group, and control group (n = 29 in each group). Subjects in the LC group received LC on infraspinatus and posterior deltoid muscles and subjects in the stretching group performed passive cross-body stretch. Stretch sensation was measured at the end range of passive IR and horizontal adduction (HA) using numerical rating scale, and the pressure pain threshold (PPT) at the infraspinatus and posterior deltoid muscles was measured using pressure algometry. Passive and active ROM of IR and HA of the glenohumeral joint were measured using an inclinometer. All measurements were performed at pre-intervention, post- intervention, and 10-min follow-up. Stretch sensation was significantly decreased and PPT was significantly increased in the LC and stretching groups at post-intervention, and these effects were maintained at 10-min follow-up, compared to the control group. Both the LC group and stretching group had a significantly greater increase in passive and active ROM of IR and HA, compared to the control group at post-intervention and 10-min follow-up. However, there were no significant differences in stretch sensation, PPT, or ROM of IR and HA between the LC group and stretching group. LC can be used to decrease the stretch sensation and increase PPT and ROM of IR and HA as much as a stretching exercise. LC could be an alternative method for increasing the restricted ROM of glenohumeral IR and HA for individuals with posterior shoulder tightness, especially for patients and sports players who have severe stretching discomfort. Key PointsLocal cryotherapy (LC) decreased the

msCentipede: Modeling Heterogeneity across Genomic Sites and Replicates Improves Accuracy in the Inference of Transcription Factor Binding.

Directory of Open Access Journals (Sweden)

Anil Raj

Full Text Available Understanding global gene regulation depends critically on accurate annotation of regulatory elements that are functional in a given cell type. CENTIPEDE, a powerful, probabilistic framework for identifying transcription factor binding sites from tissue-specific DNase I cleavage patterns and genomic sequence content, leverages the hypersensitivity of factor-bound chromatin and the information in the DNase I spatial cleavage profile characteristic of each DNA binding protein to accurately infer functional factor binding sites. However, the model for the spatial profile in this framework fails to account for the substantial variation in the DNase I cleavage profiles across different binding sites. Neither does it account for variation in the profiles at the same binding site across multiple replicate DNase I experiments, which are increasingly available. In this work, we introduce new methods, based on multi-scale models for inhomogeneous Poisson processes, to account for such variation in DNase I cleavage patterns both within and across binding sites. These models account for the spatial structure in the heterogeneity in DNase I cleavage patterns for each factor. Using DNase-seq measurements assayed in a lymphoblastoid cell line, we demonstrate the improved performance of this model for several transcription factors by comparing against the Chip-seq peaks for those factors. Finally, we explore the effects of DNase I sequence bias on inference of factor binding using a simple extension to our framework that allows for a more flexible background model. The proposed model can also be easily applied to paired-end ATAC-seq and DNase-seq data. msCentipede, a Python implementation of our algorithm, is available at http://rajanil.github.io/msCentipede.

msCentipede: Modeling Heterogeneity across Genomic Sites and Replicates Improves Accuracy in the Inference of Transcription Factor Binding.

Science.gov (United States)

Raj, Anil; Shim, Heejung; Gilad, Yoav; Pritchard, Jonathan K; Stephens, Matthew

2015-01-01

Understanding global gene regulation depends critically on accurate annotation of regulatory elements that are functional in a given cell type. CENTIPEDE, a powerful, probabilistic framework for identifying transcription factor binding sites from tissue-specific DNase I cleavage patterns and genomic sequence content, leverages the hypersensitivity of factor-bound chromatin and the information in the DNase I spatial cleavage profile characteristic of each DNA binding protein to accurately infer functional factor binding sites. However, the model for the spatial profile in this framework fails to account for the substantial variation in the DNase I cleavage profiles across different binding sites. Neither does it account for variation in the profiles at the same binding site across multiple replicate DNase I experiments, which are increasingly available. In this work, we introduce new methods, based on multi-scale models for inhomogeneous Poisson processes, to account for such variation in DNase I cleavage patterns both within and across binding sites. These models account for the spatial structure in the heterogeneity in DNase I cleavage patterns for each factor. Using DNase-seq measurements assayed in a lymphoblastoid cell line, we demonstrate the improved performance of this model for several transcription factors by comparing against the Chip-seq peaks for those factors. Finally, we explore the effects of DNase I sequence bias on inference of factor binding using a simple extension to our framework that allows for a more flexible background model. The proposed model can also be easily applied to paired-end ATAC-seq and DNase-seq data. msCentipede, a Python implementation of our algorithm, is available at http://rajanil.github.io/msCentipede.

Numerical Investigation of Cross Flow Phenomena in a Tight-Lattice Rod Bundle Using Advanced Interface Tracking Method

Science.gov (United States)

Zhang, Weizhong; Yoshida, Hiroyuki; Ose, Yasuo; Ohnuki, Akira; Akimoto, Hajime; Hotta, Akitoshi; Fujimura, Ken

In relation to the design of an innovative FLexible-fuel-cycle Water Reactor (FLWR), investigation of thermal-hydraulic performance in tight-lattice rod bundles of the FLWR is being carried out at Japan Atomic Energy Agency (JAEA). The FLWR core adopts a tight triangular lattice arrangement with about 1 mm gap clearance between adjacent fuel rods. In view of importance of accurate prediction of cross flow between subchannels in the evaluation of the boiling transition (BT) in the FLWR core, this study presents a statistical evaluation of numerical simulation results obtained by a detailed two-phase flow simulation code, TPFIT, which employs an advanced interface tracking method. In order to clarify mechanisms of cross flow in such tight lattice rod bundles, the TPFIT is applied to simulate water-steam two-phase flow in two modeled subchannels. Attention is focused on instantaneous fluctuation characteristics of cross flow. With the calculation of correlation coefficients between differential pressure and gas/liquid mixing coefficients, time scales of cross flow are evaluated, and effects of mixing section length, flow pattern and gap spacing on correlation coefficients are investigated. Differences in mechanism between gas and liquid cross flows are pointed out.

Binding, uptake, and transport of hypericin by Caco-2 cell monolayers.

Science.gov (United States)

Sattler, S; Schaefer, U; Schneider, W; Hoelzl, J; Lehr, C M

1997-10-01

The biological evaluation of hypericin in various test models is hampered by its very poor water solubility. In the present study cyclodextrin formulations and liposomal preparations were investigated for improved delivery and solubility of hypericin in aqueous buffer systems. Caco-2 cells, grown to tight monolayers on 96-well tissue culture plates as well as on Transwell polycarbonate filters, were used to study the membrane binding and the epithelial transport of hypericin. Cumulative transport of hypericin, which could not be measured without the use of cyclodextrins, in apical-to-basolateral direction from cyclodextrin-hypericin buffer solutions was 3-5% at 37 degrees C and approximately 0.12% at 4 degrees C after 5 h. After an incubation time of 1 h at 37 and 4 degrees C, 12.7% +/- 2.6% and 6.5% +/- 0.8%, respectively, of hypericin were found to be bound to or taken up by Caco-2 cells. Liposomal formulations markedly increased the solubility of hypericin in Krebs-Ringer buffer, but there was no effect observed on the binding and transport of hypericin delivered by liposomes in the Caco-2 cell model. Due to the fluorescence properties of hypericin, its interaction with the cells could be visualized by confocal laser scanning microscopy. The results indicate that a significant accumulation of the drug in the cell membrane and the cell nucleus membrane takes place. We conclude that hypericin is absorbed through the intestinal epithelium by passive transcellular diffusion and that increasing its solubility by cyclodextrin appears as a promising approach to increase its oral bioavailability for pharmaceutical formulations.

Predicting protein-binding RNA nucleotides with consideration of binding partners.

Science.gov (United States)

Tuvshinjargal, Narankhuu; Lee, Wook; Park, Byungkyu; Han, Kyungsook

2015-06-01

In recent years several computational methods have been developed to predict RNA-binding sites in protein. Most of these methods do not consider interacting partners of a protein, so they predict the same RNA-binding sites for a given protein sequence even if the protein binds to different RNAs. Unlike the problem of predicting RNA-binding sites in protein, the problem of predicting protein-binding sites in RNA has received little attention mainly because it is much more difficult and shows a lower accuracy on average. In our previous study, we developed a method that predicts protein-binding nucleotides from an RNA sequence. In an effort to improve the prediction accuracy and usefulness of the previous method, we developed a new method that uses both RNA and protein sequence data. In this study, we identified effective features of RNA and protein molecules and developed a new support vector machine (SVM) model to predict protein-binding nucleotides from RNA and protein sequence data. The new model that used both protein and RNA sequence data achieved a sensitivity of 86.5%, a specificity of 86.2%, a positive predictive value (PPV) of 72.6%, a negative predictive value (NPV) of 93.8% and Matthews correlation coefficient (MCC) of 0.69 in a 10-fold cross validation; it achieved a sensitivity of 58.8%, a specificity of 87.4%, a PPV of 65.1%, a NPV of 84.2% and MCC of 0.48 in independent testing. For comparative purpose, we built another prediction model that used RNA sequence data alone and ran it on the same dataset. In a 10 fold-cross validation it achieved a sensitivity of 85.7%, a specificity of 80.5%, a PPV of 67.7%, a NPV of 92.2% and MCC of 0.63; in independent testing it achieved a sensitivity of 67.7%, a specificity of 78.8%, a PPV of 57.6%, a NPV of 85.2% and MCC of 0.45. In both cross-validations and independent testing, the new model that used both RNA and protein sequences showed a better performance than the model that used RNA sequence data alone in

Microscopic theory of substrate-induced gap effect on real AFM ...

Indian Academy of Sciences (India)

Sivabrata Sahu

Corresponding author. E-mail: gcr@iopb.res.in. Published online 24 June 2017. Abstract. We address here a tight-binding model study of frequency-dependent real part of antiferromagnetic susceptibility for the graphene systems. The Hamiltonian consists of electron hopping upto third nearest-neighbours, substrate and ...

Effects of topical steroids on tight junction proteins and spongiosis in esophageal epithelia of patients with eosinophilic esophagitis.

Science.gov (United States)

Katzka, David A; Tadi, Ravikanth; Smyrk, Thomas C; Katarya, Eesha; Sharma, Anamay; Geno, Deborah M; Camilleri, Michael; Iyer, Prasad G; Alexander, Jeffrey A; Buttar, Navtej S

2014-11-01

The allergic response associated with eosinophilic esophagitis (EoE) occurs when food antigens permeate tight junction-mediated epithelial dilated intercellular spaces. We assessed whether levels of tight junction proteins correlate with the dilation of intercellular spaces (spongiosis) and the effects of topical steroids on these parameters. We assessed esophageal biopsy samples from 10 patients with active EoE treated with topical fluticasone, 10 untreated patients, and 10 patients without esophageal disease (controls) for degree of spongiosis. Immunohistochemical assays were used to determine the levels of the tight junction proteins filaggrin, zonula occludens (ZO)-1, ZO-2, ZO-3, and claudin-1. Histology and immunohistochemistry results were assessed blindly, with levels of tight junction proteins and degree of spongiosis rated on scales of 0 to 3. The mean degrees of spongiosis in untreated and treated patients with EoE were 1.3 and 0.4, respectively (P = .016). Esophageal epithelia did not stain significantly for ZO-1 or ZO-2. Filaggrin was observed in a predominant cytoplasmic pattern, compared with the cytoplasmic and membranous patterns of ZO-3 and claudin-1. In biopsy specimens from patients with active EoE, the mean staining intensities for filaggrin, ZO-3, and claudin-1 were 1.6, 1.4, and 0.7, respectively. In biopsy specimens from patients treated with fluticasone, levels of filaggrin, ZO-3, and claudin-1 were 2.8 (P = .002 compared with untreated patients), 1.7 (P = .46 compared with untreated patients), and 1.3 (P = .25 compared with untreated patients), respectively. The correlation between the level of filaggrin and the degree of spongiosis was r = 0.23, and between ZO-3 staining and the degree of spongiosis was r = .016 (P = .001 for filaggrin vs ZO-3 staining). Filaggrin, ZO-3, and claudin-1 (but not ZO-1 or ZO-2) are detected in the esophageal mucosa of patients with EoE treated with steroids and individuals without esophageal disease

Modeling the Alzheimer Abeta17-42 fibril architecture: tight intermolecular sheet-sheet association and intramolecular hydrated cavities.

Science.gov (United States)

Zheng, Jie; Jang, Hyunbum; Ma, Buyong; Tsai, Chung-Jun; Nussinov, Ruth

2007-11-01

We investigate Abeta(17-42) protofibril structures in solution using molecular dynamics simulations. Recently, NMR and computations modeled the Abeta protofibril as a longitudinal stack of U-shaped molecules, creating an in-parallel beta-sheet and loop spine. Here we study the molecular architecture of the fibril formed by spine-spine association. We model in-register intermolecular beta-sheet-beta-sheet associations and study the consequences of Alzheimer's mutations (E22G, E22Q, E22K, and M35A) on the organization. We assess the structural stability and association force of Abeta oligomers with different sheet-sheet interfaces. Double-layered oligomers associating through the C-terminal-C-terminal interface are energetically more favorable than those with the N-terminal-N-terminal interface, although both interfaces exhibit high structural stability. The C-terminal-C-terminal interface is essentially stabilized by hydrophobic and van der Waals (shape complementarity via M35-M35 contacts) intermolecular interactions, whereas the N-terminal-N-terminal interface is stabilized by hydrophobic and electrostatic interactions. Hence, shape complementarity, or the "steric zipper" motif plays an important role in amyloid formation. On the other hand, the intramolecular Abeta beta-strand-loop-beta-strand U-shaped motif creates a hydrophobic cavity with a diameter of 6-7 A, allowing water molecules and ions to conduct through. The hydrated hydrophobic cavities may allow optimization of the sheet association and constitute a typical feature of fibrils, in addition to the tight sheet-sheet association. Thus, we propose that Abeta fiber architecture consists of alternating layers of tight packing and hydrated cavities running along the fibrillar axis, which might be possibly detected by high-resolution imaging.

Three-dimensional model of a selective theophylline-binding RNA molecule

Energy Technology Data Exchange (ETDEWEB)

Tung, Chang-Shung; Oprea, T.I.; Hummer, G.; Garcia, A.E.

1995-07-01

We propose a three-dimensional (3D) model for an RNA molecule that selectively binds theophylline but not caffeine. This RNA, which was found using SELEX [Jenison, R.D., et al., Science (1994) 263:1425] is 10,000 times more specific for theophylline (Kd=320 nM) than for caffeine (Kd=3.5 mM), although the two ligands are identical except for a methyl group substituted at N7 (present only in caffeine). The binding affinity for ten xanthine-based ligands was used to derive a Comparative Molecular Field Analysis (CoMFA) model (R{sup 2} = 0.93 for 3 components, with cross-validated R{sup 2} of 0.73), using the SYBYL and GOLPE programs. A pharmacophoric map was generated to locate steric and electrostatic interactions between theophylline and the RNA binding site. This information was used to identify putative functional groups of the binding pocket and to generate distance constraints. Based on a model for the secondary structure (Jenison et al., idem), the 3D structure of this RNA was then generated using the following method: each helical region of the RNA molecule was treated as a rigid body; single-stranded loops with specific end-to-end distances were generated. The structures of RNA-xanthine complexes were studied using a modified Monte Carlo algorithm. The detailed structure of an RNA-ligand complex model, as well as possible explanations for the theophylline selectivity will be discussed.

Binding energy effects in cascade evolution and sputtering

International Nuclear Information System (INIS)

Robinson, M.T.

1995-06-01

The MARLOWE model was extended to include a binding energy dependent on the local crystalline order, so that atoms are bound less strongly to their lattice sites near surfaces or associated damage. Sputtering and cascade evolution were studied on the examples of self-ion irradiations of Cu and Au monocrystals. In cascades, the mean binding energy is reduced ∼8% in Cu with little dependence on the initial recoil energy; in Au, it is reduced ∼9% at 1 keV and ∼15% at 100 keV. In sputtering, the mean binding energy is reduced ∼8% in Cu and ∼15% in Au with little energy dependence; the yields are increased about half as much. Most sites from which sputtered atoms originate are isolated in both metals. Small clusters of such sites occur in Cu, but there are some large clusters in Au, especially in [111] targets. There are always more large clusters with damage-dependent binding than with a constant binding energy, but only a few clusters are compact enough to be regarded as pits

Tight-coupling of groundwater flow and transport modelling engines with spatial databases and GIS technology: a new approach integrating Feflow and ArcGIS

Directory of Open Access Journals (Sweden)

Ezio Crestaz

2012-09-01

Full Text Available Implementation of groundwater flow and transport numerical models is generally a challenge, time-consuming and financially-demanding task, in charge to specialized modelers and consulting firms. At a later stage, within clearly stated limits of applicability, these models are often expected to be made available to less knowledgeable personnel to support/design and running of predictive simulations within more familiar environments than specialized simulation systems. GIS systems coupled with spatial databases appear to be ideal candidates to address problem above, due to their much wider diffusion and expertise availability. Current paper discusses the issue from a tight-coupling architecture perspective, aimed at integration of spatial databases, GIS and numerical simulation engines, addressing both observed and computed data management, retrieval and spatio-temporal analysis issues. Observed data can be migrated to the central database repository and then used to set up transient simulation conditions in the background, at run time, while limiting additional complexity and integrity failure risks as data duplication during data transfer through proprietary file formats. Similarly, simulation scenarios can be set up in a familiar GIS system and stored to spatial database for later reference. As numerical engine is tightly coupled with the GIS, simulations can be run within the environment and results themselves saved to the database. Further tasks, as spatio-temporal analysis (i.e. for postcalibration auditing scopes, cartography production and geovisualization, can then be addressed using traditional GIS tools. Benefits of such an approach include more effective data management practices, integration and availability of modeling facilities in a familiar environment, streamlining spatial analysis processes and geovisualization requirements for the non-modelers community. Major drawbacks include limited 3D and time-dependent support in

Pre-Darcy flow in tight and shale formations

Science.gov (United States)

Dejam, Morteza; Hassanzadeh, Hassan; Chen, Zhangxin

2017-11-01

There are evidences that the fluid flow in tight and shale formations does not follow Darcy law, which is identified as pre-Darcy flow. Here, the unsteady linear flow of a slightly compressible fluid under the action of pre-Darcy flow is modeled and a generalized Boltzmann transformation technique is used to solve the corresponding highly nonlinear diffusivity equation analytically. The effect of pre-Darcy flow on the pressure diffusion in a homogenous formation is studied in terms of the nonlinear exponent, m, and the threshold pressure gradient, G1. In addition, the pressure gradient, flux, and cumulative production per unit area for different m and G1 are compared with the classical solution of the diffusivity equation based on Darcy flow. Department of Petroleum Engineering in College of Engineering and Applied Science at University of Wyoming and NSERC/AI-EES(AERI)/Foundation CMG and AITF (iCORE) Chairs in Department of Chemical and Petroleum Engineering at University of Calgary.

Specific binding of a dihydropyrimidinone derivative with DNA: Spectroscopic, calorimetric and modeling investigations

International Nuclear Information System (INIS)

Wang Gongke; Yan Changling; Wang Dongchao; Li Dan; Lu Yan

2012-01-01

One of the dihydropyrimidinone derivative 5-(ethoxycarbonyl)-6-methyl-4-(4-methoxyphenyl) -3,4-dihydropyrimidin-2(1H)-one (EMMD) was synthesized, and its binding properties with calf-thymus DNA (ctDNA) were investigated using spectroscopic, viscometric, isothermal titration calorimetric (ITC) and molecular modeling techniques. Fluorescence spectra suggested that the fluorescence enhancement of the binding interaction of EMMD to ctDNA was a static process with ground state complex formation. The binding constant determined with spectroscopic titration and ITC was found to be in the same order of 10 4 M −1 . According to the results of the viscosity analysis, fluorescence competitive binding experiment, fluorescence quenching studies, absorption spectral and ITC investigations, it can be concluded that EMMD is intercalative binding to ctDNA. Furthermore, the results of molecular modeling confirmed those obtained from spectroscopic, viscosimetric and ITC investigations. Additionally, ITC studies also indicated that the binding interaction is predominantly enthalpy driven. - Highlights: ► Medically important dihydropyrimidinones derivative EMMD is synthesized. ► EMMD is intercalative binding into ctDNA helix. ► Hydrogen bonding may play an essential role in the binding of EMCD with ctDNA. ► This binding interaction is predominantly enthalpy driven.

The media of sociology: tight or loose translations?

Science.gov (United States)

Guggenheim, Michael

2015-06-01

Sociologists have increasingly come to recognize that the discipline has unduly privileged textual representations, but efforts to incorporate visual and other media are still only in their beginning. This paper develops an analysis of the ways objects of knowledge are translated into other media, in order to understand the visual practices of sociology and to point out unused possibilities. I argue that the discourse on visual sociology, by assuming that photographs are less objective than text, is based on an asymmetric media-determinism and on a misleading notion of objectivity. Instead, I suggest to analyse media with the concept of translations. I introduce several kinds of translations, most centrally the distinction between tight and loose ones. I show that many sciences, such as biology, focus on tight translations, using a variety of media and manipulating both research objects and representations. Sociology, in contrast, uses both tight and loose translations, but uses the latter only for texts. For visuals, sociology restricts itself to what I call 'the documentary': focusing on mechanical recording technologies without manipulating either the object of research or the representation. I conclude by discussing three rare examples of what is largely excluded in sociology: visual loose translations, visual tight translations based on non-mechanical recording technologies, and visual tight translations based on mechanical recording technologies that include the manipulation of both object and representation. © London School of Economics and Political Science 2015.

Conditioned medium from LS 174T goblet cells treated with oxyresveratrol strengthens tight junctions in Caco-2 cells.

Science.gov (United States)

Hwang, Dahyun; Jo, HyunA; Hwang, Seonwook; Kim, Jeong-Keun; Kim, In-Ho; Lim, Young-Hee

2017-01-01

Strengthening of intestinal tight junctions provides an effective barrier from the external environment. Goblet cell-derived trefoil factor 3 (TFF3) increases transepithelial resistance by upregulating the expression of tight junction proteins. Oxyresveratrol (OXY) is a hydroxyl-substituted stilbene found in the roots, leaves, stems, and fruit of many plants and known to have various biological activities. In this study, we investigated the strengthening effect of OXY on intestinal tight junctions through stimulation of TFF production in goblet cells. We prepared conditioned medium from LS 174T goblet cells treated with OXY (GCO-CM) and investigated the effect of GCO-CM on strengthening tight junctions of Caco-2 cells. The mRNA and protein expression levels of major tight junction components (claudin-1, occludin, and ZO-1) were measured by quantitative real-time PCR and western blotting, respectively. Transepithelial electric resistance (TEER) was measured using an ohm/V meter. Monolayer permeability was evaluated by paracellular transport of fluorescein isothiocyanate-dextran. OXY showed a strong antioxidant activity. It significantly increased the expression level of TFF3 in LS 174T goblet cells. GCO-CM prepared by treatment with 2.5, 5, and 10μg/ml OXY did not show cytotoxicity in Caco-2 cells. GCO-CM increased the mRNA and protein expression levels of claudin-1, occludin, and ZO-1. It also significantly increased tight junction integrity and reduced permeability in a dose-dependent manner. OXY stimulates the expression of TFF3 in goblet cells, which might increase the integrity of the intestinal tight junction barrier. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Effect of increasing length on the electronic transport of an armchair graphene nano-ribbons

Directory of Open Access Journals (Sweden)

Sh Aghamiri Esfahani

2015-12-01

Full Text Available In this research, we have investigated the effect of increasing length on the electronic transport of an armchair graphene nano-ribbons with nitrogen atom impurity and without impurity. The semi-infinite, one-dimensional molecular systems are connected to two electrodes and the electron-electron interaction is ignored. The system is described by a simple tight binding model. All calculations are based on the Green's function and Landauer–Buttiker approach, and the electrodes are described in a wide band approximation.

Results on a Binding Neuron Model and Their Implications for Modified Hourglass Model for Neuronal Network

Directory of Open Access Journals (Sweden)

Viswanathan Arunachalam

2013-01-01

Full Text Available The classical models of single neuron like Hodgkin-Huxley point neuron or leaky integrate and fire neuron assume the influence of postsynaptic potentials to last till the neuron fires. Vidybida (2008 in a refreshing departure has proposed models for binding neurons in which the trace of an input is remembered only for a finite fixed period of time after which it is forgotten. The binding neurons conform to the behaviour of real neurons and are applicable in constructing fast recurrent networks for computer modeling. This paper develops explicitly several useful results for a binding neuron like the firing time distribution and other statistical characteristics. We also discuss the applicability of the developed results in constructing a modified hourglass network model in which there are interconnected neurons with excitatory as well as inhibitory inputs. Limited simulation results of the hourglass network are presented.

Tight Network Topology Dependent Bounds on Rounds of Communication

OpenAIRE

Chattopadhyay, Arkadev; Langberg, Michael; Li, Shi; Rudra, Atri

2016-01-01

We prove tight network topology dependent bounds on the round complexity of computing well studied $k$-party functions such as set disjointness and element distinctness. Unlike the usual case in the CONGEST model in distributed computing, we fix the function and then vary the underlying network topology. This complements the recent such results on total communication that have received some attention. We also present some applications to distributed graph computation problems. Our main contri...

Modelling the interdependence between the stoichiometry of receptor oligomerization and ligand binding for a coexisting dimer/tetramer receptor system.

Science.gov (United States)

Rovira, X; Vivó, M; Serra, J; Roche, D; Strange, P G; Giraldo, J

2009-01-01

Many G protein-coupled receptors have been shown to exist as oligomers, but the oligomerization state and the effects of this on receptor function are unclear. For some G protein-coupled receptors, in ligand binding assays, different radioligands provide different maximal binding capacities. Here we have developed mathematical models for co-expressed dimeric and tetrameric species of receptors. We have considered models where the dimers and tetramers are in equilibrium and where they do not interconvert and we have also considered the potential influence of the ligands on the degree of oligomerization. By analogy with agonist efficacy, we have considered ligands that promote, inhibit or have no effect on oligomerization. Cell surface receptor expression and the intrinsic capacity of receptors to oligomerize are quantitative parameters of the equations. The models can account for differences in the maximal binding capacities of radioligands in different preparations of receptors and provide a conceptual framework for simulation and data fitting in complex oligomeric receptor situations.

Field and laboratory tests of etched track detectors for 222Rn: summer-vs-winter variations and tightness effects in Maine houses

International Nuclear Information System (INIS)

Hess, C.T.; Fleischer, R.L.; Turner, L.G.

1985-01-01

Effects of tightness of homes of bedrock character on indoor 222 Rn concentrations were sought in 70 homes in the state of Maine by means of four 6- to 8-month-long surveys over a 1.5-yr period. Laboratory experiments were also performed that document the reliability of the track etching system used for the measurements. In this survey the Rn in tight homes was on the average 3.5 times that in drafty ones, and areas with granitic bedrock led to homes having 2.3 times the Rn as for homes on chlorite-biotite-rich bedrock. Winter-to-summer ratios ranged from 0.5-7, and averaged 1.5, implying that surveys of individual homes require a full year of monitoring

Binding modes of dihydroquinoxalinones in a homology model of bradykinin receptor 1.

Science.gov (United States)

Ha, Sookhee N; Hey, Pat J; Ransom, Rick W; Harrell, C Meacham; Murphy, Kathryn L; Chang, Ray; Chen, Tsing-Bau; Su, Dai-Shi; Markowitz, M Kristine; Bock, Mark G; Freidinger, Roger M; Hess, Fred J

2005-05-27

We report the first homology model of human bradykinin receptor B1 generated from the crystal structure of bovine rhodopsin as a template. Using an automated docking procedure, two B1 receptor antagonists of the dihydroquinoxalinone structural class were docked into the receptor model. Site-directed mutagenesis data of the amino acid residues in TM1, TM3, TM6, and TM7 were incorporated to place the compounds in the binding site of the homology model of the human B1 bradykinin receptor. The best pose in agreement with the mutation data was selected for detailed study of the receptor-antagonist interaction. To test the model, the calculated antagonist-receptor binding energy was correlated with the experimentally measured binding affinity (K(i)) for nine dihydroquinoxalinone analogs. The model was used to gain insight into the molecular mechanism for receptor function and to optimize the dihydroquinoxalinone analogs.

Chemical Editing of Macrocyclic Natural Products and Kinetic Profiling Reveal Slow, Tight-Binding Histone Deacetylase Inhibitors with Picomolar Affinities

DEFF Research Database (Denmark)

Kitir, Betül; Maolanon, Alex R.; Ohm, Ragnhild G.

2017-01-01

medicines. Therefore, detailed mechanistic information and precise characterization of the chemical probes used to investigate the effects of HDAC enzymes are vital. We interrogated Nature's arsenal of macrocyclic nonribosomal peptide HDAC inhibitors by chemical synthesis and evaluation of more than 30...... natural products and analogues. This furnished surprising trends in binding affinities for the various macrocycles, which were then exploited for the design of highly potent class I and IIb HDAC inhibitors. Furthermore, thorough kinetic investigation revealed unexpected inhibitory mechanisms of important...

Tight fitting garter springs-MODAR

Energy Technology Data Exchange (ETDEWEB)

Kazimer, D. [Bruce Power, Tiverton, Ontario (Canada)

2011-07-01

Annulus spacers are used in CANDU reactors to maintain the annular gap between two tubes - an inner pressure tube (PT) and the outer calandria tube (CT). Typically four annulus spacers are used in one fuel channel assembly, each at a specified axial position. Bruce Unit 8 and many other CANDU units were constructed with tight-fitting garter springs (TFGS). The TFGS were not designed to be detected or relocated by the conventional tool, Spacer Location And Repositioning (SLAR) processes. Due to non-optimal 'As Left' construction locations for the Bruce Unit 8 TFGS, PT/CT contact has been predicted to occur well prior to its End of Life (EOL). Bruce Power entered a Project with AECL-CRL to design, manufacture and test and implement a new tooling system that would detect and reposition tight fitting annulus spacers. (author)

The apical scaffold big bang binds to spectrins and regulates the growth of Drosophila melanogaster wing discs.

Science.gov (United States)

Forest, Elodie; Logeay, Rémi; Géminard, Charles; Kantar, Diala; Frayssinoux, Florence; Heron-Milhavet, Lisa; Djiane, Alexandre

2018-03-05

During development, cell numbers are tightly regulated, ensuring that tissues and organs reach their correct size and shape. Recent evidence has highlighted the intricate connections between the cytoskeleton and the regulation of the key growth control Hippo pathway. Looking for apical scaffolds regulating tissue growth, we describe that Drosophila melanogaster big bang (Bbg), a poorly characterized multi-PDZ scaffold, controls epithelial tissue growth without affecting epithelial polarity and architecture. bbg -mutant tissues are smaller, with fewer cells that are less apically constricted than normal. We show that Bbg binds to and colocalizes tightly with the β-heavy-Spectrin/Kst subunit at the apical cortex and promotes Yki activity, F-actin enrichment, and the phosphorylation of the myosin II regulatory light chain Spaghetti squash. We propose a model in which the spectrin cytoskeleton recruits Bbg to the cortex, where Bbg promotes actomyosin contractility to regulate epithelial tissue growth. © 2018 Forest et al.

Molecular modeling studies of novel retro-binding tripeptide active-site inhibitors of thrombin.

Science.gov (United States)

Lau, W F; Tabernero, L; Sack, J S; Iwanowicz, E J

1995-08-01

A novel series of retro-binding tripeptide thrombin active-site inhibitors was recently developed (Iwanowicz, E. I. et al. J. Med. Chem. 1994, 37, 2111(1)). It was hypothesized that the binding mode for these inhibitors is similar to that of the first three N-terminal residues of hirudin. This binding hypothesis was subsequently verified when the crystal structure of a member of this series, BMS-183,507 (N-[N-[N-[4-(Aminoiminomethyl)amino[-1-oxobutyl]-L- phenylalanyl]-L-allo-threonyl]-L-phenylalanine, methyl ester), was determined (Taberno, L.J. Mol. Biol. 1995, 246, 14). The methodology for developing the binding models of these inhibitors, the structure-activity relationships (SAR) and modeling studies that led to the elucidation of the proposed binding mode is described. The crystal structure of BMS-183,507/human alpha-thrombin is compared with the crystal structure of hirudin/human alpha-thrombin (Rydel, T.J. et al. Science 1990, 249,227; Rydel, T.J. et al. J. Mol Biol. 1991, 221, 583; Grutter, M.G. et al. EMBO J. 1990, 9, 2361) and with the computational binding model of BMS-183,507.

A new method in predicting productivity of multi-stage fractured horizontal well in tight gas reservoirs

Directory of Open Access Journals (Sweden)

Yunsheng Wei

2016-10-01

Full Text Available The generally accomplished technique for horizontal wells in tight gas reservoirs is by multi-stage hydraulic fracturing, not to mention, the flow characteristics of a horizontal well with multiple transverse fractures are very intricate. Conventional methods, well as an evaluation unit, are difficult to accurately predict production capacity of each fracture and productivity differences between wells with a different number of fractures. Thus, a single fracture sets the minimum evaluation unit, matrix, fractures, and lateral wellbore model that are then combined integrally to approximate horizontal well with multiple transverse hydraulic fractures in tight gas reservoirs. This paper presents a new semi-analytical methodology for predicting the production capacity of a horizontal well with multiple transverse hydraulic fractures in tight gas reservoirs. Firstly, a mathematical flow model used as a medium, which is disturbed by finite conductivity vertical fractures and rectangular shaped boundaries, is established and explained by the Fourier integral transform. Then the idea of a single stage fracture analysis is incorporated to establish linear flow model within a single fracture with a variable rate. The Fredholm integral numerical solution is applicable for the fracture conductivity function. Finally, the pipe flow model along the lateral wellbore is adapted to couple multi-stages fracture mathematical models, and the equation group of predicting productivity of a multi-stage fractured horizontal well. The whole flow process from the matrix to bottom-hole and production interference between adjacent fractures is also established. Meanwhile, the corresponding iterative algorithm of the equations is given. In this case analysis, the productions of each well and fracture are calculated under the different bottom-hole flowing pressure, and this method also contributes to obtaining the distribution of pressure drop and production for every

Characterisation of the effect of ion channel modulators on I1-imidazoline binding sites in bovine adrenal medulla

International Nuclear Information System (INIS)

Musgrave, I.F.; Kotsopoulos, D.; Hughes, R.A.

1998-01-01

Full text: The structure of I 1 -imidazoline binding sites is still unknown and we have proposed that they represent ion channels (i). In these experiments we characterised the effects of the known ion channel modulators methyltriphenylphosphonium (MTPP), 4-aminopyridine (4-AP) and tetraethyl ammonium (TEA) on [ 3 H] clonidine binding in bovine adrenal medullary membranes as these membranes have a relatively well defined I 1 -imidazoline binding site (Molderings et al, 1993). Membranes from bovine adrenal medulla's were prepared by a minor modification of the method of Rapier et al. [ 3 H] Clonidine binding was performed by the method of Ernsberger et al (3), with [ 3 H] clonidine (62 Ci/mmol) used at a final concentration of 5 nM. [ 3 H] Clonidine binding was displaced from bovine adrenal medullary membranes by adrenergic drugs with the order of potency being oxymetazoline > clonidine > moxonidine = idazoxan >> yonimbine. This order of potency is consistent with previous studies of I 1 -imidazoline binding sites (4). Non-linear curve fitting to this data was consistent with a single site model. Both TEA and 4-AP displaced [ H] clonidine with similar potency to its effect on ion channels, TEA having a EC>> of 54 ± 0.3 μM (n=3). The displacement of [ 3 H] clonidine produced by both TEA and 4-AP also fitted to a single site model. Displacement of [ 3 H] clonidine by MTPP fitted a two site model (p 1 -imidazoline binding sites defined with [ 3 H] clonidine may represent ion channels. We have used this data to perform molecular modelling and have determined a common conformation of I 1 -prefering ligands which will aid in the development of I 1 -selective ligands in the future. Copyright (1998) Australian Neuroscience Society

The effect of tight glycaemic control, during and after cardiac surgery, on patient mortality and morbidity: A systematic review and meta-analysis

Directory of Open Access Journals (Sweden)

Carter Gordon H

2011-01-01

Full Text Available Abstract Background Hyperglycaemia is a common occurrence during cardiac surgery, however, there remains some uncertainty surrounding the role of tight glycaemic control (blood glucose Method The literature was systematically reviewed, based on pre-determined search criteria, for clinical trials evaluating the effect of tight versus normal glycaemic control during and/or after cardiac surgery. Each paper was reviewed by two, independent reviewers and data extracted for statistical analysis. Data from identified studies was combined using meta-analysis (RevMan5®. The results are presented either as odds ratios (OR or mean differences (MD with 95% confidence intervals (CIs. Results A total of seven randomised controlled trials (RCTs were identified in the literature, although not all trials could be used in each analysis. Tight glycaemic control reduced the incidence of early mortality (death in ICU (OR 0.52 [95% CI 0.30, 0.91]; of post-surgical atrial fibrillation (odds ratio (OR 0.76 [95%CI 0.58, 0.99]; the use of epicardial pacing (OR 0.28 [95%CI 0.15, 0.54]; the duration of mechanical ventilation (mean difference (MD -3.69 [95% CI -3.85, -3.54] and length of stay in the intensive care unit (ICU (MD -0.57 [95%CI -0.60, -0.55] days. Measures of the time spent on mechanical ventilation (I2 94% and time spent in ICU (I2 99% both had high degrees of heterogeneity in the data. Conclusion The results from this study suggest that there may be some benefit to tight glycaemic control during and after cardiac surgery. However, due to the limited number of studies available and the significant variability in glucose levels; period of control; and the reporting of outcome measures, further research needs to be done to provide a definitive answer on the benefits of tight glycaemic control for cardiac surgery patients.

Feasibility study on application of volume acid fracturing technology to tight gas carbonate reservoir development

Directory of Open Access Journals (Sweden)

Nianyin Li

2015-09-01

Full Text Available How to effectively develop tight-gas carbonate reservoir and achieve high recovery is always a problem for the oil and gas industry. To solve this problem, domestic petroleum engineers use the combination of the successful experiences of North American shale gas pools development by stimulated reservoir volume (SRV fracturing with the research achievements of Chinese tight gas development by acid fracturing to propose volume acid fracturing technology for fractured tight-gas carbonate reservoir, which has achieved a good stimulation effect in the pilot tests. To determine what reservoir conditions are suitable to carry out volume acid fracturing, this paper firstly introduces volume acid fracturing technology by giving the stimulation mechanism and technical ideas, and initially analyzes the feasibility by the comparison of reservoir characteristics of shale gas with tight-gas carbonate. Then, this paper analyzes the validity and limitation of the volume acid fracturing technology via the analyses of control conditions for volume acid fracturing in reservoir fracturing performance, natural fracture, horizontal principal stress difference, orientation of in-situ stress and natural fracture, and gives the solution for the limitation. The study results show that the volume acid fracturing process can be used to greatly improve the flow environment of tight-gas carbonate reservoir and increase production; the incremental or stimulation response is closely related with reservoir fracturing performance, the degree of development of natural fracture, the small intersection angle between hydraulic fracture and natural fracture, the large horizontal principal stress difference is easy to form a narrow fracture zone, and it is disadvantageous to create fracture network, but the degradable fiber diversion technology may largely weaken the disadvantage. The practices indicate that the application of volume acid fracturing process to the tight-gas carbonate

Three-dimensional measurement of a tightly focused laser beam

Directory of Open Access Journals (Sweden)

Xiangsheng Xie

2013-02-01

Full Text Available The spatial structure of a tightly focused light field is measured with a double knife-edge scanning method. The measurement method is based on the use of a high-quality double knife-edge fabricated from a right-angled silicon fragment mounted on a photodetector. The reconstruction of the three-dimensional structures of tightly focused spots is carried out with both uniform and partially obstructed linearly polarized incident light beams. The optical field distribution is found to deviate substantially from the input beam profile in the tightly focused region, which is in good agreement with the results of numerical simulations.

Western tight gas sands advanced logging workshop proceedings

Energy Technology Data Exchange (ETDEWEB)

Jennings, J B; Carroll, Jr, H B [eds.

1982-04-01

An advanced logging research program is one major aspect of the Western Tight Sands Program. Purpose of this workshop is to help BETC define critical logging needs for tight gas sands and to allow free interchange of ideas on all aspects of the current logging research program. Sixteen papers and abstracts are included together with discussions. Separate abstracts have been prepared for the 12 papers. (DLC)

Exceptionally tight membrane-binding may explain the key role of the synaptotagmin-7 C ₂ A domain in asynchronous neurotransmitter release

Energy Technology Data Exchange (ETDEWEB)

Voleti, Rashmi; Tomchick, Diana R.; Südhof, Thomas C.; Rizo, Josep

2017-09-18

Synaptotagmins (Syts) act as Ca2+ sensors in neurotransmitter release by virtue of Ca2+-binding to their two C2 domains, but their mechanisms of action remain unclear. Puzzlingly, Ca2+-binding to the C2B domain appears to dominate Syt1 function in synchronous release, whereas Ca2+-binding to the C2A domain mediates Syt7 function in asynchronous release. Here we show that crystal structures of the Syt7 C2A domain and C2AB region, and analyses of intrinsic Ca2+-binding to the Syt7 C2 domains using isothermal titration calorimetry, did not reveal major differences that could explain functional differentiation between Syt7 and Syt1. However, using liposome titrations under Ca2+ saturating conditions, we show that the Syt7 C2A domain has a very high membrane affinity and dominates phospholipid binding to Syt7 in the presence or absence of L-α-phosphatidylinositol 4,5-diphosphate (PIP2). For Syt1, the two Ca2+-saturated C2 domains have similar affinities for membranes lacking PIP2, but the C2B domain dominates binding to PIP2-containing membranes. Mutagenesis revealed that the dramatic differences in membrane affinity between the Syt1 and Syt7 C2A domains arise in part from apparently conservative residue substitutions, showing how striking biochemical and functional differences can result from the cumulative effects of subtle residue substitutions. Viewed together, our results suggest that membrane affinity may be a key determinant of the functions of Syt C2 domains in neurotransmitter release.

2,3-DPG-Hb complex: a hypothesis for an asymmetric binding.

Science.gov (United States)

Pomponi, M; Bertonati, C; Fuglei, E; Wiig, O; Derocher, A E

2000-05-15

This study was undertaken to test the symmetry of 2,3-diphosphoglycerate (2,3-DPG) binding site in hemoglobin (Hb). From Arnone's study [A. Arnone, Nature (London) 237 (1972) 146] the 2,3-DPG binding site is located at the top of the cavity, that runs through the center of the deoxy-Hb molecule. However, it is possible that this symmetry reported by Arnone, for crystals of 2,3-DPG-Hb complex, might not be conserved in solution. In this paper, we report the 31P nuclear magnetic resonances of the 2,3-DPG interaction with Hb. The 2,3-DPG chemical shifts of the P2 and P3 resonance are both pH- and hemoglobin-dependent [protein from man, polar bear (Ursus maritimus), Arctic fox (Alopex lagopus) and bovine]. 2,3-DPG binds tightly to deoxyhemoglobin and weakly, nevertheless significantly, to oxyhemoglobin. In particular, our results suggest similar spatial position of the binding site of 2,3-DPG in both forms of Hb in solutions. However, the most unexpected result was the apparent loss of symmetry in the binding site, which might correlate with the ability of the hemoglobin to modulate its functional behavior. The different interactions of the phosphate groups indicate small differences in the quaternary structure of the different deoxy forms of hemoglobin. Given the above structural perturbation an asymmetric binding in the complex could justify, at least in part, different physiological properties of Hb. Regardless, functionally relevant effects of 2,3-DPG seem to be measured and best elucidated through solution studies.

Crossover between spin swapping and Hall effect in disordered systems

KAUST Repository

Saidaoui, Hamed Ben Mohamed

2015-07-16

We theoretically study the crossover between spin Hall effect and spin swapping, a recently predicted phenomenon that consists of the interchange between the current flow and its spin polarization directions [M. B. Lifshits and M. I. Dyakonov, Phys. Rev. Lett. 103, 186601 (2009)]. Using a tight-binding model with spin-orbit coupled disorder, spin Hall effect, spin relaxation, and spin swapping are treated on equal footing. We demonstrate that spin swapping and spin Hall effect present very different dependencies as a function of the spin-orbit coupling and disorder strengths and confirm that the former exceeds the latter in the parameter range considered. Three setups are proposed for the experimental observation of the spin swapping effect.

Crossover between spin swapping and Hall effect in disordered systems

KAUST Repository

Saidaoui, Hamed Ben Mohamed; Otani, Y.; Manchon, Aurelien

2015-01-01

We theoretically study the crossover between spin Hall effect and spin swapping, a recently predicted phenomenon that consists of the interchange between the current flow and its spin polarization directions [M. B. Lifshits and M. I. Dyakonov, Phys. Rev. Lett. 103, 186601 (2009)]. Using a tight-binding model with spin-orbit coupled disorder, spin Hall effect, spin relaxation, and spin swapping are treated on equal footing. We demonstrate that spin swapping and spin Hall effect present very different dependencies as a function of the spin-orbit coupling and disorder strengths and confirm that the former exceeds the latter in the parameter range considered. Three setups are proposed for the experimental observation of the spin swapping effect.

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

Science.gov (United States)

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.

A Fuzzy Adaptive Tightly-Coupled Integration Method for Mobile Target Localization Using SINS/WSN

Directory of Open Access Journals (Sweden)

Wei Li

2016-11-01

Full Text Available In recent years, mobile target localization for enclosed environments has been a growing interest. In this paper, we have proposed a fuzzy adaptive tightly-coupled integration (FATCI method for positioning and tracking applications using strapdown inertial navigation system (SINS and wireless sensor network (WSN. The wireless signal outage and severe multipath propagation of WSN often influence the accuracy of measured distance and lead to difficulties with the WSN positioning. Note also that the SINS are known for their drifted error over time. Using as a base the well-known loosely-coupled integration method, we have built a tightly-coupled integrated positioning system for SINS/WSN based on the measured distances between anchor nodes and mobile node. The measured distance value of WSN is corrected with a least squares regression (LSR algorithm, with the aim of decreasing the systematic error for measured distance. Additionally, the statistical covariance of measured distance value is used to adjust the observation covariance matrix of a Kalman filter using a fuzzy inference system (FIS, based on the statistical characteristics. Then the tightly-coupled integration model can adaptively adjust the confidence level for measurement according to the different measured accuracies of distance measurements. Hence the FATCI system is achieved using SINS/WSN. This innovative approach is verified in real scenarios. Experimental results show that the proposed positioning system has better accuracy and stability compared with the loosely-coupled and traditional tightly-coupled integration model for WSN short-term failure or normal conditions.

Study of minor actinides transmutation in heavy water cooled tight-pitch lattice

International Nuclear Information System (INIS)

Xu Xiaoqin; Shiroya, S.

2002-01-01

Minor actinides inhere long half-life and high toxicity. It is an alternative technical pathway and helpful for reducing environmental impact to incinerate minor actinides in spent fuel of nuclear power plants. Because of its high neutron, γ and β emitting rates and heat generation rate, it is necessary to imply more severe control and shielding techniques in the chemical treatment and fabrication. From economic view-point, it is suitable to transmute minor actinides in concentrated way. A technique for MA transmutation by heavy water cooled tight-pitch lattice system is proposed, and calculated with SRAC95 code system. It is shown that tight-pitch heavy water lattice can transmute MA effectively. The accelerator-driven subcritical system is practical for MA transmutation because of its low fraction of effective delay neutrons

Identification of DNA-binding protein target sequences by physical effective energy functions: free energy analysis of lambda repressor-DNA complexes.

Directory of Open Access Journals (Sweden)

Caselle Michele

2007-09-01

Full Text Available Abstract Background Specific binding of proteins to DNA is one of the most common ways gene expression is controlled. Although general rules for the DNA-protein recognition can be derived, the ambiguous and complex nature of this mechanism precludes a simple recognition code, therefore the prediction of DNA target sequences is not straightforward. DNA-protein interactions can be studied using computational methods which can complement the current experimental methods and offer some advantages. In the present work we use physical effective potentials to evaluate the DNA-protein binding affinities for the λ repressor-DNA complex for which structural and thermodynamic experimental data are available. Results The binding free energy of two molecules can be expressed as the sum of an intermolecular energy (evaluated using a molecular mechanics forcefield, a solvation free energy term and an entropic term. Different solvation models are used including distance dependent dielectric constants, solvent accessible surface tension models and the Generalized Born model. The effect of conformational sampling by Molecular Dynamics simulations on the computed binding energy is assessed; results show that this effect is in general negative and the reproducibility of the experimental values decreases with the increase of simulation time considered. The free energy of binding for non-specific complexes, estimated using the best energetic model, agrees with earlier theoretical suggestions. As a results of these analyses, we propose a protocol for the prediction of DNA-binding target sequences. The possibility of searching regulatory elements within the bacteriophage λ genome using this protocol is explored. Our analysis shows good prediction capabilities, even in absence of any thermodynamic data and information on the naturally recognized sequence. Conclusion This study supports the conclusion that physics-based methods can offer a completely complementary

The semi-empirical tight-binding model for carbon allotropes “between diamond and graphite”

Energy Technology Data Exchange (ETDEWEB)

Lytovchenko, V.; Kurchak, A.; Strikha, M., E-mail: maksym-strikha@hotmail.com [Institute of Semiconductor Physics, NAS of Ukraine, Pr. Nauky 41, Kyiv 03028 (Ukraine)

2014-06-28

The new carbon allotropes “between diamond and graphite” have come under intensive examination during the last decade due to their numerous technical applications. The modification of energy gap in thin films of these allotropes was studied experimentally using optical methods. The proposed simple model of carbon clusters with variable lengths of chemical bonds allows us to imitate the transfer from diamond and diamond-like to graphite-like structures, as well as the corresponding modification of hybridization sp{sup 3}/sp{sup 2} for diamond-like and sp{sub z} for graphite-like phases. This enables us to estimate various allotropes parameters, like the gap E{sub g}, energies of valence E{sub v}, and conduction E{sub c} band edges, and the value of electronic affinity, i.e., optical work function X, which are all of practical importance. The obtained estimations correspond to the experimental data.

Preliminary studies of 99mTc-PQQ-NMDAR binding and effect of specificity binding by mannitol

International Nuclear Information System (INIS)

Xingqin Zhou; Yanyan Kong; Guoxian Cao; Jiankang Zhang

2013-01-01

Pyrroloquinoline quinone (PQQ) is a powerful neuroprotectant that specifically binds to brain NMDA receptors and inhibits excitotoxicity. Imaging this binding reaction in the brain remains a long sought goal in this field of study, and one of the primary challenges remaining is enabling soluble labeled PQQ to pass the blood-brain barrier (BBB). Previously, our group successfully labeled PQQ with Technetium-99m ( 99m Tc), a metastable nuclear isomer used in radioactive isotope medical tests. In this work, we determined the specific binding of 99m Tc-PQQ and NMDAR by radioligand receptor assay. Ebselen (EB) and MK-801 both effectively inhibited 99m Tc-PQQ binding. We then investigated methods of opening the BBB using mannitol to enable entry to the brain by 99m Tc-PQQ. Our results showed that 7.5 mL/kg of 20 % mannitol effectively opened the BBB and 20 min was the optimum treatment time. Competition studies showed that mannitol did not affect the specific binding between 99m Tc-PQQ and NMDA receptors. Using this method, the amount of 99m Tc-PQQ uptake and retention was increased most significantly in the hippocampus and cortex, and re-opening the BBB did not affect binding. Together, our results demonstrate that the use of mannitol to open the BBB may contribute significantly to improving image quality by increasing the uptake amount of a water-soluble agent in brain. (author)

Experience in North America Tight Oil Reserves Development. Horizontal Wells and Multistage Hydraulic Fracturing

Directory of Open Access Journals (Sweden)

R.R. Ibatullin

2017-09-01

Full Text Available The accelerated development of horizontal drilling technology in combination with the multistage hydraulic fracturing of the reservoir has expanded the geological conditions for commercial oil production from tight reservoirs in North America. Geological and physical characteristics of tight reservoirs in North America are presented, as well as a comparison of the geological and physical properties of the reservoirs of the Western Canadian Sedimentary Basin and the Volga-Ural oil and gas province, in particular, in the territory of Tatarstan. The similarity of these basins is shown in terms of formation and deposition. New drilling technologies for horizontal wells (HW and multistage hydraulic fracturing are considered. The drilling in tight reservoirs is carried out exclusively on hydrocarbon-based muds The multi-stage fracturing technology with the use of sliding sleeves, and also slick water – a low-viscous carrier for proppant is the most effective solution for conditions similar to tight reservoirs in the Devonian formation of Tatarstan. Tax incentives which are actively used for the development of HW and multistage fracturing technologies in Canada are described. wells, multistage fracturing

Subchannel analysis of 37-rod tight-lattice bundle experiments for reduced-moderation water reactor

International Nuclear Information System (INIS)

Nakatsuka, Toru; Tamai, Hidesada; Akimoto, Hajime

2005-01-01

R and D project to investigate thermal-hydraulic performance of tight-lattice fuel bundles for Reduced-Moderation Water Reactor (RMWR) started at Japan Atomic Energy Research Institute (JAERI) in collaboration with utilities, reactor vendors and universities from 2002. The RMWR realizes a high conversion ratio larger than 0.1 for sustainable energy supply through plutonium multiple recycling based on the well-experienced LWR technologies. The reactor core comprises tight-lattice fuel assemblies with gap clearance of around 1.0 mm to reduce the water volume ratio to achieve the high conversion ratio. A problem of utmost importance from a thermal-hydraulic point of view is the coolability of the tight-lattice assembly with such a small gap width. JAERI has been carrying out experimental study to investigate the system parameter effects on the thermal-hydraulic performance and to confirm the feasibility of the core. In the present study, the subchannel analysis code NASCA was applied to 37-rod tight-lattice bundle experiments. The NASCA can give good predictions of critical power for the gap width of 1.3 mm while the prediction accuracy decreases for the gap width of 1.0 mm. To improve the prediction accuracy, the code will be modified to take the effect of film thickness distribution around fuel rods on boiling transition. (author)

Assessing the model transferability for prediction of transcription factor binding sites based on chromatin accessibility.

Science.gov (United States)

Liu, Sheng; Zibetti, Cristina; Wan, Jun; Wang, Guohua; Blackshaw, Seth; Qian, Jiang

2017-07-27

Computational prediction of transcription factor (TF) binding sites in different cell types is challenging. Recent technology development allows us to determine the genome-wide chromatin accessibility in various cellular and developmental contexts. The chromatin accessibility profiles provide useful information in prediction of TF binding events in various physiological conditions. Furthermore, ChIP-Seq analysis was used to determine genome-wide binding sites for a range of different TFs in multiple cell types. Integration of these two types of genomic information can improve the prediction of TF binding events. We assessed to what extent a model built upon on other TFs and/or other cell types could be used to predict the binding sites of TFs of interest. A random forest model was built using a set of cell type-independent features such as specific sequences recognized by the TFs and evolutionary conservation, as well as cell type-specific features derived from chromatin accessibility data. Our analysis suggested that the models learned from other TFs and/or cell lines performed almost as well as the model learned from the target TF in the cell type of interest. Interestingly, models based on multiple TFs performed better than single-TF models. Finally, we proposed a universal model, BPAC, which was generated using ChIP-Seq data from multiple TFs in various cell types. Integrating chromatin accessibility information with sequence information improves prediction of TF binding.The prediction of TF binding is transferable across TFs and/or cell lines suggesting there are a set of universal "rules". A computational tool was developed to predict TF binding sites based on the universal "rules".

Effects of flow changes on radiotracer binding: Simultaneous measurement of neuroreceptor binding and cerebral blood flow modulation.

Science.gov (United States)

Sander, Christin Y; Mandeville, Joseph B; Wey, Hsiao-Ying; Catana, Ciprian; Hooker, Jacob M; Rosen, Bruce R

2017-01-01

The potential effects of changes in blood flow on the delivery and washout of radiotracers has been an ongoing question in PET bolus injection studies. This study provides practical insight into this topic by experimentally measuring cerebral blood flow (CBF) and neuroreceptor binding using simultaneous PET/MRI. Hypercapnic challenges (7% CO 2 ) were administered to non-human primates in order to induce controlled increases in CBF, measured with pseudo-continuous arterial spin labeling. Simultaneously, dopamine D 2 /D 3 receptor binding of [ 11 C]raclopride or [ 18 F]fallypride was monitored with dynamic PET. Experiments showed that neither time activity curves nor quantification of binding through binding potentials ( BP ND ) were measurably affected by CBF increases, which were larger than two-fold. Simulations of experimental procedures showed that even large changes in CBF should have little effect on the time activity curves of radiotracers, given a set of realistic assumptions. The proposed method can be applied to experimentally assess the flow sensitivity of other radiotracers. Results demonstrate that CBF changes, which often occur due to behavioral tasks or pharmacological challenges, do not affect PET [ 11 C]raclopride or [ 18 F]fallypride binding studies and their quantification. The results from this study suggest flow effects may have limited impact on many PET neuroreceptor tracers with similar properties.

Outcome of tight versus standard glycemic control in coronary artery bypass patients

International Nuclear Information System (INIS)

Subhani, H.

2012-01-01

Objectives: To compare the outcome of tight versus standard glycemic control and its impact on post operative morbidity and short term mortality in patients undergoing Coronary Artery Bypass Grafting (CA-BG). Patients and Methods: A prospective surveillance of 124 patients undergoing isolated CABG surgery (on pump) was included in the study, 62 patients in each group were randomly assigned to tight and standard glucose control group. The main exposure was insulin in respect to level of blood glucose and the primary outcome measures were Sternotomy wound infection, Leg wound infection and new Myocardial Infarction. Surgical Site infection was assessed on a daily basis during the patient's stay in the Department of Cardio-thoracic Surgery, Sheikh Zayed Hospital, Lahore or within 30 days of operation prompting the patient to return to the hospital. Chi-square test or test was used to identify the significance of various short term morbidities and mortality. Results: In this study, 12 patients in the standard group and 4 patients in the tightly controlled group developed Sternal wound infection (p value 0.046). Similarly, 9 versus 2 patients in the standard and tight group respectively developed Leg wound infection (p-value 0.035). Test of proportion was applied and it was found that there was significant difference in the pro-portion of infection in the two groups (p value 0.05). However, there were no significant differences in other morbidities and the short term mortality. Conclusion: Study confirmed that tight glucose con-trol post operatively in CABG patient's results in reduced sternal and leg wound infection rates; however, there was no effect on other morbidities and short term mortality. (author)

Analysis of stress sensitivity and its influence on oil productionfrom tight reservoirs

Energy Technology Data Exchange (ETDEWEB)

Lei, Qun; Xiong, Wei; Yuan, Cui; Wu, Yu-Shu

2007-08-28

This paper presents a study of the relationship betweenpermeability and effective stress in tight petroleum reservoirformations. Specifically, a quantitative method is developed to describethe correlation between permeability and effective stress, a method basedon the original in situ reservoir effective stress rather than ondecreased effective stress during development. The experimental resultsshow that the relationship between intrinsic permeability and effectivestress in reservoirs in general follows a quadratic polynomial functionalform, found to best capture how effective stress influences formationpermeability. In addition, this experimental study reveals that changesin formation permeability, caused by both elastic and plasticdeformation, are permanent and irreversible. Related pore-deformationtests using electronic microscope scanning and constant-rate mercuryinjection techniques show that while stress variation generally has smallimpact onrock porosity, the size and shape of pore throats have asignificant impact on permeability-stress sensitivity. Based on the testresults and theoretical analyses, we believe that there exists a cone ofpressure depression in the area near production within suchstress-sensitive tight reservoirs, leading to a low-permeability zone,and that well production will decrease under the influence of stresssensitivity.

eMatchSite: sequence order-independent structure alignments of ligand binding pockets in protein models.

Directory of Open Access Journals (Sweden)

Michal Brylinski

2014-09-01

Full Text Available Detecting similarities between ligand binding sites in the absence of global homology between target proteins has been recognized as one of the critical components of modern drug discovery. Local binding site alignments can be constructed using sequence order-independent techniques, however, to achieve a high accuracy, many current algorithms for binding site comparison require high-quality experimental protein structures, preferably in the bound conformational state. This, in turn, complicates proteome scale applications, where only various quality structure models are available for the majority of gene products. To improve the state-of-the-art, we developed eMatchSite, a new method for constructing sequence order-independent alignments of ligand binding sites in protein models. Large-scale benchmarking calculations using adenine-binding pockets in crystal structures demonstrate that eMatchSite generates accurate alignments for almost three times more protein pairs than SOIPPA. More importantly, eMatchSite offers a high tolerance to structural distortions in ligand binding regions in protein models. For example, the percentage of correctly aligned pairs of adenine-binding sites in weakly homologous protein models is only 4-9% lower than those aligned using crystal structures. This represents a significant improvement over other algorithms, e.g. the performance of eMatchSite in recognizing similar binding sites is 6% and 13% higher than that of SiteEngine using high- and moderate-quality protein models, respectively. Constructing biologically correct alignments using predicted ligand binding sites in protein models opens up the possibility to investigate drug-protein interaction networks for complete proteomes with prospective systems-level applications in polypharmacology and rational drug repositioning. eMatchSite is freely available to the academic community as a web-server and a stand-alone software distribution at http://www.brylinski.org/ematchsite.

Economic evaluation on tight sandstone gas development projects in China and recommendation on fiscal and taxation support policies

Directory of Open Access Journals (Sweden)

Zhen Yang

2016-11-01

Full Text Available China is rich in tight sandstone gas resources (“tight gas” for short. For example, the Sulige Gasfield in the Ordos Basin and the Upper Triassic Xujiahe Fm gas reservoir in the Sichuan Basin are typical tight gas reservoirs. In the past decade, tight gas reserve and production both have increased rapidly in China, but tight gas reservoirs are always managed as conventional gas reservoirs without effective fiscal, taxation and policy supports. The potential of sustainable tight gas production increase is obviously restricted. The tight gas development projects represented by the Sulige Gasfield have failed to make profit for a long period, and especially tight gas production has presented a slight decline since 2015. In this paper, a new economic evaluation method was proposed for tight gas development projects. The new method was designed to verify the key parameters (e.g. production decline rate and single-well economic service life depending on tight gas development and production characteristics, and perform the depreciation by using the production method. Furthermore, the possibility that the operation cost may rise due to pressure-boosting production and intermittent opening of gas wells is considered. The method was used for the tight gas development project of Sulige Gasfield, showing that its profit level is much lower than the enterprise's cost level of capital. In order to support a sustainable development of tight gas industry in China, it is recommended that relevant authorities issue value-added tax (VAT refund policy as soon as possible. It is necessary to restore the non-resident gas gate price of the provinces where tight gas is produced to the fair and reasonable level in addition to the fiscal subsidy of CNY0.24/m3, or offer the fiscal subsidy of CNY0.32/m3 directly based on the on-going gate price. With these support policies, tax income is expected to rise directly, fiscal expenditure will not increase, and gas

Air tightness measurements in older Danish single-family houses

DEFF Research Database (Denmark)

Mortensen, Lone Hedegaard; Bergsøe, Niels Christian

2017-01-01

of the building envelope of older buildings despite the fact that the air tightness has a major influence on the energy use. In connection with renovation of the Danish building stock, the coming years will see increased focus on the air tightness of the building envelope like in other countries. This paper...

Cooperative binding mitigates the high-dose hook effect.

Science.gov (United States)

Roy, Ranjita Dutta; Rosenmund, Christian; Stefan, Melanie I

2017-08-14

The high-dose hook effect (also called prozone effect) refers to the observation that if a multivalent protein acts as a linker between two parts of a protein complex, then increasing the amount of linker protein in the mixture does not always increase the amount of fully formed complex. On the contrary, at a high enough concentration range the amount of fully formed complex actually decreases. It has been observed that allosterically regulated proteins seem less susceptible to this effect. The aim of this study was two-fold: First, to investigate the mathematical basis of how allostery mitigates the prozone effect. And second, to explore the consequences of allostery and the high-dose hook effect using the example of calmodulin, a calcium-sensing protein that regulates the switch between long-term potentiation and long-term depression in neurons. We use a combinatorial model of a "perfect linker protein" (with infinite binding affinity) to mathematically describe the hook effect and its behaviour under allosteric conditions. We show that allosteric regulation does indeed mitigate the high-dose hook effect. We then turn to calmodulin as a real-life example of an allosteric protein. Using kinetic simulations, we show that calmodulin is indeed subject to a hook effect. We also show that this effect is stronger in the presence of the allosteric activator Ca 2+ /calmodulin-dependent kinase II (CaMKII), because it reduces the overall cooperativity of the calcium-calmodulin system. It follows that, surprisingly, there are conditions where increased amounts of allosteric activator actually decrease the activity of a protein. We show that cooperative binding can indeed act as a protective mechanism against the hook effect. This will have implications in vivo where the extent of cooperativity of a protein can be modulated, for instance, by allosteric activators or inhibitors. This can result in counterintuitive effects of decreased activity with increased concentrations of

A Semi-Analytical Methodology for Multiwell Productivity Index of Well-Industry-Production-Scheme in Tight Oil Reservoirs

Directory of Open Access Journals (Sweden)

Guangfeng Liu

2018-04-01

Full Text Available Recently, the well-industry-production-scheme (WIPS has attracted more and more attention to improve tight oil recovery. However, multi-well pressure interference (MWPI induced by well-industry-production-scheme (WIPS strongly challenges the traditional transient pressure analysis methods, which focus on single multi-fractured horizontal wells (SMFHWs without MWPI. Therefore, a semi-analytical methodology for multiwell productivity index (MPI was proposed to study well performance of WIPS scheme in tight reservoir. To facilitate methodology development, the conceptual models of tight formation and WIPS scheme were firstly described. Secondly, seepage models of tight reservoir and hydraulic fractures (HFs were sequentially established and then dynamically coupled. Numerical simulation was utilized to validate our model. Finally, identification of flow regimes and sensitivity analysis were conducted. Our results showed that there was good agreement between our proposed model and numerical simulation; moreover, our approach also gave promising calculation speed over numerical simulation. Some expected flow regimes were significantly distorted due to WIPS. The slope of type curves which characterize the linear or bi-linear flow regime is bigger than 0.5 or 0.25. The horizontal line which characterize radial flow regime is also bigger 0.5. The smaller the oil rate, the more severely flow regimes were distorted. Well rate mainly determines the distortion of MPI curves, while fracture length, well spacing, fracture spacing mainly determine when the distortion of the MPI curves occurs. The bigger the well rate, the more severely the MPI curves are distorted. While as the well spacing decreases, fracture length increases, fracture spacing increases, occurrence of MWPI become earlier. Stress sensitivity coefficient mainly affects the MPI at the formation pseudo-radial flow stage, almost has no influence on the occurrence of MWPI. This work gains some

Binding of carvedilol to serum albumins investigated by multi-spectroscopic and molecular modeling methods

Energy Technology Data Exchange (ETDEWEB)

Safarnejad, Azam; Shaghaghi, Masoomeh [Department of Chemistry, Payame Noor University, P.O. Box. 19395-3697, Tehran (Iran, Islamic Republic of); Dehghan, Golamreza [Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz (Iran, Islamic Republic of); Soltani, Somaieh, E-mail: soltanisomaieh@gmail.com [Drug applied research center and pharmacy faculty, Tabriz University of Medical Sciences, Tabriz (Iran, Islamic Republic of)

2016-08-15

Carvedilol (CAR) binding to human and bovine serum albumins (HSA and BSA) was studied using fluorescence, UV–vis absorption and Fourier transform infrared spectroscopy (FTIR) and molecular docking techniques at different temperatures (288, 298 and 308 K) under physiologic pH. Results obtained from fluorescence data indicated that values of binding sites (n), effective quenching constants (Ka) and binding constants (K{sub b}) decreased under higher temperature and that the quenching mechanism was static. The thermodynamic parameters including enthalpy (ΔH), entropy (ΔS) and Gibb's free energy (ΔG) changes were calculated by the van't Hoff equation and these data showed that hydrogen bonds and Van der Waals contacts were the main binding force in HSA–CAR and BSA–CAR systems. Binding distance (r) between HSA–CAR and BSA–CAR were calculated by the Förster (fluorescence resonance energy transfer (FRET)) method. FTIR absorption studies showed that the secondary structure was changed according to the interaction of HSA/BSA and CAR. Results determined by molecular docking were in agreement with thermodynamic and FRET data and confirmed that the binding mechanism of Carvedilol to HSA and BSA is different. - Highlights: • The quenching mechanism between Carvedilol and HSA /BSA is a static process. • Hydrogen bonds and Van der Waals contacts were stabilized the Carvedilol albumin complexes. • Molecular modeling simulations confirmed the fluorescence spectroscopy and FRET analysis. • According to the binding mechanism differences between HSA and BSA, the results of BSA experiments could not be applied for HSA binding.

Tight Bound on Randomness for Violating the CHSH Inequality

OpenAIRE

Teng, Yifeng; Yang, Shenghao; Wang, Siwei; Zhao, Mingfei

2015-01-01

Free will (or randomness) has been studied to achieve loophole-free Bell's inequality test and to provide device-independent quantum key distribution security proofs. The required randomness such that a local hidden variable model (LHVM) can violate the Clauser-Horne-Shimony-Holt (CHSH) inequality has been studied, but a tight bound has not been proved for a practical case that i) the device settings of the two parties in the Bell test are independent; and ii) the device settings of each part...

Binding and functional effects of atrial natriuretic factor in isolated rat kidney

International Nuclear Information System (INIS)

Suzuki, M.; Almeida, F.A.; Nussenzveig, D.R.; Sawyer, D.; Maack, T.

1987-01-01

A new methodological approach was developed to study the relationship between specific binding and dose-response curves of the renal effects of atrial natriuretic factor (ANF) in isolated perfused rat kidneys (IK). IK were perfused with 125 I-labeled and unlabeled ANF 1-28 to determine the following: (1) distribution, capacity (C max ), and apparent affinity (S 50 ) of specific binding of ANF 1-28 in cortex, outer medulla, and papilla and (2) dose-response curves of the effects of ANF 1-28 on renal hemodynamics and excretion of fluid and electrolytes. The kidney had a very high density of high-affinity binding sites for ANF. Cortex had >90% of total binding sites whereas papilla had <2% of total binding sites with a 10-fold lower apparent affinity than in cortex. ANF-induced increases in glomerular filtration rate and excretion of fluid and electrolytes were detectable at 10-100 pM and maximal effects occurred at 1-10 nM ANF. Below 1 nM there was no dissociation between the renal hemodynamic and natriuretic effects of ANF. There was a close agreement between dose-response and binding curves of ANF to cortex. Results demonstrates that binding site occupancy in kidney cortex and renal effects of ANF occur at near physiological concentrations of the hormone

Hamstring tightness and Scheuermann's disease a pilot study.

Science.gov (United States)

Fisk, J W; Baigent, M L

1981-06-01

The lateral radiographs of the dorsal spines of 20 patients presenting with mainly low back pain are studied. These patients had clinically evident loss of flexion in the low dorsal spine and very tight hamstring muscles. 85% of them showed definite evidence of previous Scheuermann's Disease. The possibility that tight hamstrings may be an important factor in the aetiology of this disease is discussed, and a further large scale study is proposed.

Tightly Coupled Multiphysics Algorithm for Pebble Bed Reactors

International Nuclear Information System (INIS)

Park, HyeongKae; Knoll, Dana; Gaston, Derek; Martineau, Richard

2010-01-01

We have developed a tightly coupled multiphysics simulation tool for the pebble-bed reactor (PBR) concept, a type of Very High-Temperature gas-cooled Reactor (VHTR). The simulation tool, PRONGHORN, takes advantages of the Multiphysics Object-Oriented Simulation Environment library, and is capable of solving multidimensional thermal-fluid and neutronics problems implicitly with a Newton-based approach. Expensive Jacobian matrix formation is alleviated via the Jacobian-free Newton-Krylov method, and physics-based preconditioning is applied to minimize Krylov iterations. Motivation for the work is provided via analysis and numerical experiments on simpler multiphysics reactor models. We then provide detail of the physical models and numerical methods in PRONGHORN. Finally, PRONGHORN's algorithmic capability is demonstrated on a number of PBR test cases.

Catalystlike effect of orbital angular momentum on the conversion of transverse to three-dimensional spin states within tightly focused radially polarized beams

Science.gov (United States)

Han, Lei; Liu, Sheng; Li, Peng; Zhang, Yi; Cheng, Huachao; Zhao, Jianlin

2018-05-01

We report on the catalystlike effect of orbital angular momentum (OAM) on local spin-state conversion within the tightly focused radially polarized beams associated with optical spin-orbit interaction. It is theoretically demonstrated that the incident OAM can lead to a conversion of purely transverse spin state to a three-dimensional spin state on the focal plane. This conversion can be conveniently manipulated by altering the sign and value of the OAM. By comparing the total OAM and spin angular momentum (SAM) on the incident plane to those on the focal plane, it is indicated that the incident OAM have no participation in the angular momentum intertransfer, and just play a role as a catalyst of local SAM conversion. Such an effect of OAM sheds new light on the optical spin-orbit interaction in tight-focusing processes. The resultant three-dimensional spin states may provide more degrees of freedom in optical manipulation and spin-dependent directive coupling.

Detection of secondary binding sites in proteins using fragment screening.

Science.gov (United States)

Ludlow, R Frederick; Verdonk, Marcel L; Saini, Harpreet K; Tickle, Ian J; Jhoti, Harren

2015-12-29

Proteins need to be tightly regulated as they control biological processes in most normal cellular functions. The precise mechanisms of regulation are rarely completely understood but can involve binding of endogenous ligands and/or partner proteins at specific locations on a protein that can modulate function. Often, these additional secondary binding sites appear separate to the primary binding site, which, for example for an enzyme, may bind a substrate. In previous work, we have uncovered several examples in which secondary binding sites were discovered on proteins using fragment screening approaches. In each case, we were able to establish that the newly identified secondary binding site was biologically relevant as it was able to modulate function by the binding of a small molecule. In this study, we investigate how often secondary binding sites are located on proteins by analyzing 24 protein targets for which we have performed a fragment screen using X-ray crystallography. Our analysis shows that, surprisingly, the majority of proteins contain secondary binding sites based on their ability to bind fragments. Furthermore, sequence analysis of these previously unknown sites indicate high conservation, which suggests that they may have a biological function, perhaps via an allosteric mechanism. Comparing the physicochemical properties of the secondary sites with known primary ligand binding sites also shows broad similarities indicating that many of the secondary sites may be druggable in nature with small molecules that could provide new opportunities to modulate potential therapeutic targets.

Dangerous connections : on binding site models of infectious disease dynamics

NARCIS (Netherlands)

Leung, Ka Yin; Diekmann, Odo

2017-01-01

We formulate models for the spread of infection on networks that are amenable to analysis in the large population limit. We distinguish three different levels: (1) binding sites, (2) individuals, and (3) the population. In the tradition of physiologically structured population models, the

Protective Effect of 1,25-Dihydroxy Vitamin D3 on Pepsin-Trypsin-Resistant Gliadin-Induced Tight Junction Injuries.

Science.gov (United States)

Dong, Shouquan; Singh, Tikka Prabhjot; Wei, Xin; Yao, Huang; Wang, Hongling

2018-01-01

Tight junction (TJ) injuries induced by pepsin-trypsin-resistant gliadin (PT-G) play an important role in the pathogenesis of celiac disease. Previously, 1,25-dihydroxy vitamin D3 (VD3) was reported to be a TJ regulator that attenuates lipopolysaccharide- and alcohol-induced TJ injuries. However, whether VD3 can attenuate PT-G-induced TJ injuries is unknown. The aim of this study was to evaluate the effects of VD3 on PT-G-induced TJ injuries. Caco-2 monolayers were used as in vitro models. After being cultured for 21 days, the monolayers were treated with PT-G plus different concentrations of VD3. Then, the changes in trans-epithelial electrical resistance and FITC-dextran 4000 (FD-4) flux were determined to evaluate the monolayer barrier function. TJ protein levels were measured to assess TJ injury severity, and myeloid differentiation factor 88 (MyD88) expression and zonulin release levels were determined to estimate zonulin release signaling pathway activity. Additionally, a gluten-sensitized mouse model was established as an in vivo model. After the mice were treated with VD3 for 7 days, we measured serum FD-4 concentrations, TJ protein levels, MyD88 expression, and zonulin release levels to confirm the effect of VD3. Both in vitro and in vivo, VD3 significantly attenuated the TJ injury-related increase in intestinal mucosa barrier permeability. Moreover, VD3 treatment up-regulated TJ protein expression levels and significantly decreased MyD88 expression and zonulin release levels. VD3 has protective effects against PT-G-induced TJ injuries both in vitro and in vivo, which may correlate with the disturbance of the MyD88-dependent zonulin release signaling pathway.

Effect of the Flexible Regions of the Oncoprotein Mouse Double Minute X on Inhibitor Binding Affinity.

Science.gov (United States)

Qin, Lingyun; Liu, Huili; Chen, Rong; Zhou, Jingjing; Cheng, Xiyao; Chen, Yao; Huang, Yongqi; Su, Zhengding

2017-11-07

The oncoprotein MdmX (mouse double minute X) is highly homologous to Mdm2 (mouse double minute 2) in terms of their amino acid sequences and three-dimensional conformations, but Mdm2 inhibitors exhibit very weak affinity for MdmX, providing an excellent model for exploring how protein conformation distinguishes and alters inhibitor binding. The intrinsic conformation flexibility of proteins plays pivotal roles in determining and predicting the binding properties and the design of inhibitors. Although the molecular dynamics simulation approach enables us to understand protein-ligand interactions, the mechanism underlying how a flexible binding pocket adapts an inhibitor has been less explored experimentally. In this work, we have investigated how the intrinsic flexible regions of the N-terminal domain of MdmX (N-MdmX) affect the affinity of the Mdm2 inhibitor nutlin-3a using protein engineering. Guided by heteronuclear nuclear Overhauser effect measurements, we identified the flexible regions that affect inhibitor binding affinity around the ligand-binding pocket on N-MdmX. A disulfide engineering mutant, N-MdmX C25-C110/C76-C88 , which incorporated two staples to rigidify the ligand-binding pocket, allowed an affinity for nutlin-3a higher than that of wild-type N-MdmX (K d ∼ 0.48 vs K d ∼ 20.3 μM). Therefore, this mutant provides not only an effective protein model for screening and designing of MdmX inhibitors but also a valuable clue for enhancing the intermolecular interactions of the pharmacophores of a ligand with pronounced flexible regions. In addition, our results revealed an allosteric ligand-binding mechanism of N-MdmX in which the ligand initially interacts with a compact core, followed by augmenting intermolecular interactions with intrinsic flexible regions. This strategy should also be applicable to many other protein targets to accelerate drug discovery.

On the influence of reward on action-effect binding

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Paul Simon Muhle-Karbe

2012-11-01

Full Text Available Ideomotor theory states that the formation of anticipatory representations about the perceptual consequences of an action (i.e. action-effect (A-E binding provides the functional basis of voluntary action control. A host of studies has demonstrated that A-E binding occurs fast and effortlessly, yet only little is known about cognitive and affective factors that influence this learning process. In the present study, we sought to test whether the motivational value of an action modulates the acquisition of A-E associations. To this end, we associated specific actions with monetary incentives during the acquisition of novel A-E mappings. In a subsequent test phase, the degree of binding was assessed by presenting the former effect stimuli as task-irrelevant response primes in a forced-choice response task in the absence of any reward. Binding, as indexed by response priming through the former action effects, was only found for reward-related A-E mappings. Moreover, the degree to which reward associations modulated the binding strength was predicted by individuals’ trait sensitivity to reward. These observations indicate that the association of actions and their immediate outcomes depends on the motivational value of the action during learning, as well as on the motivational disposition of the individual. On a larger scale, these findings also highlight the link between ideomotor theories and reinforcement-learning theories, providing an interesting perspective for future research on anticipatory regulation of behavior.

Assessment of Density-Functional Tight-Binding Ionization Potentials and Electron Affinities of Molecules of Interest for Organic Solar Cells Against First-Principles GW Calculations

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Ala Aldin M. H. M. Darghouth

2015-12-01

Full Text Available Ionization potentials (IPs and electron affinities (EAs are important quantities input into most models for calculating the open-circuit voltage (Voc of organic solar cells. We assess the semi-empirical density-functional tight-binding (DFTB method with the third-order self-consistent charge (SCC correction and the 3ob parameter set (the third-order DFTB (DFTB3 organic and biochemistry parameter set against experiments (for smaller molecules and against first-principles GW (Green’s function, G, times the screened potential, W calculations (for larger molecules of interest in organic electronics for the calculation of IPs and EAs. Since GW calculations are relatively new for molecules of this size, we have also taken care to validate these calculations against experiments. As expected, DFTB is found to behave very much like density-functional theory (DFT, but with some loss of accuracy in predicting IPs and EAs. For small molecules, the best results were found with ΔSCF (Δ self-consistent field SCC-DFTB calculations for first IPs (good to ± 0.649 eV. When considering several IPs of the same molecule, it is convenient to use the negative of the orbital energies (which we refer to as Koopmans’ theorem (KT IPs as an indication of trends. Linear regression analysis shows that KT SCC-DFTB IPs are nearly as accurate as ΔSCF SCC-DFTB eigenvalues (± 0.852 eV for first IPs, but ± 0.706 eV for all of the IPs considered here for small molecules. For larger molecules, SCC-DFTB was also the ideal choice with IP/EA errors of ± 0.489/0.740 eV from ΔSCF calculations and of ± 0.326/0.458 eV from (KT orbital energies. Interestingly, the linear least squares fit for the KT IPs of the larger molecules also proves to have good predictive value for the lower energy KT IPs of smaller molecules, with significant deviations appearing only for IPs of 15–20 eV or larger. We believe that this quantitative analysis of errors in SCC-DFTB IPs and EAs may be of

Magnetic field effect on the ground-state binding energy in InGaN/GaN parabolic QWW

International Nuclear Information System (INIS)

El Ghazi, Haddou; Jorio, Anouar; Zorkani, Izeddine

2013-01-01

Within the framework of the effective mass scheme, the ground-state binding energy of hydrogenic shallow-donor impurity in wurtzite (WZ) (In,Ga)N/GaN parabolic transversal-section quantum-well wire (PQWW) subjected to magnetic field is investigated. The finite-difference method within the quasi-one-dimensional effective potential model is used. A cylindrical QWW effective radius is introduced to describe the lateral confinement strength. The results show that: (i) the binding energy is the largest for the impurity located at a point corresponding to the largest electron probability density and (ii) it increases with increasing external magnetic field

Magnetic field effect on the ground-state binding energy in InGaN/GaN parabolic QWW

Energy Technology Data Exchange (ETDEWEB)

El Ghazi, Haddou, E-mail: hadghazi@gmail.com [LPS, Faculty of sciences, Dhar EL Mehrez, B.P 1796 Atlas Fez (Morocco); Specials Mathematics, CPGE Kénitra, Chakib Arsalane Street, Kénitra (Morocco); Jorio, Anouar; Zorkani, Izeddine [LPS, Faculty of sciences, Dhar EL Mehrez, B.P 1796 Atlas Fez (Morocco)

2013-07-15

Within the framework of the effective mass scheme, the ground-state binding energy of hydrogenic shallow-donor impurity in wurtzite (WZ) (In,Ga)N/GaN parabolic transversal-section quantum-well wire (PQWW) subjected to magnetic field is investigated. The finite-difference method within the quasi-one-dimensional effective potential model is used. A cylindrical QWW effective radius is introduced to describe the lateral confinement strength. The results show that: (i) the binding energy is the largest for the impurity located at a point corresponding to the largest electron probability density and (ii) it increases with increasing external magnetic field.

Chondroitin sulfate addition to CD44H negatively regulates hyaluronan binding

International Nuclear Information System (INIS)

Ruffell, Brian; Johnson, Pauline

2005-01-01

CD44 is a widely expressed cell adhesion molecule that binds hyaluronan, an extracellular matrix glycosaminoglycan, in a tightly regulated manner. This regulated interaction has been implicated in inflammation and tumor metastasis. CD44 exists in the standard form, CD44H, or as higher molecular mass isoforms due to alternative splicing. Here, we identify serine 180 in human CD44H as the site of chondroitin sulfate addition and show that lack of chondroitin sulfate addition at this site enhances hyaluronan binding by CD44. A CD44H-immunoglobulin fusion protein expressed in HEK293 cells, and CD44H expressed in murine L fibroblast cells were modified by chondroitin sulfate, as determined by reduced sulfate incorporation after chondroitinase ABC treatment. Mutation of serine 180 or glycine 181 in CD44H reduced chondroitin sulfate addition and increased hyaluronan binding, indicating that serine 180 is the site for chondroitin sulfate addition in CD44H and that this negatively regulates hyaluronan binding

β-Conglycinin Reduces the Tight Junction Occludin and ZO-1 Expression in IPEC-J2

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Yuan Zhao

2014-01-01

Full Text Available Soybean allergy presents a health threat to humans and animals. The mechanism by which food/feed allergen β-conglycinin injures the intestinal barrier has not been well understood. In this study, the changes of epithelial permeability, integrity, metabolic activity, the tight junction (TJ distribution and expression induced by β-conglycinin were evaluated using IPEC-J2 model. The results showed a significant decrease of trans-epithelial electrical resistance (TEER (p < 0.001 and metabolic activity (p < 0.001 and a remarkable increase of alkaline phosphatase (AP activity (p < 0.001 in a dose-dependent manner. The expression levels of tight junction occludin and ZO-1 were decreased (p < 0.05. The reduced fluorescence of targets and change of cellular morphology were recorded. The tight junction occludin and ZO-1 mRNA expression linearly declined with increasing β-conglycinin (p < 0.001.

Sequence2Vec: A novel embedding approach for modeling transcription factor binding affinity landscape

KAUST Repository

Dai, Hanjun

2017-07-26

Motivation: An accurate characterization of transcription factor (TF)-DNA affinity landscape is crucial to a quantitative understanding of the molecular mechanisms underpinning endogenous gene regulation. While recent advances in biotechnology have brought the opportunity for building binding affinity prediction methods, the accurate characterization of TF-DNA binding affinity landscape still remains a challenging problem. Results: Here we propose a novel sequence embedding approach for modeling the transcription factor binding affinity landscape. Our method represents DNA binding sequences as a hidden Markov model (HMM) which captures both position specific information and long-range dependency in the sequence. A cornerstone of our method is a novel message passing-like embedding algorithm, called Sequence2Vec, which maps these HMMs into a common nonlinear feature space and uses these embedded features to build a predictive model. Our method is a novel combination of the strength of probabilistic graphical models, feature space embedding and deep learning. We conducted comprehensive experiments on over 90 large-scale TF-DNA data sets which were measured by different high-throughput experimental technologies. Sequence2Vec outperforms alternative machine learning methods as well as the state-of-the-art binding affinity prediction methods.

Experimental Air-Tightness Analysis in Mediterranean Buildings after Windows Retrofit

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Francesca Romana d’Ambrosio Alfano

2016-09-01

Full Text Available Energy saving and Indoor Air Quality (IAQ in buildings are strongly affected by air leakages. Several studies reveal that the energy loss owing to leaky windows can account for up to 40% of the total building energy demand. Furthermore, at the design stage, the possible infiltration of outdoor air through windows is not taken into account when determining the nominal outdoor airflow rate of the ventilation system. This practice may result in an oversizing of the ventilation system and consequent energy waste. Thus, the air-tightness class of a wall assembly should be assessed for each window component considering the type of material, the presence of the seal, the type of closure, the sealing and the maintenance condition. In this paper, the authors present the experimental results of air-tightness measurements carried out using the fan pressurization method in three residential buildings located in the Mediterranean region before and after a window retrofit. Two different window retrofits were investigated: the application of rubber seals on window frames and the substitution of existing windows with new certified high performance windows. The effectiveness of such retrofits was estimated also in terms of energy saving. Test results demonstrated a high variability of the building air tightness after window retrofits, despite the fact that air tight–certified windows were used.

Stark effect-dependent of ground-state donor binding energy in InGaN/GaN parabolic QWW

International Nuclear Information System (INIS)

El Ghazi, Haddou; Zorkani, Izeddine; Jorio, Anouar

2013-01-01

Using the finite-difference method within the quasi-one-dimensional effective potential model and effective mass approximation, the ground-state binding energy of hydrogenic shallow-donor impurity in wurtzite (WZ) (In,Ga)N/GaN parabolic transversal-section quantum-well wires (PQWWs) subjected to external electric field is investigated. An effective radius of a cylindrical QWW describing the strength of the lateral confinement is introduced. The results show that (i) the position of the largest electron probability density in x–y plane is located at a point and it is pushed along the negative sense by the electric field directed along the positive sense, (ii) the ground-state binding energy is largest for the impurity located at this point and starts to decrease when the impurity is away from this point, (iii) the ground-state binding energy decreases with increase in the external electric field and effective radius, and (iv) the Stark-shift increases with the increase of the external electric field and the effective radius

Development of Design Technology on Thermal-Hydraulic Performance in Tight-Lattice Rod Bundles: I-Master Plan and Executive Summary

Science.gov (United States)

Ohnuki, Akira; Kureta, Masatoshi; Yoshida, Hiroyuki; Tamai, Hidesada; Liu, Wei; Misawa, Takeharu; Takase, Kazuyuki; Akimoto, Hajime

R&D project to investigate thermal-hydraulic performance in tight-lattice rod bundles for Innovative Water Reactor for Flexible Fuel Cycle has been progressed at Japan Atomic Energy Agency in collaboration with power utilities, reactor vendors and universities since 2002. In this series-study, we will summarize the R&D achievements using large-scale test facility (37-rod bundle with full-height and full-pressure), model experiments and advanced numerical simulation technology. This first paper described the master plan for the development of design technology and showed an executive summary for this project up to FY2005. The thermal-hydraulic characteristics in the tight-lattice configuration were investigated and the feasibility was confirmed based on the experiments. We have developed the design technology including 3-D numerical simulation one to evaluate the effects of geometry/scale on the thermal-hydraulic behaviors.

Effect of Hydrogen Adsorption on the Stone-Wales Transformation in Small-Diameter Carbon Nanotubes

Science.gov (United States)

Openov, L. A.; Podlivaev, A. I.

2018-04-01

The effect of hydrogenation of (4, 0) and (3, 0) carbon nanotubes on the Stone-Wales transformation is studied in the framework of the nonorthogonal tight-binding model. It is shown that the atomic hydrogen adsorption can lead to both a decrease and an increase in the barriers for the direct and inverse transformations depending on the orientation of a rotating C-C bond with respect to the nanotube axis. The characteristic times of formation and annealing the Stone-Wales defects have been estimated. The Young's moduli have been calculated.

DNA-binding protects p53 from interactions with cofactors involved in transcription-independent functions.

Science.gov (United States)

Lambrughi, Matteo; De Gioia, Luca; Gervasio, Francesco Luigi; Lindorff-Larsen, Kresten; Nussinov, Ruth; Urani, Chiara; Bruschi, Maurizio; Papaleo, Elena

2016-11-02

Binding-induced conformational changes of a protein at regions distant from the binding site may play crucial roles in protein function and regulation. The p53 tumour suppressor is an example of such an allosterically regulated protein. Little is known, however, about how DNA binding can affect distal sites for transcription factors. Furthermore, the molecular details of how a local perturbation is transmitted through a protein structure are generally elusive and occur on timescales hard to explore by simulations. Thus, we employed state-of-the-art enhanced sampling atomistic simulations to unveil DNA-induced effects on p53 structure and dynamics that modulate the recruitment of cofactors and the impact of phosphorylation at Ser215. We show that DNA interaction promotes a conformational change in a region 3 nm away from the DNA binding site. Specifically, binding to DNA increases the population of an occluded minor state at this distal site by more than 4-fold, whereas phosphorylation traps the protein in its major state. In the minor conformation, the interface of p53 that binds biological partners related to p53 transcription-independent functions is not accessible. Significantly, our study reveals a mechanism of DNA-mediated protection of p53 from interactions with partners involved in the p53 transcription-independent signalling. This also suggests that conformational dynamics is tightly related to p53 signalling. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Intraoperative tight glucose control using hyperinsulinemic normoglycemia increases delirium after cardiac surgery.

Science.gov (United States)

Saager, Leif; Duncan, Andra E; Yared, Jean-Pierre; Hesler, Brian D; You, Jing; Deogaonkar, Anupa; Sessler, Daniel I; Kurz, Andrea

2015-06-01

Postoperative delirium is common in patients recovering from cardiac surgery. Tight glucose control has been shown to reduce mortality and morbidity. Therefore, the authors sought to determine the effect of tight intraoperative glucose control using a hyperinsulinemic-normoglycemic clamp approach on postoperative delirium in patients undergoing cardiac surgery. The authors enrolled 198 adult patients having cardiac surgery in this randomized, double-blind, single-center trial. Patients were randomly assigned to either tight intraoperative glucose control with a hyperinsulinemic-normoglycemic clamp (target blood glucose, 80 to 110 mg/dl) or standard therapy (conventional insulin administration with blood glucose target, battery. The authors considered patients to have experienced postoperative delirium when Confusion Assessment Method testing was positive at any assessment. A positive Confusion Assessment Method was defined by the presence of features 1 (acute onset and fluctuating course) and 2 (inattention) and either 3 (disorganized thinking) or 4 (altered consciousness). Patients randomized to tight glucose control were more likely to be diagnosed as being delirious than those assigned to routine glucose control (26 of 93 vs. 15 of 105; relative risk, 1.89; 95% CI, 1.06 to 3.37; P = 0.03), after adjusting for preoperative usage of calcium channel blocker and American Society of Anesthesiologist physical status. Delirium severity, among patients with delirium, was comparable with each glucose management strategy. Intraoperative hyperinsulinemic-normoglycemia augments the risk of delirium after cardiac surgery, but not its severity.

CaMELS: In silico prediction of calmodulin binding proteins and their binding sites.

Science.gov (United States)

Abbasi, Wajid Arshad; Asif, Amina; Andleeb, Saiqa; Minhas, Fayyaz Ul Amir Afsar

2017-09-01

Due to Ca 2+ -dependent binding and the sequence diversity of Calmodulin (CaM) binding proteins, identifying CaM interactions and binding sites in the wet-lab is tedious and costly. Therefore, computational methods for this purpose are crucial to the design of such wet-lab experiments. We present an algorithm suite called CaMELS (CalModulin intEraction Learning System) for predicting proteins that interact with CaM as well as their binding sites using sequence information alone. CaMELS offers state of the art accuracy for both CaM interaction and binding site prediction and can aid biologists in studying CaM binding proteins. For CaM interaction prediction, CaMELS uses protein sequence features coupled with a large-margin classifier. CaMELS models the binding site prediction problem using multiple instance machine learning with a custom optimization algorithm which allows more effective learning over imprecisely annotated CaM-binding sites during training. CaMELS has been extensively benchmarked using a variety of data sets, mutagenic studies, proteome-wide Gene Ontology enrichment analyses and protein structures. Our experiments indicate that CaMELS outperforms simple motif-based search and other existing methods for interaction and binding site prediction. We have also found that the whole sequence of a protein, rather than just its binding site, is important for predicting its interaction with CaM. Using the machine learning model in CaMELS, we have identified important features of protein sequences for CaM interaction prediction as well as characteristic amino acid sub-sequences and their relative position for identifying CaM binding sites. Python code for training and evaluating CaMELS together with a webserver implementation is available at the URL: http://faculty.pieas.edu.pk/fayyaz/software.html#camels. © 2017 Wiley Periodicals, Inc.

A Unified Model of the GABA(A) Receptor Comprising Agonist and Benzodiazepine Binding Sites

DEFF Research Database (Denmark)

Kongsbak, Kristine Grønning; Bergmann, Rikke; Sørensen, Pernille Louise

2013-01-01

We present a full-length a1b2c2 GABA receptor model optimized for agonists and benzodiazepine (BZD) allosteric modulators. We propose binding hypotheses for the agonists GABA, muscimol and THIP and for the allosteric modulator diazepam (DZP). The receptor model is primarily based on the glutamate......-gated chloride channel (GluCl) from C. elegans and includes additional structural information from the prokaryotic ligand-gated ion channel ELIC in a few regions. Available mutational data of the binding sites are well explained by the model and the proposed ligand binding poses. We suggest a GABA binding mode...... of the agonists in the orthosteric site. The carbonyl group of DZP is predicted to interact with two threonines a1T206 and c2T142, similar to the acidic moiety of GABA. The chlorine atom of DZP is placed near the important a1H101 and the N-methyl group near a1Y159, a1T206, and a1Y209. We present a binding mode...

Differential effect of detergents on [3H]Ro 5-4864 and [3H]PK 11195 binding to peripheral-type benzodiazepine-binding sites

International Nuclear Information System (INIS)

Awad, M.; Gavish, M.

1988-01-01

The present study demonstrates a differential effect of various detergent treatments on [ 3 H]Ro 5-4864 and [ 3 H]PK 11195 binding to peripheral benzodiazepine binding sites (PBS). Triton X-100 caused a decrease of about 70% in [ 3 H]Ro 5-4864 binding to membranes from various peripheral tissues of rat, but had only a negligible effect on [ 3 H]PK 11195 binding. A similar effect of Triton X-100 was observed on guinea pig and rabbit kidney membranes. The decrease in [ 3 H]Ro 5-4864 binding after treatment with Triton X-100 was apparently due to a decrease in the density of PBS, since the affinity remained unaltered. The detergents 3-[(3-cholamidopropyl)-dimethylammonio]-1-propane sulfonate (CHAPS), Tween 20, deoxycholic acid, or digitonin (0.0125%) caused only a minor change in [ 3 H]Ro 5-4864 and [ 3 H]PK 11195 binding to rat kidney membranes; but when concentrations were substantially increased (0.1%), all detergents caused a decrease of at least 50% in [ 3 H]Ro 5-4864 binding, while [ 3 H]PK 11195 binding to rat kidney membranes remained unaffected by the first three detergents, with only a minor decrease (15%) after treatment with digitonin

Differences between tight and loose cultures : A 33-nation study

NARCIS (Netherlands)

Gelfand, M.J.; Raver, R.L.; Nishii, L.; Leslie, L.M.; Lun, J.; Lim, B.C.; Van de Vliert, E.

2011-01-01

With data from 33 nations, we illustrate the differences between cultures that are tight (have many strong norms and a low tolerance of deviant behavior) versus loose (have weak social norms and a high tolerance of deviant behavior). Tightness-looseness is part of a complex, loosely integrated

Pyridoxal 5'-phosphate is a slow tight binding inhibitor of E. coli pyridoxal kinase.

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Mohini S Ghatge

Full Text Available Pyridoxal 5'-phosphate (PLP is a cofactor for dozens of B(6 requiring enzymes. PLP reacts with apo-B(6 enzymes by forming an aldimine linkage with the ε-amino group of an active site lysine residue, thus yielding the catalytically active holo-B(6 enzyme. During protein turnover, the PLP is salvaged by first converting it to pyridoxal by a phosphatase and then back to PLP by pyridoxal kinase. Nonetheless, PLP poses a potential toxicity problem for the cell since its reactive 4'-aldehyde moiety forms covalent adducts with other compounds and non-B(6 proteins containing thiol or amino groups. The regulation of PLP homeostasis in the cell is thus an important, yet unresolved issue. In this report, using site-directed mutagenesis, kinetic, spectroscopic and chromatographic studies we show that pyridoxal kinase from E. coli forms a complex with the product PLP to form an inactive enzyme complex. Evidence is presented that, in the inhibited complex, PLP has formed an aldimine bond with an active site lysine residue during catalytic turnover. The rate of dissociation of PLP from the complex is very slow, being only partially released after a 2-hour incubation with PLP phosphatase. Interestingly, the inactive pyridoxal kinase•PLP complex can be partially reactivated by transferring the tightly bound PLP to an apo-B(6 enzyme. These results open new perspectives on the mechanism of regulation and role of pyridoxal kinase in the Escherichia coli cell.

Effect of Chum Salmon Egg Lectin on Tight Junctions in Caco-2 Cell Monolayers

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Ryo Nemoto

2015-05-01

Full Text Available The effect of a chum salmon egg lectin (CSL3 on tight junction (TJ of Caco-2 cell monolayers was investigated. The lectin opened TJ as indicated by the decrease of the transepithelial electrical resistance (TER value and the increase of the permeation of lucifer yellow, which is transported via the TJ-mediated paracellular pathway. The effects of CSL3 were inhibited by the addition of 10 mM L-rhamnose or D-galactose which were specific sugars for CSL3. The lectin increased the intracellular Ca2+ of Caco-2 cell monolayers, that could be inhibited by the addition of L-rhamnose. The fluorescence immunostaining of β-actin in Caco-2 cell monolayers revealed that the cytoskeleton was changed by the CSL3 treatment, suggesting that CSL3 depolymerized β-actin to cause reversible TJ structural and functional disruption. Although Japanese jack bean lectin and wheat germ lectin showed similar effects in the decrease of the TER values and the increase of the intracellular Ca2+, they could not be inhibited by the same concentrations of simple sugars, such as D-glucose and N-acetyl-D-glucosamine.

Caveolin1 Is Required for Th1 Cell Infiltration, but Not Tight Junction Remodeling, at the Blood-Brain Barrier in Autoimmune Neuroinflammation

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Sarah E. Lutz

2017-11-01

Full Text Available Lymphocytes cross vascular boundaries via either disrupted tight junctions (TJs or caveolae to induce tissue inflammation. In the CNS, Th17 lymphocytes cross the blood-brain barrier (BBB before Th1 cells; yet this differential crossing is poorly understood. We have used intravital two-photon imaging of the spinal cord in wild-type and caveolae-deficient mice with fluorescently labeled endothelial tight junctions to determine how tight junction remodeling and caveolae regulate CNS entry of lymphocytes during the experimental autoimmune encephalomyelitis (EAE model for multiple sclerosis. We find that dynamic tight junction remodeling occurs early in EAE but does not depend upon caveolar transport. Moreover, Th1, but not Th17, lymphocytes are significantly reduced in the inflamed CNS of mice lacking caveolae. Therefore, tight junction remodeling facilitates Th17 migration across the BBB, whereas caveolae promote Th1 entry into the CNS. Moreover, therapies that target both tight junction degradation and caveolar transcytosis may limit lymphocyte infiltration during inflammation.

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

Science.gov (United States)

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.

Sequence-based prediction of protein-binding sites in DNA: comparative study of two SVM models.

Science.gov (United States)

Park, Byungkyu; Im, Jinyong; Tuvshinjargal, Narankhuu; Lee, Wook; Han, Kyungsook

2014-11-01

As many structures of protein-DNA complexes have been known in the past years, several computational methods have been developed to predict DNA-binding sites in proteins. However, its inverse problem (i.e., predicting protein-binding sites in DNA) has received much less attention. One of the reasons is that the differences between the interaction propensities of nucleotides are much smaller than those between amino acids. Another reason is that DNA exhibits less diverse sequence patterns than protein. Therefore, predicting protein-binding DNA nucleotides is much harder than predicting DNA-binding amino acids. We computed the interaction propensity (IP) of nucleotide triplets with amino acids using an extensive dataset of protein-DNA complexes, and developed two support vector machine (SVM) models that predict protein-binding nucleotides from sequence data alone. One SVM model predicts protein-binding nucleotides using DNA sequence data alone, and the other SVM model predicts protein-binding nucleotides using both DNA and protein sequences. In a 10-fold cross-validation with 1519 DNA sequences, the SVM model that uses DNA sequence data only predicted protein-binding nucleotides with an accuracy of 67.0%, an F-measure of 67.1%, and a Matthews correlation coefficient (MCC) of 0.340. With an independent dataset of 181 DNAs that were not used in training, it achieved an accuracy of 66.2%, an F-measure 66.3% and a MCC of 0.324. Another SVM model that uses both DNA and protein sequences achieved an accuracy of 69.6%, an F-measure of 69.6%, and a MCC of 0.383 in a 10-fold cross-validation with 1519 DNA sequences and 859 protein sequences. With an independent dataset of 181 DNAs and 143 proteins, it showed an accuracy of 67.3%, an F-measure of 66.5% and a MCC of 0.329. Both in cross-validation and independent testing, the second SVM model that used both DNA and protein sequence data showed better performance than the first model that used DNA sequence data. To the best of

Revenue Risk of U.S. Tight-Oil Firms

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