Evidence for W=0 pairing in repulsive Hubbard square and hexagonal geometries

NASA Astrophysics Data System (ADS)

Perfetto, Enrico; Stefanucci, Gianluca; Callegari, Agnese; Cini, Michele

2004-08-01

Square and hexagonal lattices with purely repulsive on-site interactions on all sites and appropriate fillings show W=0 pairing, and the effective attractive interaction is due to a symmetry driven correlation effect; the W=0 pairs are two-body singlet eigenstates of the Hamiltonian with vanishing on-site repulsion. We can set up gedanken experiments with these bound pairs. Chains of CuO 4 units connected by weak links provide a test case which displays bound pair hopping and superconducting flux quantization (SFQ). Focusing on the low-energy sector, one obtains an accurate description in terms of an effective hard-core boson Hamiltonian which naturally describes itinerant pairs and SFQ in mesoscopic rings. For the numerical calculations, we take advantage of a recently proposed exact spin-disentangled diagonalization technique which can be generally applied to many-fermion problems and drastically reduces the size of the matrices to be handled. Remarkably, the very same pairing mechanism also works neatly with the wrapped honeycomb lattice, suitable for armchair carbon nanotubes; the binding energy of W=0 pairs depends strongly on the filling and decreases towards a small but non-zero value in the graphite limit.

Paired and interacting galaxies: Conference summary

NASA Technical Reports Server (NTRS)

Norman, Colin A.

1990-01-01

The author gives a summary of the conference proceedings. The conference began with the presentation of the basic data sets on pairs, groups, and interacting galaxies with the latter being further discussed with respect to both global properties and properties of the galactic nuclei. Then followed the theory, modelling and interpretation using analytic techniques, simulations and general modelling for spirals and ellipticals, starbursts and active galactic nuclei. Before the conference the author wrote down the three questions concerning pairs, groups and interacting galaxies that he hoped would be answered at the meeting: (1) How do they form, including the role of initial conditions, the importance of subclustering, the evolution of groups to compact groups, and the fate of compact groups; (2) How do they evolve, including issues such as relevant timescales, the role of halos and the problem of overmerging, the triggering and enhancement of star formation and activity in the galactic nuclei, and the relative importance of dwarf versus giant encounters; and (3) Are they important, including the frequency of pairs and interactions, whether merging and interactions are very important aspects of the life of a normal galaxy at formation, during its evolution, in forming bars, shells, rings, bulges, etc., and in the formation and evolution of active galaxies? Where possible he focuses on these three central issues in the summary.

Ionic fluids with r-6 pair interactions have power-law electrostatic screening

NASA Astrophysics Data System (ADS)

Kjellander, Roland; Forsberg, Björn

2005-06-01

The decay behaviour of radial distribution functions for large distances r is investigated for classical Coulomb fluids where the ions interact with an r-6 potential (e.g. a dispersion interaction) in addition to the Coulombic and the short-range repulsive potentials (e.g. a hard core). The pair distributions and the density-density (NN), charge-density (QN) and charge-charge (QQ) correlation functions are investigated analytically and by Monte Carlo simulations. It is found that the NN correlation function ultimately decays like r-6 for large r, just as it does for fluids of electroneutral particles interacting with an r-6 potential. The prefactor is proportional to the squared compressibility in both cases. The QN correlations decay in general like r-8 and the QQ correlations like r-10 in the ionic fluid. The average charge density around an ion decays generally like r-8 and the average electrostatic potential like r-6. This behaviour is in stark contrast to the decay behaviour for classical Coulomb fluids in the absence of the r-6 potential, where all these functions decay exponentially for large r. The power-law decays are, however, the same as for quantum Coulomb fluids. This indicates that the inclusion of the dispersion interaction as an effective r-6 interaction potential in classical systems yields the same decay behaviour for the pair correlations as in quantum ionic systems. An exceptional case is the completely symmetric binary electrolyte for which only the NN correlation has a power-law decay but not the QQ correlations. These features are shown by an analysis of the bridge function.

Galaxy And Mass Assembly (GAMA): the life and times of L★ galaxies

NASA Astrophysics Data System (ADS)

Robotham, A. S. G.; Liske, J.; Driver, S. P.; Sansom, A. E.; Baldry, I. K.; Bauer, A. E.; Bland-Hawthorn, J.; Brough, S.; Brown, M. J. I.; Colless, M.; Christodoulou, L.; Drinkwater, M. J.; Grootes, M. W.; Hopkins, A. M.; Kelvin, L. S.; Norberg, P.; Loveday, J.; Phillipps, S.; Sharp, R.; Taylor, E. N.; Tuffs, R. J.

2013-05-01

In this work, we investigate in detail the effects the local environment (groups and pairs) has on galaxies with stellar mass similar to the Milky Way (L* galaxies). A volume limited sample of 6150 galaxies are visually classified to determine the emission features, morphological type and presence of a disc. This large sample allows for the significant characteristics of galaxies to be isolated (e.g. stellar mass and group halo mass), and their codependencies determined. We observe that galaxy-galaxy interactions play the most important role in shaping the evolution within a group halo; the main role of halo mass is in gathering the galaxies together to encourage such interactions. Dominant pair galaxies find their overall star formation enhanced when the pair's mass ratio is close to 1; otherwise, we observe the same galaxies as we would in an unpaired system. The minor galaxy in a pair is greatly affected by its companion galaxy, and while the star-forming fraction is always suppressed relative to equivalent stellar mass unpaired galaxies, it becomes lower still when the mass ratio of a pair system increases. We find that, in general, the close galaxy-galaxy interaction rate drops as a function of halo mass for a given amount of stellar mass. We find evidence of a local peak of interactions for Milky Way stellar mass galaxies in Milky Way halo mass groups. Low-mass haloes, and in particular Local Group mass haloes, are an important environment for understanding the typical evolutionary path of a unit of stellar mass. We find compelling evidence for galaxy conformity in both groups and pairs, where morphological type conformity is dominant in groups, and emission class conformity is dominant in pairs. This suggests that group scale conformity is the result of many galaxy encounters over an extended period of time, while pair conformity is a fairly instantaneous response to a transitory interaction.

Enhancer Sharing Promotes Neighborhoods of Transcriptional Regulation Across Eukaryotes

PubMed Central

Quintero-Cadena, Porfirio; Sternberg, Paul W.

2016-01-01

Enhancers physically interact with transcriptional promoters, looping over distances that can span multiple regulatory elements. Given that enhancer–promoter (EP) interactions generally occur via common protein complexes, it is unclear whether EP pairing is predominantly deterministic or proximity guided. Here, we present cross-organismic evidence suggesting that most EP pairs are compatible, largely determined by physical proximity rather than specific interactions. By reanalyzing transcriptome datasets, we find that the transcription of gene neighbors is correlated over distances that scale with genome size. We experimentally show that nonspecific EP interactions can explain such correlation, and that EP distance acts as a scaling factor for the transcriptional influence of an enhancer. We propose that enhancer sharing is commonplace among eukaryotes, and that EP distance is an important layer of information in gene regulation. PMID:27799341

Plant-pollinator interactions in a biodiverse meadow are rather stable and tight for 3 consecutive years.

PubMed

Fang, Qiang; Huang, Shuangquan

2016-05-01

Plant-pollinator interactions can be highly variable across years in natural communities. Although variation in the species composition and its basic structure has been investigated to understand the dynamic nature of pollination networks, little is known about the temporal dynamic of interaction strength between the same plant and pollinator species in any natural community. Pollinator-mediated selection on the evolution of floral traits could be diminished if plant-pollinator interactions vary temporally. To quantify the temporal variation in plant-pollinator interactions and the interaction strength (observed visits), we compared weighted networks between plants and pollinators in a biodiverse alpine meadow in Shangri-La, southwest China for 3 consecutive years. Although plant-pollinator interactions were highly dynamic such that identical interactions only accounted for 10.7% of the total between pair years, the diversity of interactions was stable. These identical interactions contributed 41.2% of total visits and were similar in strength and weighted nestedness. For plant species, 72.6% of species were visited by identical pollinator species between pair years, accounting for over half of the total visits and three-quarters at the functional group level. More generalized pollinators contributed more connectiveness and were more central in networks across years. However, there was no similar or even opposite trend for plant species, which suggested that specialized plant species may also be central in pollinator networks. The variation in pollinator composition decreased as pollinator species numbers increased, suggesting that generalized plants experienced stable pollinator partition. The stable, tight interactions between generalized pollinators and specialized plants represent cornerstones of the studied community. © 2016 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and John Wiley & Sons Australia, Ltd.

Fission and fusion interaction phenomena of mixed lump kink solutions for a generalized (3+1)-dimensional B-type Kadomtsev-Petviashvili equation

NASA Astrophysics Data System (ADS)

Liu, Yaqing; Wen, Xiaoyong

2018-05-01

In this paper, a generalized (3+1)-dimensional B-type Kadomtsev-Petviashvili (gBKP) equation is investigated by using the Hirota’s bilinear method. With the aid of symbolic computation, some new lump, mixed lump kink and periodic lump solutions are derived. Based on the derived solutions, some novel interaction phenomena like the fission and fusion interactions between one lump soliton and one kink soliton, the fission and fusion interactions between one lump soliton and a pair of kink solitons and the interactions between two periodic lump solitons are discussed graphically. Results might be helpful for understanding the propagation of the shallow water wave.

Moving Beyond Quantum Mechanics in Search for a Generalized Theory of Superconductivity

NASA Astrophysics Data System (ADS)

Akpojotor, Godfrey; Animalu, Alexander

2012-02-01

Though there are infinite number of theories currently in the literature in the search for a generalized theory of superconductivity (SC), there may be three domineering mechanisms for the Cooper pair formation (CPF) and their emergent theories of SC. Two of these mechanisms, electron-phonon interactions and electron-electron correlations which are based on the quantum theory axiom of action-at-a distance, may be only an approximation of the third mechanism which is contact interaction of the wavepackets of the two electrons forming the Cooper pair as envisaged in hadronic mechanics to be responsible for natural bonding of elements. The application of this hydronic --type interaction to the superconducting cuprates, iron based compounds and heavy fermions leads to interesting results. It is therefore suggested that the future of the search for the theory of SC may be considered from this natural possible bonding that at short distances, the CPF is by a nonlinear, nonlocal and nonhamiltonian strong hadronic-type interactions due to deep wave-overlapping of spinning particles leading to Hulthen potential that is attractive between two electrons in singlet couplings while at large distances the CPF is by superexchange interaction which is purely a quantum mechanical affairs.

Pairing phase diagram of three holes in the generalized Hubbard model

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

Navarro, O.; Espinosa, J.E.

Investigations of high-{Tc} superconductors suggest that the electronic correlation may play a significant role in the formation of pairs. Although the main interest is on the physic of two-dimensional highly correlated electron systems, the one-dimensional models related to high temperature superconductivity are very popular due to the conjecture that properties of the 1D and 2D variants of certain models have common aspects. Within the models for correlated electron systems, that attempt to capture the essential physics of high-temperature superconductors and parent compounds, the Hubbard model is one of the simplest. Here, the pairing problem of a three electrons system hasmore » been studied by using a real-space method and the generalized Hubbard Hamiltonian. This method includes the correlated hopping interactions as an extension of the previously proposed mapping method, and is based on mapping the correlated many body problem onto an equivalent site- and bond-impurity tight-binding one in a higher dimensional space, where the problem was solved in a non-perturbative way. In a linear chain, the authors analyzed the pairing phase diagram of three correlated holes for different values of the Hamiltonian parameters. For some value of the hopping parameters they obtain an analytical solution for all kind of interactions.« less

Hole superconductivity in a generalized two-band model

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

Hong, X.Q.; Hirsch, J.E.

1992-06-01

We study superconductivity in a two-band model that generalizes the model introduced by Suhl, Matthias, and Walker: All possible interaction terms coupling both bands are included. The pairing interaction is assumed to originate in the momentum dependence of the intraband interactions that arises in the model of hole superconductivity. The model generically displays a single critical temperature and two gaps, with the larger gap associated with the band with strongest holelike character to the carriers. The dependence of the critical temperature and of the magnitudes of the gaps on the various parameters in the Hamiltonian is studied.

Brief Introduction to Higher Education Institutions in China.

DTIC Science & Technology

1984-01-12

were sent to foreign countries to study. Through these activities, the friendship and interaction with foreign scholars and experts have been promoted...the interaction between each pair of echoes was presented for the first time. The paper (overall reactance = general theory on opposing end networks...the school for a visit. The number of people reached over 500. These exchange and interaction activities promoted the friendship with foreign scholars

Common misconceptions about the dynamical theory of crystal lattices: Cauchy relations, lattice potentials and infinite crystals

NASA Astrophysics Data System (ADS)

Elcoro, Luis; Etxebarria, Jesús

2011-01-01

The requirement of rotational invariance for lattice potential energies is investigated. Starting from this condition, it is shown that the Cauchy relations for the elastic constants are fulfilled if the lattice potential is built from pair interactions or when the first-neighbour approximation is adopted. This is seldom recognized in widely used solid-state textbooks. Frequently, pair interaction is even considered to be the most general situation. In addition, it is shown that the demand of rotational invariance in an infinite crystal leads to inconsistencies in the symmetry of the elastic tensor. However, for finite crystals, no problems arise, and the Huang conditions are deduced using exclusively a microscopic approach for the elasticity theory, without making any reference to macroscopic parameters. This work may be useful in both undergraduate and graduate level courses to point out the crudeness of the pair-potential interaction and to explore the limits of the infinite-crystal approximation.

The Radical Pair Mechanism and the Avian Chemical Compass: Quantum Coherence and Entanglement

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

Zhang, Yiteng; Kais, Sabre; Berman, Gennady Petrovich

2015-02-02

We review the spin radical pair mechanism which is a promising explanation of avian navigation. This mechanism is based on the dependence of product yields on 1) the hyperfine interaction involving electron spins and neighboring nuclear spins and 2) the intensity and orientation of the geomagnetic field. One surprising result is that even at ambient conditions quantum entanglement of electron spins can play an important role in avian magnetoreception. This review describes the general scheme of chemical reactions involving radical pairs generated from singlet and triplet precursors; the spin dynamics of the radical pairs; and the magnetic field dependence ofmore » product yields caused by the radical pair mechanism. The main part of the review includes a description of the chemical compass in birds. We review: the general properties of the avian compass; the basic scheme of the radical pair mechanism; the reaction kinetics in cryptochrome; quantum coherence and entanglement in the avian compass; and the effects of noise. We believe that the quantum avian compass can play an important role in avian navigation and can also provide the foundation for a new generation of sensitive and selective magnetic-sensing nano-devices.« less

Control of Nonlinear Systems

DTIC Science & Technology

2004-01-01

variables reinforce each other (positive feedback) as well as certain more general systems in which each pair of variables may affect each other in...characteristics, and applied to presented small-gain theorems guaranteeing the lack of oscillatory or more complicated behavior in a large class of Lotka ... Volterra systems with predator-prey interactions as well as chemostats, which describe the interaction between microbial species which are competing

Pairing versus quarteting coherence length

NASA Astrophysics Data System (ADS)

Delion, D. S.; Baran, V. V.

2015-02-01

We systematically analyze the coherence length in even-even nuclei. The pairing coherence length in the spin-singlet channel for the effective density-dependent delta (DDD) and Gaussian interaction is estimated. We consider in our calculations bound states as well as narrow resonances. It turns out that the pairing gaps given by the DDD interaction are similar to those of the Gaussian potential if one renormalizes the radial width to the nuclear radius. The correlations induced by the pairing interaction have, in all considered cases, a long-range character inside the nucleus and a decrease towards the surface. The mean coherence length is larger than the geometrical radius for light nuclei and approaches this value for heavy nuclei. The effect of the temperature and states in the continuum is investigated. Strong shell effects are put in evidence, especially for protons. We generalize this concept to quartets by considering similar relations, but between proton and neutron pairs. The quartet coherence length has a similar shape, but with larger values on the nuclear surface. We provide evidence of the important role of proton-neutron correlations by estimating the so-called alpha coherence length, which takes into account the overlap with the proton-neutron part of the α -particle wave function. It turns out that it does not depend on the nuclear size and has a value comparable to the free α -particle radius. We have shown that pairing correlations are mainly concentrated inside the nucleus, while quarteting correlations are connected to the nuclear surface.

Topological Nodal Cooper Pairing in Doped Weyl Metals

NASA Astrophysics Data System (ADS)

Li, Yi; Haldane, F. D. M.

2018-02-01

We generalize the concept of Berry connection of the single-electron band structure to that of a two-particle Cooper pairing state between two Fermi surfaces with opposite Chern numbers. Because of underlying Fermi surface topology, the pairing Berry phase acquires nontrivial monopole structure. Consequently, pairing gap functions have topologically protected nodal structure as vortices in the momentum space with the total vorticity solely determined by the pair monopole charge qp. The nodes of gap function behave as the Weyl-Majorana points of the Bogoliubov-de Gennes pairing Hamiltonian. Their relation with the connection patterns of the surface modes from the Weyl band structure and the Majorana surface modes inside the pairing gap is also discussed. Under the approximation of spherical Fermi surfaces, the pairing symmetry are represented by monopole harmonic functions. The lowest possible pairing channel carries angular momentum number j =|qp|, and the corresponding gap functions are holomorphic or antiholomorphic functions on Fermi surfaces. After projected on the Fermi surfaces with nontrivial topology, all the partial-wave channels of pairing interactions acquire the monopole charge qp independent of concrete pairing mechanism.

Interactive effects of prey and weather on golden eagle reproduction

USGS Publications Warehouse

Steenhof, Karen; Kochert, Michael N.; McDonald, T.L.

1997-01-01

1. The reproduction of the golden eagle Aquila chrysaetos was studied in southwestern Idaho for 23 years, and the relationship between eagle reproduction and jackrabbit Lepus californicus abundance, weather factors, and their interactions, was modelled using general linear models. Backward elimination procedures were used to arrive at parsimonious models.2. The number of golden eagle pairs occupying nesting territories each year showed a significant decline through time that was unrelated to either annual rabbit abundance or winter severity. However, eagle hatching dates were significantly related to both winter severity and jackrabbit abundance. Eagles hatched earlier when jackrabbits were abundant, and they hatched later after severe winters.3. Jackrabbit abundance influenced the proportion of pairs that laid eggs, the proportion of pairs that were successful, mean brood size at fledging, and the number of young fledged per pair. Weather interacted with prey to influence eagle reproductive rates.4. Both jackrabbit abundance and winter severity were important in predicting the percentage of eagle pairs that laid eggs. Percentage laying was related positively to jackrabbit abundance and inversely related to winter severity.5. The variables most useful in predicting percentage of laying pairs successful were rabbit abundance and the number of extremely hot days during brood-rearing. The number of hot days and rabbit abundance were also significant in a model predicting eagle brood size at fledging. Both success and brood size were positively related to jackrabbit abundance and inversely related to the frequency of hot days in spring.6. Eagle reproduction was limited by rabbit abundance during approximately twothirds of the years studied. Weather influenced how severely eagle reproduction declined in those years.7. This study demonstrates that prey and weather can interact to limit a large raptor population's productivity. Smaller raptors could be affected more strongly, especially in colder or wetter climates.

DNA hybridization kinetics: zippering, internal displacement and sequence dependence.

PubMed

Ouldridge, Thomas E; Sulc, Petr; Romano, Flavio; Doye, Jonathan P K; Louis, Ard A

2013-10-01

Although the thermodynamics of DNA hybridization is generally well established, the kinetics of this classic transition is less well understood. Providing such understanding has new urgency because DNA nanotechnology often depends critically on binding rates. Here, we explore DNA oligomer hybridization kinetics using a coarse-grained model. Strand association proceeds through a complex set of intermediate states, with successful binding events initiated by a few metastable base-pairing interactions, followed by zippering of the remaining bonds. But despite reasonably strong interstrand interactions, initial contacts frequently dissociate because typical configurations in which they form differ from typical states of similar enthalpy in the double-stranded equilibrium ensemble. Initial contacts must be stabilized by two or three base pairs before full zippering is likely, resulting in negative effective activation enthalpies. Non-Arrhenius behavior arises because the number of base pairs required for nucleation increases with temperature. In addition, we observe two alternative pathways-pseudoknot and inchworm internal displacement-through which misaligned duplexes can rearrange to form duplexes. These pathways accelerate hybridization. Our results explain why experimentally observed association rates of GC-rich oligomers are higher than rates of AT- rich equivalents, and more generally demonstrate how association rates can be modulated by sequence choice.

Thermal motion in proteins: Large effects on the time-averaged interaction energies

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

Goethe, Martin, E-mail: martingoethe@ub.edu; Rubi, J. Miguel; Fita, Ignacio

As a consequence of thermal motion, inter-atomic distances in proteins fluctuate strongly around their average values, and hence, also interaction energies (i.e. the pair-potentials evaluated at the fluctuating distances) are not constant in time but exhibit pronounced fluctuations. These fluctuations cause that time-averaged interaction energies do generally not coincide with the energy values obtained by evaluating the pair-potentials at the average distances. More precisely, time-averaged interaction energies behave typically smoother in terms of the average distance than the corresponding pair-potentials. This averaging effect is referred to as the thermal smoothing effect. Here, we estimate the strength of the thermal smoothingmore » effect on the Lennard-Jones pair-potential for globular proteins at ambient conditions using x-ray diffraction and simulation data of a representative set of proteins. For specific atom species, we find a significant smoothing effect where the time-averaged interaction energy of a single atom pair can differ by various tens of cal/mol from the Lennard-Jones potential at the average distance. Importantly, we observe a dependency of the effect on the local environment of the involved atoms. The effect is typically weaker for bulky backbone atoms in beta sheets than for side-chain atoms belonging to other secondary structure on the surface of the protein. The results of this work have important practical implications for protein software relying on free energy expressions. We show that the accuracy of free energy expressions can largely be increased by introducing environment specific Lennard-Jones parameters accounting for the fact that the typical thermal motion of protein atoms depends strongly on their local environment.« less

Thermal motion in proteins: Large effects on the time-averaged interaction energies

NASA Astrophysics Data System (ADS)

Goethe, Martin; Fita, Ignacio; Rubi, J. Miguel

2016-03-01

As a consequence of thermal motion, inter-atomic distances in proteins fluctuate strongly around their average values, and hence, also interaction energies (i.e. the pair-potentials evaluated at the fluctuating distances) are not constant in time but exhibit pronounced fluctuations. These fluctuations cause that time-averaged interaction energies do generally not coincide with the energy values obtained by evaluating the pair-potentials at the average distances. More precisely, time-averaged interaction energies behave typically smoother in terms of the average distance than the corresponding pair-potentials. This averaging effect is referred to as the thermal smoothing effect. Here, we estimate the strength of the thermal smoothing effect on the Lennard-Jones pair-potential for globular proteins at ambient conditions using x-ray diffraction and simulation data of a representative set of proteins. For specific atom species, we find a significant smoothing effect where the time-averaged interaction energy of a single atom pair can differ by various tens of cal/mol from the Lennard-Jones potential at the average distance. Importantly, we observe a dependency of the effect on the local environment of the involved atoms. The effect is typically weaker for bulky backbone atoms in beta sheets than for side-chain atoms belonging to other secondary structure on the surface of the protein. The results of this work have important practical implications for protein software relying on free energy expressions. We show that the accuracy of free energy expressions can largely be increased by introducing environment specific Lennard-Jones parameters accounting for the fact that the typical thermal motion of protein atoms depends strongly on their local environment.

Resonance production in. gamma gamma. collisions

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

Renard, F.M.

1983-04-01

The processes ..gamma gamma.. ..-->.. hadrons can be depicted as follows. One photon creates a q anti q pair which starts to evolve; the other photon can either (A) make its own q anti q pair and the (q anti q q anti q) system continue to evolve or (B) interact with the quarks of the first pair and lead to a modified (q anti q) system in interaction with C = +1 quantum numbers. A review of the recent theoretical activity concerning resonance production and related problems is given under the following headings: hadronic C = +1 spectroscopy (qmore » anti q, qq anti q anti q, q anti q g, gg, ggg bound states and mixing effects); exclusive ..gamma gamma.. processes (generalities, unitarized Born method, VDM and QCD); total cross section (soft and hard contributions); q/sup 2/ dependence of soft processes (soft/hard separation, 1/sup +- +/ resonances); and polarization effects. (WHK)« less

Spin-Triplet Pairing Induced by Spin-Singlet Interactions in Noncentrosymmetric Superconductors

NASA Astrophysics Data System (ADS)

Matsuzaki, Tomoaki; Shimahara, Hiroshi

2017-02-01

In noncentrosymmetric superconductors, we examine the effect of the difference between the intraband and interband interactions, which becomes more important when the band splitting increases. We define the difference ΔVμ between their coupling constants, i.e., that between the intraband and interband hopping energies of intraband Cooper pairs. Here, the subscript μ of ΔVμ indicates that the interactions scatter the spin-singlet and spin-triplet pairs when μ = 0 and μ = 1,2,3, respectively. It is shown that the strong antisymmetric spin-orbit interaction reverses the target spin parity of the interaction: it converts the spin-singlet and spin-triplet interactions represented by ΔV0 and ΔVμ>0 into effective spin-triplet and spin-singlet pairing interactions, respectively. Hence, for example, triplet pairing can be induced solely by the singlet interaction ΔV0. We name the pairing symmetry of the system after that of the intraband Cooper pair wave function, but with an odd-parity phase factor excluded. The pairing symmetry must then be even, even for the triplet component, and the following results are obtained. When ΔVμ is small, the spin-triplet p-wave interactions induce spin-triplet s-wave and spin-triplet d-wave pairings in the regions where the repulsive singlet s-wave interaction is weak and strong, respectively. When ΔV0 is large, a repulsive interband spin-singlet interaction can stabilize spin-triplet pairing. When the Rashba interaction is adopted for the spin-orbit interaction, the spin-triplet pairing interactions mediated by transverse magnetic fluctuations do not contribute to triplet pairing.

Some Interaction Solutions of a Reduced Generalised (3+1)-Dimensional Shallow Water Wave Equation for Lump Solutions and a Pair of Resonance Solitons

NASA Astrophysics Data System (ADS)

Wang, Yao; Chen, Mei-Dan; Li, Xian; Li, Biao

2017-05-01

Through Hirota bilinear transformation and symbolic computation with Maple, a class of lump solutions, rationally localised in all directions in the space, to a reduced generalised (3+1)-dimensional shallow water wave (SWW) equation are prensented. The resulting lump solutions all contain six parameters, two of which are free due to the translation invariance of the SWW equation and the other four of which must satisfy a nonzero determinant condition guaranteeing analyticity and rational localisation of the solutions. Then we derived the interaction solutions for lump solutions and one stripe soliton and the result shows that the particular lump solutions with specific values of the involved parameters will be drowned or swallowed by the stripe soliton. Furthermore, we extend this method to a more general combination of positive quadratic function and hyperbolic functions. Especially, it is interesting that a rogue wave is found to be aroused by the interaction between lump solutions and a pair of resonance stripe solitons. By choosing the values of the parameters, the dynamic properties of lump solutions, interaction solutions for lump solutions and one stripe soliton and interaction solutions for lump solutions and a pair of resonance solitons, are shown by dynamic graphs.

Effective fragment potential study of the interaction of DNA bases.

PubMed

Smith, Quentin A; Gordon, Mark S; Slipchenko, Lyudmila V

2011-10-20

Hydrogen-bonded and stacked structures of adenine-thymine and guanine-cytosine nucleotide base pairs, along with their methylated analogues, are examined with the ab inito based general effective fragment potential (EFP2) method. A comparison of coupled cluster with single, double, and perturbative triple (CCSD(T)) energies is presented, along with an EFP2 energy decomposition to illustrate the components of the interaction energy.

Protein-protein interactions in paralogues: Electrostatics modulates specificity on a conserved steric scaffold

PubMed Central

Huber, Roland G.; Bond, Peter J.

2017-01-01

An improved knowledge of protein-protein interactions is essential for better understanding of metabolic and signaling networks, and cellular function. Progress tends to be based on structure determination and predictions using known structures, along with computational methods based on evolutionary information or detailed atomistic descriptions. We hypothesized that for the case of interactions across a common interface, between proteins from a pair of paralogue families or within a family of paralogues, a relatively simple interface description could distinguish between binding and non-binding pairs. Using binding data for several systems, and large-scale comparative modeling based on known template complex structures, it is found that charge-charge interactions (for groups bearing net charge) are generally a better discriminant than buried non-polar surface. This is particularly the case for paralogue families that are less divergent, with more reliable comparative modeling. We suggest that electrostatic interactions are major determinants of specificity in such systems, an observation that could be used to predict binding partners. PMID:29016650

Protein-protein interactions in paralogues: Electrostatics modulates specificity on a conserved steric scaffold.

PubMed

Ivanov, Stefan M; Cawley, Andrew; Huber, Roland G; Bond, Peter J; Warwicker, Jim

2017-01-01

An improved knowledge of protein-protein interactions is essential for better understanding of metabolic and signaling networks, and cellular function. Progress tends to be based on structure determination and predictions using known structures, along with computational methods based on evolutionary information or detailed atomistic descriptions. We hypothesized that for the case of interactions across a common interface, between proteins from a pair of paralogue families or within a family of paralogues, a relatively simple interface description could distinguish between binding and non-binding pairs. Using binding data for several systems, and large-scale comparative modeling based on known template complex structures, it is found that charge-charge interactions (for groups bearing net charge) are generally a better discriminant than buried non-polar surface. This is particularly the case for paralogue families that are less divergent, with more reliable comparative modeling. We suggest that electrostatic interactions are major determinants of specificity in such systems, an observation that could be used to predict binding partners.

Corresponding-states laws for protein solutions.

PubMed

Katsonis, Panagiotis; Brandon, Simon; Vekilov, Peter G

2006-09-07

The solvent around protein molecules in solutions is structured and this structuring introduces a repulsion in the intermolecular interaction potential at intermediate separations. We use Monte Carlo simulations with isotropic, pair-additive systems interacting with such potentials. We test if the liquid-liquid and liquid-solid phase lines in model protein solutions can be predicted from universal curves and a pair of experimentally determined parameters, as done for atomic and colloid materials using several laws of corresponding states. As predictors, we test three properties at the critical point for liquid-liquid separation: temperature, as in the original van der Waals law, the second virial coefficient, and a modified second virial coefficient, all paired with the critical volume fraction. We find that the van der Waals law is best obeyed and appears more general than its original formulation: A single universal curve describes all tested nonconformal isotropic pair-additive systems. Published experimental data for the liquid-liquid equilibrium for several proteins at various conditions follow a single van der Waals curve. For the solid-liquid equilibrium, we find that no single system property serves as its predictor. We go beyond corresponding-states correlations and put forth semiempirical laws, which allow prediction of the critical temperature and volume fraction solely based on the range of attraction of the intermolecular interaction potential.

Modulational instability, beak-shaped rogue waves, multi-dark-dark solitons and dynamics in pair-transition-coupled nonlinear Schrödinger equations.

PubMed

Zhang, Guoqiang; Yan, Zhenya; Wen, Xiao-Yong

2017-07-01

The integrable coupled nonlinear Schrödinger equations with four-wave mixing are investigated. We first explore the conditions for modulational instability of continuous waves of this system. Secondly, based on the generalized N -fold Darboux transformation (DT), beak-shaped higher-order rogue waves (RWs) and beak-shaped higher-order rogue wave pairs are derived for the coupled model with attractive interaction in terms of simple determinants. Moreover, we derive the simple multi-dark-dark and kink-shaped multi-dark-dark solitons for the coupled model with repulsive interaction through the generalizing DT. We explore their dynamics and classifications by different kinds of spatial-temporal distribution structures including triangular, pentagonal, 'claw-like' and heptagonal patterns. Finally, we perform the numerical simulations to predict that some dark solitons and RWs are stable enough to develop within a short time. The results would enrich our understanding on nonlinear excitations in many coupled nonlinear wave systems with transition coupling effects.

BCS-Bose model of exotic superconductors: Generalized coherence length

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

Casas, M.; Getino, J.M.; de Llano, M.

1994-12-01

Analytic expressions are derived for the root-mean-square (rms) radius of a pair of fermions in a BCS many-fermion state in one, two, and three dimensions, in terms of the BCS gap energy and the associated chemical potential. These expressions are valid for any coupling strength of [ital any] pair interaction model implying a momentum-independent gap energy. The latter holds, e.g., for an attractive [delta] pair potential examined in the one-dimensional (1D) case (whose [ital N]-fermion ground state can be determined exactly) or for the BCS (electron-phonon) model interaction in any dimension. Weak-coupling and/or high-density limits for the rms radius aremore » identical in 1D, 2D, and 3D, and reduce to the familiar well-known Pippard result to within a factor of order unity. In contrast, strong-coupling and/or low-density limits coincide in 1D and 3D, but differ by a factor of order unity in the 2D limit, and in each case are essentially the size of a single, isolated pair. The 1D [delta] interaction McGuire-Yang-Gaudin many-fermion model is studied in detail. The interaction renormalization scheme of Miyake and of Randeria, Duan, and Shieh, and the BCS interaction model, both in 2D, are employed to analyze cuprate superconductor empirical results. Reasonable agreement between theoretical rms radii with experimental coherence lengths suggests that cuprates can be described moderately well as [ital weakly] [ital coupled] superconductors within the BCS-Bose formalism.« less

Griffiths' inequalities for Ashkin-Teller model

NASA Technical Reports Server (NTRS)

Lee, C. T.

1973-01-01

The two Griffiths' (1967) inequalities for the correlation functions of Ising ferromagnets with two-body interactions, and two other inequalities obtained by Kelly and Sherman (1968) and by Sherman (1969) are shown to hold not only for the Ashkin-Teller (1943) model but also for a generalized Ashkin-Teller model (Kihara et al., 1954) with many-body interactions involving arbitrary clusters of particles. A cluster of particles is understood to mean a collection of pairs of particles rather than a group of particles. The four generalized inequalities under consideration are presented in the form of theorems, and a new inequality is obtained.

A multilevel-skin neighbor list algorithm for molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Zhang, Chenglong; Zhao, Mingcan; Hou, Chaofeng; Ge, Wei

2018-01-01

Searching of the interaction pairs and organization of the interaction processes are important steps in molecular dynamics (MD) algorithms and are critical to the overall efficiency of the simulation. Neighbor lists are widely used for these steps, where thicker skin can reduce the frequency of list updating but is discounted by more computation in distance check for the particle pairs. In this paper, we propose a new neighbor-list-based algorithm with a precisely designed multilevel skin which can reduce unnecessary computation on inter-particle distances. The performance advantages over traditional methods are then analyzed against the main simulation parameters on Intel CPUs and MICs (many integrated cores), and are clearly demonstrated. The algorithm can be generalized for various discrete simulations using neighbor lists.

Role of the pair potential for the saturation of generalized Pauli constraints

NASA Astrophysics Data System (ADS)

Legeza, Örs; Schilling, Christian

2018-05-01

The dependence of the (quasi-)saturation of the generalized Pauli constraints on the pair potential is studied for ground states of few-fermion systems. For this, we consider spinless fermions in one dimension which are harmonically confined and interact by pair potentials of the form | xi-xj|s with -1 ≤s ≤5 . We use the density matrix renormalization group approach and large orbital basis to achieve the convergence on more than ten digits of both the variational energy and the natural occupation numbers. Our results confirm that the conflict between energy minimization and fermionic exchange symmetry results in a universal and nontrivial quasisaturation of the generalized Pauli constraints (quasipinning), implying tremendous structural simplifications of the fermionic ground state for all s . Those numerically exact results are complemented by an analytical study based on a self-consistent perturbation theory which we develop for this purpose. The respective results for the weak-coupling regime eventually elucidate the singular behavior found for the specific values s =2 ,4 ,..., resulting in an extremely strong quasipinning.

From bare to renormalized order parameter in gauge space: Structure and reactions

NASA Astrophysics Data System (ADS)

Potel, G.; Idini, A.; Barranco, F.; Vigezzi, E.; Broglia, R. A.

2017-09-01

It is not physically obvious why one can calculate with similar accuracy, as compared to the experimental data, the absolute cross section associated with two-nucleon transfer processes between members of pairing rotational bands, making use of simple BCS (constant matrix elements) or of many-body [Nambu-Gorkov (NG), nuclear field theory (NFT)] spectroscopic amplitudes. Restoration of spontaneous symmetry breaking and associated emergent generalized rigidity in gauge space provides the answer and points to a new emergence: A physical sum rule resulting from the intertwining of structure and reaction processes, closely connected with the central role induced pairing interaction plays in structure, together with the fact that successive transfer dominates Cooper pair tunneling.

Boosting compound-protein interaction prediction by deep learning.

PubMed

Tian, Kai; Shao, Mingyu; Wang, Yang; Guan, Jihong; Zhou, Shuigeng

2016-11-01

The identification of interactions between compounds and proteins plays an important role in network pharmacology and drug discovery. However, experimentally identifying compound-protein interactions (CPIs) is generally expensive and time-consuming, computational approaches are thus introduced. Among these, machine-learning based methods have achieved a considerable success. However, due to the nonlinear and imbalanced nature of biological data, many machine learning approaches have their own limitations. Recently, deep learning techniques show advantages over many state-of-the-art machine learning methods in some applications. In this study, we aim at improving the performance of CPI prediction based on deep learning, and propose a method called DL-CPI (the abbreviation of Deep Learning for Compound-Protein Interactions prediction), which employs deep neural network (DNN) to effectively learn the representations of compound-protein pairs. Extensive experiments show that DL-CPI can learn useful features of compound-protein pairs by a layerwise abstraction, and thus achieves better prediction performance than existing methods on both balanced and imbalanced datasets. Copyright © 2016 Elsevier Inc. All rights reserved.

Spectral properties of excitons in the bilayer graphene

NASA Astrophysics Data System (ADS)

Apinyan, V.; Kopeć, T. K.

2018-01-01

In this paper, we consider the spectral properties of the bilayer graphene with the local excitonic pairing interaction between the electrons and holes. We consider the generalized Hubbard model, which includes both intralayer and interlayer Coulomb interaction parameters. The solution of the excitonic gap parameter is used to calculate the electronic band structure, single-particle spectral functions, the hybridization gap, and the excitonic coherence length in the bilayer graphene. We show that the local interlayer Coulomb interaction is responsible for the semimetal-semiconductor transition in the double layer system, and we calculate the hybridization gap in the band structure above the critical interaction value. The formation of the excitonic band gap is reported as the threshold process and the momentum distribution functions have been calculated numerically. We show that in the weak coupling limit the system is governed by the Bardeen-Cooper-Schrieffer (BCS)-like pairing state. Contrary, in the strong coupling limit the excitonic condensate states appear in the semiconducting phase, by forming the Dirac's pockets in the reciprocal space.

Effects of ligand electronegativity on recoupled pair bonds with application to sulfurane precursors.

PubMed

Lindquist, Beth A; Woon, David E; Dunning, Thom H

2014-07-31

Recoupled pair bonds (RPBs) are conditional bonds-they only form for selected central atoms and ligands. A complete theoretical description of RPBs requires an understanding of the properties of the central atom and ligands that enable such bonds to be formed. In this work, we show that ligand electronegativity is positively correlated with recoupled pair bond strength for a variety of ligands interacting with the 3p(2) pair of sulfur. We also describe substituent (X) effects on the SF(a(4)Σ(-)) state by investigating X2SF species. These effects generally mirror those observed for covalently bound analogues, but we found that recoupled pair bonding can lead to breakdowns in the expected relationships among bond length, strength, and force constant for some of these species. Finally, we compare the properties of two molecules of practical interest that are bound by recoupled pair bonds: the dimethyl sulfur fluoride and hydroxide radicals (DMS-F and DMS-OH).

Genome-Scale Screening of Drug-Target Associations Relevant to Ki Using a Chemogenomics Approach

PubMed Central

Cao, Dong-Sheng; Liang, Yi-Zeng; Deng, Zhe; Hu, Qian-Nan; He, Min; Xu, Qing-Song; Zhou, Guang-Hua; Zhang, Liu-Xia; Deng, Zi-xin; Liu, Shao

2013-01-01

The identification of interactions between drugs and target proteins plays a key role in genomic drug discovery. In the present study, the quantitative binding affinities of drug-target pairs are differentiated as a measurement to define whether a drug interacts with a protein or not, and then a chemogenomics framework using an unbiased set of general integrated features and random forest (RF) is employed to construct a predictive model which can accurately classify drug-target pairs. The predictability of the model is further investigated and validated by several independent validation sets. The built model is used to predict drug-target associations, some of which were confirmed by comparing experimental data from public biological resources. A drug-target interaction network with high confidence drug-target pairs was also reconstructed. This network provides further insight for the action of drugs and targets. Finally, a web-based server called PreDPI-Ki was developed to predict drug-target interactions for drug discovery. In addition to providing a high-confidence list of drug-target associations for subsequent experimental investigation guidance, these results also contribute to the understanding of drug-target interactions. We can also see that quantitative information of drug-target associations could greatly promote the development of more accurate models. The PreDPI-Ki server is freely available via: http://sdd.whu.edu.cn/dpiki. PMID:23577055

Profiling cellular protein complexes by proximity ligation with dual tag microarray readout.

PubMed

Hammond, Maria; Nong, Rachel Yuan; Ericsson, Olle; Pardali, Katerina; Landegren, Ulf

2012-01-01

Patterns of protein interactions provide important insights in basic biology, and their analysis plays an increasing role in drug development and diagnostics of disease. We have established a scalable technique to compare two biological samples for the levels of all pairwise interactions among a set of targeted protein molecules. The technique is a combination of the proximity ligation assay with readout via dual tag microarrays. In the proximity ligation assay protein identities are encoded as DNA sequences by attaching DNA oligonucleotides to antibodies directed against the proteins of interest. Upon binding by pairs of antibodies to proteins present in the same molecular complexes, ligation reactions give rise to reporter DNA molecules that contain the combined sequence information from the two DNA strands. The ligation reactions also serve to incorporate a sample barcode in the reporter molecules to allow for direct comparison between pairs of samples. The samples are evaluated using a dual tag microarray where information is decoded, revealing which pairs of tags that have become joined. As a proof-of-concept we demonstrate that this approach can be used to detect a set of five proteins and their pairwise interactions both in cellular lysates and in fixed tissue culture cells. This paper provides a general strategy to analyze the extent of any pairwise interactions in large sets of molecules by decoding reporter DNA strands that identify the interacting molecules.

Guide-substrate base-pairing requirement for box H/ACA RNA-guided RNA pseudouridylation.

PubMed

De Zoysa, Meemanage D; Wu, Guowei; Katz, Raviv; Yu, Yi-Tao

2018-06-05

Box H/ACA RNAs are a group of small RNAs found in abundance in eukaryotes (as well as in archaea). Although their sequences differ, eukaryotic box H/ACA RNAs all share the same unique hairpin-hinge-hairpin-tail structure. Almost all of them function as guides that primarily direct pseudouridylation of rRNAs and spliceosomal snRNAs at specific sites. Although box H/ACA RNA-guided pseudouridylation has been extensively studied, the detailed rules governing this reaction, especially those concerning the guide RNA-substrate RNA base-pairing interactions that determine the specificity and efficiency of pseudouridylation, are still not exactly clear. This is particularly relevant given that the lengths of the guide sequences involved in base-pairing vary from one box H/ACA RNA to another. Here, we carry out a detailed investigation into guide-substrate base-pairing interactions, and identify the minimum number of base-pairs (8), required for RNA-guided pseudouridylation. In addition, we find that the pseudouridylation pocket, present in each hairpin of box H/ACA RNA, exhibits flexibility in fitting slightly different substrate sequences. Our results are consistent across three independent pseudouridylation pockets tested, suggesting that our findings are generally applicable to box H/ACA RNA-guided RNA pseudouridylation. Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Genome-Wide Analysis of Gene-Gene and Gene-Environment Interactions Using Closed-Form Wald Tests.

PubMed

Yu, Zhaoxia; Demetriou, Michael; Gillen, Daniel L

2015-09-01

Despite the successful discovery of hundreds of variants for complex human traits using genome-wide association studies, the degree to which genes and environmental risk factors jointly affect disease risk is largely unknown. One obstacle toward this goal is that the computational effort required for testing gene-gene and gene-environment interactions is enormous. As a result, numerous computationally efficient tests were recently proposed. However, the validity of these methods often relies on unrealistic assumptions such as additive main effects, main effects at only one variable, no linkage disequilibrium between the two single-nucleotide polymorphisms (SNPs) in a pair or gene-environment independence. Here, we derive closed-form and consistent estimates for interaction parameters and propose to use Wald tests for testing interactions. The Wald tests are asymptotically equivalent to the likelihood ratio tests (LRTs), largely considered to be the gold standard tests but generally too computationally demanding for genome-wide interaction analysis. Simulation studies show that the proposed Wald tests have very similar performances with the LRTs but are much more computationally efficient. Applying the proposed tests to a genome-wide study of multiple sclerosis, we identify interactions within the major histocompatibility complex region. In this application, we find that (1) focusing on pairs where both SNPs are marginally significant leads to more significant interactions when compared to focusing on pairs where at least one SNP is marginally significant; and (2) parsimonious parameterization of interaction effects might decrease, rather than increase, statistical power. © 2015 WILEY PERIODICALS, INC.

A Survey of Aspartate Phenylalanine and Glutamate Phenylalanine Interactions in the Protein Data Bank: Searching for Anion Pairs

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

Philip, Vivek M; Harris, Jason B; Adams, Rachel M

Protein structures are stabilized using noncovalent interactions. In addition to the traditional noncovalent interactions, newer types of interactions are thought to be present in proteins. One such interaction, an anion pair, in which the positively charged edge of an aromatic ring interacts with an anion, forming a favorable anion quadrupole interaction, has been previously proposed [Jackson, M. R., et al. (2007) J. Phys. Chem. B111, 8242 8249]. To study the role of anion interactions in stabilizing protein structure, we analyzed pairwise interactions between phenylalanine (Phe) and the anionic amino acids, aspartate (Asp) and glutamate (Glu). Particular emphasis was focused onmore » identification of Phe Asp or Glu pairs separated by less than 7 in the high-resolution, nonredundant Protein Data Bank. Simplifying Phe to benzene and Asp or Glu to formate molecules facilitated in silico analysis of the pairs. Kitaura Morokuma energy calculations were performed on roughly 19000 benzene formate pairs and the resulting energies analyzed as a function of distance and angle. Edgewise interactions typically produced strongly stabilizing interaction energies (2 to 7.3 kcal/mol), while interactions involving the ring face resulted in weakly stabilizing to repulsive interaction energies. The strongest, most stabilizing interactions were identified as preferentially occurring in buried residues. Anion pairs are found throughout protein structures, in helices as well as strands. Numerous pairs also had nearby cation interactions as well as potential stacking. While more than 1000 structures did not contain an anion pair, the 3134 remaining structures contained approximately 2.6 anion pairs per protein, suggesting it is a reasonably common motif that could contribute to the overall structural stability of a protein.« less

A Survey of Aspartate-Phenylalanine and Glutamate-Phenylalanine Interactions in the Protein Data Bank: Searching for Anion-pi Pairs

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

Philip, Vivek M; Harris, Jason B; Adams, Rachel M

Protein structures are stabilized using noncovalent interactions. In addition to the traditional noncovalent interactions, newer types of interactions are thought to be present in proteins. One such interaction, an anion-{pi} pair, in which the positively charged edge of an aromatic ring interacts with an anion, forming a favorable anion-quadrupole interaction, has been previously proposed [Jackson, M. R., et al. (2007) J. Phys. Chem. B111, 8242-8249]. To study the role of anion-{pi} interactions in stabilizing protein structure, we analyzed pairwise interactions between phenylalanine (Phe) and the anionic amino acids, aspartate (Asp) and glutamate (Glu). Particular emphasis was focused on identification ofmore » Phe-Asp or -Glu pairs separated by less than 7 {angstrom} in the high-resolution, nonredundant Protein Data Bank. Simplifying Phe to benzene and Asp or Glu to formate molecules facilitated in silico analysis of the pairs. Kitaura-Morokuma energy calculations were performed on roughly 19000 benzene-formate pairs and the resulting energies analyzed as a function of distance and angle. Edgewise interactions typically produced strongly stabilizing interaction energies (-2 to -7.3 kcal/mol), while interactions involving the ring face resulted in weakly stabilizing to repulsive interaction energies. The strongest, most stabilizing interactions were identified as preferentially occurring in buried residues. Anion-{pi} pairs are found throughout protein structures, in helices as well as {beta} strands. Numerous pairs also had nearby cation-{pi} interactions as well as potential {pi}-{pi} stacking. While more than 1000 structures did not contain an anion-{pi} pair, the 3134 remaining structures contained approximately 2.6 anion-{pi} pairs per protein, suggesting it is a reasonably common motif that could contribute to the overall structural stability of a protein.« less

A survey of aspartate-phenylalanine and glutamate-phenylalanine interactions in the protein data bank: searching for anion-π pairs.

PubMed

Philip, Vivek; Harris, Jason; Adams, Rachel; Nguyen, Don; Spiers, Jeremy; Baudry, Jerome; Howell, Elizabeth E; Hinde, Robert J

2011-04-12

Protein structures are stabilized using noncovalent interactions. In addition to the traditional noncovalent interactions, newer types of interactions are thought to be present in proteins. One such interaction, an anion-π pair, in which the positively charged edge of an aromatic ring interacts with an anion, forming a favorable anion-quadrupole interaction, has been previously proposed [Jackson, M. R., et al. (2007) J. Phys. Chem. B111, 8242-8249]. To study the role of anion-π interactions in stabilizing protein structure, we analyzed pairwise interactions between phenylalanine (Phe) and the anionic amino acids, aspartate (Asp) and glutamate (Glu). Particular emphasis was focused on identification of Phe-Asp or -Glu pairs separated by less than 7 Å in the high-resolution, nonredundant Protein Data Bank. Simplifying Phe to benzene and Asp or Glu to formate molecules facilitated in silico analysis of the pairs. Kitaura-Morokuma energy calculations were performed on roughly 19000 benzene-formate pairs and the resulting energies analyzed as a function of distance and angle. Edgewise interactions typically produced strongly stabilizing interaction energies (-2 to -7.3 kcal/mol), while interactions involving the ring face resulted in weakly stabilizing to repulsive interaction energies. The strongest, most stabilizing interactions were identified as preferentially occurring in buried residues. Anion-π pairs are found throughout protein structures, in helices as well as β strands. Numerous pairs also had nearby cation-π interactions as well as potential π-π stacking. While more than 1000 structures did not contain an anion-π pair, the 3134 remaining structures contained approximately 2.6 anion-π pairs per protein, suggesting it is a reasonably common motif that could contribute to the overall structural stability of a protein.

Origins of coevolution between residues distant in protein 3D structures

PubMed Central

Ovchinnikov, Sergey; Kamisetty, Hetunandan; Baker, David

2017-01-01

Residue pairs that directly coevolve in protein families are generally close in protein 3D structures. Here we study the exceptions to this general trend—directly coevolving residue pairs that are distant in protein structures—to determine the origins of evolutionary pressure on spatially distant residues and to understand the sources of error in contact-based structure prediction. Over a set of 4,000 protein families, we find that 25% of directly coevolving residue pairs are separated by more than 5 Å in protein structures and 3% by more than 15 Å. The majority (91%) of directly coevolving residue pairs in the 5–15 Å range are found to be in contact in at least one homologous structure—these exceptions arise from structural variation in the family in the region containing the residues. Thirty-five percent of the exceptions greater than 15 Å are at homo-oligomeric interfaces, 19% arise from family structural variation, and 27% are in repeat proteins likely reflecting alignment errors. Of the remaining long-range exceptions (<1% of the total number of coupled pairs), many can be attributed to close interactions in an oligomeric state. Overall, the results suggest that directly coevolving residue pairs not in repeat proteins are spatially proximal in at least one biologically relevant protein conformation within the family; we find little evidence for direct coupling between residues at spatially separated allosteric and functional sites or for increased direct coupling between residue pairs on putative allosteric pathways connecting them. PMID:28784799

Theory of the Knight Shift and Flux Quantization in Superconductors

DOE R&D Accomplishments Database

Cooper, L. N.; Lee, H. J.; Schwartz, B. B.; Silvert, W.

1962-05-01

Consequences of a generalization of the theory of superconductivity that yields a finite Knight shift are presented. In this theory, by introducing an electron-electron interaction that is not spatially invariant, the pairing of electrons with varying total momentum is made possible. An expression for Xs (the spin susceptibility in the superconducting state) is derived. In general Xs is smaller than Xn, but is not necessarily zero. The precise magnitude of Xs will vary from sample to sample and will depend on the nonuniformity of the samples. There should be no marked size dependence and no marked dependence on the strength of the magnetic field; this is in accord with observation. The basic superconducting properties are retained, but there are modifications in the various electromagnetic and thermal properties since the electrons paired are not time sequences of this generalized theory on flux quantization arguments are presented.(auth)

Electron-hole pair effects in methane dissociative chemisorption on Ni(111)

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

Luo, Xuan; Jiang, Bin, E-mail: bjiangch@ustc.edu.cn; Juaristi, J. Iñaki

The dissociative chemisorption of methane on metal surfaces has attracted much attention in recent years as a prototype of gas-surface reactions in understanding the mode specific and bond selective chemistry. In this work, we systematically investigate the influence of electron-hole pair excitations on the dissociative chemisorption of CH{sub 4}/CH{sub 3}D/CHD{sub 3} on Ni(111). The energy dissipation induced by surface electron-hole pair excitations is modeled as a friction force introduced in the generalized Langevin equation, in which the independent atomic friction coefficients are determined within the local-density friction approximation. Quasi-classical trajectory calculations for CH{sub 4}/CH{sub 3}D/CHD{sub 3} have been carried outmore » on a recently developed twelve-dimensional potential energy surface. Comparing the dissociation probabilities obtained with and without friction, our results clearly indicate that the electron-hole pair effects are generally small, both on absolute reactivity of each vibrational state and on the mode specificity and bond selectivity. Given similar observations in both water and methane dissociation processes, we conclude that electron-hole pair excitations would not play an important role as long as the reaction is direct and the interaction time between the molecule and metal electrons is relatively short.« less

Analysis of functional redundancies within the Arabidopsis TCP transcription factor family.

PubMed

Danisman, Selahattin; van Dijk, Aalt D J; Bimbo, Andrea; van der Wal, Froukje; Hennig, Lars; de Folter, Stefan; Angenent, Gerco C; Immink, Richard G H

2013-12-01

Analyses of the functions of TEOSINTE-LIKE1, CYCLOIDEA, and PROLIFERATING CELL FACTOR1 (TCP) transcription factors have been hampered by functional redundancy between its individual members. In general, putative functionally redundant genes are predicted based on sequence similarity and confirmed by genetic analysis. In the TCP family, however, identification is impeded by relatively low overall sequence similarity. In a search for functionally redundant TCP pairs that control Arabidopsis leaf development, this work performed an integrative bioinformatics analysis, combining protein sequence similarities, gene expression data, and results of pair-wise protein-protein interaction studies for the 24 members of the Arabidopsis TCP transcription factor family. For this, the work completed any lacking gene expression and protein-protein interaction data experimentally and then performed a comprehensive prediction of potential functional redundant TCP pairs. Subsequently, redundant functions could be confirmed for selected predicted TCP pairs by genetic and molecular analyses. It is demonstrated that the previously uncharacterized class I TCP19 gene plays a role in the control of leaf senescence in a redundant fashion with TCP20. Altogether, this work shows the power of combining classical genetic and molecular approaches with bioinformatics predictions to unravel functional redundancies in the TCP transcription factor family.

Analysis of functional redundancies within the Arabidopsis TCP transcription factor family

PubMed Central

Danisman, Selahattin; de Folter, Stefan; Immink, Richard G. H.

2013-01-01

Analyses of the functions of TEOSINTE-LIKE1, CYCLOIDEA, and PROLIFERATING CELL FACTOR1 (TCP) transcription factors have been hampered by functional redundancy between its individual members. In general, putative functionally redundant genes are predicted based on sequence similarity and confirmed by genetic analysis. In the TCP family, however, identification is impeded by relatively low overall sequence similarity. In a search for functionally redundant TCP pairs that control Arabidopsis leaf development, this work performed an integrative bioinformatics analysis, combining protein sequence similarities, gene expression data, and results of pair-wise protein–protein interaction studies for the 24 members of the Arabidopsis TCP transcription factor family. For this, the work completed any lacking gene expression and protein–protein interaction data experimentally and then performed a comprehensive prediction of potential functional redundant TCP pairs. Subsequently, redundant functions could be confirmed for selected predicted TCP pairs by genetic and molecular analyses. It is demonstrated that the previously uncharacterized class I TCP19 gene plays a role in the control of leaf senescence in a redundant fashion with TCP20. Altogether, this work shows the power of combining classical genetic and molecular approaches with bioinformatics predictions to unravel functional redundancies in the TCP transcription factor family. PMID:24129704

Combination of the pair density approximation and the Takahashi–Imada approximation for path integral Monte Carlo simulations

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

Zillich, Robert E., E-mail: robert.zillich@jku.at

2015-11-15

We construct an accurate imaginary time propagator for path integral Monte Carlo simulations for heterogeneous systems consisting of a mixture of atoms and molecules. We combine the pair density approximation, which is highly accurate but feasible only for the isotropic interactions between atoms, with the Takahashi–Imada approximation for general interactions. We present finite temperature simulations results for energy and structure of molecules–helium clusters X{sup 4}He{sub 20} (X=HCCH and LiH) which show a marked improvement over the Trotter approximation which has a 2nd-order time step bias. We show that the 4th-order corrections of the Takahashi–Imada approximation can also be applied perturbativelymore » to a 2nd-order simulation.« less

Linking Spatial Structure and Community-Level Biotic Interactions through Cooccurrence and Time Series Modeling of the Human Intestinal Microbiota.

PubMed

de Muinck, Eric J; Lundin, Knut E A; Trosvik, Pål

2017-01-01

The gastrointestinal (GI) microbiome is a densely populated ecosystem where dynamics are determined by interactions between microbial community members, as well as host factors. The spatial organization of this system is thought to be important in human health, yet this aspect of our resident microbiome is still poorly understood. In this study, we report significant spatial structure of the GI microbiota, and we identify general categories of spatial patterning in the distribution of microbial taxa along a healthy human GI tract. We further estimate the biotic interaction structure in the GI microbiota, both through time series and cooccurrence modeling of microbial community data derived from a large number of sequentially collected fecal samples. Comparison of these two approaches showed that species pairs involved in significant negative interactions had strong positive contemporaneous correlations and vice versa, while for species pairs without significant interactions, contemporaneous correlations were distributed around zero. We observed similar patterns when comparing these models to the spatial correlations between taxa identified in the adherent microbiota. This suggests that colocalization of microbial taxon pairs, and thus the spatial organization of the GI microbiota, is driven, at least in part, by direct or indirect biotic interactions. Thus, our study can provide a basis for an ecological interpretation of the biogeography of the human gut. IMPORTANCE The human gut microbiome is the subject of intense study due to its importance in health and disease. The majority of these studies have been based on the analysis of feces. However, little is known about how the microbial composition in fecal samples relates to the spatial distribution of microbial taxa along the gastrointestinal tract. By characterizing the microbial content both in intestinal tissue samples and in fecal samples obtained daily, we provide a conceptual framework for how the spatial structure relates to biotic interactions on the community level. We further describe general categories of spatial distribution patterns and identify taxa conforming to these categories. To our knowledge, this is the first study combining spatial and temporal analyses of the human gut microbiome. This type of analysis can be used for identifying candidate probiotics and designing strategies for clinical intervention.

Interacting steps with finite-range interactions: Analytical approximation and numerical results

NASA Astrophysics Data System (ADS)

Jaramillo, Diego Felipe; Téllez, Gabriel; González, Diego Luis; Einstein, T. L.

2013-05-01

We calculate an analytical expression for the terrace-width distribution P(s) for an interacting step system with nearest- and next-nearest-neighbor interactions. Our model is derived by mapping the step system onto a statistically equivalent one-dimensional system of classical particles. The validity of the model is tested with several numerical simulations and experimental results. We explore the effect of the range of interactions q on the functional form of the terrace-width distribution and pair correlation functions. For physically plausible interactions, we find modest changes when next-nearest neighbor interactions are included and generally negligible changes when more distant interactions are allowed. We discuss methods for extracting from simulated experimental data the characteristic scale-setting terms in assumed potential forms.

Two-photon production of dilepton pairs in peripheral heavy ion collisions

NASA Astrophysics Data System (ADS)

Klein, Spencer R.

2018-05-01

The STAR collaboration has observed an excess production of e+e- pairs in relativistic heavy ion collisions, over the expectations from hadronic production models. The excess pairs have transverse momenta pT<150 MeV /c and are most prominent in peripheral gold-gold and uranium-uranium collisions. The pairs exhibit a peak at the J /ψ mass, but include a wide continuum, with pair invariant masses from 400 MeV/c 2 up to 2.6 GeV/c 2 . The ALICE Collaboration observes a similar excess in peripheral lead-lead collisions, but only at the J /ψ mass, without a corresponding continuum. This paper presents a calculation of the cross section and kinematic for two-photon production of e+e- pairs, and find general agreement with the STAR data. The calculation is based on the starlight simulation code, which is based on the Weizsäcker-Williams virtual photon approach. The STAR continuum observations are compatible with two-photon production of e+e- pairs. The ALICE analysis required individual muon pT be greater than 1 GeV/c; this eliminated almost all of the pairs from two-photon interactions, while leaving most of the J /ψ decays.

Differential effects of pair housing on voluntary nicotine consumption: a comparison between male and female adolescent rats.

PubMed

Lee, Hyunchan; Jang, Minji; Kim, Woonhee; Noh, Jihyun

2017-08-01

Tobacco smoking occurs in a wide array of social circumstances. Social support for quitting is generally used to stop smoking, while peer interactions may be a crucial factor in triggering tobacco use among adolescents. To determine the role of social factors on nicotine dependence, we compared single- and pair-housed rats subjected to voluntary oral nicotine consumption tests. Six-week-old adolescent rats were subjected to experimental procedures and assigned to one of the following groups: a male single group, a male pair group with a sibling, a female single group, and a female pair group with a sibling. To measure voluntary nicotine intake, we adopted a two-bottle free-choice paradigm for each two days using 25 μg/ml and 100 μg/ml nicotine solution. There were no differences in change in body weight or food intake between the two groups of either sex. Pair-housed female rats showed a reduction in nicotine consumption and preference for both low- and high-dose nicotine solution, while pair-housed male rats showed only reduced consumption and preference for high-dose nicotine solution, but not low-dose solution, as compared to single-housed male rats. Nicotine consumption is sex-dependently controlled by the social circumstances of rats. This study broadens our perspectives on the role of social interactions as a therapeutic strategy to treat nicotine addiction-related behaviors depending on sex.

Transitive inference in adults with autism spectrum disorders

PubMed Central

Solomon, Marjorie; Frank, Michael J.; Smith, Anne C.; Ly, Stanford; Carter, Cameron S.

2012-01-01

Individuals with autism spectrum disorders (ASDs) exhibit intact rote learning with impaired generalization. A transitive inference paradigm, involving training on four sequentially presented stimulus pairs containing overlapping items, with subsequent testing on two novel pairs, was used to investigate this pattern of learning in 27 young adults with ASDs and 31 matched neurotypical individuals (TYPs). On the basis of findings about memory and neuropathology, we hypothesized that individuals with ASDs would use a relational flexibility/conjunctive strategy reliant on an intact hippocampus, versus an associative strength/value transfer strategy requiring intact interactions between the prefrontal cortex and the striatum. Hypotheses were largely confirmed. ASDs demonstrated reduced interference from intervening pairs in early training; only TYPs formed a serial position curve by test; and ASDs exhibited impairments on the novel test pair consisting of end items with intact performance on the inner test pair. However, comparable serial position curves formed for both groups by the end of the first block. PMID:21656344

Anisotropic Surface State Mediated RKKY Interaction Between Adatoms on a Hexagonal Lattice

NASA Astrophysics Data System (ADS)

Einstein, Theodore; Patrone, Paul

2012-02-01

Motivated by recent numerical studies of Ag on Pt(111), we derive a far-field expression for the RKKY interaction mediated by surface states on a (111) FCC surface, considering the effect of anisotropy in the Fermi edge. The main contribution to the interaction comes from electrons whose Fermi velocity vF is parallel to the vector R connecting the interacting adatoms; we show that in general, the corresponding Fermi wave-vector kF is not parallel to R. The interaction is oscillatory; the amplitude and wavelength of oscillations have angular dependence arising from the anisotropy of the surface state band structure. The wavelength, in particular, is determined by the component of the aforementioned kF that is parallel to R. Our analysis is easily generalized to other systems. For Ag on Pt(111), our results indicate that the RKKY interaction between pairs of adatoms should be nearly isotropic and so cannot account for the anisotropy found in the studies motivating our work.

Fermion Cooper pairing with unequal masses: Standard field theory approach

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

He Lianyi; Jin Meng; Zhuang Pengfei

Fermion Cooper pairing with unequal masses is investigated in a standard field theory approach. We derived the superfluid density and Meissner mass squared of the U(1) gauge field in a general two-species model and found that the often used proportional relation between the two quantities is broken when the fermion masses are unequal. In the weak-coupling region, the superfluid density is always negative but the Meissner mass squared becomes mostly positive when the mass ratio between the pairing fermions is large enough. We established a proper momentum configuration of the LOFF pairing with unequal masses and showed that the LOFFmore » state is energetically favored due to the negative superfluid density. The single-plane-wave LOFF state is physically equivalent to an anisotropic state with a spontaneously generated superflow. The extension to a finite-range interaction is briefly discussed.« less

General Anesthetics Have Additive Actions on Three Ligand-Gated Ion Channels

PubMed Central

Jenkins, Andrew; Lobo, Ingrid A.; Gong, Diane; Trudell, James R.; Solt, Ken; Harris, R. Adron; Eger, Edmond I

2008-01-01

Background The purpose of this study was to determine whether pairs of compounds, including general anesthetics, could simultaneously modulate receptor function in a synergistic manner, thus demonstrating the existence of multiple intra-protein anesthetic binding sites. Methods Using standard electrophysiologic methods, we measured the effects of at least one combination of benzene, isoflurane, halothane, chloroform, flunitrazepam, zinc and pentobarbital on at least one of the following ligand gated ion channels: N-methyl-D-aspartate receptors (NMDARs), glycine receptors (GlyRs) and γ-aminobutyric acid type A receptors (GABAARs). Results All drug-drug-receptor combinations were found to exhibit additive, not synergistic modulation. Isoflurane with benzene additively depressed NMDAR function. Isoflurane with halothane additively enhanced GlyR function, as did isoflurane with zinc. Isoflurane with halothane additively enhanced GABAAR function as did all of the following: halothane with chloroform, pentobarbital with isoflurane, and flunitrazepam with isoflurane. Conclusions The simultaneous allosteric modulation of ligand gated ion channels by general anesthetics is entirely additive. Where pairs of general anesthetic drugs interact synergistically to produce general anesthesia, they must do so on systems more complex than a single receptor. PMID:18633027

From Additivity to Cooperativity in Chemistry: Can Cooperativity Be Measured?

PubMed

Tebben, Ludger; Mück-Lichtenfeld, Christian; Fernández, Gustavo; Grimme, Stefan; Studer, Armido

2017-05-02

Cooperative effects can be observed in various research areas in chemistry; cooperative catalysis is well-established, the assembly of compounds on surfaces can be steered by cooperative effects, and supramolecular polymerization can proceed in a cooperative manner. In biological systems, cooperativity is observed in protein-protein, protein-lipid and protein-molecule interactions. Synergistic effects are relevant in frustrated Lewis pairs, organic multispin systems, multimetallic clusters and also in nanoparticles. However, a general approach to determine cooperativity in the different chemical systems is currently not known. In the present concept paper it is suggested that, at least for simpler systems that can be described at the molecular level, cooperativity can be defined based on energy considerations. For systems in which no chemical transformation occurs, determination of interaction energies of the whole system with respect to the interaction energies between all individual component pairs (subsystems) will allow determination of cooperativity. For systems comprising of chemical transformations, cooperativity can be evaluated by determining the activation energy of the synergistic system and by comparing this with activation energies of the corresponding subsystems that lack an activating moiety. For more complex systems, cooperativity is generally determined at a qualitative level. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Superfluid transition in the attractive Hofstadter-Hubbard model

NASA Astrophysics Data System (ADS)

Umucalılar, R. O.; Iskin, M.

2016-08-01

We consider a Fermi gas that is loaded onto a square optical lattice and subjected to a perpendicular artificial magnetic field, and determine its superfluid transition boundary by adopting a BCS-like mean-field approach in momentum space. The multiband structure of the single-particle Hofstadter spectrum is taken explicitly into account while deriving a generalized pairing equation. We present the numerical solutions as functions of the artificial magnetic flux, interaction strength, Zeeman field, chemical potential, and temperature, with a special emphasis on the roles played by the density of single-particle states and center-of-mass momentum of Cooper pairs.

DNA base dimers are stabilized by hydrogen-bonding interactions including non-Watson-Crick pairing near graphite surfaces.

PubMed

Shankar, Akshaya; Jagota, Anand; Mittal, Jeetain

2012-10-11

Single- and double-stranded DNA are increasingly being paired with surfaces and nanoparticles for numerous applications, such as sensing, imaging, and drug delivery. Unlike the majority of DNA structures in bulk that are stabilized by canonical Watson-Crick pairing between Ade-Thy and Gua-Cyt, those adsorbed on surfaces are often stabilized by noncanonical base pairing, quartet formation, and base-surface stacking. Not much is known about these kinds of interactions. To build an understanding of the role of non-Watson-Crick pairing on DNA behavior near surfaces, one requires basic information on DNA base pair stacking and hydrogen-bonding interactions. All-atom molecular simulations of DNA bases in two cases--in bulk water and strongly adsorbed on a graphite surface--are conducted to study the relative strengths of stacking and hydrogen bond interactions for each of the 10 possible combinations of base pairs. The key information obtained from these simulations is the free energy as a function of distance between two bases in a pair. We find that stacking interactions exert the dominant influence on the stability of DNA base pairs in bulk water as expected. The strength of stability for these stacking interactions is found to decrease in the order Gua-Gua > Ade-Gua > Ade-Ade > Gua-Thy > Gua-Cyt > Ade-Thy > Ade-Cyt > Thy-Thy > Cyt-Thy > Cyt-Cyt. On the other hand, mutual interactions of surface-adsorbed base pairs are stabilized mostly by hydrogen-bonding interactions in the order Gua-Cyt > Ade-Gua > Ade-Thy > Ade-Ade > Cyt-Thy > Gua-Gua > Cyt-Cyt > Ade-Cyt > Thy-Thy > Gua-Thy. Interestingly, several non-Watson-Crick base pairings, which are commonly ignored, have similar stabilization free energies due to interbase hydrogen bonding as Watson-Crick pairs. This clearly highlights the importance of non-Watson-Crick base pairing in the development of secondary structures of oligonucleotides near surfaces.

Effects of stress and social support on mothers and premature and full-term infants.

PubMed

Crnic, K A; Greenberg, M T; Ragozin, A S; Robinson, N M; Basham, R B

1983-02-01

This study examined the relationships of stress and social support to maternal attitudes and early mother-infant interactive behavior. 52 mother-premature infant pairs and 53 mother-full-term infant pairs were seen for structured home interviews at 1 month, and behavioral interactions at 4 months. Maternal life stress, social support, life satisfaction, and satisfaction with parenting were assessed at the 1-month home visit. Although no group differences were found, both stress and support significantly predicted maternal attitudes at 1 month and interactive behavior at 4 months when data were pooled. Mothers with greater stress were less positive in their attitudes and behavior, while mothers with greater support were significantly more positive. Intimate support proved to have the most general positive effects. Additionally, social support moderated the adverse effects of stress on mother's life satisfaction and on several behavioral variables. Maternal social support was further found to have several significant effects on infant interactive behavior. Results are discussed in terms of the ecological significance of social support to parenting and infants' early development.

Concurrent choice for social interaction and amphetamine using conditioned place preference in rats: effects of age and housing condition.

PubMed

Yates, Justin R; Beckmann, Joshua S; Meyer, Andrew C; Bardo, Michael T

2013-05-01

Social interaction can serve as a natural reward that attenuates drug reward in rats; however, it is unknown if age or housing conditions alter the choice between social interaction and drug. Individually- and pair-housed adolescent and adult male rats were tested using conditioned place preference (CPP) in separate experiments in which: (1) social interaction was conditioned against no social interaction; (2) amphetamine (AMPH; 1mg/kg, s.c.) was conditioned against saline; or (3) social interaction was conditioned against AMPH. Social interaction CPP was obtained only in individually-housed adolescents, whereas AMPH CPP was obtained in both individually-housed adolescents and adults; however, the effect of AMPH was not statistically significant in pair-housed adults. When allowed to choose concurrently between compartments paired with either social interaction or AMPH, individually-housed adolescents preferred the compartment paired with social interaction, whereas pair-housed adolescents preferred the compartment paired with AMPH. Regardless of housing condition, adults showed a similar preference for the compartments paired with either social interaction or AMPH. Although some caution is needed in interpreting cross-experiment comparisons, the overall results suggest that individually-housed adolescents were most sensitive to the rewarding effect of social interaction, and this hypersensitivity to social reward effectively competed with AMPH reward. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Inferring Domain-Domain Interactions from Protein-Protein Interactions with Formal Concept Analysis

PubMed Central

Khor, Susan

2014-01-01

Identifying reliable domain-domain interactions will increase our ability to predict novel protein-protein interactions, to unravel interactions in protein complexes, and thus gain more information about the function and behavior of genes. One of the challenges of identifying reliable domain-domain interactions is domain promiscuity. Promiscuous domains are domains that can occur in many domain architectures and are therefore found in many proteins. This becomes a problem for a method where the score of a domain-pair is the ratio between observed and expected frequencies because the protein-protein interaction network is sparse. As such, many protein-pairs will be non-interacting and domain-pairs with promiscuous domains will be penalized. This domain promiscuity challenge to the problem of inferring reliable domain-domain interactions from protein-protein interactions has been recognized, and a number of work-arounds have been proposed. This paper reports on an application of Formal Concept Analysis to this problem. It is found that the relationship between formal concepts provides a natural way for rare domains to elevate the rank of promiscuous domain-pairs and enrich highly ranked domain-pairs with reliable domain-domain interactions. This piggybacking of promiscuous domain-pairs onto less promiscuous domain-pairs is possible only with concept lattices whose attribute-labels are not reduced and is enhanced by the presence of proteins that comprise both promiscuous and rare domains. PMID:24586450

Derivation of the density functional theory from the cluster expansion.

PubMed

Hsu, J Y

2003-09-26

The density functional theory is derived from a cluster expansion by truncating the higher-order correlations in one and only one term in the kinetic energy. The formulation allows self-consistent calculation of the exchange correlation effect without imposing additional assumptions to generalize the local density approximation. The pair correlation is described as a two-body collision of bound-state electrons, and modifies the electron- electron interaction energy as well as the kinetic energy. The theory admits excited states, and has no self-interaction energy.

FAST TRACK COMMUNICATION: The nonlinear fragmentation equation

NASA Astrophysics Data System (ADS)

Ernst, Matthieu H.; Pagonabarraga, Ignacio

2007-04-01

We study the kinetics of nonlinear irreversible fragmentation. Here, fragmentation is induced by interactions/collisions between pairs of particles and modelled by general classes of interaction kernels, for several types of breakage models. We construct initial value and scaling solutions of the fragmentation equations, and apply the 'non-vanishing mass flux' criterion for the occurrence of shattering transitions. These properties enable us to determine the phase diagram for the occurrence of shattering states and of scaling states in the phase space of model parameters.

Thin Film Evaporation Model with Retarded Van Der Waals Interaction (Postprint)

DTIC Science & Technology

2013-11-01

Waals interaction. The retarded van der Waals interaction is derived from Hamaker theory, the summation of retarded pair potentials for all molecules...interaction is derived from Hamaker theory, the summation of retarded pair potentials for all molecules for a given geometry. When combined, the governing...interaction force is the negative derivative with respect to distance of the interaction energy. The method due to Hamaker essentially sums all pair

Improving strand pairing prediction through exploring folding cooperativity

PubMed Central

Jeong, Jieun; Berman, Piotr; Przytycka, Teresa M.

2008-01-01

The topology of β-sheets is defined by the pattern of hydrogen-bonded strand pairing. Therefore, predicting hydrogen bonded strand partners is a fundamental step towards predicting β-sheet topology. At the same time, finding the correct partners is very difficult due to long range interactions involved in strand pairing. Additionally, patterns of aminoacids observed in β-sheet formations are very general and therefore difficult to use for computational recognition of specific contacts between strands. In this work, we report a new strand pairing algorithm. To address above mentioned difficulties, our algorithm attempts to mimic elements of the folding process. Namely, in addition to ensuring that the predicted hydrogen bonded strand pairs satisfy basic global consistency constraints, it takes into account hypothetical folding pathways. Consistently with this view, introducing hydrogen bonds between a pair of strands changes the probabilities of forming hydrogen bonds between other pairs of strand. We demonstrate that this approach provides an improvement over previously proposed algorithms. We also compare the performance of this method to that of a global optimization algorithm that poses the problem as integer linear programming optimization problem and solves it using ILOG CPLEX™ package. PMID:18989036

Specificity and autoregulation of Notch binding by tandem WW domains in suppressor of Deltex.

PubMed

Jennings, Martin D; Blankley, Richard T; Baron, Martin; Golovanov, Alexander P; Avis, Johanna M

2007-09-28

WW domains target proline-tyrosine (PY) motifs and frequently function as tandem pairs. When studied in isolation, single WW domains are notably promiscuous and regulatory mechanisms are undoubtedly required to ensure selective interactions. Here, we show that the fourth WW domain (WW4) of Suppressor of Deltex, a modular Nedd4-like protein that down-regulates the Notch receptor, is the primary mediator of a direct interaction with a Notch-PY motif. A natural Trp to Phe substitution in WW4 reduces its affinity for general PY sequences and enhances selective interaction with the Notch-PY motif via compensatory specificity-determining interactions with PY-flanking residues. When WW4 is paired with WW3, domain-domain association, impeding proper folding, competes with Notch-PY binding to WW4. This novel mode of autoinhibition is relieved by binding of another ligand to WW3. Such cooperativity may facilitate the transient regulatory interactions observed in vivo between Su(dx) and Notch in the endocytic pathway. The highly conserved tandem arrangement of WW domains in Nedd4 proteins, and similar arrangements in more diverse proteins, suggests domain-domain communication may be integral to regulation of their associated cellular activities.

Social affiliation in same-class and cross-class interactions.

PubMed

Côté, Stéphane; Kraus, Michael W; Carpenter, Nichelle C; Piff, Paul K; Beermann, Ursula; Keltner, Dacher

2017-02-01

Historically high levels of economic inequality likely have important consequences for relationships between people of the same and different social class backgrounds. Here, we test the prediction that social affiliation among same-class partners is stronger at the extremes of the class spectrum, given that these groups are highly distinctive and most separated from others by institutional and economic forces. An internal meta-analysis of 4 studies (N = 723) provided support for this hypothesis. Participant and partner social class were interactively, rather than additively, associated with social affiliation, indexed by affiliative behaviors and emotions during structured laboratory interactions and in daily life. Further, response surface analyses revealed that paired upper or lower class partners generally affiliated more than average-class pairs. Analyses with separate class indices suggested that these patterns are driven more by parental income and subjective social class than by parental education. The findings illuminate the dynamics of same- and cross-class interactions, revealing that not all same-class interactions feature the same degree of affiliation. They also reveal the importance of studying social class from an intergroup perspective. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Helix-length compensation studies reveal the adaptability of the VS ribozyme architecture.

PubMed

Lacroix-Labonté, Julie; Girard, Nicolas; Lemieux, Sébastien; Legault, Pascale

2012-03-01

Compensatory mutations in RNA are generally regarded as those that maintain base pairing, and their identification forms the basis of phylogenetic predictions of RNA secondary structure. However, other types of compensatory mutations can provide higher-order structural and evolutionary information. Here, we present a helix-length compensation study for investigating structure-function relationships in RNA. The approach is demonstrated for stem-loop I and stem-loop V of the Neurospora VS ribozyme, which form a kissing-loop interaction important for substrate recognition. To rapidly characterize the substrate specificity (k(cat)/K(M)) of several substrate/ribozyme pairs, a procedure was established for simultaneous kinetic characterization of multiple substrates. Several active substrate/ribozyme pairs were identified, indicating the presence of limited substrate promiscuity for stem Ib variants and helix-length compensation between stems Ib and V. 3D models of the I/V interaction were generated that are compatible with the kinetic data. These models further illustrate the adaptability of the VS ribozyme architecture for substrate cleavage and provide global structural information on the I/V kissing-loop interaction. By exploring higher-order compensatory mutations in RNA our approach brings a deeper understanding of the adaptability of RNA structure, while opening new avenues for RNA research.

Broadband photon pair generation in green fluorescent proteins through spontaneous four-wave mixing

PubMed Central

Shi, Siyuan; Thomas, Abu; Corzo, Neil V.; Kumar, Prem; Huang, Yuping; Lee, Kim Fook

2016-01-01

Recent studies in quantum biology suggest that quantum mechanics help us to explore quantum processes in biological system. Here, we demonstrate generation of photon pairs through spontaneous four-wave mixing process in naturally occurring fluorescent proteins. We develop a general empirical method for analyzing the relative strength of nonlinear optical interaction processes in five different organic fluorophores. Our results indicate that the generation of photon pairs in green fluorescent proteins is subject to less background noises than in other fluorophores, leading to a coincidence-to-accidental ratio ~145. As such proteins can be genetically engineered and fused to many biological cells, our experiment enables a new platform for quantum information processing in a biological environment such as biomimetic quantum networks and quantum sensors. PMID:27076032

The lateral mesodermal divide: an epigenetic model of the origin of paired fins.

PubMed

Nuño de la Rosa, Laura; Müller, Gerd B; Metscher, Brian D

2014-01-01

By examining development at the level of tissues and processes, rather than focusing on gene expression, we have formulated a general hypothesis to explain the dorso-ventral and anterior-posterior placement of paired appendage initiation sites in vertebrates. According to our model, the number and position of paired appendages are due to a commonality of embryonic tissue environments determined by the global interactions involving the two separated layers (somatic and visceral) of lateral plate mesoderm along the dorso-ventral and anterior-posterior axes of the embryo. We identify this distribution of developmental conditions, as modulated by the separation/contact of the two LPM layers and their interactions with somitic mesoderm, ectoderm, and endoderm as a dynamic developmental entity which we have termed the lateral mesodermal divide (LMD). Where the divide results in a certain tissue environment, fin bud initiation can occur. According to our hypothesis, the influence of the developing gut suppresses limb initiation along the midgut region and the ventral body wall owing to an "endodermal predominance." From an evolutionary perspective, the lack of gut regionalization in agnathans reflects the ancestral absence of these conditions, and the elaboration of the gut together with the concomitant changes to the LMD in the gnathostomes could have led to the origin of paired fins. © 2013 Wiley Periodicals, Inc.

Introducing a model of pairing based on base pair specific interactions between identical DNA sequences

NASA Astrophysics Data System (ADS)

(O' Lee, Dominic J.

2018-02-01

At present, there have been suggested two types of physical mechanism that may facilitate preferential pairing between DNA molecules, with identical or similar base pair texts, without separation of base pairs. One mechanism solely relies on base pair specific patterns of helix distortion being the same on the two molecules, discussed extensively in the past. The other mechanism proposes that there are preferential interactions between base pairs of the same composition. We introduce a model, built on this second mechanism, where both thermal stretching and twisting fluctuations are included, as well as the base pair specific helix distortions. Firstly, we consider an approximation for weak pairing interactions, or short molecules. This yields a dependence of the energy on the square root of the molecular length, which could explain recent experimental data. However, analysis suggests that this approximation is no longer valid at large DNA lengths. In a second approximation, for long molecules, we define two adaptation lengths for twisting and stretching, over which the pairing interaction can limit the accumulation of helix disorder. When the pairing interaction is sufficiently strong, both adaptation lengths are finite; however, as we reduce pairing strength, the stretching adaptation length remains finite but the torsional one becomes infinite. This second state persists to arbitrarily weak values of the pairing strength; suggesting that, if the molecules are long enough, the pairing energy scales as length. To probe differences between the two pairing mechanisms, we also construct a model of similar form. However, now, pairing between identical sequences solely relies on the intrinsic helix distortion patterns. Between the two models, we see interesting qualitative differences. We discuss our findings, and suggest new work to distinguish between the two mechanisms.

Exact solutions for a type of electron pairing model with spin-orbit interactions and Zeeman coupling.

PubMed

Liu, Jia; Han, Qiang; Shao, L B; Wang, Z D

2011-07-08

A type of electron pairing model with spin-orbit interactions or Zeeman coupling is solved exactly in the framework of the Richardson ansatz. Based on the exact solutions for the case with spin-orbit interactions, it is shown rigorously that the pairing symmetry is of the p + ip wave and the ground state possesses time-reversal symmetry, regardless of the strength of the pairing interaction. Intriguingly, how Majorana fermions can emerge in the system is also elaborated. Exact results are illustrated for two systems, respectively, with spin-orbit interactions and Zeeman coupling.

Bilinearization of the generalized coupled nonlinear Schrödinger equation with variable coefficients and gain and dark-bright pair soliton solutions.

PubMed

Chakraborty, Sushmita; Nandy, Sudipta; Barthakur, Abhijit

2015-02-01

We investigate coupled nonlinear Schrödinger equations (NLSEs) with variable coefficients and gain. The coupled NLSE is a model equation for optical soliton propagation and their interaction in a multimode fiber medium or in a fiber array. By using Hirota's bilinear method, we obtain the bright-bright, dark-bright combinations of a one-soliton solution (1SS) and two-soliton solutions (2SS) for an n-coupled NLSE with variable coefficients and gain. Crucial properties of two-soliton (dark-bright pair) interactions, such as elastic and inelastic interactions and the dynamics of soliton bound states, are studied using asymptotic analysis and graphical analysis. We show that a bright 2-soliton, in addition to elastic interactions, also exhibits multiple inelastic interactions. A dark 2-soliton, on the other hand, exhibits only elastic interactions. We also observe a breatherlike structure of a bright 2-soliton, a feature that become prominent with gain and disappears as the amplitude acquires a minimum value, and after that the solitons remain parallel. The dark 2-soliton, however, remains parallel irrespective of the gain. The results found by us might be useful for applications in soliton control, a fiber amplifier, all optical switching, and optical computing.

Anion-π Catalysis of Enolate Chemistry: Rigidified Leonard Turns as a General Motif to Run Reactions on Aromatic Surfaces.

PubMed

Cotelle, Yoann; Benz, Sebastian; Avestro, Alyssa-Jennifer; Ward, Thomas R; Sakai, Naomi; Matile, Stefan

2016-03-18

To integrate anion-π, cation-π, and ion pair-π interactions in catalysis, the fundamental challenge is to run reactions reliably on aromatic surfaces. Addressing a specific question concerning enolate addition to nitroolefins, this study elaborates on Leonard turns to tackle this problem in a general manner. Increasingly refined turns are constructed to position malonate half thioesters as close as possible on π-acidic surfaces. The resulting preorganization of reactive intermediates is shown to support the disfavored addition to enolate acceptors to an absolutely unexpected extent. This decisive impact on anion-π catalysis increases with the rigidity of the turns. The new, rigidified Leonard turns are most effective with weak anion-π interactions, whereas stronger interactions do not require such ideal substrate positioning to operate well. The stunning simplicity of the motif and its surprisingly strong relevance for function should render the introduced approach generally useful. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mental health, constraints, and organization of work as interactive variables. A study of word processing secretaries.

PubMed

Billette, A; Carrier, M; Bernier, M; de Sève, M

1992-07-01

The effect of a work constraint is specific to the type of work organization. This article deals with the effects of different types of work organization on the mental health of secretaries. The advantage of choosing secretarial work as a research subject lies in the fact that we can identify three distinct types of work organization: (1) a secretary working directly for someone (the "paired" secretary-boss), (2) the "pool," geared toward keyboard input with no specific pairing of secretaries and authors, and (3) the departmental "team," a hybrid of the two preceding types, characterized by the presence of several secretaries, each one assigned to several authors. A study was conducted on the health problems reported by secretaries in the Québec civil service. Data available from a Santé Québec study, carried out at the same time, allowed us to constitute a general population reference group of secretaries and other working women. The findings indicate that secretaries in the general population are no more at risk than are other similar working women, but that secretaries in the provincial civil service are at risk. Regression analysis shows that the same traditional constraints do not affect secretaries in the same way regardless of whether they are members of pair, pool, or team organizations. This suggests that the context of work organization is an interactive or a "specifying variable" of the effect of work constraints on the secretaries' mental health.

Relativistic elliptic matrix tops and finite Fourier transformations

NASA Astrophysics Data System (ADS)

Zotov, A.

2017-10-01

We consider a family of classical elliptic integrable systems including (relativistic) tops and their matrix extensions of different types. These models can be obtained from the “off-shell” Lax pairs, which do not satisfy the Lax equations in general case but become true Lax pairs under various conditions (reductions). At the level of the off-shell Lax matrix, there is a natural symmetry between the spectral parameter z and relativistic parameter η. It is generated by the finite Fourier transformation, which we describe in detail. The symmetry allows one to consider z and η on an equal footing. Depending on the type of integrable reduction, any of the parameters can be chosen to be the spectral one. Then another one is the relativistic deformation parameter. As a by-product, we describe the model of N2 interacting GL(M) matrix tops and/or M2 interacting GL(N) matrix tops depending on a choice of the spectral parameter.

Population interactions between parietal and primary motor cortices during reach

PubMed Central

Rao, Naveen G.; Bondy, Adrian; Truccolo, Wilson; Donoghue, John P.

2014-01-01

Neural interactions between parietal area 2/5 and primary motor cortex (M1) were examined to determine the timing and behavioral correlates of cortico-cortical interactions. Neural activity in areas 2/5 and M1 was simultaneously recorded with 96-channel microelectrode arrays in three rhesus monkeys performing a center-out reach task. We introduce a new method to reveal parietal-motor interactions at a population level using partial spike-field coherence (PSFC) between ensembles of neurons in one area and a local field potential (LFP) in another. PSFC reflects the extent of phase locking between spike times and LFP, after removing the coherence between LFPs in the two areas. Spectral analysis of M1 LFP revealed three bands: low, medium, and high, differing in power between movement preparation and performance. We focus on PSFC in the 1–10 Hz band, in which coherence was strongest. PSFC was also present in the 10–40 Hz band during movement preparation in many channels but generally nonsignificant in the 60–200 Hz band. Ensemble PSFC revealed stronger interactions than single cell-LFP pairings. PSFC of area 2/5 ensembles with M1 LFP typically rose around movement onset and peaked ∼500 ms afterward. PSFC was typically stronger for subsets of area 2/5 neurons and M1 LFPs with similar directional bias than for those with opposite bias, indicating that area 2/5 contributes movement direction information. Together with linear prediction of M1 LFP by area 2/5 spiking, the ensemble-LFP pairing approach reveals interactions missed by single neuron-LFP pairing, demonstrating that cortico-cortical communication can be more readily observed at the ensemble level. PMID:25210154

Three-Nucleon Forces and Triplet Pairing in Neutron Matter

NASA Astrophysics Data System (ADS)

Papakonstantinou, P.; Clark, J. W.

2017-12-01

The existence of superfluidity of the neutron component in the core of a neutron star, associated specifically with triplet P-wave pairing, is currently an open question that is central to interpretation of the observed cooling curves and other neutron-star observables. Ab initio theoretical calculations aimed at resolving this issue face unique challenges in the relevant high-density domain, which reaches beyond the saturation density of symmetrical nuclear matter. These issues include uncertainties in the three-nucleon (3N) interaction and in the effects of strong short-range correlations—and more generally of in-medium modification of nucleonic self-energies and interactions. A survey of existing solutions of the gap equations in the triplet channel demonstrates that the net impact on the gap magnitude of 3N forces, coupled channels, and mass renormalization shows extreme variation dependent on specific theoretical inputs, in some cases even pointing to the absence of a triplet gap, thus motivating a detailed analysis of competing effects within a well-controlled model. In the present study, we track the effects of the 3N force and in-medium modifications in the representative case of the ^3P_2 channel, based on the Argonne v_{18} two-nucleon (2N) interaction supplemented by 3N interactions of the Urbana IX family. Sensitivity of the results to the input interaction is clearly demonstrated. We point out consistency issues with respect to the simultaneous treatment of 3N forces and in-medium effects, which warrant further investigation. We consider this pilot study as the first step toward a systematic and comprehensive exploration of coupled-channel ^3P F_2 pairing using a broad range of 2N and 3N interactions from the current generation of refined semi-phenomenological models and models derived from chiral effective field theory.

Pair bond characteristics and maintenance in free-flying jackdaws Corvus monedula: effects of social context and season

PubMed Central

Kubitza, Robin J.; Bugnyar, Thomas; Schwab, Christine

2015-01-01

Most birds rely on cooperation between pair partners for breeding. In long-term monogamous species, pair bonds are considered the basic units of social organization, albeit these birds often form foraging, roosting or breeding groups in which they repeatedly interact with numerous conspecifics. Focusing on jackdaws Corvus monedula, we here investigated 1) the interplay between pair bond and group dynamics in several social contexts and 2) how pair partners differ in individual effort of pair bond maintenance. Based on long-term data on free-flying birds, we quantified social interactions between group members within three positive contexts (spatial proximity, feeding and sociopositive interactions) for different periods of the year (non-breeding, pre-breeding, parental care). On the group level, we found that the number of interaction partners was highest in the spatial proximity context while in the feeding and sociopositive contexts the number of interaction partners was low and moderately low, respectively. Interactions were reciprocated within almost all contexts and periods. Investigating subgrouping within the flock, results showed that interactions were preferentially directed towards the respective pair partner compared to unmated adults. When determining pair partner effort, both sexes similarly invested most into mutual proximity during late winter, thereby refreshing their bond before the onset of breeding. Paired males fed their mates over the entire year at similar rates while paired females hardly fed their mates at all but engaged in sociopositive behaviors instead. We conclude that jackdaws actively seek out positive social ties to flock members (close proximity, sociopositive behavior), at certain times of the year. Thus, the group functions as a dynamic social unit, nested within are highly cooperative pair bonds. Both sexes invested into the bond with different social behaviors and different levels of effort, yet these are likely male and female proximate mechanisms aimed at maintaining and perpetuating the pair bond. PMID:25892848

Superconductivity in three-dimensional spin-orbit coupled semimetals

NASA Astrophysics Data System (ADS)

Savary, Lucile; Ruhman, Jonathan; Venderbos, Jörn W. F.; Fu, Liang; Lee, Patrick A.

2017-12-01

Motivated by the experimental detection of superconductivity in the low-carrier density half-Heusler compound YPtBi, we study the pairing instabilities of three-dimensional strongly spin-orbit coupled semimetals with a quadratic band touching point. In these semimetals the electronic structure at the Fermi energy is described by spin j =3/2 quasiparticles, which are fundamentally different from those in ordinary metals with spin j =1/2 . For both local and nonlocal pairing channels in j =3/2 materials we develop a general approach to analyzing pairing instabilities, thereby providing the computational tools needed to investigate the physics of these systems beyond phenomenological considerations. Furthermore, applying our method to a generic density-density interaction, we establish that: (i) The pairing strengths in the different symmetry channels uniquely encode the j =3/2 nature of the Fermi surface band structure—a manifestation of the fundamental difference with ordinary metals. (ii) The leading odd-parity pairing instabilities are different for electron doping and hole doping. Finally, we argue that polar phonons, i.e., Coulomb interactions mediated by the long-ranged electric polarization of the optical phonon modes, provide a coupling strength large enough to account for a Kelvin-range transition temperature in the s -wave channel, and are likely to play an important role in the overall attraction in non-s -wave channels. Moreover, the explicit calculation of the coupling strengths allows us to conclude that the two largest non-s -wave contributions occur in nonlocal channels, in contrast with what has been commonly assumed.

Closing loop base pairs in RNA loop-loop complexes: structural behavior, interaction energy and solvation analysis through molecular dynamics simulations.

PubMed

Golebiowski, Jérôme; Antonczak, Serge; Fernandez-Carmona, Juan; Condom, Roger; Cabrol-Bass, Daniel

2004-12-01

Nanosecond molecular dynamics using the Ewald summation method have been performed to elucidate the structural and energetic role of the closing base pair in loop-loop RNA duplexes neutralized by Mg2+ counterions in aqueous phases. Mismatches GA, CU and Watson-Crick GC base pairs have been considered for closing the loop of an RNA in complementary interaction with HIV-1 TAR. The simulations reveal that the mismatch GA base, mediated by a water molecule, leads to a complex that presents the best compromise between flexibility and energetic contributions. The mismatch CU base pair, in spite of the presence of an inserted water molecule, is too short to achieve a tight interaction at the closing-loop junction and seems to force TAR to reorganize upon binding. An energetic analysis has allowed us to quantify the strength of the interactions of the closing and the loop-loop pairs throughout the simulations. Although the water-mediated GA closing base pair presents an interaction energy similar to that found on fully geometry-optimized structure, the water-mediated CU closing base pair energy interaction reaches less than half the optimal value.

Super-resolution imaging and tracking of protein-protein interactions in sub-diffraction cellular space

NASA Astrophysics Data System (ADS)

Liu, Zhen; Xing, Dong; Su, Qian Peter; Zhu, Yun; Zhang, Jiamei; Kong, Xinyu; Xue, Boxin; Wang, Sheng; Sun, Hao; Tao, Yile; Sun, Yujie

2014-07-01

Imaging the location and dynamics of individual interacting protein pairs is essential but often difficult because of the fluorescent background from other paired and non-paired molecules, particularly in the sub-diffraction cellular space. Here we develop a new method combining bimolecular fluorescence complementation and photoactivated localization microscopy for super-resolution imaging and single-molecule tracking of specific protein-protein interactions. The method is used to study the interaction of two abundant proteins, MreB and EF-Tu, in Escherichia coli cells. The super-resolution imaging shows interesting distribution and domain sizes of interacting MreB-EF-Tu pairs as a subpopulation of total EF-Tu. The single-molecule tracking of MreB, EF-Tu and MreB-EF-Tu pairs reveals intriguing localization-dependent heterogonous dynamics and provides valuable insights to understanding the roles of MreB-EF-Tu interactions.

Super-resolution imaging and tracking of protein–protein interactions in sub-diffraction cellular space

PubMed Central

Liu, Zhen; Xing, Dong; Su, Qian Peter; Zhu, Yun; Zhang, Jiamei; Kong, Xinyu; Xue, Boxin; Wang, Sheng; Sun, Hao; Tao, Yile; Sun, Yujie

2014-01-01

Imaging the location and dynamics of individual interacting protein pairs is essential but often difficult because of the fluorescent background from other paired and non-paired molecules, particularly in the sub-diffraction cellular space. Here we develop a new method combining bimolecular fluorescence complementation and photoactivated localization microscopy for super-resolution imaging and single-molecule tracking of specific protein–protein interactions. The method is used to study the interaction of two abundant proteins, MreB and EF-Tu, in Escherichia coli cells. The super-resolution imaging shows interesting distribution and domain sizes of interacting MreB–EF-Tu pairs as a subpopulation of total EF-Tu. The single-molecule tracking of MreB, EF-Tu and MreB–EF-Tu pairs reveals intriguing localization-dependent heterogonous dynamics and provides valuable insights to understanding the roles of MreB–EF-Tu interactions. PMID:25030837

Food Web Assembly Rules for Generalized Lotka-Volterra Equations.

PubMed

Haerter, Jan O; Mitarai, Namiko; Sneppen, Kim

2016-02-01

In food webs, many interacting species coexist despite the restrictions imposed by the competitive exclusion principle and apparent competition. For the generalized Lotka-Volterra equations, sustainable coexistence necessitates nonzero determinant of the interaction matrix. Here we show that this requirement is equivalent to demanding that each species be part of a non-overlapping pairing, which substantially constrains the food web structure. We demonstrate that a stable food web can always be obtained if a non-overlapping pairing exists. If it does not, the matrix rank can be used to quantify the lack of niches, corresponding to unpaired species. For the species richness at each trophic level, we derive the food web assembly rules, which specify sustainable combinations. In neighboring levels, these rules allow the higher level to avert competitive exclusion at the lower, thereby incorporating apparent competition. In agreement with data, the assembly rules predict high species numbers at intermediate levels and thinning at the top and bottom. Using comprehensive food web data, we demonstrate how omnivores or parasites with hosts at multiple trophic levels can loosen the constraints and help obtain coexistence in food webs. Hence, omnivory may be the glue that keeps communities intact even under extinction or ecological release of species.

Food Web Assembly Rules for Generalized Lotka-Volterra Equations

PubMed Central

Haerter, Jan O.; Mitarai, Namiko; Sneppen, Kim

2016-01-01

In food webs, many interacting species coexist despite the restrictions imposed by the competitive exclusion principle and apparent competition. For the generalized Lotka-Volterra equations, sustainable coexistence necessitates nonzero determinant of the interaction matrix. Here we show that this requirement is equivalent to demanding that each species be part of a non-overlapping pairing, which substantially constrains the food web structure. We demonstrate that a stable food web can always be obtained if a non-overlapping pairing exists. If it does not, the matrix rank can be used to quantify the lack of niches, corresponding to unpaired species. For the species richness at each trophic level, we derive the food web assembly rules, which specify sustainable combinations. In neighboring levels, these rules allow the higher level to avert competitive exclusion at the lower, thereby incorporating apparent competition. In agreement with data, the assembly rules predict high species numbers at intermediate levels and thinning at the top and bottom. Using comprehensive food web data, we demonstrate how omnivores or parasites with hosts at multiple trophic levels can loosen the constraints and help obtain coexistence in food webs. Hence, omnivory may be the glue that keeps communities intact even under extinction or ecological release of species. PMID:26828363

Using diets of Canis breeding pairs to assess resource partitioning between sympatric red wolves and coyotes

USGS Publications Warehouse

Hinton, Joseph W.; Ashley, Annaliese K.; Dellinger, Justin A.; Gittleman, John L.; van Manen, Frank T.; Chamberlain, Michael J.

2017-01-01

Foraging behaviors of red wolves (Canis rufus) and coyotes (Canis latrans) are complex and their ability to form congeneric breeding pairs and hybridize further complicates our understanding of factors influencing their diets. Through scat analysis, we assessed prey selection of red wolf, coyote, and congeneric breeding pairs formed by red wolves and coyotes, and found that all 3 had similar diets. However, red wolf and congeneric pairs consumed more white-tailed deer (Odocoileus virginianus) than coyote pairs. Coyotes forming breeding pairs with red wolves had 12% more white-tailed deer in their diet than conspecifics paired with coyotes. Contrary to many studies on coyotes in the southeastern United States, we found coyotes in eastern North Carolina to be primarily carnivorous with increased consumption of deer during winter. Although prey selection was generally similar among the 3 groups, differences in diet among different breeding pairs were strongly associated with body mass. Larger breeding pairs consumed more white-tailed deer, and fewer rabbits (Sylvilagus spp.) and other small mammals. Partitioning of food resources by sympatric red wolves and coyotes is likely via differences in the proportions of similar prey consumed, rather than differences in types of prey exploited. Consequently, our results suggest coexistence of red wolves and coyotes in the southeastern United States may not be possible because there are limited opportunities for niche partitioning to reduce competitive interactions.

Interaction effects on galaxy pairs with Gemini/GMOS- III: stellar population synthesis

NASA Astrophysics Data System (ADS)

Krabbe, A. C.; Rosa, D. A.; Pastoriza, M. G.; Hägele, G. F.; Cardaci, M. V.; Dors, O. L., Jr.; Winge, C.

2017-05-01

We present an observational study of the impacts of interactions on the stellar population in a sample of galaxy pairs. Long-slit spectra in the wavelength range 3440-7300 Å obtained with the Gemini Multi-Object Spectrograph (GMOS) at Gemini South for 15 galaxies in nine close pairs were used. The spatial distributions of the stellar population contributions were obtained using the stellar population synthesis code starlight. Taking into account the different contributions to the emitted light, we found that most of the galaxies in our sample are dominated by young/intermediate stellar populations. This result differs from the one derived for isolated galaxies, where the old stellar population dominates the disc surface brightness. We interpreted such different behaviour as being due to the effect of gas inflows along the discs of interacting galaxies on the star formation over a time-scale of the order of about 2 Gyr. We also found that, in general, the secondary galaxy of a pair has a higher contribution from the young stellar population than the primary one. We compared the estimated values of stellar and nebular extinction derived from the synthesis method and the Hα/Hβ emission-line ratio, finding that nebular extinctions are systematically higher than stellar ones by about a factor of 2. We did not find any correlation between nebular and stellar metallicities. Neither did we find a correlation between stellar metallicities and ages, while a positive correlation between nebular metallicities and stellar ages was obtained, with older regions being the most metal-rich.

Enhancement of superexchange pairing in the periodically driven Hubbard model

NASA Astrophysics Data System (ADS)

Coulthard, J. R.; Clark, S. R.; Al-Assam, S.; Cavalleri, A.; Jaksch, D.

2017-08-01

Recent experiments performed on cuprates and alkali-doped fullerides have demonstrated that key signatures of superconductivity can be induced above the equilibrium critical temperature by optical modulation. These observations in disparate physical systems may indicate a general underlying mechanism. Multiple theories have been proposed, but these either consider specific features, such as competing instabilities, or focus on conventional BCS-type superconductivity. Here we show that periodic driving can enhance electron pairing in strongly correlated systems. Focusing on the strongly repulsive limit of the doped Hubbard model, we investigate in-gap, spatially inhomogeneous, on-site modulations. We demonstrate that such modulations substantially reduce electronic hopping, while simultaneously sustaining superexchange interactions and pair hopping via driving-induced virtual charge excitations. We calculate real-time dynamics for the one-dimensional case, starting from zero- and finite-temperature initial states, and we show that enhanced singlet-pair correlations emerge quickly and robustly in the out-of-equilibrium many-body state. Our results reveal a fundamental pairing mechanism that might underpin optically induced superconductivity in some strongly correlated quantum materials.

Theory of inhomogeneous quantum systems. III. Variational wave functions for Fermi fluids

NASA Astrophysics Data System (ADS)

Krotscheck, E.

1985-04-01

We develop a general variational theory for inhomogeneous Fermi systems such as the electron gas in a metal surface, the surface of liquid 3He, or simple models of heavy nuclei. The ground-state wave function is expressed in terms of two-body correlations, a one-body attenuation factor, and a model-system Slater determinant. Massive partial summations of cluster expansions are performed by means of Born-Green-Yvon and hypernetted-chain techniques. An optimal single-particle basis is generated by a generalized Hartree-Fock equation in which the two-body correlations screen the bare interparticle interaction. The optimization of the pair correlations leads to a state-averaged random-phase-approximation equation and a strictly microscopic determination of the particle-hole interaction.

Biochemical investigations into the mutagenic potential of 8-oxo-2'-deoxyguanosine using nucleotide analogues.

PubMed

Hamm, Michelle L; Crowley, Kelly A; Ghio, Michael; Lindell, Maria A M; McFadden, Emily J; Silberg, Jordan S L; Weaver, Amelia M

2012-11-19

8-Oxo-2'-deoxyguanosine (OdG) is an abundant DNA lesion produced during oxidative damage to DNA. It can form relatively stable base pairs with both dC and dA that mimic natural dG:dC and dT:dA base pairs, respectively. Thus, when in the template strand, OdG can direct the insertion of either dCTP or dATP during replication, the latter of which can lead to a dG → T transversion. The potential for OdG to cause mutation is dependent on the preference for dCTP or dATP insertion opposite OdG, as well as the ability to extend past the resulting base pairs. The C2-amine and C8-oxygen could play major roles during these reactions since both would lie outside the Watson-Crick cognate base pairs shape in the major groove when OdG base pairs to dA and dC, respectively, and both have the ability to form strong interactions, like hydrogen bonds. To gain a more generalized understanding of how the C2-amine and C8-oxygen of OdG affect its mutagenic potential, the incorporation opposite and extension past seven analogues of dG/OdG that vary at C2 and/or C8 were characterized for three DNA polymerases, including an exonuclease-deficient version of the replicative polymerase from RB69 (RB69), human polymerase (pol) β, and polymerase IV from Sulfolobus solfataricus P2 (Dpo4). Based on the results from these studies, as well as those from previous studies with RB69, pol β, Dpo4, and two A-family polymerases, the influence of the C2-amine and C8-oxygen during each incorporation and extension reaction with each polymerase is discussed. In general, it appears that when the C2-amine and the C8-oxygen are in the minor groove, they allow OdG to retain interactions that are normally present during insertion and extension. However, when the two groups are in the major groove, they each tend to form novel active site interactions, both stabilizing and destabilizing, that are not present during insertion and extension with natural DNA.

Electron-phonon Interactions in HTSC Cuprates

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

Egami, T.; Chung, J.-H.; McQueeny, R. J.

Phonons have been generally considered to be irrelevant to the high-temperature superconductivity in the cuprates. However, such a bias is usually based upon the assumption of conventional electron-phonon coupling, while in the cuprates the coupling can be rather unconventional because of strong electron correlation. We present the results of our recent measurements of phonon dispersion in YBa{sub 2}Cu{sub 3}O{sub 6+x} by inelastic neutron scattering. These suggest certain phonon modes interact strongly with electrons and are closely involved in the superconductivity phenomenon with possible contribution to pairing.

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

Ghosh, Tarini Shankar; Chaitanya, S. Krishna; Sankararamakrishnan, Ramasubbu, E-mail: rsankar@iitk.ac.in

New classes of helix–helix interactions in protein structures are reported in which interactions only occur at the terminal regions or between the terminal region of one helix and the middle region of another helix. Helix–helix interactions are important for the structure, stability and function of α-helical proteins. Helices that either cross in the middle or show extensive contacts between each other, such as coiled coils, have been investigated in previous studies. Interactions between two helices can also occur only at the terminal regions or between the terminal region of one helix and the middle region of another helix. Examples ofmore » such helix pairs are found in aquaporin, H{sup +}/Cl{sup −} transporter and Bcl-2 proteins. The frequency of the occurrence of such ‘end-to-end’ (EE) and ‘end-to-middle’ (EM) helix pairs in protein structures is not known. Questions regarding the residue preferences in the interface and the mode of interhelical interactions in such helix pairs also remain unanswered. In this study, high-resolution structures of all-α proteins from the PDB have been systematically analyzed and the helix pairs that interact only in EE or EM fashion have been extracted. EE and EM helix pairs have been categorized into five classes (N–N, N–C, C–C, N–MID and C–MID) depending on the region of interaction. Nearly 13% of 5725 helix pairs belonged to one of the five classes. Analysis of single-residue propensities indicated that hydrophobic and polar residues prefer to occur in the C-terminal and N-terminal regions, respectively. Hydrophobic C-terminal interacting residues and polar N-terminal interacting residues are also highly conserved. A strong correlation exists between some of the residue properties (surface area/volume and length of side chains) and their preferences for occurring in the interface of EE and EM helix pairs. In contrast to interacting non-EE/EM helix pairs, helices in EE and EM pairs are farther apart. In these helix pairs, residues with large surface area/volume and longer side chains are preferred in the interfacial region.« less

It's not just lunch: extra-pair commensality can trigger sexual jealousy.

PubMed

Kniffin, Kevin M; Wansink, Brian

2012-01-01

Do people believe that sharing food might involve sharing more than just food? To investigate this, participants were asked to rate how jealous they (Study 1)--or their best friend (Study 2)--would be if their current romantic partner were contacted by an ex-romantic partner and subsequently engaged in an array of food- and drink-based activities. We consistently find--across both men and women--that meals elicit more jealousy than face-to-face interactions that do not involve eating, such as having coffee. These findings suggest that people generally presume that sharing a meal enhances cooperation. In the context of romantic pairs, we find that participants are attuned to relationship risks that extra-pair commensality can present. For romantic partners left out of a meal, we find a common view that lunch, for example, is not "just lunch."

Interaction of a parabolic-shaped pulse pair in a passively mode-locked Yb-doped fiber laser

NASA Astrophysics Data System (ADS)

Wang, Da-Shuai; Wu, Ge; Gao, Bo; Tian, Xiao-Jian

2013-01-01

We numerically investigate the formation and interaction of a parabolic-shaped pulse pair in a passively mode-locked Yb-doped fiber laser. Based on a lumped model, the parabolic-shaped pulse pair is obtained by controlling the inter-cavity average dispersion and gain saturation energy, Moreover, pulse repulsive and attractive motion are also achieved with different pulse separations. Simulation results show that the phase shift plays an important role in pulse interaction, and the interaction is determined by the inter-cavity average dispersion and gain saturation energy, i.e., the strength of the interaction is proportional to the gain saturation energy, a stronger gain saturation energy will result in a higher interaction intensity. On the contrary, the increase of the inter-cavity dispersion will counterbalance some interaction force. The results also show that the interaction of a parabolic-shaped pulse pair has a larger interaction distance compared to conventional solitons.

Generalized rules for the optimization of elastic network models

NASA Astrophysics Data System (ADS)

Lezon, Timothy; Eyal, Eran; Bahar, Ivet

2009-03-01

Elastic network models (ENMs) are widely employed for approximating the coarse-grained equilibrium dynamics of proteins using only a few parameters. An area of current focus is improving the predictive accuracy of ENMs by fine-tuning their force constants to fit specific systems. Here we introduce a set of general rules for assigning ENM force constants to residue pairs. Using a novel method, we construct ENMs that optimally reproduce experimental residue covariances from NMR models of 68 proteins. We analyze the optimal interactions in terms of amino acid types, pair distances and local protein structures to identify key factors in determining the effective spring constants. When applied to several unrelated globular proteins, our method shows an improved correlation with experiment over a standard ENM. We discuss the physical interpretation of our findings as well as its implications in the fields of protein folding and dynamics.

Flexible modulation of network connectivity related to cognition in Alzheimer's disease.

PubMed

McLaren, Donald G; Sperling, Reisa A; Atri, Alireza

2014-10-15

Functional neuroimaging tools, such as fMRI methods, may elucidate the neural correlates of clinical, behavioral, and cognitive performance. Most functional imaging studies focus on regional task-related activity or resting state connectivity rather than how changes in functional connectivity across conditions and tasks are related to cognitive and behavioral performance. To investigate the promise of characterizing context-dependent connectivity-behavior relationships, this study applies the method of generalized psychophysiological interactions (gPPI) to assess the patterns of associative-memory-related fMRI hippocampal functional connectivity in Alzheimer's disease (AD) associated with performance on memory and other cognitively demanding neuropsychological tests and clinical measures. Twenty-four subjects with mild AD dementia (ages 54-82, nine females) participated in a face-name paired-associate encoding memory study. Generalized PPI analysis was used to estimate the connectivity between the hippocampus and the whole brain during encoding. The difference in hippocampal-whole brain connectivity between encoding novel and encoding repeated face-name pairs was used in multiple-regression analyses as an independent predictor for 10 behavioral, neuropsychological and clinical tests. The analysis revealed connectivity-behavior relationships that were distributed, dynamically overlapping, and task-specific within and across intrinsic networks; hippocampal-whole brain connectivity-behavior relationships were not isolated to single networks, but spanned multiple brain networks. Importantly, these spatially distributed performance patterns were unique for each measure. In general, out-of-network behavioral associations with encoding novel greater than repeated face-name pairs hippocampal-connectivity were observed in the default-mode network, while correlations with encoding repeated greater than novel face-name pairs hippocampal-connectivity were observed in the executive control network (p<0.05, cluster corrected). Psychophysiological interactions revealed significantly more extensive and robust associations between paired-associate encoding task-dependent hippocampal-whole brain connectivity and performance on memory and behavioral/clinical measures than previously revealed by standard activity-behavior analysis. Compared to resting state and task-activation methods, gPPI analyses may be more sensitive to reveal additional complementary information regarding subtle within- and between-network relations. The patterns of robust correlations between hippocampal-whole brain connectivity and behavioral measures identified here suggest that there are 'coordinated states' in the brain; that the dynamic range of these states is related to behavior and cognition; and that these states can be observed and quantified, even in individuals with mild AD. Copyright © 2014 Elsevier Inc. All rights reserved.

Freed by interaction kinetic states in the Harper model

NASA Astrophysics Data System (ADS)

Frahm, Klaus M.; Shepelyansky, Dima L.

2015-12-01

We study the problem of two interacting particles in a one-dimensional quasiperiodic lattice of the Harper model. We show that a short or long range interaction between particles leads to emergence of delocalized pairs in the non-interacting localized phase. The properties of these freed by interaction kinetic states (FIKS) are analyzed numerically including the advanced Arnoldi method. We find that the number of sites populated by FIKS pairs grows algebraically with the system size with the maximal exponent b = 1, up to a largest lattice size N = 10 946 reached in our numerical simulations, thus corresponding to a complete delocalization of pairs. For delocalized FIKS pairs the spectral properties of such quasiperiodic operators represent a deep mathematical problem. We argue that FIKS pairs can be detected in the framework of recent cold atom experiments [M. Schreiber et al., Science 349, 842 (2015)] by a simple setup modification. We also discuss possible implications of FIKS pairs for electron transport in the regime of charge-density wave and high T c superconductivity.

Receptor-mediated membrane adhesion of lipid-polymer hybrid (LPH) nanoparticles studied by dissipative particle dynamics simulations

NASA Astrophysics Data System (ADS)

Li, Zhenlong; Gorfe, Alemayehu A.

2014-12-01

Lipid-polymer hybrid (LPH) nanoparticles represent a novel class of targeted drug delivery platforms that combine the advantages of liposomes and biodegradable polymeric nanoparticles. However, the molecular details of the interaction between LPHs and their target cell membranes remain poorly understood. We have investigated the receptor-mediated membrane adhesion process of a ligand-tethered LPH nanoparticle using extensive dissipative particle dynamics (DPD) simulations. We found that the spontaneous adhesion process follows a first-order kinetics characterized by two distinct stages: a rapid nanoparticle-membrane engagement, followed by a slow growth in the number of ligand-receptor pairs coupled with structural re-organization of both the nanoparticle and the membrane. The number of ligand-receptor pairs increases with the dynamic segregation of ligands and receptors toward the adhesion zone causing an out-of-plane deformation of the membrane. Moreover, the fluidity of the lipid shell allows for strong nanoparticle-membrane interactions to occur even when the ligand density is low. The LPH-membrane avidity is enhanced by the increased stability of each receptor-ligand pair due to the geometric confinement and the cooperative effect arising from multiple binding events. Thus, our results reveal the unique advantages of LPH nanoparticles as active cell-targeting nanocarriers and provide some general principles governing nanoparticle-cell interactions that may aid future design of LPHs with improved affinity and specificity for a given target of interest.

An Analytical Model for Determining Two-Dimensional Receptor-Ligand Kinetics

PubMed Central

Cheung, Luthur Siu-Lun; Konstantopoulos, Konstantinos

2011-01-01

Cell-cell adhesive interactions play a pivotal role in major pathophysiological vascular processes, such as inflammation, infection, thrombosis, and cancer metastasis, and are regulated by hemodynamic forces generated by blood flow. Cell adhesion is mediated by the binding of receptors to ligands, which are both anchored on two-dimensional (2-D) membranes of apposing cells. Biophysical assays have been developed to determine the unstressed (no-force) 2-D affinity but fail to disclose its dependence on force. Here we develop an analytical model to estimate the 2-D kinetics of diverse receptor-ligand pairs as a function of force, including antibody-antigen, vascular selectin-ligand, and bacterial adhesin-ligand interactions. The model can account for multiple bond interactions necessary to mediate adhesion and resist detachment amid high hemodynamic forces. Using this model, we provide a generalized biophysical interpretation of the counterintuitive force-induced stabilization of cell rolling observed by a select subset of receptor-ligand pairs with specific intrinsic kinetic properties. This study enables us to understand how single-molecule and multibond biophysics modulate the macroscopic cell behavior in diverse pathophysiological processes. PMID:21575567

Interacting preformed Cooper pairs in resonant Fermi gases

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

Gubbels, K. B.; Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, NL-6525 AJ Nijmegen; Institute for Theoretical Physics, Utrecht University, Leuvenlaan 4, NL-3584 CE Utrecht

2011-07-15

We consider the normal phase of a strongly interacting Fermi gas, which can have either an equal or an unequal number of atoms in its two accessible spin states. Due to the unitarity-limited attractive interaction between particles with different spin, noncondensed Cooper pairs are formed. The starting point in treating preformed pairs is the Nozieres-Schmitt-Rink (NSR) theory, which approximates the pairs as being noninteracting. Here, we consider the effects of the interactions between the Cooper pairs in a Wilsonian renormalization-group scheme. Starting from the exact bosonic action for the pairs, we calculate the Cooper-pair self-energy by combining the NSR formalismmore » with the Wilsonian approach. We compare our findings with the recent experiments by Harikoshi et al. [Science 327, 442 (2010)] and Nascimbene et al. [Nature (London) 463, 1057 (2010)], and find very good agreement. We also make predictions for the population-imbalanced case, which can be tested in experiments.« less

Base pairing and base mis-pairing in nucleic acids

NASA Technical Reports Server (NTRS)

Wang, A. H. J.; Rich, A.

1986-01-01

In recent years we have learned that DNA is conformationally active. It can exist in a number of different stable conformations including both right-handed and left-handed forms. Using single crystal X-ray diffraction analysis we are able to discover not only additional conformations of the nucleic acids but also different types of hydrogen bonded base-base interactions. Although Watson-Crick base pairings are the predominant type of interaction in double helical DNA, they are not the only types. Recently, we have been able to examine mismatching of guanine-thymine base pairs in left-handed Z-DNA at atomic resolution (1A). A minimum amount of distortion of the sugar phosphate backbone is found in the G x T pairing in which the bases are held together by two hydrogen bonds in the wobble pairing interaction. Because of the high resolution of the analysis we can visualize water molecules which fill in to accommodate the other hydrogen bonding positions in the bases which are not used in the base-base interactions. Studies on other DNA oligomers have revealed that other types of non-Watson-Crick hydrogen bonding interactions can occur. In the structure of a DNA octamer with the sequence d(GCGTACGC) complexed to an antibiotic triostin A, it was found that the two central AT base pairs are held together by Hoogsteen rather than Watson-Crick base pairs. Similarly, the G x C base pairs at the ends are also Hoogsteen rather than Watson-Crick pairing. Hoogsteen base pairs make a modified helix which is distinct from the Watson-Crick double helix.

Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse.

PubMed

Peng, Tao; Xue, Chenghai; Bi, Jianning; Li, Tingting; Wang, Xiaowo; Zhang, Xuegong; Li, Yanda

2008-04-26

Alternative splicing expands transcriptome diversity and plays an important role in regulation of gene expression. Previous studies focus on the regulation of a single cassette exon, but recent experiments indicate that multiple cassette exons within a gene may interact with each other. This interaction can increase the potential to generate various transcripts and adds an extra layer of complexity to gene regulation. Several cases of exon interaction have been discovered. However, the extent to which the cassette exons coordinate with each other remains unknown. Based on EST data, we employed a metric of correlation coefficients to describe the interaction between two adjacent cassette exons and then categorized these exon pairs into three different groups by their interaction (correlation) patterns. Sequence analysis demonstrates that strongly-correlated groups are more conserved and contain a higher proportion of pairs with reading frame preservation in a combinatorial manner. Multiple genome comparison further indicates that different groups of correlated pairs have different evolutionary courses: (1) The vast majority of positively-correlated pairs are old, (2) most of the weakly-correlated pairs are relatively young, and (3) negatively-correlated pairs are a mixture of old and young events. We performed a large-scale analysis of interactions between adjacent cassette exons. Compared with weakly-correlated pairs, the strongly-correlated pairs, including both the positively and negatively correlated ones, show more evidence that they are under delicate splicing control and tend to be functionally important. Additionally, the positively-correlated pairs bear strong resemblance to constitutive exons, which suggests that they may evolve from ancient constitutive exons, while negatively and weakly correlated pairs are more likely to contain newly emerging exons.

Variational Approach in the Theory of Liquid-Crystal State

NASA Astrophysics Data System (ADS)

Gevorkyan, E. V.

2018-03-01

The variational calculus by Leonhard Euler is the basis for modern mathematics and theoretical physics. The efficiency of variational approach in statistical theory of liquid-crystal state and in general case in condensed state theory is shown. The developed approach in particular allows us to introduce correctly effective pair interactions and optimize the simple models of liquid crystals with help of realistic intermolecular potentials.

MESIC GROUP AND CONSERVATION OF PARITY (in French)

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

Petermann, A.; Ruegg, H.

1960-01-01

A principle of invariance under a continuous local group of transformations, the mesic group, is investigated. This principle has the following influences: 1. For the pseudoscslar Yukawa interaction of two Fermiore with the pseudoscalar pi -meson it entails PC invariance. 2. If the Fermions have equal bare masses with respect to electromagnetic interaction (a hypothesis which is plausible for the nucleons), the principle imposes, for the ps interaction with pi , the conservation of isotopic spin and separate P and C invariance. 3. For the Fermi interactions of the pairs (pn), nonconservation of parity. Arguments leading to this principle aremore » based on a generalization of the demonstration of the Dyson-Foldy equivalence theorem as given by Stueckelberg and Petermann. (auth)« less

Probing long-range carrier-pair spin–spin interactions in a conjugated polymer by detuning of electrically detected spin beating

PubMed Central

van Schooten, Kipp J.; Baird, Douglas L.; Limes, Mark E.; Lupton, John M.; Boehme, Christoph

2015-01-01

Weakly coupled electron spin pairs that experience weak spin–orbit interaction can control electronic transitions in molecular and solid-state systems. Known to determine radical pair reactions, they have been invoked to explain phenomena ranging from avian magnetoreception to spin-dependent charge-carrier recombination and transport. Spin pairs exhibit persistent spin coherence, allowing minute magnetic fields to perturb spin precession and thus recombination rates and photoreaction yields, giving rise to a range of magneto-optoelectronic effects in devices. Little is known, however, about interparticle magnetic interactions within such pairs. Here we present pulsed electrically detected electron spin resonance experiments on poly(styrene-sulfonate)-doped poly(3,4-ethylenedioxythiophene) (PEDOT:PSS) devices, which show how interparticle spin–spin interactions (magnetic-dipolar and spin-exchange) between charge-carrier spin pairs can be probed through the detuning of spin-Rabi oscillations. The deviation from uncoupled precession frequencies quantifies both the exchange (<30 neV) and dipolar (23.5±1.5 neV) interaction energies responsible for the pair's zero-field splitting, implying quantum mechanical entanglement of charge-carrier spins over distances of 2.1±0.1 nm. PMID:25868686

Stacking interactions and DNA intercalation

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

Li, Dr. Shen; Cooper, Valentino R; Thonhauser, Prof. Timo

2009-01-01

The relationship between stacking interactions and the intercalation of proflavine and ellipticine within DNA is investigated using a nonempirical van der Waals density functional for the correlation energy. Our results, employing a binary stack model, highlight fundamental, qualitative differences between base-pair base-pair interactions and that of the stacked intercalator base pair system. Most notable result is the paucity of torque which so distinctively defines the Twist of DNA. Surprisingly, this model, when combined with a constraint on the twist of the surrounding base-pair steps to match the observed unwinding of the sugar-phosphate backbone, was sufficient for explaining the experimentally observedmore » proflavine intercalator configuration. Our extensive mapping of the potential energy surface of base-pair intercalator interactions can provide valuable information for future nonempirical studies of DNA intercalation dynamics.« less

Anisotropic surface-state-mediated RKKY interaction between adatoms on a hexagonal lattice

NASA Astrophysics Data System (ADS)

Patrone, Paul N.; Einstein, T. L.

2012-01-01

Motivated by recent numerical studies of Ag on Pt(111), we derive an expression for the RKKY interaction mediated by surface states, considering the effect of anisotropy in the Fermi edge. Our analysis is based on a stationary phase approximation. The main contribution to the interaction comes from electrons whose Fermi velocity vF is parallel to the vector R connecting the interacting adatoms; we show that, in general, the corresponding Fermi wave vector kF is not parallel to R. The interaction is oscillatory; the amplitude and wavelength of oscillations have angular dependence arising from the anisotropy of the surface-state band structure. The wavelength, in particular, is determined by the projection of this kF (corresponding to vF) onto the direction of R. Our analysis is easily generalized to other systems. For Ag on Pt(111), our results indicate that the RKKY interaction between pairs of adatoms should be nearly isotropic and so cannot account for the anisotropy found in the studies motivating our work. However, for metals with surface-state dispersions similar to Be(101¯0), we show that the RKKY interaction should have considerable anisotropy.

A combined theoretical and Cambridge Structural Database study of π-hole pnicogen bonding complexes between electron rich molecules and both nitro compounds and inorganic bromides (YO2Br, Y = N, P, and As).

PubMed

Bauzá, Antonio; Ramis, Rafael; Frontera, Antonio

2014-04-17

Quantum calculations at the DFT-D3/def2-TZVPD level of theory have been used to examine complexes between O2YBr (Y═N, P, and As) molecules and several Lewis bases, that is, NH3, H2O, and HF. The interactions of the lone pair of the ammonia, water, and hydrogen fluoride with the σ-hole and π-hole of O2YBr molecules have been considered. In general, the complexes where the Lewis base lone pair interacts with the π-hole are more favorable than those with σ-hole. The nature of the interactions has been characterized with the Bader theory of atoms in molecules (AIM). We have also studied the ability of trifluoronitromethane and nitromethane to interact with anions using their π-hole along with an analysis the Cambridge Structural Database. We have found a large number of hits that provide strong experimental support for ability of the nitryl (-NO2) group to interact with anions and Lewis bases. In some X-ray structures, the π-hole interaction is crucial in the crystal packing and has a strong influence in the solid state architecture of the complexes. Finally, due to the relevance in atmospheric chemistry, we have studied noncovalent σ/π-hole complexes of nitryl bromide with ozone.

Probing the tides in interacting galaxy pairs

NASA Technical Reports Server (NTRS)

Borne, Kirk D.

1990-01-01

Detailed spectroscopic and imaging observations of colliding elliptical galaxies revealed unmistakable diagnostic signatures of the tidal interactions. It is possible to compare both the distorted luminosity distributions and the disturbed internal rotation profiles with numerical simulations in order to model the strength of the tidal gravitational field acting within a given pair of galaxies. Using the best-fit numerical model, one can then measure directly the mass of a specific interacting binary system. This technique applies to individual pairs and therefore complements the classical methods of measuring the masses of galaxy pairs in well-defined statistical samples. The 'personalized' modeling of galaxy pairs also permits the derivation of each binary's orbit, spatial orientation, and interaction timescale. Similarly, one can probe the tides in less-detailed observations of disturbed galaxies in order to estimate some of the physical parameters for larger samples of interacting galaxy pairs. These parameters are useful inputs to the more universal problems of (1) the galaxy merger rate, (2) the strength and duration of the driving forces behind tidally stimulated phenomena (e.g., starbursts and maybe quasi steller objects), and (3) the identification of long-lived signatures of interaction/merger events.

It’s Not Just Lunch: Extra-Pair Commensality Can Trigger Sexual Jealousy

PubMed Central

Kniffin, Kevin M.; Wansink, Brian

2012-01-01

Do people believe that sharing food might involve sharing more than just food? To investigate this, participants were asked to rate how jealous they (Study 1) – or their best friend (Study 2) – would be if their current romantic partner were contacted by an ex-romantic partner and subsequently engaged in an array of food- and drink-based activities. We consistently find – across both men and women – that meals elicit more jealousy than face-to-face interactions that do not involve eating, such as having coffee. These findings suggest that people generally presume that sharing a meal enhances cooperation. In the context of romantic pairs, we find that participants are attuned to relationship risks that extra-pair commensality can present. For romantic partners left out of a meal, we find a common view that lunch, for example, is not “just lunch.” PMID:22792327

Tetrylones: An Intriguing Class of Monoatomic Zero-valent Group 14 Compounds.

PubMed

Majhi, Paresh Kumar; Sasamori, Takahiro

2018-02-13

Tetrylones (ylidones) represent a class of zero-valent group 14 compounds with the general formula EL 2 (E=C, Si, Ge, Sn, or Pb; L=neutral σ-donating ligand), wherein the tetrel atom, E(0), possess its four valence electrons in the form of two electron lone pairs, and is moreover coordinated by two ligands (L) via donor-acceptor interactions (L→E←L). This review focuses on the synthesis, structure, reactivity, and computational examination of the isolable heavier tetrylones (Si, Ge, Sn) that have been discovered recently. A comprehensive review on carbone chemistry is beyond the scope of this review. It should also be noted that tetrylones contain two different types of lone pairs, that is, one that exhibits p-type and one that exhibits s-type characteristics. Different behavior should thus be expected when these lone pairs react with Lewis acids. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Orthogonal Luciferase-Luciferin Pairs for Bioluminescence Imaging.

PubMed

Jones, Krysten A; Porterfield, William B; Rathbun, Colin M; McCutcheon, David C; Paley, Miranda A; Prescher, Jennifer A

2017-02-15

Bioluminescence imaging with luciferase-luciferin pairs is widely used in biomedical research. Several luciferases have been identified in nature, and many have been adapted for tracking cells in whole animals. Unfortunately, the optimal luciferases for imaging in vivo utilize the same substrate and therefore cannot easily differentiate multiple cell types in a single subject. To develop a broader set of distinguishable probes, we crafted custom luciferins that can be selectively processed by engineered luciferases. Libraries of mutant enzymes were iteratively screened with sterically modified luciferins, and orthogonal enzyme-substrate "hits" were identified. These tools produced light when complementary enzyme-substrate partners interacted both in vitro and in cultured cell models. Based on their selectivity, these designer pairs will bolster multicomponent imaging and enable the direct interrogation of cell networks not currently possible with existing tools. Our screening platform is also general and will expedite the identification of more unique luciferases and luciferins, further expanding the bioluminescence toolkit.

Lone pair-π interactions in biological systems: occurrence, function, and physical origin.

PubMed

Kozelka, Jiří

2017-12-01

Lone pair-π interactions are now recognized as a supramolecular bond whose existence in biological systems is documented by a growing number of examples. They are commonly attributed to electrostatic forces. This review attempts to highlight some recent discoveries evidencing the important role which lone pair-π interactions, and anion-π interactions in particular, play in stabilizing the structure and affecting the function of biomolecules. Special attention is paid to studies exploring the physical origin of these at first glance counterintuitive interactions between a lone pair of electrons of one residue and the π-cloud of another. Recent theoretical work went beyond the popular electrostatic model and inquired the extent to which orbital interactions have to be taken into account. In at least one biologically relevant case-that of anion-flavin interactions-a substantial charge-transfer component has been shown to operate.

Zero-range effective field theory for resonant wino dark matter. Part III. Annihilation effects

NASA Astrophysics Data System (ADS)

Braaten, Eric; Johnson, Evan; Zhang, Hong

2018-05-01

Near a critical value of the wino mass where there is a zero-energy S-wave resonance at the neutral-wino-pair threshold, low-energy winos can be described by a zero-range effective field theory (ZREFT) in which the winos interact nonperturbatively through a contact interaction and through Coulomb interactions. The effects of wino-pair annihilation into electroweak gauge bosons are taken into account through the analytic continuation of the real parameters for the contact interaction to complex values. The parameters of ZREFT can be determined by matching wino-wino scattering amplitudes calculated by solving the Schrödinger equation for winos interacting through a real potential due to the exchange of electroweak gauge bosons and an imaginary potential due to wino-pair annihilation into electroweak gauge bosons. ZREFT at leading order gives an accurate analytic description of low-energy wino-wino scattering, inclusive wino-pair annihilation, and a wino-pair bound state. ZREFT can also be applied to partial annihilation rates, such as the Sommerfeld enhancement of the annihilation rate of wino pairs into monochromatic photons.

Reducing interaction in simultaneous paired stimulation with CI.

PubMed

Vellinga, Dirk; Bruijn, Saskia; Briaire, Jeroen J; Kalkman, Randy K; Frijns, Johan H M

2017-01-01

In this study simultaneous paired stimulation of electrodes in cochlear implants is investigated by psychophysical experiments in 8 post-lingually deaf subjects (and one extra subject who only participated in part of the experiments). Simultaneous and sequential monopolar stimulation modes are used as references and are compared to channel interaction compensation, partial tripolar stimulation and a novel sequential stimulation strategy named phased array compensation. Psychophysical experiments are performed to investigate both the loudness integration during paired stimulation at the main electrodes as well as the interaction with the electrode contact located halfway between the stimulating pair. The study shows that simultaneous monopolar stimulation has more loudness integration on the main electrodes and more interaction in between the electrodes than sequential stimulation. Channel interaction compensation works to reduce the loudness integration at the main electrodes, but does not reduce the interaction in between the electrodes caused by paired stimulation. Partial tripolar stimulation uses much more current to reach the needed loudness, but shows the same interaction in between the electrodes as sequential monopolar stimulation. In phased array compensation we have used the individual impedance matrix of each subject to calculate the current needed on each electrode to exactly match the stimulation voltage along the array to that of sequential stimulation. The results show that the interaction in between the electrodes is the same as monopolar stimulation. The strategy uses less current than partial tripolar stimulation, but more than monopolar stimulation. In conclusion, the paper shows that paired stimulation is possible if the interaction is compensated.

Ab initio calculation of atomic interactions on Al(110): implications for epitaxial growth

NASA Astrophysics Data System (ADS)

Fichthorn, Kristen; Tiwary, Yogesh

2007-03-01

Using first-principles calculations based on density-functional theory, we resolved atomic interactions between adsorbed Al atoms on Al(110). Relevant pair and trio interactions were quantified. We find that pair interactions extend to the third in-channel and second cross-channel neighbor on the anisotropic (110) surface. Beyond these distances, pair interactions are negligible. The nearest-neighbor interaction in the in-channel direction is attractive, but nearest-neighbor cross-channel interaction is repulsive. While nearest-neighbor, cross-channel repulsion does not support the experimental observation of 3D hut formation in Al/Al(110) homoepitaxial growth [1], we find that trio interactions can be significant and attractive and they support cross-channel bonding. The pair and trio interactions have direct and indirect components. We have quantified the electronic and elastic components of the indirect, substrate-mediated interactions. We also probe the influence of these interactions on the energy barriers for adatom hopping. [1] F. Buatier de Mongeot, W. Zhu, A. Molle, R. Buzio, C. Boragno, U. Valbusa, E. Wang, and Z. Zhang, Phys. Rev. Lett. 91, 016102 (2003).

The interaction between vocabulary size and phonotactic probability effects on children's production accuracy and fluency in nonword repetition.

PubMed

Edwards, Jan; Beckman, Mary E; Munson, Benjamin

2004-04-01

Adults' performance on a variety of tasks suggests that phonological processing of nonwords is grounded in generalizations about sublexical patterns over all known words. A small body of research suggests that children's phonological acquisition is similarly based on generalizations over the lexicon. To test this account, production accuracy and fluency were examined in nonword repetitions by 104 children and 22 adults. Stimuli were 22 pairs of nonwords, in which one nonword contained a low-frequency or unattested two-phoneme sequence and the other contained a high-frequency sequence. For a subset of these nonword pairs, segment durations were measured. The same sound was produced with a longer duration (less fluently) when it appeared in a low-frequency sequence, as compared to a high-frequency sequence. Low-frequency sequences were also repeated with lower accuracy than high-frequency sequences. Moreover, children with smaller vocabularies showed a larger influence of frequency on accuracy than children with larger vocabularies. Taken together, these results provide support for a model of phonological acquisition in which knowledge of sublexical units emerges from generalizations made over lexical items.

Sign Reversal of Coulom Interaction Between Two Quasiparticles in Momentum Space

NASA Astrophysics Data System (ADS)

Fan, J. D.; Malozovsky, Yuriy M.

2013-06-01

The main misconception regarding the interaction between quasiparticles stems from the assertion that the interaction energy between two quasiparticles is exactly identical to that of the renormalized interaction between two particles due to interparticle interaction in the Fermi system. If the main concept regarding the definition of quasiparticle as a weakly excited state of the Fermi system with conservation of charge and spin is paramount (except for the charge and spin separation models), the concept of the interaction between quasiparticles is very different from the assumption in the common sense. In this paper, we will prove a general theorem that the interaction between two quasiparticles is very much different from the renormalized interaction between two particles. The major difference lies in two places: the interaction between two quasiparticles is just negative to the renormalized interaction between two particles, and the interaction energy between the two particles is proportional to the product of two Fermi liquid renormalization factors. The result shed light on the reinterpretation of Cooper's pairing without invoking electron-photon interaction.

Interprofessional collaboration between residents and nurses in general internal medicine: a qualitative study on behaviours enhancing teamwork quality.

PubMed

Muller-Juge, Virginie; Cullati, Stéphane; Blondon, Katherine S; Hudelson, Patricia; Maître, Fabienne; Vu, Nu V; Savoldelli, Georges L; Nendaz, Mathieu R

2014-01-01

Effective teamwork is necessary for optimal patient care. There is insufficient understanding of interactions between physicians and nurses on internal medicine wards. To describe resident physicians' and nurses' actual behaviours contributing to teamwork quality in the setting of a simulated internal medicine ward. A volunteer sample of 14 pairs of residents and nurses in internal medicine was asked to manage one non-urgent and one urgent clinical case in a simulated ward, using a high-fidelity manikin. After the simulation, participants attended a stimulated-recall session during which they viewed the videotape of the simulation and explained their actions and perceptions. All simulations were transcribed, coded, and analyzed, using a qualitative method (template analysis). Quality of teamwork was assessed, based on patient management efficiency and presence of shared management goals and of team spirit. Most resident-nurse pairs tended to interact in a traditional way, with residents taking the leadership and nurses executing medical prescriptions and assuming their own specific role. They also demonstrated different types of interactions involving shared responsibilities and decision making, constructive suggestions, active communication and listening, and manifestations of positive team building. The presence of a leader in the pair or a truly shared leadership between resident and nurse contributed to teamwork quality only if both members of the pair demonstrated sufficient autonomy. In case of a lack of autonomy of one member, the other member could compensate for it, if his/her own autonomy was sufficiently strong and if there were demonstrations of mutual listening, information sharing, and positive team building. Although they often relied on traditional types of interaction, residents and nurses also demonstrated readiness for increased sharing of responsibilities. Interprofessional education should insist on better redefinition of respective roles and reinforce behaviours shown to enhance teamwork quality.

Interprofessional Collaboration between Residents and Nurses in General Internal Medicine: A Qualitative Study on Behaviours Enhancing Teamwork Quality

PubMed Central

Muller-Juge, Virginie; Cullati, Stéphane; Blondon, Katherine S.; Hudelson, Patricia; Maître, Fabienne; Vu, Nu V.; Savoldelli, Georges L.; Nendaz, Mathieu R.

2014-01-01

Background Effective teamwork is necessary for optimal patient care. There is insufficient understanding of interactions between physicians and nurses on internal medicine wards. Objective To describe resident physicians’ and nurses’ actual behaviours contributing to teamwork quality in the setting of a simulated internal medicine ward. Methods A volunteer sample of 14 pairs of residents and nurses in internal medicine was asked to manage one non-urgent and one urgent clinical case in a simulated ward, using a high-fidelity manikin. After the simulation, participants attended a stimulated-recall session during which they viewed the videotape of the simulation and explained their actions and perceptions. All simulations were transcribed, coded, and analyzed, using a qualitative method (template analysis). Quality of teamwork was assessed, based on patient management efficiency and presence of shared management goals and of team spirit. Results Most resident-nurse pairs tended to interact in a traditional way, with residents taking the leadership and nurses executing medical prescriptions and assuming their own specific role. They also demonstrated different types of interactions involving shared responsibilities and decision making, constructive suggestions, active communication and listening, and manifestations of positive team building. The presence of a leader in the pair or a truly shared leadership between resident and nurse contributed to teamwork quality only if both members of the pair demonstrated sufficient autonomy. In case of a lack of autonomy of one member, the other member could compensate for it, if his/her own autonomy was sufficiently strong and if there were demonstrations of mutual listening, information sharing, and positive team building. Conclusions Although they often relied on traditional types of interaction, residents and nurses also demonstrated readiness for increased sharing of responsibilities. Interprofessional education should insist on better redefinition of respective roles and reinforce behaviours shown to enhance teamwork quality. PMID:24769672

Extracting joint weak values with local, single-particle measurements.

PubMed

Resch, K J; Steinberg, A M

2004-04-02

Weak measurement is a new technique which allows one to describe the evolution of postselected quantum systems. It appears to be useful for resolving a variety of thorny quantum paradoxes, particularly when used to study properties of pairs of particles. Unfortunately, such nonlocal or joint observables often prove difficult to measure directly in practice (for instance, in optics-a common testing ground for this technique-strong photon-photon interactions would be needed to implement an appropriate von Neumann interaction). Here we derive a general, experimentally feasible, method for extracting these joint weak values from correlations between single-particle observables.

Intermolecular interactions of trifluorohalomethanes with Lewis bases in the gas phase: an ab initio study.

PubMed

Wang, Yi-Siang; Yin, Chih-Chien; Chao, Sheng D

2014-10-07

We perform an ab initio computational study of molecular complexes with the general formula CF3X-B that involve one trifluorohalomethane CF3X (X = Cl or Br) and one of a series of Lewis bases B in the gas phase. The Lewis bases are so chosen that they provide a range of electron-donating abilities for comparison. Based on the characteristics of their electron pairs, we consider the Lewis bases with a single n-pair (NH3 and PH3), two n-pairs (H2O and H2S), two n-pairs with an unsaturated bond (H2CO and H2CS), and a single π-pair (C2H4) and two π-pairs (C2H2). The aim is to systematically investigate the influence of the electron pair characteristics and the central atom substitution effects on the geometries and energetics of the formed complexes. The counterpoise-corrected supermolecule MP2 and coupled-cluster single double with perturbative triple [CCSD(T)] levels of theory have been employed, together with a series of basis sets up to aug-cc-pVTZ. The angular and radial configurations, the binding energies, and the electrostatic potentials of the stable complexes have been compared and discussed as the Lewis base varies. For those complexes where halogen bonding plays a significant role, the calculated geometries and energetics are consistent with the σ-hole model. Upon formation of stable complexes, the C-X bond lengths shorten, while the C-X vibrational frequencies increase, thus rendering blueshifting halogen bonds. The central atom substitution usually enlarges the intermolecular bond distances while it reduces the net charge transfers, thus weakening the bond strengths. The analysis based on the σ-hole model is grossly reliable but requires suitable modifications incorporating the central atom substitution effects, in particular, when interaction components other than electrostatic contributions are involved.

Orbitally limited pair-density-wave phase of multilayer superconductors

NASA Astrophysics Data System (ADS)

Möckli, David; Yanase, Youichi; Sigrist, Manfred

2018-04-01

We investigate the magnetic field dependence of an ideal superconducting vortex lattice in the parity-mixed pair-density-wave phase of multilayer superconductors within a circular cell Ginzburg-Landau approach. In multilayer systems, due to local inversion symmetry breaking, a Rashba spin-orbit coupling is induced at the outer layers. This combined with a perpendicular paramagnetic (Pauli) limiting magnetic field stabilizes a staggered layer dependent pair-density-wave phase in the superconducting singlet channel. The high-field pair-density-wave phase is separated from the low-field BCS phase by a first-order phase transition. The motivating guiding question in this paper is: What is the minimal necessary Maki parameter αM for the appearance of the pair-density-wave phase of a superconducting trilayer system? To address this problem we generalize the circular cell method for the regular flux-line lattice of a type-II superconductor to include paramagnetic depairing effects. Then, we apply the model to the trilayer system, where each of the layers are characterized by Ginzburg-Landau parameter κ0 and a Maki parameter αM. We find that when the spin-orbit Rashba interaction compares to the superconducting condensation energy, the orbitally limited pair-density-wave phase stabilizes for Maki parameters αM>10 .

Regime of validity of the pairing Hamiltonian in the study of Fermi gases

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

Chang, S. Y.; Pandharipande, V. R.

2006-06-01

The ground state energy and pairing gap of the interacting Fermi gases calculated by the ab initio stochastic method are compared with those estimated from the Bardeen-Cooper-Schrieffer pairing Hamiltonian. We discuss the ingredients of this Hamiltonian in various regimes of interaction strength. In the weakly interacting (1/ak{sub F}<<0) regime the BCS Hamiltonian should describe Landau quasiparticle energies and interactions, on the other hand, in the strongly pairing regime, that is, 1/ak{sub F} > or approx. 0, it becomes part of the bare Hamiltonian. However, the bare BCS Hamiltonian is not adequate for describing atomic gases in the regime of weakmore » to moderate interaction strength -{infinity}<1/ak{sub F}<0 such as ak{sub F}{approx}-1.« less

Intermittent pair-housing, pair relationship qualities, and HPA activity in adult female rhesus macaques.

PubMed

Hannibal, Darcy L; Cassidy, Lauren C; Vandeleest, Jessica; Semple, Stuart; Barnard, Allison; Chun, Katie; Winkler, Sasha; McCowan, Brenda

2018-05-02

Laboratory rhesus macaques are often housed in pairs and may be temporarily or permanently separated for research, health, or management reasons. While both long-term social separations and introductions can stimulate a stress response that impacts inflammation and immune function, the effects of short-term overnight separations and whether qualities of the pair relationship mediate these effects are unknown. In this study, we investigated the effects of overnight separations on the urinary cortisol concentration of 20 differentially paired adult female rhesus macaques (Macaca mulatta) at the California National Primate Research Center. These females were initially kept in either continuous (no overnight separation) or intermittent (with overnight separation) pair-housing and then switched to the alternate pair-housing condition part way through the study. Each study subject was observed for 5 weeks, during which we collected measures of affiliative, aggressive, anxious, abnormal, and activity-state behaviors in both pair-housing conditions. Additionally, up to three urine samples were collected from each subject per week and assayed for urinary free cortisol and creatinine. Lastly, the behavioral observer scored each pair on four relationship quality attributes ("Anxious," "Tense," "Well-meshed," and "Friendly") using a seven-point scale. Data were analyzed using a generalized linear model with gamma distribution and an information theoretic approach to determine the best model set. An interaction between the intermittent pairing condition and tense pair adjective rating was in the top three models of the best model set. Dominance and rates of affiliation were also important for explaining urinary cortisol variation. Our results suggest that to prevent significant changes in HPA-axis activation in rhesus macaque females, which could have unintended effects on research outcomes, pairs with "Tense" relationships and overnight separations preventing tactile contact should be avoided. © 2018 Wiley Periodicals, Inc.

A Synthetic Coiled-Coil Interactome Provides Heterospecific Modules for Molecular Engineering

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

Reinke, Aaron W.; Grant, Robert A.; Keating, Amy E.

2010-06-21

The versatile coiled-coil protein motif is widely used to induce and control macromolecular interactions in biology and materials science. Yet the types of interaction patterns that can be constructed using known coiled coils are limited. Here we greatly expand the coiled-coil toolkit by measuring the complete pairwise interactions of 48 synthetic coiled coils and 7 human bZIP coiled coils using peptide microarrays. The resulting 55-member protein 'interactome' includes 27 pairs of interacting peptides that preferentially heteroassociate. The 27 pairs can be used in combinations to assemble sets of 3 to 6 proteins that compose networks of varying topologies. Of specialmore » interest are heterospecific peptide pairs that participate in mutually orthogonal interactions. Such pairs provide the opportunity to dimerize two separate molecular systems without undesired crosstalk. Solution and structural characterization of two such sets of orthogonal heterodimers provide details of their interaction geometries. The orthogonal pair, along with the many other network motifs discovered in our screen, provide new capabilities for synthetic biology and other applications.« less

In vivo versus simulation training: an interactional analysis of range and type of training exemplars.

PubMed Central

Neef, N A; Lensbower, J; Hockersmith, I; DePalma, V; Gray, K

1990-01-01

We analyzed the role of the range of variation in training exemplars as a contextual variable influencing the effects of in vivo versus simulation training in producing generalized responding. Four mentally retarded adults received single case instruction, followed by general case instruction, on washing machine and dryer use; one task was taught using actual appliances (in vivo) and the other using simulation. In vivo and simulation training were counterbalanced across the two tasks for the 2 subject pairs, using a within-subjects Latin square design. With both paradigms, more errors were made after single case than after general case instruction during probe sessions with untrained washing machines and dryers. These results suggest that generalization errors were affected by the range of training exemplars and not by the use of simulated versus natural training stimuli. Although both general case simulation and general case in vivo training facilitated generalized performance of laundry skills, an analysis of training time and costs indicated that the former approach was more efficient. The study illustrates a methodology for studying complex interactions and guiding decisions on the optimal use of instructional alternatives. PMID:2074236

Signatures of pairing in the magnetic excitation spectrum of strongly correlated two-leg ladders [Signatures of pairing in the magnetic excitation spectrum of strongly correlated ladders

DOE PAGES

Nocera, Alberto; Patel, Niravkumar D.; Dagotto, Elbio R.; ...

2017-11-13

Magnetic interactions are widely believed to play a crucial role in the microscopic mechanism leading to high critical temperature superconductivity. It is therefore important to study the signatures of pairing in the magnetic excitation spectrum of simple models known to show unconventional superconducting tendencies. Using the density matrix renormalization group technique, we calculate the dynamical spin structure factor S(k,ω) of a generalized t–U–J Hubbard model away from half filling in a two-leg ladder geometry. The addition of J enhances pairing tendencies. We analyze quantitatively the signatures of pairing in the magnetic excitation spectra. We found that the superconducting pair-correlation strength,more » that can be estimated independently from ground state properties, is closely correlated with the integrated low-energy magnetic spectral weight in the vicinity of (π,π). In this wave-vector region, robust spin incommensurate features develop with increasing doping. The branch of the spectrum with rung direction wave vector k rung=0 does not change substantially with doping where pairing dominates and thus plays a minor role. As a result, we discuss the implications of our results for neutron scattering experiments, where the spin excitation dynamics of hole-doped quasi-one-dimensional magnetic materials can be measured and also address implications for recent resonant inelastic x-ray scattering experiments.« less

Signatures of pairing in the magnetic excitation spectrum of strongly correlated two-leg ladders [Signatures of pairing in the magnetic excitation spectrum of strongly correlated ladders

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

Nocera, Alberto; Patel, Niravkumar D.; Dagotto, Elbio R.

Magnetic interactions are widely believed to play a crucial role in the microscopic mechanism leading to high critical temperature superconductivity. It is therefore important to study the signatures of pairing in the magnetic excitation spectrum of simple models known to show unconventional superconducting tendencies. Using the density matrix renormalization group technique, we calculate the dynamical spin structure factor S(k,ω) of a generalized t–U–J Hubbard model away from half filling in a two-leg ladder geometry. The addition of J enhances pairing tendencies. We analyze quantitatively the signatures of pairing in the magnetic excitation spectra. We found that the superconducting pair-correlation strength,more » that can be estimated independently from ground state properties, is closely correlated with the integrated low-energy magnetic spectral weight in the vicinity of (π,π). In this wave-vector region, robust spin incommensurate features develop with increasing doping. The branch of the spectrum with rung direction wave vector k rung=0 does not change substantially with doping where pairing dominates and thus plays a minor role. As a result, we discuss the implications of our results for neutron scattering experiments, where the spin excitation dynamics of hole-doped quasi-one-dimensional magnetic materials can be measured and also address implications for recent resonant inelastic x-ray scattering experiments.« less

Molecular electrostatics for probing lone pair-π interactions.

PubMed

Mohan, Neetha; Suresh, Cherumuttathu H; Kumar, Anmol; Gadre, Shridhar R

2013-11-14

An electrostatics-based approach has been proposed for probing the weak interactions between lone pair containing molecules and π deficient molecular systems. For electron-rich molecules, the negative minima in molecular electrostatic potential (MESP) topography give the location of electron localization and the MESP value at the minimum (Vmin) quantifies the electron-rich character of that region. Interactive behavior of a lone pair bearing molecule with electron deficient π-systems, such as hexafluorobenzene, 1,3,5-trinitrobenzene, 2,4,6-trifluoro-1,3,5-triazine and 1,2,4,5-tetracyanobenzene explored within DFT brings out good correlation of the lone pair-π interaction energy (E(int)) with the Vmin value of the electron-rich system. Such interaction is found to be portrayed well with the Electrostatic Potential for Intermolecular Complexation (EPIC) model. On the basis of the precise location of MESP minimum, a prediction for the orientation of a lone pair bearing molecule with an electron deficient π-system is possible in the majority of the cases studied.

Cation specific binding with protein surface charges

PubMed Central

Hess, Berk; van der Vegt, Nico F. A.

2009-01-01

Biological organization depends on a sensitive balance of noncovalent interactions, in particular also those involving interactions between ions. Ion-pairing is qualitatively described by the law of “matching water affinities.” This law predicts that cations and anions (with equal valence) form stable contact ion pairs if their sizes match. We show that this simple physical model fails to describe the interaction of cations with (molecular) anions of weak carboxylic acids, which are present on the surfaces of many intra- and extracellular proteins. We performed molecular simulations with quantitatively accurate models and observed that the order K+ < Na+ < Li+ of increasing binding affinity with carboxylate ions is caused by a stronger preference for forming weak solvent-shared ion pairs. The relative insignificance of contact pair interactions with protein surfaces indicates that thermodynamic stability and interactions between proteins in alkali salt solutions is governed by interactions mediated through hydration water molecules. PMID:19666545

The crack-inclusion interaction problem

NASA Technical Reports Server (NTRS)

Liu, X.-H.; Erdogan, F.

1986-01-01

The general plane elastostatic problem of interaction between a crack and an inclusion is considered. The Green's functions for a pair of dislocations and a pair of concentrated body forces are used to generate the crack and the inclusion. Integral equations are obtained for a line crack and an elastic line inclusion having an arbitrary relative orientation and size. The nature of stress singularity around the end points of rigid and elastic inclusions is described and three special cases of this intersection problem are studied. The problem is solved for an arbitrary uniform stress state away from the crack-inclusion region. The nonintersecting crack-inclusion problem is considered for various relative size, orientation, and stiffness parameters, and the stress intensity factors at the ends of the inclusion and the crack are calculated. For the crack-inclusion intersection case, special stress intensity factors are defined and are calculated for various values of the parameters defining the relative size and orientation of the crack and the inclusion and the stiffness of the inclusion.

The crack-inclusion interaction problem

NASA Technical Reports Server (NTRS)

Xue-Hui, L.; Erdogan, F.

1984-01-01

The general plane elastostatic problem of interaction between a crack and an inclusion is considered. The Green's functions for a pair of dislocations and a pair of concentrated body forces are used to generate the crack and the inclusion. Integral equations are obtained for a line crack and an elastic line inclusion having an arbitrary relative orientation and size. The nature of stress singularity around the end points of rigid and elastic inclusions is described and three special cases of this intersection problem are studied. The problem is solved for an arbitrary uniform stress state away from the crack-inclusion region. The nonintersecting crack-inclusion problem is considered for various relative size, orientation, and stiffness parameters, and the stress intensity factors at the ends of the inclusion and the crack are calculated. For the crack-inclusion intersection case, special stress intensity factors are defined and are calculated for various values of the parameters defining the relative size and orientation of the crack and the inclusion and the stiffness of the inclusion.

Twin Brothers with Autism and Their Intra-Pair Interactions in a Pre-School Special Education Class

ERIC Educational Resources Information Center

Markodimitraki, Maria; Ampartzaki, Maria; Kypriotaki, Maria; Linardakis, Michalis

2017-01-01

The present study focused on the intra-pair interaction of a pair of dizygotic twins with autism in pre-school age and explored: (a) the type of play and the level of symbolic play the twins prefer and are most frequently engaged with; (b) the attitudes the twins usually display; (c) the most frequent initiator of interactions; and (d) the way the…

Spin interactions in InAs quantum dots

NASA Astrophysics Data System (ADS)

Doty, M. F.; Ware, M. E.; Stinaff, E. A.; Scheibner, M.; Bracker, A. S.; Gammon, D.; Ponomarev, I. V.; Reinecke, T. L.; Korenev, V. L.

2006-03-01

Fine structure splittings in optical spectra of self-assembled InAs quantum dots (QDs) generally arise from spin interactions between particles confined in the dots. We present experimental studies of the fine structure that arises from multiple charges confined in a single dot [1] or in molecular orbitals of coupled pairs of dots. To probe the underlying spin interactions we inject particles with a known spin orientation (by using polarized light to perform photoluminescence excitation spectroscopy experiments) or use a magnetic field to orient and/or mix the spin states. We develop a model of the spin interactions that aids in the development of quantum information processing applications based on controllable interactions between spins confined to QDs. [1] Polarized Fine Structure in the Photoluminescence Excitation Spectrum of a Negatively Charged Quantum Dot, Phys. Rev. Lett. 95, 177403 (2005)

Designing heteropolymers to fold into unique structures via water-mediated interactions.

PubMed

Jamadagni, Sumanth N; Bosoy, Christian; Garde, Shekhar

2010-10-28

Hydrophobic homopolymers collapse into globular structures in water driven by hydrophobic interactions. Here we employ extensive molecular dynamics simulations to study the collapse of heteropolymers containing one or two pairs of oppositely charged monomers. We show that charging a pair of monomers can dramatically alter the most stable conformations from compact globular to more open hairpin-like. We systematically explore a subset of the sequence space of one- and two-charge-pair polymers, focusing on the locations of the charge pairs. Conformational stability is governed by a balance of hydrophobic interactions, hydration and interactions of charge groups, water-mediated charged-hydrophobic monomer repulsions, and other factors. As a result, placing charge pairs in the middle, away from the hairpin ends, leads to stable hairpin-like structures. Turning off the monomer-water attractions enhances hydrophobic interactions significantly leading to a collapse into compact globular structures even for two-charge-pair heteropolymers. In contrast, the addition of salt leads to open and extended structures, suggesting that solvation of charged monomer sites by salt ions dominates the salt-induced enhancement of hydrophobic interactions. We also test the ability of a predictive scheme based on the additivity of free energy of contact formation. The success of the scheme for symmetric two-charge-pair sequences and the failure for their flipped versions highlight the complexity of the heteropolymer conformation space and of the design problem. Collectively, our results underscore the ability of tuning water-mediated interactions to design stable nonglobular structures in water and present model heteropolymers for further studies in the extended thermodynamic space and in inhomogeneous environments.

The choice of product indicators in latent variable interaction models: post hoc analyses.

PubMed

Foldnes, Njål; Hagtvet, Knut Arne

2014-09-01

The unconstrained product indicator (PI) approach is a simple and popular approach for modeling nonlinear effects among latent variables. This approach leaves the practitioner to choose the PIs to be included in the model, introducing arbitrariness into the modeling. In contrast to previous Monte Carlo studies, we evaluated the PI approach by 3 post hoc analyses applied to a real-world case adopted from a research effort in social psychology. The measurement design applied 3 and 4 indicators for the 2 latent 1st-order variables, leaving the researcher with a choice among more than 4,000 possible PI configurations. Sixty so-called matched-pair configurations that have been recommended in previous literature are of special interest. In the 1st post hoc analysis we estimated the interaction effect for all PI configurations, keeping the real-world sample fixed. The estimated interaction effect was substantially affected by the choice of PIs, also across matched-pair configurations. Subsequently, a post hoc Monte Carlo study was conducted, with varying sample sizes and data distributions. Convergence, bias, Type I error and power of the interaction test were investigated for each matched-pair configuration and the all-pairs configuration. Variation in estimates across matched-pair configurations for a typical sample was substantial. The choice of specific configuration significantly affected convergence and the interaction test's outcome. The all-pairs configuration performed overall better than the matched-pair configurations. A further advantage of the all-pairs over the matched-pairs approach is its unambiguity. The final study evaluates the all-pairs configuration for small sample sizes and compares it to the non-PI approach of latent moderated structural equations. PsycINFO Database Record (c) 2014 APA, all rights reserved.

Preadolescent Girls' and Boys' Virtual MUD Play

ERIC Educational Resources Information Center

Calvert, Sandra L.; Strouse, Gabrielle A.; Strong, Bonnie L.; Huffaker, David A.; Lai, Sean

2009-01-01

Same and opposite-sex pairs of preadolescents interacted twice in a MUD, a virtual domain where they created characters known as avatars and socially interacted with one another. Boys interacted primarily through rapid scene shifts and playful exchanges; girls interacted with one another through written dialogue. Opposite-sex pairs lagged behind…

Framing matters: contextual influences on interracial interaction outcomes.

PubMed

Babbitt, Laura G; Sommers, Samuel R

2011-09-01

Previous studies indicate that interracial interactions frequently have negative outcomes but have typically focused on social contexts. The current studies examined the effect of manipulating interaction context. In Study 1, Black and White participants worked together with instructions that created either a social focus or a task focus. With a task focus, interracial pairs were more consistently synchronized, Black participants showed less executive function depletion, and White participants generally showed reduced implicit bias. Follow-up studies suggested that prejudice concerns help explain these findings: White participants reported fewer concerns about appearing prejudiced when they imagined an interracial interaction with a task focus rather than a social focus (Study 2a), and Black participants reported less vigilance against prejudice in an imagined interracial interaction with a task focus rather than a social focus (Study 2b). Taken together, these studies illustrate the importance of interaction context for the experiences of both Blacks and Whites.

Probing long-range carrier-pair spin–spin interactions in a conjugated polymer by detuning of electrically detected spin beating

DOE PAGES

van Schooten, Kipp J.; Baird, Douglas L.; Limes, Mark E.; ...

2015-04-14

Here, weakly coupled electron spin pairs that experience weak spin–orbit interaction can control electronic transitions in molecular and solid-state systems. Known to determine radical pair reactions, they have been invoked to explain phenomena ranging from avian magnetoreception to spin-dependent charge-carrier recombination and transport. Spin pairs exhibit persistent spin coherence, allowing minute magnetic fields to perturb spin precession and thus recombination rates and photoreaction yields, giving rise to a range of magneto-optoelectronic effects in devices. Little is known, however, about interparticle magnetic interactions within such pairs. Here we present pulsed electrically detected electron spin resonance experiments on poly(styrene-sulfonate)-doped poly(3,4-ethylenedioxythiophene) (PEDOT:PSS) devices,more » which show how interparticle spin–spin interactions (magnetic-dipolar and spin-exchange) between charge-carrier spin pairs can be probed through the detuning of spin-Rabi oscillations. The deviation from uncoupled precession frequencies quantifies both the exchange (<30 neV) and dipolar (23.5±1.5 neV) interaction energies responsible for the pair’s zero-field splitting, implying quantum mechanical entanglement of charge-carrier spins over distances of 2.1±0.1 nm.« less

Hierarchical structure of biological systems

PubMed Central

Alcocer-Cuarón, Carlos; Rivera, Ana L; Castaño, Victor M

2014-01-01

A general theory of biological systems, based on few fundamental propositions, allows a generalization of both Wierner and Berthalanffy approaches to theoretical biology. Here, a biological system is defined as a set of self-organized, differentiated elements that interact pair-wise through various networks and media, isolated from other sets by boundaries. Their relation to other systems can be described as a closed loop in a steady-state, which leads to a hierarchical structure and functioning of the biological system. Our thermodynamical approach of hierarchical character can be applied to biological systems of varying sizes through some general principles, based on the exchange of energy information and/or mass from and within the systems. PMID:24145961

Hierarchical structure of biological systems: a bioengineering approach.

PubMed

Alcocer-Cuarón, Carlos; Rivera, Ana L; Castaño, Victor M

2014-01-01

A general theory of biological systems, based on few fundamental propositions, allows a generalization of both Wierner and Berthalanffy approaches to theoretical biology. Here, a biological system is defined as a set of self-organized, differentiated elements that interact pair-wise through various networks and media, isolated from other sets by boundaries. Their relation to other systems can be described as a closed loop in a steady-state, which leads to a hierarchical structure and functioning of the biological system. Our thermodynamical approach of hierarchical character can be applied to biological systems of varying sizes through some general principles, based on the exchange of energy information and/or mass from and within the systems.

Accurate, precise, and efficient theoretical methods to calculate anion-π interaction energies in model structures.

PubMed

Mezei, Pál D; Csonka, Gábor I; Ruzsinszky, Adrienn; Sun, Jianwei

2015-01-13

A correct description of the anion-π interaction is essential for the design of selective anion receptors and channels and important for advances in the field of supramolecular chemistry. However, it is challenging to do accurate, precise, and efficient calculations of this interaction, which are lacking in the literature. In this article, by testing sets of 20 binary anion-π complexes of fluoride, chloride, bromide, nitrate, or carbonate ions with hexafluorobenzene, 1,3,5-trifluorobenzene, 2,4,6-trifluoro-1,3,5-triazine, or 1,3,5-triazine and 30 ternary π-anion-π' sandwich complexes composed from the same monomers, we suggest domain-based local-pair natural orbital coupled cluster energies extrapolated to the complete basis-set limit as reference values. We give a detailed explanation of the origin of anion-π interactions, using the permanent quadrupole moments, static dipole polarizabilities, and electrostatic potential maps. We use symmetry-adapted perturbation theory (SAPT) to calculate the components of the anion-π interaction energies. We examine the performance of the direct random phase approximation (dRPA), the second-order screened exchange (SOSEX), local-pair natural-orbital (LPNO) coupled electron pair approximation (CEPA), and several dispersion-corrected density functionals (including generalized gradient approximation (GGA), meta-GGA, and double hybrid density functional). The LPNO-CEPA/1 results show the best agreement with the reference results. The dRPA method is only slightly less accurate and precise than the LPNO-CEPA/1, but it is considerably more efficient (6-17 times faster) for the binary complexes studied in this paper. For 30 ternary π-anion-π' sandwich complexes, we give dRPA interaction energies as reference values. The double hybrid functionals are much more efficient but less accurate and precise than dRPA. The dispersion-corrected double hybrid PWPB95-D3(BJ) and B2PLYP-D3(BJ) functionals perform better than the GGA and meta-GGA functionals for the present test set.

Coupled bipolarons and optical phonons as a model for high-Tc superconductors

NASA Technical Reports Server (NTRS)

Kasperczyk, J.

1991-01-01

The coherence length of the new high-temperature superconductors reaches a small value which is comparable to the dimensions of the unit cell of the compound. This means that a pair consists of two holes occupying the same site or two adjacent sites. Such a situation is described by a model of the local-pairs (bipolarons). The origin of local-pairs may come not only from strong enough electron or hole-phonon interaction but also from other interactions. Independent of the specific nature of such local-pairs, they can undergo a Bose-like condensation to the superconducting state at a critical temperature which is usually much lower than the temperature of the pair formation. An interplay of ferroelectric and superconducting properties is considered within the model of hole-like local-pairs interacting with optical phonons. Therefore, researchers extend the usual local-pair Hamiltonian by including a direct interaction between the local-pairs and the optical phonons. These optical phonons are known to play an important role in the ferroelectric transition and they transform into an additional pseudo-acoustic branch at the ferroelectric critical temperature. (This is associated with nonzero electric polarization due to the existence of two separate lattices composed of negative and positive ions, respectively.)

Predicting human genetic interactions from cancer genome evolution.

PubMed

Lu, Xiaowen; Megchelenbrink, Wout; Notebaart, Richard A; Huynen, Martijn A

2015-01-01

Synthetic Lethal (SL) genetic interactions play a key role in various types of biological research, ranging from understanding genotype-phenotype relationships to identifying drug-targets against cancer. Despite recent advances in empirical measuring SL interactions in human cells, the human genetic interaction map is far from complete. Here, we present a novel approach to predict this map by exploiting patterns in cancer genome evolution. First, we show that empirically determined SL interactions are reflected in various gene presence, absence, and duplication patterns in hundreds of cancer genomes. The most evident pattern that we discovered is that when one member of an SL interaction gene pair is lost, the other gene tends not to be lost, i.e. the absence of co-loss. This observation is in line with expectation, because the loss of an SL interacting pair will be lethal to the cancer cell. SL interactions are also reflected in gene expression profiles, such as an under representation of cases where the genes in an SL pair are both under expressed, and an over representation of cases where one gene of an SL pair is under expressed, while the other one is over expressed. We integrated the various previously unknown cancer genome patterns and the gene expression patterns into a computational model to identify SL pairs. This simple, genome-wide model achieves a high prediction power (AUC = 0.75) for known genetic interactions. It allows us to present for the first time a comprehensive genome-wide list of SL interactions with a high estimated prediction precision, covering up to 591,000 gene pairs. This unique list can potentially be used in various application areas ranging from biotechnology to medical genetics.

Systematics of ground state multiplets of atomic nuclei in the delta-interaction approach

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

Imasheva, L. T.; Ishkhanov, B. S.; Stepanov, M. E., E-mail: stepanov@depni.sinp.msu.ru

2015-12-15

Pairing forces between nucleons in an atomic nucleus strongly influence its structure. One of the manifestations of pair interaction is the ground state multiplet (GSM) formation in the spectrum of low-lying excited states of even–even nuclei. The value of GSM splitting is determined by the value of pair interaction of nucleons; for each isotope, it can be estimated on the basis of experimental nuclear masses. The quality of this estimate is characterized by the degree of reproduction of GSM levels in the nucleus. The GSM systematics in even–even nuclei with a pair of identical nucleons in addition to the filledmore » nuclear core is considered on the basis of delta interaction.« less

Interpersonal Responses Among Sibling Dyads Tested for BRCA1/BRCA2 Gene Mutations

PubMed Central

Hamann, Heidi A.; Croyle, Robert T.; Smith, Timothy W.; Smith, Ken R.; Ruiz, John M.; Kircher, John C.; Botkin, Jeffrey R.

2013-01-01

Objective The familial context plays an important role in psychosocial responses to genetic testing. The purpose of this study was to compare sibling pairs with different combinations of BRCA1/BRCA2 test results on measures of affect, interpersonal responses, and physiological reactions. Design Forty-nine sibling dyads with different combinations of BRCA1/BRCA2 test results (i.e., mixed, positive, negative) completed a questionnaire, and 35 of the dyads also participated in a laboratory-based discussion of genetic testing. Main Outcome Measures The primary outcome variables included participant reports of supportive actions toward their sibling, state anger and anxiety, perceptions of sibling behavior, and electrodermal responses. Results Compared to positive and negative dyads, mixed pairs reported less friendly general support actions, noted more anger, and perceived their sibling to be less friendly and more dominant during the interactions. In comparisons between same-result (i.e., positive, negative) pairs, positive dyads reported more dominant support behaviors and perceived their sibling to be friendlier during the interactions. Conclusion Data suggest that siblings who have different test results may experience more interpersonal strain than siblings who have the same test result. Future research on genetic testing and family relationships can expand upon these findings. PMID:18230020

Adsorbate-induced lifting of substrate relaxation is a general mechanism governing titania surface chemistry.

PubMed

Silber, David; Kowalski, Piotr M; Traeger, Franziska; Buchholz, Maria; Bebensee, Fabian; Meyer, Bernd; Wöll, Christof

2016-09-30

Under ambient conditions, almost all metals are coated by an oxide. These coatings, the result of a chemical reaction, are not passive. Many of them bind, activate and modify adsorbed molecules, processes that are exploited, for example, in heterogeneous catalysis and photochemistry. Here we report an effect of general importance that governs the bonding, structure formation and dissociation of molecules on oxidic substrates. For a specific example, methanol adsorbed on the rutile TiO 2 (110) single crystal surface, we demonstrate by using a combination of experimental and theoretical techniques that strongly bonding adsorbates can lift surface relaxations beyond their adsorption site, which leads to a significant substrate-mediated interaction between adsorbates. The result is a complex superstructure consisting of pairs of methanol molecules and unoccupied adsorption sites. Infrared spectroscopy reveals that the paired methanol molecules remain intact and do not deprotonate on the defect-free terraces of the rutile TiO 2 (110) surface.

Adsorbate-induced lifting of substrate relaxation is a general mechanism governing titania surface chemistry

NASA Astrophysics Data System (ADS)

Silber, David; Kowalski, Piotr M.; Traeger, Franziska; Buchholz, Maria; Bebensee, Fabian; Meyer, Bernd; Wöll, Christof

2016-09-01

Under ambient conditions, almost all metals are coated by an oxide. These coatings, the result of a chemical reaction, are not passive. Many of them bind, activate and modify adsorbed molecules, processes that are exploited, for example, in heterogeneous catalysis and photochemistry. Here we report an effect of general importance that governs the bonding, structure formation and dissociation of molecules on oxidic substrates. For a specific example, methanol adsorbed on the rutile TiO2(110) single crystal surface, we demonstrate by using a combination of experimental and theoretical techniques that strongly bonding adsorbates can lift surface relaxations beyond their adsorption site, which leads to a significant substrate-mediated interaction between adsorbates. The result is a complex superstructure consisting of pairs of methanol molecules and unoccupied adsorption sites. Infrared spectroscopy reveals that the paired methanol molecules remain intact and do not deprotonate on the defect-free terraces of the rutile TiO2(110) surface.

Latino Teen Theater: A Theater Intervention to Promote Latino Parent-Adolescent Sexual Communication.

PubMed

Noone, Joanne; Castillo, Nancy; Allen, Tiffany L; Esqueda, Teresa

2015-01-01

Latina teen pregnancy rates continue to be a health disparity in the United States. This study evaluated a parenting intervention using interactive theater to facilitate Latino parent-adolescent communication about sexuality and pregnancy prevention. The intervention, conducted in Spanish and with teen actors, consisted of scenes involving the audience. Fifty-nine parents participated in this 3-month prospective study. Spanish measures of comfort with communication, general communication, and parent-child sexual communication were employed comparing paired t tests for each scale. Acceptability of the intervention was assessed and demonstrated. Eighty-six percent of parents used information from the performance to talk to their child. Improvements in general communication (p < .02), sexual communication (p < .001), and comfort (p < .001) occurred. Interactive theater is an innovative approach to facilitate Latino parent communication about sexuality and pregnancy prevention.

Hydrodynamic interactions in freely suspended liquid crystal films

NASA Astrophysics Data System (ADS)

Kuriabova, Tatiana; Powers, Thomas R.; Qi, Zhiyuan; Goldfain, Aaron; Park, Cheol Soo; Glaser, Matthew A.; Maclennan, Joseph E.; Clark, Noel A.

2016-11-01

Hydrodynamic interactions play an important role in biological processes in cellular membranes, a large separation of length scales often allowing such membranes to be treated as continuous, two-dimensional (2D) fluids. We study experimentally and theoretically the hydrodynamic interaction of pairs of inclusions in two-dimensional, fluid smectic liquid crystal films suspended in air. Such smectic membranes are ideal systems for performing controlled experiments as they are mechanically stable, of highly uniform structure, and have well-defined, variable thickness, enabling experimental investigation of the crossover from 2D to 3D hydrodynamics. Our theoretical model generalizes the Levine-MacKintosh theory of point-force response functions and uses a boundary-element approach to calculate the mobility matrix for inclusions of finite extent. We describe in detail the theoretical and computational approach previously outlined in Z. Qi et al., Phys. Rev. Lett. 113, 128304 (2014), 10.1103/PhysRevLett.113.128304 and extend the method to study the mutual mobilities of inclusions with asymmetric shapes. The model predicts well the observed mutual mobilities of pairs of circular inclusions in films and the self-mobility of a circular inclusion in the vicinity of a linear boundary.

Classwide peer tutoring: an integration strategy to improve reading skills and promote peer interactions among students with autism and general education peers.

PubMed Central

Kamps, D M; Barbetta, P M; Leonard, B R; Delquadri, J

1994-01-01

A multiple baseline design across subjects with a reversal was used to examine the effects of classwide peer tutoring relative to traditional reading instruction on reading skills and social interaction time for 3 high-functioning students with autism and their typical peers in integrated, general education classrooms. Traditional reading instruction consisted largely of teacher-led instruction with individual student participation and seat work. Classwide peer tutoring consisted of 25 to 30 min of well-specified instruction in which tutor-learner pairs worked together on a classwide basis on reading fluency and comprehension skills. All students participated in 15- to 20-min unstructured free-time activities immediately following reading instruction. Results of reading assessments demonstrated that classwide peer tutoring increased reading fluency and correct responses to reading comprehension questions for students with autism and their peers. The procedure further increased the total duration of free-time social interactions for students with autism and typical peers, with individual variation in performance. PMID:8188563

Building up the spin - orbit alignment of interacting galaxy pairs

NASA Astrophysics Data System (ADS)

Moon, Jun-Sung; Yoon, Suk-Jin

2018-01-01

Galaxies are not just randomly distributed throughout space. Instead, they are in alignment over a wide range of scales from the cosmic web down to a pair of galaxies. Motivated by recent findings that the spin and the orbital angular momentum vectors of galaxy pairs tend to be parallel, we here investigate the spin - orbit orientation in close pairs using the Illustris cosmological simulation. We find that since z ~ 1, the parallel alignment has become progressively stronger with time through repetitive encounters. The pair Interactions are preferentially in prograde at z = 0 (over 5 sigma significance). The prograde fraction at z = 0 is larger for the pairs influenced more heavily by each other during their evolution. We find no correlation between the spin - orbit orientation and the surrounding large-scale structure. Our results favor the scenario in which the alignment in close pairs is caused by tidal interactions later on, rather than the primordial torquing by the large-scale structures.

Final state interactions at the threshold of Higgs boson pair production

NASA Astrophysics Data System (ADS)

Zhang, Zhentao

2015-11-01

We study the effect of final state interactions at the threshold of Higgs boson pair production in the Glashow-Weinberg-Salam model. We consider three major processes of the pair production in the model: lepton pair annihilation, ZZ fusion, and WW fusion. We find that the corrections caused by the effect for these processes are markedly different. According to our results, the effect can cause non-negligible corrections to the cross sections for lepton pair annihilation and small corrections for ZZ fusion, and this effect is negligible for WW fusion.

An investigation on the physicochemical properties of the nanostructured [(4-X)PMAT][N(CN)2] ion pairs as energetic and tunable aryl alkyl amino tetrazolium based ionic liquids

NASA Astrophysics Data System (ADS)

Khalili, Behzad; Rimaz, Mehdi

2017-06-01

In this study the different class of tunable and high nitrogen content ionic liquids termed TAMATILs (Tunable Aryl Methyl Amino Tetrazolium based Ionic Liquids) were designed. The physicochemical properties of the nanostructured TAMATILs composed of para substituted phenyl methyl amino tetrazolium cations [(4-X)PMAT]+ (X = H, Me, OCH3, OH, NH2, NO2, F, CN, CHO, CF3, COMe and CO2Me) and dicyanimide anion [N(CN)2]- were fully investigated using M06-2X functional in conjunction with the 6-311++G(2d,2p) basis set. For all of the studied nanostructured ILs the structural parameters, interaction energy, cation's enthalpy of formation, natural charges, charge transfer values and topological properties were calculated and discussed. The substituent effect on the interaction energy and physicochemical properties also is taking into account. The results showed that the strength of interaction has a linear correlation with electron content of the phenyl ring in a way the substituents with electron withdrawing effects lead to make more stable ion pairs with higher interaction energies. Some of the main physical properties of ILs such as surface tension, melting point, critical-point temperature, electrochemical stability and conductivity are discussed and estimated for studying ion pairs using quantum chemical computationally obtained thermochemical data. Finally the enthalpy and Gibbs free energy of formation for twelve nanostructured individual cations with the general formula of [(4-X)PMAT]+ (X = 4-H, 4-Me, 4-OMe, 4-OH, 4-NH2, 4-NO2, 4-F, 4-CN, 4-CHO, 4-CF3, 4-COMe and 4-CO2Me) are calculated.

Unconventional pairing symmetry of interacting Dirac fermions on a π -flux lattice

NASA Astrophysics Data System (ADS)

Guo, Huaiming; Khatami, Ehsan; Wang, Yao; Devereaux, Thomas P.; Singh, Rajiv R. P.; Scalettar, Richard T.

2018-04-01

The pairing symmetry of interacting Dirac fermions on the π -flux lattice is studied with the determinant quantum Monte Carlo and numerical linked-cluster expansion methods. The s*- (i.e., extended s -) and d -wave pairing symmetries, which are distinct in the conventional square lattice, are degenerate under the Landau gauge. We demonstrate that the dominant pairing channel at strong interactions is an unconventional d s* -wave phase consisting of alternating stripes of s*- and d -wave phases. A complementary mean-field analysis shows that while the s*- and d -wave symmetries individually have nodes in the energy spectrum, the d s* channel is fully gapped. The results represent a new realization of pairing in Dirac systems, connected to the problem of chiral d -wave pairing on the honeycomb lattice, which might be more readily accessed by cold-atom experiments.

Unconventional pairing symmetry of interacting Dirac fermions on a π -flux lattice

DOE PAGES

Guo, Huaiming; Khatami, Ehsan; Wang, Yao; ...

2018-04-20

The pairing symmetry of interacting Dirac fermions on the π-flux lattice is studied with the determinant quantum Monte Carlo and numerical linked-cluster expansion methods. The s*- (i.e., extended s-) and d-wave pairing symmetries, which are distinct in the conventional square lattice, are degenerate under the Landau gauge. We demonstrate that the dominant pairing channel at strong interactions is an unconventional ds*-wave phase consisting of alternating stripes of s*- and d-wave phases. A complementary mean-field analysis shows that while the s*- and d-wave symmetries individually have nodes in the energy spectrum, the ds* channel is fully gapped. The results represent amore » new realization of pairing in Dirac systems, connected to the problem of chiral d-wave pairing on the honeycomb lattice, which might be more readily accessed by cold-atom experiments.« less

Interactional Competence in a Paired Speaking Test: Features Salient to Raters

ERIC Educational Resources Information Center

May, Lyn

2011-01-01

Paired speaking tests are now commonly used in both high-stakes testing and classroom assessment contexts. The co-construction of discourse by candidates is regarded as a strength of paired speaking tests, as candidates have the opportunity to display a wider range of interactional competencies, including turn taking, initiating topics, and…

Modeling the mechanical properties of DNA nanostructures.

PubMed

Arbona, Jean Michel; Aimé, Jean-Pierre; Elezgaray, Juan

2012-11-01

We discuss generalizations of a previously published coarse-grained description [Mergell et al., Phys. Rev. E 68, 021911 (2003)] of double stranded DNA (dsDNA). The model is defined at the base-pair level and includes the electrostatic repulsion between neighbor helices. We show that the model reproduces mechanical and elastic properties of several DNA nanostructures (DNA origamis). We also show that electrostatic interactions are necessary to reproduce atomic force microscopy measurements on planar DNA origamis.

Bioassays Based on Molecular Nanomechanics

DOE PAGES

Majumdar, Arun

2002-01-01

Recent experiments have shown that when specific biomolecular interactions are confined to one surface of a microcantilever beam, changes in intermolecular nanomechanical forces provide sufficient differential torque to bend the cantilever beam. This has been used to detect single base pair mismatches during DNA hybridization, as well as prostate specific antigen (PSA) at concentrations and conditions that are clinically relevant for prostate cancer diagnosis. Since cantilever motion originates from free energy change induced by specific biomolecular binding, this technique is now offering a common platform for label-free quantitative analysis of protein-protein binding, DNA hybridization DNA-protein interactions, and in general receptor-ligandmore » interactions. Current work is focused on developing “universal microarrays” of microcantilever beams for high-throughput multiplexed bioassays.« less

Global limits and interference patterns in dark matter direct detection

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

Catena, Riccardo; Gondolo, Paolo

2015-08-13

We compare the general effective theory of one-body dark matter nucleon interactions to current direct detection experiments in a global multidimensional statistical analysis. We derive exclusion limits on the 28 isoscalar and isovector coupling constants of the theory, and show that current data place interesting constraints on dark matter-nucleon interaction operators usually neglected in this context. We characterize the interference patterns that can arise in dark matter direct detection from pairs of dark matter-nucleon interaction operators, or from isoscalar and isovector components of the same operator. We find that commonly neglected destructive interference effects weaken standard direct detection exclusion limitsmore » by up to one order of magnitude in the coupling constants.« less

Global limits and interference patterns in dark matter direct detection

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

Catena, Riccardo; Gondolo, Paolo, E-mail: riccardo.catena@theorie.physik.uni-goettingen.de, E-mail: paolo.gondolo@utah.edu

2015-08-01

We compare the general effective theory of one-body dark matter nucleon interactions to current direct detection experiments in a global multidimensional statistical analysis. We derive exclusion limits on the 28 isoscalar and isovector coupling constants of the theory, and show that current data place interesting constraints on dark matter-nucleon interaction operators usually neglected in this context. We characterize the interference patterns that can arise in dark matter direct detection from pairs of dark matter-nucleon interaction operators, or from isoscalar and isovector components of the same operator. We find that commonly neglected destructive interference effects weaken standard direct detection exclusion limitsmore » by up to one order of magnitude in the coupling constants.« less

Correlation Decay in Fermionic Lattice Systems with Power-Law Interactions at Nonzero Temperature

NASA Astrophysics Data System (ADS)

Hernández-Santana, Senaida; Gogolin, Christian; Cirac, J. Ignacio; Acín, Antonio

2017-09-01

We study correlations in fermionic lattice systems with long-range interactions in thermal equilibrium. We prove a bound on the correlation decay between anticommuting operators and generalize a long-range Lieb-Robinson-type bound. Our results show that in these systems of spatial dimension D with, not necessarily translation invariant, two-site interactions decaying algebraically with the distance with an exponent α ≥2 D , correlations between such operators decay at least algebraically to 0 with an exponent arbitrarily close to α at any nonzero temperature. Our bound is asymptotically tight, which we demonstrate by a high temperature expansion and by numerically analyzing density-density correlations in the one-dimensional quadratic (free, exactly solvable) Kitaev chain with long-range pairing.

Strongly exchange-coupled triplet pairs in an organic semiconductor

NASA Astrophysics Data System (ADS)

Weiss, Leah R.; Bayliss, Sam L.; Kraffert, Felix; Thorley, Karl J.; Anthony, John E.; Bittl, Robert; Friend, Richard H.; Rao, Akshay; Greenham, Neil C.; Behrends, Jan

2017-02-01

From biological complexes to devices based on organic semiconductors, spin interactions play a key role in the function of molecular systems. For instance, triplet-pair reactions impact operation of organic light-emitting diodes as well as photovoltaic devices. Conventional models for triplet pairs assume they interact only weakly. Here, using electron spin resonance, we observe long-lived, strongly interacting triplet pairs in an organic semiconductor, generated via singlet fission. Using coherent spin manipulation of these two-triplet states, we identify exchange-coupled (spin-2) quintet complexes coexisting with weakly coupled (spin-1) triplets. We measure strongly coupled pairs with a lifetime approaching 3 μs and a spin coherence time approaching 1 μs, at 10 K. Our results pave the way for the utilization of high-spin systems in organic semiconductors.

Pair Interaction of Dislocations in Two-Dimensional Crystals

NASA Astrophysics Data System (ADS)

Eisenmann, C.; Gasser, U.; Keim, P.; Maret, G.; von Grünberg, H. H.

2005-10-01

The pair interaction between crystal dislocations is systematically explored by analyzing particle trajectories of two-dimensional colloidal crystals measured by video microscopy. The resulting pair energies are compared to Monte Carlo data and to predictions derived from the standard Hamiltonian of the elastic theory of dislocations. Good agreement is found with respect to the distance and temperature dependence of the interaction potential, but not regarding the angle dependence where discrete lattice effects become important. Our results on the whole confirm that the dislocation Hamiltonian allows a quantitative understanding of the formation and interaction energies of dislocations in two-dimensional crystals.

Numerical approach for finite volume three-body interaction

NASA Astrophysics Data System (ADS)

Guo, Peng; Gasparian, Vladimir

2018-01-01

In the present work, we study a numerical approach to one dimensional finite volume three-body interaction, the method is demonstrated by considering a toy model of three spinless particles interacting with pair-wise δ -function potentials. The numerical results are compared with the exact solutions of three spinless bosons interaction when the strength of short-range interactions are set equal for all pairs.

Intermolecular interactions of trifluorohalomethanes with Lewis bases in the gas phase: An ab initio study

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

Wang, Yi-Siang; Yin, Chih-Chien; Chao, Sheng D., E-mail: sdchao@spring.iam.ntu.edu.tw

2014-10-07

We perform an ab initio computational study of molecular complexes with the general formula CF{sub 3}X—B that involve one trifluorohalomethane CF{sub 3}X (X = Cl or Br) and one of a series of Lewis bases B in the gas phase. The Lewis bases are so chosen that they provide a range of electron-donating abilities for comparison. Based on the characteristics of their electron pairs, we consider the Lewis bases with a single n-pair (NH{sub 3} and PH{sub 3}), two n-pairs (H{sub 2}O and H{sub 2}S), two n-pairs with an unsaturated bond (H{sub 2}CO and H{sub 2}CS), and a single π-pairmore » (C{sub 2}H{sub 4}) and two π-pairs (C{sub 2}H{sub 2}). The aim is to systematically investigate the influence of the electron pair characteristics and the central atom substitution effects on the geometries and energetics of the formed complexes. The counterpoise-corrected supermolecule MP2 and coupled-cluster single double with perturbative triple [CCSD(T)] levels of theory have been employed, together with a series of basis sets up to aug-cc-pVTZ. The angular and radial configurations, the binding energies, and the electrostatic potentials of the stable complexes have been compared and discussed as the Lewis base varies. For those complexes where halogen bonding plays a significant role, the calculated geometries and energetics are consistent with the σ-hole model. Upon formation of stable complexes, the C–X bond lengths shorten, while the C–X vibrational frequencies increase, thus rendering blueshifting halogen bonds. The central atom substitution usually enlarges the intermolecular bond distances while it reduces the net charge transfers, thus weakening the bond strengths. The analysis based on the σ-hole model is grossly reliable but requires suitable modifications incorporating the central atom substitution effects, in particular, when interaction components other than electrostatic contributions are involved.« less

Mediated Activity in the Primary Classroom: Girls, Boys and Computers.

ERIC Educational Resources Information Center

Fitzpatrick, Helen; Hardman, Margaret

2000-01-01

Studied the social interaction of 7- and 9-year-olds working in the same or mixed gender pairs on language-based computer and noncomputer tasks. At both ages, mixed gender pairs showed more assertive and less transactive (collaborative) interaction than same gender pairs on both tasks. Discusses the mediational role of the computer and the social…

A Macroscopic Analogue of the Nuclear Pairing Potential

ERIC Educational Resources Information Center

Dunlap, Richard A.

2013-01-01

A macroscopic system involving permanent magnets is used as an analogue to nucleons in a nucleus to illustrate the significance of the pairing interaction. This illustrates that the view of the total nuclear energy based only on the nucleon occupancy of the energy levels can yield erroneous results and it is only when the pairing interaction is…

Modeling plant interspecific interactions from experiments with perennial crop mixtures to predict optimal combinations.

PubMed

Halty, Virginia; Valdés, Matías; Tejera, Mauricio; Picasso, Valentín; Fort, Hugo

2017-12-01

The contribution of plant species richness to productivity and ecosystem functioning is a longstanding issue in ecology, with relevant implications for both conservation and agriculture. Both experiments and quantitative modeling are fundamental to the design of sustainable agroecosystems and the optimization of crop production. We modeled communities of perennial crop mixtures by using a generalized Lotka-Volterra model, i.e., a model such that the interspecific interactions are more general than purely competitive. We estimated model parameters -carrying capacities and interaction coefficients- from, respectively, the observed biomass of monocultures and bicultures measured in a large diversity experiment of seven perennial forage species in Iowa, United States. The sign and absolute value of the interaction coefficients showed that the biological interactions between species pairs included amensalism, competition, and parasitism (asymmetric positive-negative interaction), with various degrees of intensity. We tested the model fit by simulating the combinations of more than two species and comparing them with the polycultures experimental data. Overall, theoretical predictions are in good agreement with the experiments. Using this model, we also simulated species combinations that were not sown. From all possible mixtures (sown and not sown) we identified which are the most productive species combinations. Our results demonstrate that a combination of experiments and modeling can contribute to the design of sustainable agricultural systems in general and to the optimization of crop production in particular. © 2017 by the Ecological Society of America.

Magnetically actuated and controlled colloidal sphere-pair swimmer

NASA Astrophysics Data System (ADS)

Ran, Sijie; Guez, Allon; Friedman, Gary

2016-12-01

Magnetically actuated swimming of microscopic objects has been attracting attention partly due to its promising applications in the bio-medical field and partly due to interesting physics of swimming in general. While colloidal particles that are free to move in fluid can be an attractive swimming system due it its simplicity and ability to assemble in situ, stability of their dynamics and the possibility of stable swimming behavior in periodically varying magnetic fields has not been considered. Dynamic behavior of two magnetically interacting colloidal particles subjected to rotating magnetic field of switching frequency is analyzed here and is shown to result in stable swimming without any stabilizing feedback. A new mechanism of swimming that relies only on rotations of the particles themselves and of the particle pair axis is found to dominate the swimming dynamics of the colloidal particle pair. Simulation results and analytical arguments demonstrate that this swimming strategy compares favorably to dragging the particles with an external magnetic force when colloidal particle sizes are reduced.

MicroRNA Targeting Specificity in Mammals: Determinants Beyond Seed Pairing

PubMed Central

Grimson, Andrew; Farh, Kyle Kai-How; Johnston, Wendy K.; Garrett-Engele, Philip; Lim, Lee P.; Bartel, David P.

2013-01-01

Summary Mammalian microRNAs (miRNAs) pair to 3'UTRs of mRNAs to direct their posttranscriptional repression. Important for target recognition are ~7-nt sites that match the seed region of the miRNA. However, these seed matches are not always sufficient for repression, indicating that other characteristics help specify targeting. By combining computational and experimental approaches, we uncovered five general features of site context that boost site efficacy: AU-rich nucleotide composition near the site, proximity to sites for co-expressed miRNAs (which leads to cooperative action), proximity to residues pairing to miRNA nucleotides 13–16, and positioning within the 3'UTR at least 15 nt from the stop codon and away from the center of long UTRs. A model combining these context determinants quantitatively predicts site performance both for exogenously added miRNAs and for endogenous miRNA-message interactions. Because it predicts site efficacy without recourse to evolutionary conservation, the model also identifies effective nonconserved sites and siRNA off-targets. PMID:17612493

Prediction of Spin-Polarization Effects in Quantum Wire Transport

NASA Astrophysics Data System (ADS)

Fasol, Gerhard; Sakaki, Hiroyuki

1994-01-01

We predict a new effect for transport in quantum wires: spontaneous spin polarization. Most work on transport in mesoscopic devices has assumed a model of non interacting, spin-free electrons. We introduce spin, electron pair scattering and microscopic crystal properties into the design of mesoscopic devices. The new spin polarization effect results from the fact that in a single mode quantum wire, electron and hole bands still have two spin subbands. In general, these two spin subbands are expected to be split even in zero magnetic field. At sufficiently low temperatures the electron pair scattering rates for one spin subband ( e.g., the spin-down) can be much larger than for the other spin subband. This effect can be used for an active spin polarizer device: hot electrons in one subband ( e.g., `spin up') pass with weak pair scattering, while electrons in the opposite subband ( e.g., `spin down'), have high probability of scattering into the `spin-up' subband, resulting in spin polarization of a hot electron beam.

Exploiting Bounded Signal Flow for Graph Orientation Based on Cause-Effect Pairs

NASA Astrophysics Data System (ADS)

Dorn, Britta; Hüffner, Falk; Krüger, Dominikus; Niedermeier, Rolf; Uhlmann, Johannes

We consider the following problem: Given an undirected network and a set of sender-receiver pairs, direct all edges such that the maximum number of "signal flows" defined by the pairs can be routed respecting edge directions. This problem has applications in communication networks and in understanding protein interaction based cell regulation mechanisms. Since this problem is NP-hard, research so far concentrated on polynomial-time approximation algorithms and tractable special cases. We take the viewpoint of parameterized algorithmics and examine several parameters related to the maximum signal flow over vertices or edges. We provide several fixed-parameter tractability results, and in one case a sharp complexity dichotomy between a linear-time solvable case and a slightly more general NP-hard case. We examine the value of these parameters for several real-world network instances. For many relevant cases, the NP-hard problem can be solved to optimality. In this way, parameterized analysis yields both deeper insight into the computational complexity and practical solving strategies.

Structural studies of CNG repeats

PubMed Central

Kiliszek, Agnieszka; Rypniewski, Wojciech

2014-01-01

CNG repeats (where N denotes one of the four natural nucleotides) are abundant in the human genome. Their tendency to undergo expansion can lead to hereditary diseases known as TREDs (trinucleotide repeat expansion disorders). The toxic factor can be protein, if the abnormal gene is expressed, or the gene transcript, or both. The gene transcripts have attracted much attention in the biomedical community, but their molecular structures have only recently been investigated. Model RNA molecules comprising CNG repeats fold into long hairpins whose stems generally conform to an A-type helix, in which the non-canonical N-N pairs are flanked by C-G and G-C pairs. Each homobasic pair is accommodated in the helical context in a unique manner, with consequences for the local helical parameters, solvent structure, electrostatic potential and potential to interact with ligands. The detailed three-dimensional profiles of RNA CNG repeats can be used in screening of compound libraries for potential therapeutics and in structure-based drug design. Here is a brief survey of the CNG structures published to date. PMID:24939898

Control of box C/D snoRNP assembly by N6-methylation of adenine.

PubMed

Huang, Lin; Ashraf, Saira; Wang, Jia; Lilley, David Mj

2017-09-01

N 6 -methyladenine is the most widespread mRNA modification. A subset of human box C/D snoRNA species have target GAC sequences that lead to formation of N 6 -methyladenine at a key trans Hoogsteen-sugar A·G base pair, of which half are methylated in vivo The GAC target is conserved only in those that are methylated. Methylation prevents binding of the 15.5-kDa protein and the induced folding of the RNA Thus, the assembly of the box C/D snoRNP could in principle be regulated by RNA methylation at its critical first stage. Crystallography reveals that N 6 -methylation of adenine prevents the formation of trans Hoogsteen-sugar A·G base pairs, explaining why the box C/D RNA cannot adopt its kinked conformation. More generally, our data indicate that sheared A·G base pairs (but not Watson-Crick base pairs) are more susceptible to disruption by N 6 mA methylation and are therefore possible regulatory sites. The human signal recognition particle RNA and many related Alu retrotransposon RNA species are also methylated at N6 of an adenine that forms a sheared base pair with guanine and mediates a key tertiary interaction. © 2017 The Authors. Published under the terms of the CC BY 4.0 license.

Nanoparticle interaction potentials constructed by multiscale computation

NASA Astrophysics Data System (ADS)

Lee, Cheng K.; Hua, Chi C.

2010-06-01

The van der Waals (vdW) potentials governing macroscopic objects have long been formulated in the context of classical theories, such as Hamaker's microscopic theory and Lifshitz's continuum theory. This work addresses the possibility of constructing the vdW interaction potentials of nanoparticle species using multiscale simulation schemes. Amorphous silica nanoparticles were considered as a benchmark example for which a series of (SiO2)n (n being an integer) has been systematically surveyed as the potential candidates of the packing units that reproduce known bulk material properties in atomistic molecular dynamics simulations. This strategy led to the identification of spherical Si6O12 molecules, later utilized as the elementary coarse-grained (CG) particles to compute the pair interaction potentials of silica nanoparticles ranging from 0.62 to 100 nm in diameter. The model nanoparticles so built may, in turn, serve as the children CG particles to construct nanoparticles assuming arbitrary sizes and shapes. Major observations are as follows. The pair interaction potentials for all the investigated spherical silica nanoparticles can be cast into a semiempirical, generalized Lennard-Jones 2α-α potential (α being a size-dependent, large integral number). In its reduced form, we discuss the implied universalities for the vdW potentials governing a certain range of amorphous nanoparticle species as well as how thermodynamic transferability can be fulfilled automatically. In view of future applications with colloidal suspensions, we briefly evaluated the vdW potential in the presence of a "screening" medium mimicking the effects of electrical double layers or grafting materials atop the nanoparticle core. The general observations shed new light on strategies to attain a microscopic control over interparticle attractions. In future perspectives, the proposed multiscale computation scheme shall help bridge the current gap between the modeling of polymer chains and macroscopic objects by introducing molecular models coarse-grained at a similar level so that the interactions between these two can be treated in a consistent and faithful way.

Drug-target interaction prediction via class imbalance-aware ensemble learning.

PubMed

Ezzat, Ali; Wu, Min; Li, Xiao-Li; Kwoh, Chee-Keong

2016-12-22

Multiple computational methods for predicting drug-target interactions have been developed to facilitate the drug discovery process. These methods use available data on known drug-target interactions to train classifiers with the purpose of predicting new undiscovered interactions. However, a key challenge regarding this data that has not yet been addressed by these methods, namely class imbalance, is potentially degrading the prediction performance. Class imbalance can be divided into two sub-problems. Firstly, the number of known interacting drug-target pairs is much smaller than that of non-interacting drug-target pairs. This imbalance ratio between interacting and non-interacting drug-target pairs is referred to as the between-class imbalance. Between-class imbalance degrades prediction performance due to the bias in prediction results towards the majority class (i.e. the non-interacting pairs), leading to more prediction errors in the minority class (i.e. the interacting pairs). Secondly, there are multiple types of drug-target interactions in the data with some types having relatively fewer members (or are less represented) than others. This variation in representation of the different interaction types leads to another kind of imbalance referred to as the within-class imbalance. In within-class imbalance, prediction results are biased towards the better represented interaction types, leading to more prediction errors in the less represented interaction types. We propose an ensemble learning method that incorporates techniques to address the issues of between-class imbalance and within-class imbalance. Experiments show that the proposed method improves results over 4 state-of-the-art methods. In addition, we simulated cases for new drugs and targets to see how our method would perform in predicting their interactions. New drugs and targets are those for which no prior interactions are known. Our method displayed satisfactory prediction performance and was able to predict many of the interactions successfully. Our proposed method has improved the prediction performance over the existing work, thus proving the importance of addressing problems pertaining to class imbalance in the data.

Sequence co-evolution gives 3D contacts and structures of protein complexes

PubMed Central

Hopf, Thomas A; Schärfe, Charlotta P I; Rodrigues, João P G L M; Green, Anna G; Kohlbacher, Oliver; Sander, Chris; Bonvin, Alexandre M J J; Marks, Debora S

2014-01-01

Protein–protein interactions are fundamental to many biological processes. Experimental screens have identified tens of thousands of interactions, and structural biology has provided detailed functional insight for select 3D protein complexes. An alternative rich source of information about protein interactions is the evolutionary sequence record. Building on earlier work, we show that analysis of correlated evolutionary sequence changes across proteins identifies residues that are close in space with sufficient accuracy to determine the three-dimensional structure of the protein complexes. We evaluate prediction performance in blinded tests on 76 complexes of known 3D structure, predict protein–protein contacts in 32 complexes of unknown structure, and demonstrate how evolutionary couplings can be used to distinguish between interacting and non-interacting protein pairs in a large complex. With the current growth of sequences, we expect that the method can be generalized to genome-wide elucidation of protein–protein interaction networks and used for interaction predictions at residue resolution. DOI: http://dx.doi.org/10.7554/eLife.03430.001 PMID:25255213

In vitro colony interactions among species of Trichoderma with inference toward biological control.

Treesearch

Jimmy L. Reaves

1994-01-01

Colony interactions among 15 isolates representing seven species of Trichoderma were evaluated in vitro. Interactions characterized by zones of inhibition, demarcation lines, ridges of conidia, overgrowth, intermingling, anastomosis, and hyphal coiling in self-pairings and intraspecific and interspecific pairings of the seven species were recorded...

Benefits of pair housing are consistent across a diverse population of rhesus macaques

PubMed Central

Baker, Kate C.; Bloomsmith, Mollie A.; Oettinger, Brooke; Neu, Kimberly; Griffis, Caroline; Schoof, Valérie; Maloney, Margaret

2015-01-01

Introducing singly housed rhesus macaques (Macaca mulatta) into isosexual pairs is widely considered to improve welfare. The population of laboratory rhesus macaques is heterogeneous on a variety of factors and there is little literature available to directly evaluate the influence of many of these factors on the benefits of pair housing. Subjects were 46 adult female and 18 adult male rhesus macaques housed at the Tulane National Primate Research Center and the Yerkes National Primate Research Center. Behavioral data totalling 859 h and serum cortisol levels derived from 312 serum samples were analyzed for main effects of housing condition, comparing single housing to pair housing. In addition, a series of analyses were performed to test for interactions between housing condition and seven independent variables: sex, age, prior duration of single housing, presence or absence of a history of self-injurious behavior, and dominance rank, levels of affiliation and agonism in the paired setting. After the collection of 4–8 h of baseline data and three serum cortisol samples, pairs of individuals were introduced to one another and data collection was repeated, no earlier than 4 weeks after introduction. In pair housing both female and male subjects showed decrease in abnormal behavior (females: 54% reduction; P = 0.001; males: 18% reduction; P = 0.0007) and anxiety-related behavior (females: 35% reduction; P = 0.0001; males: 41% reduction; P = 0.0001), and increases in locomotion (females: 41% increase; P = 0.0001; males: 76% increase: P = 0.002). In pair housing, there were no significant sex differences in social behavior. Descriptively, paired females spent 12% of samples engaged in affiliative behavior and 0.5% engaged in agonistic behavior (back-transformed arcsin square root means). The corresponding values for males were 12% and 0.3%. No interaction effects were detected with any of the independent variables tested in this study. Cortisol values varied with sex but did not differ between housing conditions; no differences were detected when any of the above variables were included in the statistical model. Results support the general consensus among those studying the welfare of captive primates that social housing is a potent means for promoting behavioral indicators of the psychological well-being of laboratory primates. These results are of considerable practical significance and include information that refutes common perceptions about the unsuitability of males as socialization candidates, perceived negative PMID:25635151

Collapse of resilience patterns in generalized Lotka-Volterra dynamics and beyond.

PubMed

Tu, Chengyi; Grilli, Jacopo; Schuessler, Friedrich; Suweis, Samir

2017-06-01

Recently, a theoretical framework aimed at separating the roles of dynamics and topology in multidimensional systems has been developed [Gao et al., Nature (London) 530, 307 (2016)10.1038/nature16948]. The validity of their method is assumed to hold depending on two main hypotheses: (i) The network determined by the the interaction between pairs of nodes has negligible degree correlations; (ii) the node activities are uniform across nodes on both the drift and the pairwise interaction functions. Moreover, the authors consider only positive (mutualistic) interactions. Here we show the conditions proposed by Gao and collaborators [Nature (London) 530, 307 (2016)10.1038/nature16948] are neither sufficient nor necessary to guarantee that their method works in general and validity of their results are not independent of the model chosen within the class of dynamics they considered. Indeed we find that a new condition poses effective limitations to their framework and we provide quantitative predictions of the quality of the one-dimensional collapse as a function of the properties of interaction networks and stable dynamics using results from random matrix theory. We also find that multidimensional reduction may work also for an interaction matrix with a mixture of positive and negative signs, opening up an application of the framework to food webs, neuronal networks, and social and economic interactions.

Collapse of resilience patterns in generalized Lotka-Volterra dynamics and beyond

NASA Astrophysics Data System (ADS)

Tu, Chengyi; Grilli, Jacopo; Schuessler, Friedrich; Suweis, Samir

2017-06-01

Recently, a theoretical framework aimed at separating the roles of dynamics and topology in multidimensional systems has been developed [Gao et al., Nature (London) 530, 307 (2016), 10.1038/nature16948]. The validity of their method is assumed to hold depending on two main hypotheses: (i) The network determined by the the interaction between pairs of nodes has negligible degree correlations; (ii) the node activities are uniform across nodes on both the drift and the pairwise interaction functions. Moreover, the authors consider only positive (mutualistic) interactions. Here we show the conditions proposed by Gao and collaborators [Nature (London) 530, 307 (2016), 10.1038/nature16948] are neither sufficient nor necessary to guarantee that their method works in general and validity of their results are not independent of the model chosen within the class of dynamics they considered. Indeed we find that a new condition poses effective limitations to their framework and we provide quantitative predictions of the quality of the one-dimensional collapse as a function of the properties of interaction networks and stable dynamics using results from random matrix theory. We also find that multidimensional reduction may work also for an interaction matrix with a mixture of positive and negative signs, opening up an application of the framework to food webs, neuronal networks, and social and economic interactions.

Establishing and Maintaining Treatment Effects with Less Intrusive Consequences VIA a Pairing Procedure

PubMed Central

Vorndran, Christina M; Lerman, Dorothea C

2006-01-01

The generality and long-term maintenance of a pairing procedure designed to improve the efficacy of less intrusive procedures were evaluated for the treatment of problem behavior maintained by automatic reinforcement exhibited by 2 individuals with developmental disabilities. Results suggested that a less intrusive procedure could be established as a conditioned punisher by pairing it with an effective punisher contingent on problem behavior. Generalization across multiple therapists was demonstrated for both participants. However, generalization to another setting was not achieved for 1 participant until pairing was conducted in the second setting. Long-term maintenance was observed with 1 participant in the absence of further pairing trials. Maintenance via intermittent pairing trials was successful for the other participant. PMID:16602384

Multipole Algorithms for Molecular Dynamics Simulation on High Performance Computers.

NASA Astrophysics Data System (ADS)

Elliott, William Dewey

1995-01-01

A fundamental problem in modeling large molecular systems with molecular dynamics (MD) simulations is the underlying N-body problem of computing the interactions between all pairs of N atoms. The simplest algorithm to compute pair-wise atomic interactions scales in runtime {cal O}(N^2), making it impractical for interesting biomolecular systems, which can contain millions of atoms. Recently, several algorithms have become available that solve the N-body problem by computing the effects of all pair-wise interactions while scaling in runtime less than {cal O}(N^2). One algorithm, which scales {cal O}(N) for a uniform distribution of particles, is called the Greengard-Rokhlin Fast Multipole Algorithm (FMA). This work describes an FMA-like algorithm called the Molecular Dynamics Multipole Algorithm (MDMA). The algorithm contains several features that are new to N-body algorithms. MDMA uses new, efficient series expansion equations to compute general 1/r^{n } potentials to arbitrary accuracy. In particular, the 1/r Coulomb potential and the 1/r^6 portion of the Lennard-Jones potential are implemented. The new equations are based on multivariate Taylor series expansions. In addition, MDMA uses a cell-to-cell interaction region of cells that is closely tied to worst case error bounds. The worst case error bounds for MDMA are derived in this work also. These bounds apply to other multipole algorithms as well. Several implementation enhancements are described which apply to MDMA as well as other N-body algorithms such as FMA and tree codes. The mathematics of the cell -to-cell interactions are converted to the Fourier domain for reduced operation count and faster computation. A relative indexing scheme was devised to locate cells in the interaction region which allows efficient pre-computation of redundant information and prestorage of much of the cell-to-cell interaction. Also, MDMA was integrated into the MD program SIgMA to demonstrate the performance of the program over several simulation timesteps. One MD application described here highlights the utility of including long range contributions to Lennard-Jones potential in constant pressure simulations. Another application shows the time dependence of long range forces in a multiple time step MD simulation.

Explicit ions/implicit water generalized Born model for nucleic acids

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

Tolokh, Igor S.; Thomas, Dennis G.; Onufriev, Alexey V.

Ion atmosphere around highly charged nucleic acid molecules plays a significant role in their dynamics, structure and interactions. Here we utilized the implicit solvent framework to develop a model for the explicit treatment of ions interacting with nucleic acid molecules. The proposed explicit ions/implicit water model is based on a significantly modified generalized Born (GB) model, and utilizes a non-standard approach to defining the solute/solvent dielectric boundary. Specifically, the model includes modifications to the GB interaction terms for the case of multiple interacting solutes – disconnected dielectric boundary around the solute-ion or ion-ion pairs. Fully analytical description of all energymore » components for charge-charge interactions is provided. The effectiveness of the approach is demonstrated by calculating the potential of mean force (PMF) for Na+-Cl− ion pair and by carrying out a set of Monte Carlo (MC) simulations of mono- and trivalent ions interacting with DNA and RNA duplexes. The monovalent (Na+) and trivalent (CoHex3+) counterion distributions predicted by the model are in close quantitative agreement with all-atom explicit water molecular dynamics simulations used as reference. Expressed in the units of energy, the maximum deviations of local ion concentrations from the reference are within kBT. The proposed explicit ions/implicit water GB model is able to resolve subtle features and differences of CoHex distributions around DNA and RNA duplexes. These features include preferential CoHex binding inside the major groove of RNA duplex, in contrast to CoHex biding at the "external" surface of the sugar-phosphate backbone of DNA duplex; these differences in the counterion binding patters were shown earlier to be responsible for the observed drastic differences in condensation propensities between short DNA and RNA duplexes. MC simulations of CoHex ions interacting with homopolymeric poly(dA·dT) DNA duplex with modified (de-methylated) and native Thymine bases are used to explore the physics behind CoHex-Thymine interactions. The simulations suggest that the ion desolvation penalty due to proximity to the low dielectric volume of the methyl group can contribute significantly to CoHex-Thymine interactions. Compared to the steric repulsion between the ion and the methyl group, the desolvation penalty interaction has a longer range, and may be important to consider in the context of methylation effects on DNA condensation.« less

Explicit ions/implicit water generalized Born model for nucleic acids

NASA Astrophysics Data System (ADS)

Tolokh, Igor S.; Thomas, Dennis G.; Onufriev, Alexey V.

2018-05-01

The ion atmosphere around highly charged nucleic acid molecules plays a significant role in their dynamics, structure, and interactions. Here we utilized the implicit solvent framework to develop a model for the explicit treatment of ions interacting with nucleic acid molecules. The proposed explicit ions/implicit water model is based on a significantly modified generalized Born (GB) model and utilizes a non-standard approach to define the solute/solvent dielectric boundary. Specifically, the model includes modifications to the GB interaction terms for the case of multiple interacting solutes—disconnected dielectric boundary around the solute-ion or ion-ion pairs. A fully analytical description of all energy components for charge-charge interactions is provided. The effectiveness of the approach is demonstrated by calculating the potential of mean force for Na+-Cl- ion pair and by carrying out a set of Monte Carlo (MC) simulations of mono- and trivalent ions interacting with DNA and RNA duplexes. The monovalent (Na+) and trivalent (CoHex3+) counterion distributions predicted by the model are in close quantitative agreement with all-atom explicit water molecular dynamics simulations used as reference. Expressed in the units of energy, the maximum deviations of local ion concentrations from the reference are within kBT. The proposed explicit ions/implicit water GB model is able to resolve subtle features and differences of CoHex distributions around DNA and RNA duplexes. These features include preferential CoHex binding inside the major groove of the RNA duplex, in contrast to CoHex biding at the "external" surface of the sugar-phosphate backbone of the DNA duplex; these differences in the counterion binding patters were earlier shown to be responsible for the observed drastic differences in condensation propensities between short DNA and RNA duplexes. MC simulations of CoHex ions interacting with the homopolymeric poly(dA.dT) DNA duplex with modified (de-methylated) and native thymine bases are used to explore the physics behind CoHex-thymine interactions. The simulations suggest that the ion desolvation penalty due to proximity to the low dielectric volume of the methyl group can contribute significantly to CoHex-thymine interactions. Compared to the steric repulsion between the ion and the methyl group, the desolvation penalty interaction has a longer range and may be important to consider in the context of methylation effects on DNA condensation.

Pair Interactions and Mode of Communication: Comparing Face-to-Face and Computer Mediated Communication

ERIC Educational Resources Information Center

Tan, Lan Liana; Wigglesworth, Gillian; Storch, Neomy

2010-01-01

In today's second language classrooms, students are often asked to work in pairs or small groups. Such collaboration can take place face-to-face, but now more often via computer mediated communication. This paper reports on a study which investigated the effect of the medium of communication on the nature of pair interaction. The study involved…

A Bayesian mixture model for chromatin interaction data.

PubMed

Niu, Liang; Lin, Shili

2015-02-01

Chromatin interactions mediated by a particular protein are of interest for studying gene regulation, especially the regulation of genes that are associated with, or known to be causative of, a disease. A recent molecular technique, Chromatin interaction analysis by paired-end tag sequencing (ChIA-PET), that uses chromatin immunoprecipitation (ChIP) and high throughput paired-end sequencing, is able to detect such chromatin interactions genomewide. However, ChIA-PET may generate noise (i.e., pairings of DNA fragments by random chance) in addition to true signal (i.e., pairings of DNA fragments by interactions). In this paper, we propose MC_DIST based on a mixture modeling framework to identify true chromatin interactions from ChIA-PET count data (counts of DNA fragment pairs). The model is cast into a Bayesian framework to take into account the dependency among the data and the available information on protein binding sites and gene promoters to reduce false positives. A simulation study showed that MC_DIST outperforms the previously proposed hypergeometric model in terms of both power and type I error rate. A real data study showed that MC_DIST may identify potential chromatin interactions between protein binding sites and gene promoters that may be missed by the hypergeometric model. An R package implementing the MC_DIST model is available at http://www.stat.osu.edu/~statgen/SOFTWARE/MDM.

Nanoscale swimmers: hydrodynamic interactions and propulsion of molecular machines

NASA Astrophysics Data System (ADS)

Sakaue, T.; Kapral, R.; Mikhailov, A. S.

2010-06-01

Molecular machines execute nearly regular cyclic conformational changes as a result of ligand binding and product release. This cyclic conformational dynamics is generally non-reciprocal so that under time reversal a different sequence of machine conformations is visited. Since such changes occur in a solvent, coupling to solvent hydrodynamic modes will generally result in self-propulsion of the molecular machine. These effects are investigated for a class of coarse grained models of protein machines consisting of a set of beads interacting through pair-wise additive potentials. Hydrodynamic effects are incorporated through a configuration-dependent mobility tensor, and expressions for the propulsion linear and angular velocities, as well as the stall force, are obtained. In the limit where conformational changes are small so that linear response theory is applicable, it is shown that propulsion is exponentially small; thus, propulsion is nonlinear phenomenon. The results are illustrated by computations on a simple model molecular machine.

The modeling of piezoceramic patch interactions with shells, plates and beams

NASA Technical Reports Server (NTRS)

Banks, H. T.; Smith, R. C.

1992-01-01

General models describing the interactions between a pair of piezoceramic patches and elastic substructures consisting of a cylindrical shell, plate and beam are presented. In each case, the manner in which the patch loads enter both the strong and weak forms of the time-dependent structural equations of motion is described. Through force and moment balancing, these loads are then determined in terms of material properties of the patch and substructure (thickness, elastic properties, Poisson ratios), the geometry of the patch placement, and the voltages into the patches. In the case of the shell, the coupling between banding and inplane deformations, which is due to the curvature, is retained. These models are sufficiently general to allow for potentially different patch voltages which implies that they can be suitably employed when using piezoceramic patches for controlling system dynamics when both extensional and bending vibrations are present.

Overview of hybrid fiber-coaxial network deployment in the deregulated UK environment

NASA Astrophysics Data System (ADS)

Cox, Alan L.

1995-11-01

Cable operators in the U.K. enjoy unprecedented license to construct networks and operate cable TV and telecommunications services within their franchise areas. In general, operators have built hybrid-fiber-coax (HFC) networks for cable TV in parallel with fiber-copper-pair networks for telephony. The commonly used network architectures are reviewed, together with their present and future capacities. Despite this dual-technology approach, there is considerable interest in the integration of telephony services onto the HFC network and the development of new interactive services for which HFC may be more suitable than copper pairs. Certain technological and commercial developments may have considerable significance for HFC networks and their operators. These include the digitalization of TV distribution and the rising demand for high-rate digital access lines. Possible scenarios are discussed.

Coherent States for Kronecker Products of Non Compact Groups: Formulation and Applications

NASA Technical Reports Server (NTRS)

Bambah, Bindu A.; Agarwal, Girish S.

1996-01-01

We introduce and study the properties of a class of coherent states for the group SU(1,1) X SU(1,1) and derive explicit expressions for these using the Clebsch-Gordan algebra for the SU(1,1) group. We restrict ourselves to the discrete series representations of SU(1,1). These are the generalization of the 'Barut Girardello' coherent states to the Kronecker Product of two non-compact groups. The resolution of the identity and the analytic phase space representation of these states is presented. This phase space representation is based on the basis of products of 'pair coherent states' rather than the standard number state canonical basis. We discuss the utility of the resulting 'bi-pair coherent states' in the context of four-mode interactions in quantum optics.

Human-Human Interaction Forces and Interlimb Coordination During Side-by-Side Walking With Hand Contact.

PubMed

Sylos-Labini, Francesca; d'Avella, Andrea; Lacquaniti, Francesco; Ivanenko, Yury

2018-01-01

Handholding can naturally occur between two walkers. When people walk side-by-side, either with or without hand contact, they often synchronize their steps. However, despite the importance of haptic interaction in general and the natural use of hand contact between humans during walking, few studies have investigated forces arising from physical interactions. Eight pairs of adult subjects participated in this study. They walked on side-by-side treadmills at 4 km/h independently and with hand contact. Only hand contact-related sensory information was available for unintentional synchronization, while visual and auditory communication was obstructed. Subjects walked at their natural cadences or following a metronome. Limb kinematics, hand contact 3D interaction forces and EMG activity of 12 upper limb muscles were recorded. Overall, unintentional step frequency locking was observed during about 40% of time in 88% of pairs walking with hand contact. On average, the amplitude of contact arm oscillations decreased while the contralateral (free) arm oscillated in the same way as during normal walking. Interestingly, EMG activity of the shoulder muscles of the contact arm did not decrease, and their synergistic pattern remained similar. The amplitude of interaction forces and of trunk oscillations was similar for synchronized and non-synchronized steps, though the synchronized steps were characterized by significantly more regular orientations of interaction forces. Our results further support the notion that gait synchronization during natural walking is common, and that it may occur through interaction forces. Conservation of the proximal muscle activity of the contact (not oscillating) arm is consistent with neural coupling between cervical and lumbosacral pattern generation circuitries ("quadrupedal" arm-leg coordination) during human gait. Overall, the findings suggest that individuals might integrate force interaction cues to communicate and coordinate steps during walking.

Human-Human Interaction Forces and Interlimb Coordination During Side-by-Side Walking With Hand Contact

PubMed Central

Sylos-Labini, Francesca; d'Avella, Andrea; Lacquaniti, Francesco; Ivanenko, Yury

2018-01-01

Handholding can naturally occur between two walkers. When people walk side-by-side, either with or without hand contact, they often synchronize their steps. However, despite the importance of haptic interaction in general and the natural use of hand contact between humans during walking, few studies have investigated forces arising from physical interactions. Eight pairs of adult subjects participated in this study. They walked on side-by-side treadmills at 4 km/h independently and with hand contact. Only hand contact-related sensory information was available for unintentional synchronization, while visual and auditory communication was obstructed. Subjects walked at their natural cadences or following a metronome. Limb kinematics, hand contact 3D interaction forces and EMG activity of 12 upper limb muscles were recorded. Overall, unintentional step frequency locking was observed during about 40% of time in 88% of pairs walking with hand contact. On average, the amplitude of contact arm oscillations decreased while the contralateral (free) arm oscillated in the same way as during normal walking. Interestingly, EMG activity of the shoulder muscles of the contact arm did not decrease, and their synergistic pattern remained similar. The amplitude of interaction forces and of trunk oscillations was similar for synchronized and non-synchronized steps, though the synchronized steps were characterized by significantly more regular orientations of interaction forces. Our results further support the notion that gait synchronization during natural walking is common, and that it may occur through interaction forces. Conservation of the proximal muscle activity of the contact (not oscillating) arm is consistent with neural coupling between cervical and lumbosacral pattern generation circuitries (“quadrupedal” arm-leg coordination) during human gait. Overall, the findings suggest that individuals might integrate force interaction cues to communicate and coordinate steps during walking. PMID:29563883

Magnon-induced superconductivity in a topological insulator coupled to ferromagnetic and antiferromagnetic insulators

NASA Astrophysics Data System (ADS)

Hugdal, Henning G.; Rex, Stefan; Nogueira, Flavio S.; Sudbø, Asle

2018-05-01

We study the effective interactions between Dirac fermions on the surface of a three-dimensional topological insulator due to the proximity coupling to the magnetic fluctuations in a ferromagnetic or antiferromagnetic insulator. Our results show that the magnetic fluctuations can mediate attractive interactions between Dirac fermions of both Amperean and BCS types. In the ferromagnetic case, we find pairing between fermions with parallel momenta, so-called Amperean pairing, whenever the effective Lagrangian for the magnetic fluctuations does not contain a quadratic term. The pairing interaction also increases with increasing Fermi momentum and is in agreement with previous studies in the limit of high chemical potential. If a quadratic term is present, the pairing is instead of BCS type above a certain chemical potential. In the antiferromagnetic case, BCS pairing occurs when the ferromagnetic coupling between magnons on the same sublattice exceeds the antiferromagnetic coupling between magnons on different sublattices. Outside this region in parameter space, we again find that Amperean pairing is realized.

Photofragmentation, state interaction, and energetics of Rydberg and ion-pair states: Resonance enhanced multiphoton ionization of HI

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

Hróðmarsson, Helgi Rafn; Wang, Huasheng; Kvaran, Ágúst, E-mail: agust@hi.is

2014-06-28

Mass resolved resonance enhanced multiphoton ionization data for hydrogen iodide (HI), for two-photon resonance excitation to Rydberg and ion-pair states in the 69 600–72 400 cm{sup −1} region were recorded and analyzed. Spectral perturbations due to homogeneous and heterogeneous interactions between Rydberg and ion-pair states, showing as deformations in line-positions, line-intensities, and line-widths, were focused on. Parameters relevant to photodissociation processes, state interaction strengths and spectroscopic parameters for deperturbed states were derived. Overall interaction and dynamical schemes to describe the observations are proposed.

In search of functional association from time-series microarray data based on the change trend and level of gene expression

PubMed Central

He, Feng; Zeng, An-Ping

2006-01-01

Background The increasing availability of time-series expression data opens up new possibilities to study functional linkages of genes. Present methods used to infer functional linkages between genes from expression data are mainly based on a point-to-point comparison. Change trends between consecutive time points in time-series data have been so far not well explored. Results In this work we present a new method based on extracting main features of the change trend and level of gene expression between consecutive time points. The method, termed as trend correlation (TC), includes two major steps: 1, calculating a maximal local alignment of change trend score by dynamic programming and a change trend correlation coefficient between the maximal matched change levels of each gene pair; 2, inferring relationships of gene pairs based on two statistical extraction procedures. The new method considers time shifts and inverted relationships in a similar way as the local clustering (LC) method but the latter is merely based on a point-to-point comparison. The TC method is demonstrated with data from yeast cell cycle and compared with the LC method and the widely used Pearson correlation coefficient (PCC) based clustering method. The biological significance of the gene pairs is examined with several large-scale yeast databases. Although the TC method predicts an overall lower number of gene pairs than the other two methods at a same p-value threshold, the additional number of gene pairs inferred by the TC method is considerable: e.g. 20.5% compared with the LC method and 49.6% with the PCC method for a p-value threshold of 2.7E-3. Moreover, the percentage of the inferred gene pairs consistent with databases by our method is generally higher than the LC method and similar to the PCC method. A significant number of the gene pairs only inferred by the TC method are process-identity or function-similarity pairs or have well-documented biological interactions, including 443 known protein interactions and some known cell cycle related regulatory interactions. It should be emphasized that the overlapping of gene pairs detected by the three methods is normally not very high, indicating a necessity of combining the different methods in search of functional association of genes from time-series data. For a p-value threshold of 1E-5 the percentage of process-identity and function-similarity gene pairs among the shared part of the three methods reaches 60.2% and 55.6% respectively, building a good basis for further experimental and functional study. Furthermore, the combined use of methods is important to infer more complete regulatory circuits and network as exemplified in this study. Conclusion The TC method can significantly augment the current major methods to infer functional linkages and biological network and is well suitable for exploring temporal relationships of gene expression in time-series data. PMID:16478547

The Effects of Dominance on Leadership and Energetic Gain: A Dynamic Game between Pairs of Social Foragers

PubMed Central

Rands, Sean A.

2011-01-01

Although social behaviour can bring many benefits to an individual, there are also costs that may be incurred whenever the members of a social group interact. The formation of dominance hierarchies could offer a means of reducing some of the costs of social interaction, but individuals within the hierarchy may end up paying differing costs dependent upon their position within the hierarchy. These differing interaction costs may therefore influence the behaviour of the group, as subordinate individuals may experience very different benefits and costs to dominants when the group is conducting a given behaviour. Here, a state-dependent dynamic game is described which considers a pair of social foragers where there is a set dominance relationship within the pair. The model considers the case where the subordinate member of the pair pays an interference cost when it and the dominant individual conduct specific pairs of behaviours together. The model demonstrates that if the subordinate individual pays these energetic costs when it interacts with the dominant individual, this has effects upon the behaviour of both subordinate and the dominant individuals. Including interaction costs increases the amount of foraging behaviour both individuals conduct, with the behaviour of the pair being driven by the subordinate individual. The subordinate will tend to be the lighter individual for longer periods of time when interaction costs are imposed. This supports earlier suggestions that lighter individuals should act as the decision-maker within the pair, giving leadership-like behaviours that are based upon energetic state. Pre-existing properties of individuals such as their dominance will be less important for determining which individual makes the decisions for the pair. This suggests that, even with strict behavioural hierarchies, identifying which individual is the dominant one is not sufficient for identifying which one is the leader. PMID:22028645

Seasonal differences of corticosterone metabolite concentrations and parasite burden in northern bald ibis (Geronticus eremita): The role of affiliative interactions

PubMed Central

Wascher, Claudia A. F.; Loretto, Matthias-Claudio; Palme, Rupert; Stoewe, Mareike; Kotrschal, Kurt; Frigerio, Didone

2018-01-01

The reproductive season is energetically costly as revealed by elevated glucocorticoid concentrations, constrained immune functions and an increased risk of infections. Social allies and affiliative interactions may buffer physiological stress responses and thereby alleviate associated effects. In the present study, we investigated the seasonal differences of immune reactive corticosterone metabolite concentrations, endoparasite burden (nematode eggs and coccidian oocysts) and affiliative interactions in northern bald ibis (Geronticus eremita), a critically endangered bird. In total, 43 individually marked focal animals from a free-ranging colony were investigated. The analyses included a description of initiated and received affiliative interactions, pair bond status as well as seasonal patterns of hormone and endoparasite levels. During the reproductive season, droppings contained parasite eggs more often and corticosterone metabolite levels were higher as compared to the period after reproduction. The excretion rate of endoparasite products was lower in paired individuals than in unpaired ones, but paired animals exhibited higher corticosterone metabolite concentrations than unpaired individuals. Furthermore, paired individuals initiated affiliative behaviour more frequently than unpaired ones. This suggests that the reproductive season influences the excretion patterns of endoparasite products and corticosterone metabolites and that affiliative interactions between pair partners may positively affect endoparasite burden during periods of elevated glucocorticoid levels. Being embedded in a pair bond may have a positive impact on individual immune system and parasite resistance. PMID:29364951

The interactive evolution of human communication systems.

PubMed

Fay, Nicolas; Garrod, Simon; Roberts, Leo; Swoboda, Nik

2010-04-01

This paper compares two explanations of the process by which human communication systems evolve: iterated learning and social collaboration. It then reports an experiment testing the social collaboration account. Participants engaged in a graphical communication task either as a member of a community, where they interacted with seven different partners drawn from the same pool, or as a member of an isolated pair, where they interacted with the same partner across the same number of games. Participants' horizontal, pair-wise interactions led "bottom up" to the creation of an effective and efficient shared sign system in the community condition. Furthermore, the community-evolved sign systems were as effective and efficient as the local sign systems developed by isolated pairs. Finally, and as predicted by a social collaboration account, and not by an iterated learning account, interaction was critical to the creation of shared sign systems, with different isolated pairs establishing different local sign systems and different communities establishing different global sign systems. Copyright © 2010 Cognitive Science Society, Inc.

Highly Dynamic Anion-Quadrupole Networks in Proteins.

PubMed

Kapoor, Karan; Duff, Michael R; Upadhyay, Amit; Bucci, Joel C; Saxton, Arnold M; Hinde, Robert J; Howell, Elizabeth E; Baudry, Jerome

2016-11-01

The dynamics of anion-quadrupole (or anion-π) interactions formed between negatively charged (Asp/Glu) and aromatic (Phe) side chains are for the first time computationally characterized in RmlC (Protein Data Bank entry 1EP0 ), a homodimeric epimerase. Empirical force field-based molecular dynamics simulations predict anion-quadrupole pairs and triplets (anion-anion-π and anion-π-π) are formed by the protein during the simulated trajectory, which suggests that the anion-quadrupole interactions may provide a significant contribution to the overall stability of the protein, with an average of -1.6 kcal/mol per pair. Some anion-π interactions are predicted to form during the trajectory, extending the number of anion-quadrupole interactions beyond those predicted from crystal structure analysis. At the same time, some anion-π pairs observed in the crystal structure exhibit marginal stability. Overall, most anion-π interactions alternate between an "on" state, with significantly stabilizing energies, and an "off" state, with marginal or null stabilizing energies. The way proteins possibly compensate for transient loss of anion-quadrupole interactions is characterized in the RmlC aspartate 84-phenylalanine 112 anion-quadrupole pair observed in the crystal structure. A double-mutant cycle analysis of the thermal stability suggests a possible loss of anion-π interactions compensated by variations of hydration of the residues and formation of compensating electrostatic interactions. These results suggest that near-planar anion-quadrupole pairs can exist, sometimes transiently, which may play a role in maintaining the structural stability and function of the protein, in an otherwise very dynamic interplay of a nonbonded interaction network as well as solvent effects.

[The study of complex-formation of DNA with the antimicrobial drug decamethoxine].

PubMed

Sorokin, V A; Blagoĭ, Iu P; Valeev, V A; Gladchenko, G O; Sukhodub, L F; Volianskiĭ, Iu L

1990-01-01

The interaction of effective antibacterial drug decametoxyn with natural DNA was studied by UV-spectroscopy. Decametoxyn shows a specificity to nucleotides: it decreases the cooperativity of melting and the thermal stability of DNA parts enriched by AT pairs. The characteristics of the helix-coil transition on the DNA parts enriched by GC-pairs are invariable. Interaction with AT-pairs results in their partial or complete melting at room temperature, followed by intermolecule aggregation. Interacting with phosphates decametoxyn manifests itself not as a dication but as two single-charged ions.

Superconductivity in the Penson-Kolb Model on a Triangular Lattice

NASA Astrophysics Data System (ADS)

Ptok, A.; Mierzejewski, M.

2008-07-01

We investigate properties of the two-dimensional Penson-Kolb model with repulsive pair hopping interaction. In the case of a bipartite square lattice this interaction may lead to the η-type pairing, when the phase of superconducting order parameter changes from one lattice site to the neighboring one. We show that this interaction may be responsible for the onset of superconductivity also for a triangular lattice. We discuss the spatial dependence of the superconducting order parameter and demonstrate that the total momentum of the paired electrons is determined by the lattice geometry.

Single top quarks and dark matter

NASA Astrophysics Data System (ADS)

Pinna, Deborah; Zucchetta, Alberto; Buckley, Matthew R.; Canelli, Florencia

2017-08-01

Processes with dark matter interacting with the standard model fermions through new scalars or pseudoscalars with flavor-diagonal couplings proportional to fermion mass are well motivated theoretically, and provide a useful phenomenological model with which to interpret experimental results. Two modes of dark matter production from these models have been considered in the existing literature: pairs of dark matter produced through top quark loops with an associated monojet in the event, and pair production of dark matter with pairs of heavy flavored quarks (tops or bottoms). In this paper, we demonstrate that a third, previously overlooked channel yields a non-negligible contribution to LHC dark matter searches in these models. In spite of a generally lower production cross section at LHC when compared to the associated top-pair channel, non-flavor violating single top quark processes are kinematically favored and can significantly increase the sensitivity to these models. Including dark matter production in association with a single top quark through scalar or pseudoscalar mediators, the exclusion limit set by the LHC searches for dark matter can be improved by 30% up to a factor of two, depending on the mass assumed for the mediator particle.

Long-range interactions, wobbles, and phase defects in chains of model cilia

NASA Astrophysics Data System (ADS)

Brumley, Douglas R.; Bruot, Nicolas; Kotar, Jurij; Goldstein, Raymond E.; Cicuta, Pietro; Polin, Marco

2016-12-01

Eukaryotic cilia and flagella are chemo-mechanical oscillators capable of generating long-range coordinated motions known as metachronal waves. Pair synchronization is a fundamental requirement for these collective dynamics, but it is generally not sufficient for collective phase-locking, chiefly due to the effect of long-range interactions. Here we explore experimentally and numerically a minimal model for a ciliated surface: hydrodynamically coupled oscillators rotating above a no-slip plane. Increasing their distance from the wall profoundly affects the global dynamics, due to variations in hydrodynamic interaction range. The array undergoes a transition from a traveling wave to either a steady chevron pattern or one punctuated by periodic phase defects. Within the transition between these regimes the system displays behavior reminiscent of chimera states.

Fluctuations in Mass-Action Equilibrium of Protein Binding Networks

NASA Astrophysics Data System (ADS)

Yan, Koon-Kiu; Walker, Dylan; Maslov, Sergei

2008-12-01

We consider two types of fluctuations in the mass-action equilibrium in protein binding networks. The first type is driven by slow changes in total concentrations of interacting proteins. The second type (spontaneous) is caused by quickly decaying thermodynamic deviations away from equilibrium. We investigate the effects of network connectivity on fluctuations by comparing them to scenarios in which the interacting pair is isolated from the network and analytically derives bounds on fluctuations. Collective effects are shown to sometimes lead to large amplification of spontaneous fluctuations. The strength of both types of fluctuations is positively correlated with the complex connectivity and negatively correlated with complex concentration. Our general findings are illustrated using a curated network of protein interactions and multiprotein complexes in baker’s yeast, with empirical protein concentrations.

Abasic pivot substitution harnesses target specificity of RNA interference

PubMed Central

Lee, Hye-Sook; Seok, Heeyoung; Lee, Dong Ha; Ham, Juyoung; Lee, Wooje; Youm, Emilia Moonkyung; Yoo, Jin Seon; Lee, Yong-Seung; Jang, Eun-Sook; Chi, Sung Wook

2015-01-01

Gene silencing via RNA interference inadvertently represses hundreds of off-target transcripts. Because small interfering RNAs (siRNAs) can function as microRNAs, avoiding miRNA-like off-target repression is a major challenge. Functional miRNA–target interactions are known to pre-require transitional nucleation, base pairs from position 2 to the pivot (position 6). Here, by substituting nucleotide in pivot with abasic spacers, which prevent base pairing and alleviate steric hindrance, we eliminate miRNA-like off-target repression while preserving on-target activity at ∼80–100%. Specifically, miR-124 containing dSpacer pivot substitution (6pi) loses seed-mediated transcriptome-wide target interactions, repression activity and biological function, whereas other conventional modifications are ineffective. Application of 6pi allows PCSK9 siRNA to efficiently lower plasma cholesterol concentration in vivo, and abolish potentially deleterious off-target phenotypes. The smallest spacer, C3, also shows the same improvement in target specificity. Abasic pivot substitution serves as a general means to harness the specificity of siRNA experiments and therapeutic applications. PMID:26679372

Color Superconductivity and Charge Neutrality in Yukawa Theory

NASA Astrophysics Data System (ADS)

Alford, Mark G.; Pangeni, Kamal; Windisch, Andreas

2018-02-01

It is generally believed that when Cooper pairing occurs between two different species of fermions, their Fermi surfaces become locked together so that the resultant state remains "neutral," with equal number densities of the two species, even when subjected to a chemical potential that couples to the difference in number densities. This belief is based on mean-field calculations in models with a zero-range interaction, where the anomalous self-energy is independent of energy and momentum. Following up on an early report of a deviation from neutrality in a Dyson-Schwinger calculation of color-flavor-locked quark matter, we investigate the neutrality of a two-species condensate using a Yukawa model which has a finite-range interaction. In a mean field calculation we obtain the full energy-momentum dependence of the self-energy and find that the energy dependence leads to a population imbalance in the Cooper-paired phase when it is stressed by a species-dependent chemical potential. This gives some support to the suggestion that the color-flavor-locked phase of quark matter might not be an insulator.

Centromere pairing precedes meiotic chromosome pairing in plants.

PubMed

Zhang, Jing; Han, Fangpu

2017-11-01

Meiosis is a specialized eukaryotic cell division, in which diploid cells undergo a single round of DNA replication and two rounds of nuclear division to produce haploid gametes. In most eukaryotes, the core events of meiotic prophase I are chromosomal pairing, synapsis and recombination. To ensure accurate chromosomal segregation, homologs have to identify and align along each other at the onset of meiosis. Although much progress has been made in elucidating meiotic processes, information on the mechanisms underlying chromosome pairing is limited in contrast to the meiotic recombination and synapsis events. Recent research in many organisms indicated that centromere interactions during early meiotic prophase facilitate homologous chromosome pairing, and functional centromere is a prerequisite for centromere pairing such as in maize. Here, we summarize the recent achievements of chromosome pairing research on plants and other organisms, and outline centromere interactions, nuclear chromosome orientation, and meiotic cohesin, as main determinants of chromosome pairing in early meiotic prophase.

Quantifying Electrical Interactions between Cardiomyocytes and Other Cells in Micropatterned Cell Pairs

PubMed Central

Nguyen, Hung; Badie, Nima; McSpadden, Luke; Pedrotty, Dawn; Bursac, Nenad

2014-01-01

Micropatterning is a powerful technique to control cell shape and position on a culture substrate. In this chapter, we describe the method to reproducibly create large numbers of micropatterned heterotypic cell pairs with defined size, shape, and length of cell–cell contact. These cell pairs can be utilized in patch clamp recordings to quantify electrical interactions between cardiomyocytes and non-cardiomyocytes. PMID:25070342

Unconventional Cooper pairing results in a pseudogap-like phase in s-wave superconductors

NASA Astrophysics Data System (ADS)

Springer, Daniel; Cheong, Siew Ann

2015-10-01

The impact of disorder on the superconducting (SC) pairing mechanism is the centre of much debate. Some evidence suggests a loss of phase coherence of pairs while others point towards the formation of a competing phase. In our work we show that the two perspectives may be different sides of the same coin. Using an extension of the perturbative renormalization group approach we compare the impact of different disorder-induced interactions on a SC ground state. We find that in the strongly disordered regime an interaction between paired fermions and their respective disordered environment replaces conventional Cooper pairing. For these unconventional Cooper pairs the phase coherence condition, required for the formation of a SC condensate, is not satisfied.

Attractive interaction between Mn atoms on the GaAs(110) surface observed by scanning tunneling microscopy.

PubMed

Taninaka, Atsushi; Yoshida, Shoji; Kanazawa, Ken; Hayaki, Eiko; Takeuchi, Osamu; Shigekawa, Hidemi

2016-06-16

Scanning tunneling microscopy/spectroscopy (STM/STS) was carried out to investigate the structures of Mn atoms deposited on a GaAs(110) surface at room temperature to directly observe the characteristics of interactions between Mn atoms in GaAs. Mn atoms were paired with a probability higher than the random distribution, indicating an attractive interaction between them. In fact, re-pairing of unpaired Mn atoms was observed during STS measurement. The pair initially had a new structure, which was transformed during STS measurement into one of those formed by atom manipulation at 4 K. Mn atoms in pairs and trimers were aligned in the <110> direction, which is theoretically predicted to produce a high Curie temperature.

Beyond BCS pairing in high-density neutron matter

NASA Astrophysics Data System (ADS)

Rios, A.; Ding, D.; Dussan, H.; Dickhoff, W. H.; Witte, S. J.; Polls, A.

2018-01-01

Pairing gaps in neutron matter need to be computed in a wide range of densities to address open questions in neutron star phenomenology. Traditionally, the Bardeen-Cooper-Schrieffer approach has been used to compute gaps from bare nucleon-nucleon interactions. Here, we incorporate the influence of short- and long-range correlations into pairing properties. Short-range correlations are treated including the appropriate fragmentation of single-particle states, and they suppress the gaps substantially. Long-range correlations dress the pairing interaction via density and spin modes, and provide a relatively small correction. We use three different interactions as a starting point to control for any systematic effects. Results are relevant for neutron-star cooling scenarios, in particular in view of the recent observational data on Cassiopeia A.

Predicting Physical Interactions between Protein Complexes*

PubMed Central

Clancy, Trevor; Rødland, Einar Andreas; Nygard, Ståle; Hovig, Eivind

2013-01-01

Protein complexes enact most biochemical functions in the cell. Dynamic interactions between protein complexes are frequent in many cellular processes. As they are often of a transient nature, they may be difficult to detect using current genome-wide screens. Here, we describe a method to computationally predict physical interactions between protein complexes, applied to both humans and yeast. We integrated manually curated protein complexes and physical protein interaction networks, and we designed a statistical method to identify pairs of protein complexes where the number of protein interactions between a complex pair is due to an actual physical interaction between the complexes. An evaluation against manually curated physical complex-complex interactions in yeast revealed that 50% of these interactions could be predicted in this manner. A community network analysis of the highest scoring pairs revealed a biologically sensible organization of physical complex-complex interactions in the cell. Such analyses of proteomes may serve as a guide to the discovery of novel functional cellular relationships. PMID:23438732

Large-Scale Identification and Analysis of Suppressive Drug Interactions

PubMed Central

Cokol, Murat; Weinstein, Zohar B.; Yilancioglu, Kaan; Tasan, Murat; Doak, Allison; Cansever, Dilay; Mutlu, Beste; Li, Siyang; Rodriguez-Esteban, Raul; Akhmedov, Murodzhon; Guvenek, Aysegul; Cokol, Melike; Cetiner, Selim; Giaever, Guri; Iossifov, Ivan; Nislow, Corey; Shoichet, Brian; Roth, Frederick P.

2014-01-01

SUMMARY One drug may suppress the effects of another. Although knowledge of drug suppression is vital to avoid efficacy-reducing drug interactions or discover countermeasures for chemical toxins, drug-drug suppression relationships have not been systematically mapped. Here, we analyze the growth response of Saccharomyces cerevisiae to anti-fungal compound (“drug”) pairs. Among 440 ordered drug pairs, we identified 94 suppressive drug interactions. Using only pairs not selected on the basis of their suppression behavior, we provide an estimate of the prevalence of suppressive interactions between anti-fungal compounds as 17%. Analysis of the drug suppression network suggested that Bromopyruvate is a frequently suppressive drug and Staurosporine is a frequently suppressed drug. We investigated potential explanations for suppressive drug interactions, including chemogenomic analysis, coaggregation, and pH effects, allowing us to explain the interaction tendencies of Bromopyruvate. PMID:24704506

Double binding energy differences: Mean-field or pairing effect?

NASA Astrophysics Data System (ADS)

Qi, Chong

2012-10-01

In this Letter we present a systematic analysis on the average interaction between the last protons and neutrons in atomic nuclei, which can be extracted from the double differences of nuclear binding energies. The empirical average proton-neutron interaction Vpn thus derived from experimental data can be described in a very simple form as the interplay of the nuclear mean field and the pairing interaction. It is found that the smooth behavior as well as the local fluctuations of the Vpn in even-even nuclei with N ≠ Z are dominated by the contribution from the proton-neutron monopole interactions. A strong additional contribution from the isoscalar monopole interaction and isovector proton-neutron pairing interaction is seen in the Vpn for even-even N = Z nuclei and for the adjacent odd-A nuclei with one neutron or proton being subtracted.

A Pair of Resonance Stripe Solitons and Lump Solutions to a Reduced (3+1)-Dimensional Nonlinear Evolution Equation

NASA Astrophysics Data System (ADS)

Chen, Mei-Dan; Li, Xian; Wang, Yao; Li, Biao

2017-06-01

With symbolic computation, some lump solutions are presented to a (3+1)-dimensional nonlinear evolution equation by searching the positive quadratic function from the Hirota bilinear form of equation. The quadratic function contains six free parameters, four of which satisfy two determinant conditions guaranteeing analyticity and rational localization of the solutions, while the others are free. Then, by combining positive quadratic function with exponential function, the interaction solutions between lump solutions and the stripe solitons are presented on the basis of some conditions. Furthermore, we extend this method to obtain more general solutions by combining of positive quadratic function and hyperbolic cosine function. Thus the interaction solutions between lump solutions and a pair of resonance stripe solitons are derived and asymptotic property of the interaction solutions are analyzed under some specific conditions. Finally, the dynamic properties of these solutions are shown in figures by choosing the values of the parameters. Supported by National Natural Science Foundation of China under Grant Nos. 11271211, 11275072, and 11435005, Ningbo Natural Science Foundation under Grant No. 2015A610159 and the Opening Project of Zhejiang Provincial Top Key Discipline of Physics Sciences in Ningbo University under Grant No. xkzw11502 and K.C. Wong Magna Fund in Ningbo University

Developing force fields when experimental data is sparse: AMBER/GAFF-compatible parameters for inorganic and alkyl oxoanions.

PubMed

Kashefolgheta, Sadra; Vila Verde, Ana

2017-08-09

We present a set of Lennard-Jones parameters for classical, all-atom models of acetate and various alkylated and non-alkylated forms of sulfate, sulfonate and phosphate ions, optimized to reproduce their interactions with water and with the physiologically relevant sodium, ammonium and methylammonium cations. The parameters are internally consistent and are fully compatible with the Generalized Amber Force Field (GAFF), the AMBER force field for proteins, the accompanying TIP3P water model and the sodium model of Joung and Cheatham. The parameters were developed primarily relying on experimental information - hydration free energies and solution activity derivatives at 0.5 m concentration - with ab initio, gas phase calculations being used for the cases where experimental information is missing. The ab initio parameterization scheme presented here is distinct from other approaches because it explicitly connects gas phase binding energies to intermolecular interactions in solution. We demonstrate that the original GAFF/AMBER parameters often overestimate anion-cation interactions, leading to an excessive number of contact ion pairs in solutions of carboxylate ions, and to aggregation in solutions of divalent ions. GAFF/AMBER parameters lead to excessive numbers of salt bridges in proteins and of contact ion pairs between sodium and acidic protein groups, issues that are resolved by using the optimized parameters presented here.

Voluntary physical exercise alters attentional orienting and social behavior in a rat model of attention-deficit/hyperactivity disorder.

PubMed

Hopkins, Michael E; Sharma, Mita; Evans, Gretchen C; Bucci, David J

2009-06-01

The effects of voluntary physical exercise on attentional function and social behavior were examined in male and female spontaneously hypertensive rats (SHR), a commonly used animal model of attention-deficit/hyperactivity disorder (ADHD). Rats in the exercise groups had free access to a running wheel for 2 weeks and then all rats received nonreinforced presentations of a visual stimulus (light) during the 1st training session, followed by daily sessions in which the light was paired with food. Nonexercising male and female SHR rats exhibited more unconditioned orienting behavior than Wistar-Kyoto rats. SHRs also exhibited impaired conditioning when the light was paired with food. Exercise reduced orienting in female SHRs but not in male SHRs. In the social interaction task, nonexercising male and female SHRs interacted more with an unfamiliar rat than Wistar-Kyoto rats. Exercise reduced the number of social interactions in female SHRs but not male SHRs. There were no differences in general locomotor activity observed between the nonexercising and exercising SHRs. These data indicate that exercise may preferentially benefit female SHRs, and has implications for using exercise as an intervention for ADHD and for understanding sex differences in the effects of exercise on behavior. Copyright (c) 2009 APA, all rights reserved.

Deep eutectic solvent formation: a structural view using molecular dynamics simulations with classical force fields

NASA Astrophysics Data System (ADS)

Mainberger, Sebastian; Kindlein, Moritz; Bezold, Franziska; Elts, Ekaterina; Minceva, Mirjana; Briesen, Heiko

2017-06-01

Deep eutectic solvents (DES) have gained a reputation as inexpensive and easy to handle ionic liquid analogues. This work employs molecular dynamics (MD) to simulate a variety of DES. The hydrogen bond acceptor (HBA) choline chloride was paired with the hydrogen bond donors (HBD) glycerol, 1,4-butanediol, and levulinic acid. Levulinic acid was also paired with the zwitterionic HBA betaine. In order to evaluate the reliability of data MD simulations can provide for DES, two force fields were compared: the Merck Molecular Force Field and the General Amber Force Field with two different sets of partial charges for the latter. The force fields were evaluated by comparing available experimental thermodynamic and transport properties against simulated values. Structural analysis was performed on the eutectic systems and compared to non-eutectic compositions. All force fields could be validated against certain experimental properties, but performance varied depending on the system and property in question. While extensive hydrogen bonding was found for all systems, details about the contribution of individual groups strongly varied among force fields. Interaction potentials revealed that HBA-HBA interactions weaken linearly with increasing HBD ratio, while HBD-HBD interactions grew disproportionally in magnitude, which might hint at the eutectic composition of a system.

Response trajectories capture the continuous dynamics of the size congruity effect.

PubMed

Faulkenberry, Thomas J; Cruise, Alexander; Lavro, Dmitri; Shaki, Samuel

2016-01-01

In a comparison task involving numbers, the size congruity effect refers to the general finding that responses are usually faster when there is a match between numerical size and physical size (e.g., 2-8) than when there is a mismatch (e.g., 2-8). In the present study, we used computer mouse tracking to test two competing models of the size congruity effect: an early interaction model, where interference occurs at an early representational stage, and a late interaction model, where interference occurs as dynamic competition between response options. In three experiments, we found that the curvature of responses for incongruent trials was greater than for congruent trials. In Experiment 2 we showed that this curvature effect was reliably modulated by the numerical distance between the two stimulus numbers, with large distance pairs exhibiting a larger curvature effect than small distance pairs. In Experiment 3 we demonstrated that the congruity effects persist into response execution. These findings indicate that incongruities between numerical and physical sizes are carried throughout the response process and result from competition between parallel and partially active response options, lending further support to a late interaction model of the size congruity effect. Copyright © 2015 Elsevier B.V. All rights reserved.

Analog of the Milky Way and the Magellanic Clouds

NASA Astrophysics Data System (ADS)

Kohler, Susanna

2017-11-01

A hunt for merging dwarf galaxies has yielded an intriguing result: 180 million light-years away, a galaxy very similar to the Milky Way with two dwarf-galaxy satellites just like our own Magellanic clouds.Unusual SatellitesThe Large and Small Magellanic clouds, as observed from Earth. [ESO/S. Brunier]The Large and Small Magellanic clouds (LMC and SMC), the only bright and star-forming satellite galaxies around the Milky Way, have proven unusual in the universe: satellite pairs of LMCSMC mass are neither common in observation nor typically produced in numerical simulations of galaxy formation and evolution.Since the probability of having such an interacting pair of satellites in a massive halo is so low, this raises questions about how our system came about. Did the Magellanic clouds form independently around the Milky Way and then interact? Were they more recently captured as an already-merging pair of dwarf galaxies? Or is there some other explanation?If we could find other systems that look like the LMCSMCMilky-Way system, we might be able to learn more about pairs of dwarf galaxies and how they interact near the halos of large galaxies like the Milky Way. Conveniently, two researchers from Yonsei University in South Korea, Sanjaya Paudel and Chandreyee Sengupta, have now identified exactly such a system.The UGC 4703 pair of dwarf galaxies show a stellar bridge connecting them a sign of their past interaction, when tidal forces stripped material from them as they passed each other. [Adapted from Paudel Sengupta 2017]An Interacting PairHunting for merging dwarf galaxies in various environments, Paudel and Sengupta found UGC 4703, an interacting pair of dwarf galaxies that are located near the isolated spiral galaxy NGC 2718. This pair of satellites around the massive spiral bear a striking resemblance to the LMCSMC system around the Milky-Way.The authors performed a multi-wavelength study of the system using archival images from the Sloan Digital Sky Survey, The Galaxy Evolutionary Explorer spacecraft, and the Spitzer Space Telescope. They also gather new observations of the H I gas distribution in the system using the Giant Metrewave Radio Telescope in India.Paudel and Sengupta find that NGC 2718 and the Milky Way have similar stellar masses, and the stellar mass ratio of the UGC 4703 interacting pair is around 5:1, similar to the mass ratio of the LMC to the SMC. The separation of the UGC 4703 pair is also roughly the same as that of the LMC and SMC: 70,000 light-years.Similarities and DifferencesThe H I gas distribution in UGC 4703 reveals both similarities and differences between this system and the LMCSMC system. [Paudel Sengupta 2017]The stellar bridge connecting the components of the UGC 4703 system are a sign of their past interaction, but a comparison of the optical and H I morphology between the UGC 4703 pair and the LMCSMC pair suggests that the UGC 4703 galaxies are either interacting more slowly than the Magellanic clouds or that the interaction is at a more advanced stage than we see with the LMCSMC.Understanding these similarities and differences between the LMCSMCMilky-Way system and this analog are an important first step to studying dwarf galaxy pairs as they interact near the massive halos of their large spiral hosts. In the future, further observations of UGC 4703 and detailed modeling of the system may help continue to puzzle out how our own Magellanic clouds came about.CitationSanjaya Paudel and C. Sengupta 2017 ApJL 849 L28. doi:10.3847/2041-8213/aa95bf

Theoretical Probing of Weak Anion-Cation Interactions in Certain Pyridinium-Based Ionic Liquid Ion Pairs and the Application of Molecular Electrostatic Potential in Their Ionic Crystal Density Determination: A Comparative Study Using Density Functional Approach.

PubMed

Joseph, Aswathy; Thomas, Vibin Ipe; Żyła, Gaweł; Padmanabhan, A S; Mathew, Suresh

2018-01-11

A comprehensive study on the structure, nature of interaction, and properties of six ionic pairs of 1-butylpyridinium and 1-butyl-4-methylpyridinium cations in combination with tetrafluoroborate (BF 4 - ), chloride (Cl - ), and bromide (Br - ) anions have been carried out using density functional theory (DFT). The anion-cation interaction energy (ΔE int ), thermochemistry values, theoretical band gap, molecular orbital energy order, DFT-based chemical activity descriptors [chemical potential (μ), chemical hardness (η), and electrophilicity index (ω)], and distribution of density of states (DOS) of these ion pairs were investigated. The ascendancy of the -CH 3 substituent at the fourth position of the 1-butylpyridinium cation ring on the values of ΔE int , theoretical band gap and chemical activity descriptors was evaluated. The ΔE int values were negative for all six ion pairs and were highest for Cl - containing ion pairs. The theoretical band gap value after -CH 3 substitution increased from 3.78 to 3.96 eV (for Cl - ) and from 2.74 to 2.88 eV (for Br - ) and decreased from 4.9 to 4.89 eV (for BF 4 - ). Ion pairs of BF 4 - were more susceptible to charge transfer processes as inferred from their significantly high η values and comparatively small difference in ω value after -CH 3 substitution. The change in η and μ values due to the -CH 3 substituent is negligibly small in all cases except for the ion pairs of Cl - . Critical-point (CP) analyses were carried out to investigate the AIM topological parameters at the interionic bond critical points (BCPs). The RDG isosurface analysis indicated that the anion-cation interaction was dominated by strong H cat ···X ani and C cat ···X ani interactions in ion pairs of Cl - and Br - whereas a weak van der Waal's effect dominated in ion pairs of BF 4 - . The molecular electrostatic potential (MESP)-based parameter ΔΔV min measuring the anion-cation interaction strength showed a good linear correlation with ΔE int for all 1-butylpyridinium ion pairs (R 2 = 0.9918). The ionic crystal density values calculated by using DFT-based MESP showed only slight variations from experimentally reported values.

1+1 Gaudin Model

NASA Astrophysics Data System (ADS)

Zotov, Andrei V.

2011-07-01

We study 1+1 field-generalizations of the rational and elliptic Gaudin models. For sl(N) case we introduce equations of motion and L-A pair with spectral parameter on the Riemann sphere and elliptic curve. In sl(2) case we study the equations in detail and find the corresponding Hamiltonian densities. The n-site model describes n interacting Landau-Lifshitz models of magnets. The interaction depends on position of the sites (marked points on the curve). We also analyze the 2-site case in its own right and describe its relation to the principal chiral model. We emphasize that 1+1 version impose a restriction on a choice of flows on the level of the corresponding 0+1 classical mechanics.

Higher order structural effects stabilizing the reverse Watson–Crick Guanine-Cytosine base pair in functional RNAs

PubMed Central

Chawla, Mohit; Abdel-Azeim, Safwat; Oliva, Romina; Cavallo, Luigi

2014-01-01

The G:C reverse Watson–Crick (W:W trans) base pair, also known as Levitt base pair in the context of tRNAs, is a structurally and functionally important base pair that contributes to tertiary interactions joining distant domains in functional RNA molecules and also participates in metabolite binding in riboswitches. We previously indicated that the isolated G:C W:W trans base pair is a rather unstable geometry, and that dicationic metal binding to the Guanine base or posttranscriptional modification of the Guanine can increase its stability. Herein, we extend our survey and report on other H-bonding interactions that can increase the stability of this base pair. To this aim, we performed a bioinformatics search of the PDB to locate all the occurencies of G:C trans base pairs. Interestingly, 66% of the G:C trans base pairs in the PDB are engaged in additional H-bonding interactions with other bases, the RNA backbone or structured water molecules. High level quantum mechanical calculations on a data set of representative crystal structures were performed to shed light on the structural stability and energetics of the various crystallographic motifs. This analysis was extended to the binding of the preQ1 metabolite to a preQ1-II riboswitch. PMID:24121683

Pgltools: a genomic arithmetic tool suite for manipulation of Hi-C peak and other chromatin interaction data.

PubMed

Greenwald, William W; Li, He; Smith, Erin N; Benaglio, Paola; Nariai, Naoki; Frazer, Kelly A

2017-04-07

Genomic interaction studies use next-generation sequencing (NGS) to examine the interactions between two loci on the genome, with subsequent bioinformatics analyses typically including annotation, intersection, and merging of data from multiple experiments. While many file types and analysis tools exist for storing and manipulating single locus NGS data, there is currently no file standard or analysis tool suite for manipulating and storing paired-genomic-loci: the data type resulting from "genomic interaction" studies. As genomic interaction sequencing data are becoming prevalent, a standard file format and tools for working with these data conveniently and efficiently are needed. This article details a file standard and novel software tool suite for working with paired-genomic-loci data. We present the paired-genomic-loci (PGL) file standard for genomic-interactions data, and the accompanying analysis tool suite "pgltools": a cross platform, pypy compatible python package available both as an easy-to-use UNIX package, and as a python module, for integration into pipelines of paired-genomic-loci analyses. Pgltools is a freely available, open source tool suite for manipulating paired-genomic-loci data. Source code, an in-depth manual, and a tutorial are available publicly at www.github.com/billgreenwald/pgltools , and a python module of the operations can be installed from PyPI via the PyGLtools module.

UGC 4703 Interacting Pair Near the Isolated Spiral Galaxy NGC 2718: A Milky Way Magellanic Cloud Analog

NASA Astrophysics Data System (ADS)

Paudel, Sanjaya; Sengupta, C.

2017-11-01

We present an analysis of physical and morphological properties of an interacting pair of dwarf galaxies, UGC 4703, located in the vicinity of an isolated Milky Way (MW) type spiral galaxy NGC 2718. Based on the comparison of physical and morphological properties with that of the Large and Small Magellanic Clouds (LMC and SMC), we report that the UGC 4703 pair-NGC 2718 system is probably an LMC-SMC-MW analog. Located at a sky-projected distance of 81 kpc from NGC 2718, we find that UGC 4703 is clearly interacting with its nearby lower-mass companion UGC 4703B, forming a bridge of stellar stream between them. Total B-band luminosity of UGC 4703 and its companion is -17.75 and -16.25 mag, respectively. We obtained H I 21 cm line data of UGC 4703 using the GMRT to get a more detailed view of neutral hydrogen (H I) emission. The H I image revealed evidence of interaction between the dwarf galaxy pair but no extended emission, such as the Magellanic Stream. We also detected star-forming regions along the UGC 4703/4703B bridge with stellar mass exceeding 107 M ⊙. While comparing the optical and H I morphology of the interacting dwarf pairs (UGC 4703-4703B and LMC-SMC), we discuss possible differences in interaction histories of these systems.

Velocity statistics for interacting edge dislocations in one dimension from Dyson's Coulomb gas model.

PubMed

Jafarpour, Farshid; Angheluta, Luiza; Goldenfeld, Nigel

2013-10-01

The dynamics of edge dislocations with parallel Burgers vectors, moving in the same slip plane, is mapped onto Dyson's model of a two-dimensional Coulomb gas confined in one dimension. We show that the tail distribution of the velocity of dislocations is power law in form, as a consequence of the pair interaction of nearest neighbors in one dimension. In two dimensions, we show the presence of a pairing phase transition in a system of interacting dislocations with parallel Burgers vectors. The scaling exponent of the velocity distribution at effective temperatures well below this pairing transition temperature can be derived from the nearest-neighbor interaction, while near the transition temperature, the distribution deviates from the form predicted by the nearest-neighbor interaction, suggesting the presence of collective effects.

Residue frequencies and pairing preferences at protein-protein interfaces.

PubMed

Glaser, F; Steinberg, D M; Vakser, I A; Ben-Tal, N

2001-05-01

We used a nonredundant set of 621 protein-protein interfaces of known high-resolution structure to derive residue composition and residue-residue contact preferences. The residue composition at the interfaces, in entire proteins and in whole genomes correlates well, indicating the statistical strength of the data set. Differences between amino acid distributions were observed for interfaces with buried surface area of less than 1,000 A(2) versus interfaces with area of more than 5,000 A(2). Hydrophobic residues were abundant in large interfaces while polar residues were more abundant in small interfaces. The largest residue-residue preferences at the interface were recorded for interactions between pairs of large hydrophobic residues, such as Trp and Leu, and the smallest preferences for pairs of small residues, such as Gly and Ala. On average, contacts between pairs of hydrophobic and polar residues were unfavorable, and the charged residues tended to pair subject to charge complementarity, in agreement with previous reports. A bootstrap procedure, lacking from previous studies, was used for error estimation. It showed that the statistical errors in the set of pairing preferences are generally small; the average standard error is approximately 0.2, i.e., about 8% of the average value of the pairwise index (2.9). However, for a few pairs (e.g., Ser-Ser and Glu-Asp) the standard error is larger in magnitude than the pairing index, which makes it impossible to tell whether contact formation is favorable or unfavorable. The results are interpreted using physicochemical factors and their implications for the energetics of complex formation and for protein docking are discussed. Proteins 2001;43:89-102. Copyright 2001 Wiley-Liss, Inc.

Insights into the Electronic Structure of Ozone and Sulfur Dioxide from Generalized Valence Bond Theory: Bonding in O3 and SO2.

PubMed

Takeshita, Tyler Y; Lindquist, Beth A; Dunning, Thom H

2015-07-16

There are many well-known differences in the physical and chemical properties of ozone (O3) and sulfur dioxide (SO2). O3 has longer and weaker bonds than O2, whereas SO2 has shorter and stronger bonds than SO. The O-O2 bond is dramatically weaker than the O-SO bond, and the singlet-triplet gap in SO2 is more than double that in O3. In addition, O3 is a very reactive species, while SO2 is far less so. These disparities have been attributed to variations in the amount of diradical character in the two molecules. In this work, we use generalized valence bond (GVB) theory to characterize the electronic structure of ozone and sulfur dioxide, showing O3 does indeed possess significant diradical character, whereas SO2 is effectively a closed shell molecule. The GVB results provide critical insights into the genesis of the observed difference in these two isoelectronic species. SO2 possesses a recoupled pair bond dyad in the a"(π) system, resulting in SO double bonds. The π system of O3, on the other hand, has a lone pair on the central oxygen atom plus a pair of electrons in orbitals on the terminal oxygen atoms that give rise to a relatively weak π interaction.

Electrohydrodynamic deformation and interaction of a pair of emulsion drops

NASA Technical Reports Server (NTRS)

Baygents, James C.

1994-01-01

The response of a pair of emulsion drops to the imposition of a uniform electric field is examined. The case studied is that of equal-sized drops whose line of centers is parallel to the axis of the applied field. A new boundary integral solution to the governing equations of the leaky dielectric model is developed; the formulation accounts for the electrostatic and hydrodynamic interactions between the drops, as well as their deformations. Numerical calculations show that, after an initial transient during which the drops primarily deform, the pair drift slowly together due to their electrostatic interactions.

Complete particle-pair annihilation as a dynamical signature of the spectral singularity

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

Li, G.R.; Zhang, X.Z.; Song, Z., E-mail: nkquantum@gmail.com

2014-10-15

Motivated by the physical relevance of a spectral singularity of interacting many-particle system, we explore the dynamics of two bosons as well as fermions in one-dimensional system with imaginary delta interaction strength. Based on the exact solution, it shows that the two-particle collision leads to amplitude-reduction of the wave function. For fermion pair, the amplitude-reduction depends on the spin configuration of two particles. In both cases, the residual amplitude can vanish when the relative group velocity of two single-particle Gaussian wave packets with equal width reaches the magnitude of the interaction strength, exhibiting complete particle-pair annihilation at the spectral singularity.more » - Highlights: • We investigate the physical relevance of a spectral singularity. • The two-particle collision leads to amplitude-reduction of the wave function. • There is a singularity spectrum which leads to complete particle-pair annihilation. • Complete particle-pair annihilation can only occur for two distinguishable bosons and singlet fermions. • Pair annihilation provides a detection method of the spectral singularity in the experiment.« less

Interlayer Pairing Symmetry of Composite Fermions in Quantum Hall Bilayers

DOE PAGES

Isobe, Hiroki; Fu, Liang

2017-04-17

Here, we study the pairing symmetry of the interlayer paired state of composite fermions in quantum Hall bilayers. Based on the Halperin-Lee-Read (HLR) theory, the effect of the long-range Coulomb interaction and the internal Chern-Simons gauge fluctuation is analyzed with the random-phase approximation beyond the leading order contribution in small momentum expansion, and we observe that the interlayer paired states with a relative angular momentummore » $l=+1$ are energetically favored for filling ν=$$\\frac{1}2$$+$$\\frac{1}2$$ and $$\\frac{1}4$$+$$\\frac{1}4$$. The degeneracy between states with $±l$ is lifted by the interlayer density-current interaction arising from the interplay of the long-range Coulomb interaction and the Chern-Simons term in the HLR theory.« less

BVR photometric investigation of galaxy pair KPG 562

NASA Astrophysics Data System (ADS)

Hendy, Y. H. M.

2018-06-01

This work presents BVR photometric observations and analyses for galaxy pair KPG 562 selected from the Karachentsev Catalog of Isolated Pairs of Galaxies. The observations were obtained using the 1.88-m Telescope of the Kottamia Astronomical Observatory (KAO), Egypt. There is no interaction signs assigned for this pair as reported by Karachentsev Catalog. We used the surface photometry technique to obtain photometric parameters for each galaxy of the pair. The isophotal contours, the luminosity profiles, color profiles (B-V, V-R), ellipticity profiles, position angle (PA) profiles and isophotal center-shift (xc, yc) profiles have been presented. The total and absolute magnitude, ellipticity and position angle (PA) were also obtained from the studied galaxy pair. The studied galaxy pair is clearly showing signs of interaction opposed to that found by Karachentsev. We found that the galaxy KPG 562b contains one tidal tail. The length and thickness of tidal tail were obtained and presented in this study.

Spin polarization transfer by the radical pair mechanism

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

Zarea, Mehdi, E-mail: m-zarea@northwestern.edu; Ratner, Mark A.; Wasielewski, Michael R.

2015-08-07

In a three-site representation, we study a spin polarization transfer from radical pair spins to a nearby electron or nuclear spin. The quantum dynamics of the radical pair spins is governed by a constant exchange interaction between the radical pair spins which have different Zeeman frequencies. Radical pair spins can recombine to the singlet ground state or to lower energy triplet states. It is then shown that the coherent dynamics of the radical pair induces spin polarization on the nearby third spin in the presence of a magnetic field. The spin polarization transfer depends on the difference between Zeeman frequencies,more » the singlet and triplet recombination rates, and on the exchange and dipole-dipole interactions between the different spins. In particular, the sign of the polarization depends on the exchange coupling between radical pair spins and also on the difference between singlet and triplet recombination rate constants.« less

Active galactic nuclei and galaxy interactions

NASA Astrophysics Data System (ADS)

Alonso, M. Sol; Lambas, Diego G.; Tissera, Patricia; Coldwell, Georgina

2007-03-01

We perform a statistical analysis of active galactic nucleus (AGN) host characteristics and nuclear activity for AGNs in pairs and without companions. Our study concerns a sample of AGNs derived from the Sloan Digital Sky Survey Data Release 4 data by Kauffmann et al. and pair galaxies obtained from the same data set by Alonso et al. An eye-ball classification of images of 1607 close pairs (rp < 25 kpc h-1,ΔV < 350 km s-1) according to the evidence of interaction through distorted morphologies and tidal features provides us with a more confident assessment of galaxy interactions from this sample. We notice that, at a given luminosity or stellar mass content, the fraction of AGNs is larger for pair galaxies exhibiting evidence for strong interaction and tidal features which also show signs of strong star formation activity. Nevertheless, this process accounts only for a ~10per cent increase of the fraction of AGNs. As in previous works, we find AGN hosts to be redder and with a larger concentration morphological index than non-AGN galaxies. This effect does not depend on whether AGN hosts are in pairs or in isolation. The OIII luminosity of AGNs with strong interaction features is found to be significantly larger than that of other AGNs, either in pairs or in isolation. Estimations of the accretion rate, L[OIII]/MBH, show that AGNs in merging pairs are actively feeding their black holes, regardless of their stellar masses. We also find that the luminosity of the companion galaxy seems to be a key parameter in the determination of the black hole activity. At a given host luminosity, both the OIII luminosity and the L[ OIII]/MBH are significantly larger in AGNs with a bright companion (Mr < -20) than otherwise.

Calix[4]pyrrole: A New Ion-Pair Receptor As Demonstrated by Liquid-Liquid Extraction

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

Wintergerst, Mr. Matthieu; Levitskaia, Tatiana G.; Moyer, Bruce A

Solvent extraction studies provide confirming evidence that meso-octamethylcalix[4]pyrrole acts as an ion-pair receptor for cesium chloride and cesium bromide in nitrobenzene solution. The stoichiometry of the interaction under extraction conditions from water to nitrobenzene was determined from plots of the cesium distribution ratios vs. cesium salt and receptor concentration, indicating the formation of an ion-paired 1:1:1 cesium:calix[4]pyrrole:halide complex. The extraction results were modeled to evaluate the equilibria inherent to the solvent extraction system, either with chloride or bromide. The binding energy between the halide anion and the calix[4]pyrrole was found to be about 7 kJ/mol larger for cesium chloride thanmore » for the cesium bromide. The ion-pairing free energies between the calix[4]pyrrole-halide complex and the cesium cation are nearly the same within experimental uncertainty for either halide, consistent with a structural model in which the Cs+ cation resides in the calix bowl. These results are unexpected since nitrobenzene is a very polar solvent that generally leads to dissociated complexes in the organic phase when used as a diluent in extraction studies of univalent ions. Control studies involving nitrate revealed no evidence of ion-pairing for CsNO3 under conditions identical to those where it is observed for CsCl and CsBr.« less

Understanding Task-in-Process through the Lens of Laughter: Activity Designs, Instructional Materials, Learner Orientations, and Interpersonal Relationships

ERIC Educational Resources Information Center

Hasegawa, Atsushi

2018-01-01

Using the framework of conversation analysis, this study investigated the interactional workings of laughter in task-based interactions. The analysis was drawn from 160 cases of pair work interactions, collected in 2nd-semester Japanese-as-a-foreign-language classrooms. The pair work activities examined in this study are mostly grammar-focused,…

Symmetry-Enforced Line Nodes in Unconventional Superconductors [Nodal-Line Superconductors and Band-Sticking

DOE PAGES

Micklitz, T.; Norman, M. R.

2017-05-18

We classify line nodes in superconductors with strong spin-orbit interactions and time-reversal symmetry, where the latter may include nonprimitive translations in the magnetic Brillouin zone to account for coexistence with antiferromagnetic order. We find four possible combinations of irreducible representations of the order parameter on high-symmetry planes, two of which allow for line nodes in pseudospin-triplet pairs and two that exclude conventional fully gapped pseudospin-singlet pairs. We show that the former can only be realized in the presence of band-sticking degeneracies, and we verify their topological stability using arguments based on Clifford algebra extensions. Lastly, our classification exhausts all possiblemore » symmetry protected line nodes in the presence of spin-orbit coupling and a (generalized) time-reversal symmetry. Implications for existing nonsymmorphic and antiferromagnetic superconductors are discussed.« less

Corona emission thresholds for three types of hydrometeor interaction in thunderclouds

NASA Astrophysics Data System (ADS)

Blyth, A. M.; Christian, H. J.; Latham, J.

1998-06-01

Laboratory studies have been conducted of the conditions under which glancing collisions, at relative velocities V characteristic of those occurring in thunderstorms, of three types of hydrometeor pairs of precipitation dimension (such as (1) warm drop pairs, (2) supercooled drop pairs, and (3) a supercooled drop and a graupel pellet) produce a corona discharge in an electric field E. In each case, the observed corona is emitted at the tip of an ephemeral liquid filament, of length greater than the dimensions of the interacting hydrometeors, drawn out during each interaction. For each type of hydrometeor pair, the probability f that corona was produced during an interaction increased steadily from zero for increasing values of E above about 150 kV/m, and was significantly in excess of 50% for values of E = 400 kV/m, which is probably about the maximum ambient value occurring in a thunderstorm. We conclude that if the associated hydrometeors are present in strongly electrified regions of thunderstorms (unlikely for interaction type 1 but manifestly possible for types 2 and 3, corona initiation leading to the production of lightning could result from each of the three types of interaction studied.

Mapping IR Enhancements in Closely Interacting Spiral-Spiral Pairs: I. ISO CAM and ISO SWS Observations

NASA Technical Reports Server (NTRS)

Xu, C.; Gao, Y.; Mazzarella, J.; Lu, N.; Sulentic, J.; Domingue, D.

2000-01-01

Mid-infrared (MIR) imaging and spectroscopic observations are presented for a well defined sample of eight closely interacting (CLO) pairs of spiral galaxies that have overlapping disks and show enhanced far-infrared (FIR) emission.

The short range anion-H interaction is the driving force for crystal formation of ions in water.

PubMed

Alejandre, José; Chapela, Gustavo A; Bresme, Fernando; Hansen, Jean-Pierre

2009-05-07

The crystal formation of NaCl in water is studied by extensive molecular dynamics simulations. Ionic solutions at room temperature and various concentrations are studied using the SPC/E and TIP4P/2005 water models and seven force fields of NaCl. Most force fields of pure NaCl fail to reproduce the experimental density of the crystal, and in solution some favor dissociation at saturated conditions, while others favor crystal formation at low concentration. A new force field of NaCl is proposed, which reproduces the experimental phase diagram in the solid, liquid, and vapor regions. This force field overestimates the solubility of NaCl in water at saturation conditions when used with standard Lorentz-Berthelot combining rules for the ion-water pair potentials. It is shown that precipitation of ions is driven by the short range interaction between Cl-H pairs, a term which is generally missing in the simulation of ionic solutions. The effects of intramolecular flexibility of water on the solubility of NaCl ions are analyzed and is found to be small compared to rigid models. A flexible water model, extending the rigid SPC/E, is proposed, which incorporates Lennard-Jones interactions centered on the hydrogen atoms. This force field gives liquid-vapor coexisting densities and surface tensions in better agreement with experimental data than the rigid SPC/E model. The Cl-H, Na-O, and Cl-O pair distribution functions of the rigid and flexible models agree well with experiment. The predicted concentration dependence of the electric conductivity is in fair agreement with available experimental data.

Familial Analysis of Epistatic and Sex-Dependent Association of Genes of the Renin-Angiotensin-Aldosterone System and Blood Pressure.

PubMed

Scurrah, Katrina J; Lamantia, Angela; Ellis, Justine A; Harrap, Stephen B

2017-06-01

Renin-angiotensin-aldosterone system genes have been inconsistently associated with blood pressure, possibly because of unrecognized influences of sex-dependent genetic effects or gene-gene interactions (epistasis). We tested association of systolic blood pressure with single-nucleotide polymorphisms (SNPs) at renin ( REN ), angiotensinogen ( AGT ), angiotensin-converting enzyme ( ACE ), angiotensin II type 1 receptor ( AGTR1 ), and aldosterone synthase ( CYP11B2 ), including sex-SNP or SNP-SNP interactions. Eighty-eight tagSNPs were tested in 2872 white individuals in 809 pedigrees from the Victorian Family Heart Study using variance components models. Three SNPs (rs8075924 and rs4277404 at ACE and rs12721297 at AGTR1 ) were individually associated with lower systolic blood pressure with significant ( P <0.00076) effect sizes ≈1.7 to 2.5 mm Hg. Sex-specific associations were seen for 3 SNPs in men (rs2468523 and rs2478544 at AGT and rs11658531 at ACE ) and 1 SNP in women (rs12451328 at ACE ). SNP-SNP interaction was suggested ( P <0.005) for 14 SNP pairs, none of which had shown individual association with systolic blood pressure. Four SNP pairs were at the same gene (2 for REN , 1 for AGT , and 1 for AGTR1 ). The SNP rs3097 at CYP11B2 was represented in 5 separate pairs. SNPs at key renin-angiotensin-aldosterone system genes associate with systolic blood pressure individually in both sexes, individually in one sex only and only when combined with another SNP. Analyses that incorporate sex-dependent and epistatic effects could reconcile past inconsistencies and account for some of the missing heritability of blood pressure and are generally relevant to SNP association studies for any phenotype. © 2017 American Heart Association, Inc.

BKT phase transition in a 2D system with long-range dipole-dipole interaction

NASA Astrophysics Data System (ADS)

Fedichev, P. O.; Men'shikov, L. I.

2012-01-01

We consider phase transitions in 2D XY-like systems with long-range dipole-dipole interactions and demonstrate that BKT-type phase transition always occurs separating the ordered (ferroelectric) and the disordered (paraelectric) phases. The low-temperature phase corresponds to a thermal state with bound vortex-antivortex pairs characterized by linear attraction at large distances. Using the Maier-Schwabl topological charge model, we show that bound vortex pairs polarize and screen the vortex-antivortex interaction, leaving only the logarithmic attraction at sufficiently large separations between the vortices. At higher temperatures the pairs dissociate and the phase transition similar to BKT occurs, though at a larger temperature than in a system without the dipole-dipole interaction.

Dynamical Bayesian inference of time-evolving interactions: from a pair of coupled oscillators to networks of oscillators.

PubMed

Duggento, Andrea; Stankovski, Tomislav; McClintock, Peter V E; Stefanovska, Aneta

2012-12-01

Living systems have time-evolving interactions that, until recently, could not be identified accurately from recorded time series in the presence of noise. Stankovski et al. [Phys. Rev. Lett. 109, 024101 (2012)] introduced a method based on dynamical Bayesian inference that facilitates the simultaneous detection of time-varying synchronization, directionality of influence, and coupling functions. It can distinguish unsynchronized dynamics from noise-induced phase slips. The method is based on phase dynamics, with Bayesian inference of the time-evolving parameters being achieved by shaping the prior densities to incorporate knowledge of previous samples. We now present the method in detail using numerically generated data, data from an analog electronic circuit, and cardiorespiratory data. We also generalize the method to encompass networks of interacting oscillators and thus demonstrate its applicability to small-scale networks.

How multiple causes combine: independence constraints on causal inference.

PubMed

Liljeholm, Mimi

2015-01-01

According to the causal power view, two core constraints-that causes occur independently (i.e., no confounding) and influence their effects independently-serve as boundary conditions for causal induction. This study investigated how violations of these constraints modulate uncertainty about the existence and strength of a causal relationship. Participants were presented with pairs of candidate causes that were either confounded or not, and that either interacted or exerted their influences independently. Consistent with the causal power view, uncertainty about the existence and strength of causal relationships was greater when causes were confounded or interacted than when unconfounded and acting independently. An elemental Bayesian causal model captured differences in uncertainty due to confounding but not those due to an interaction. Implications of distinct sources of uncertainty for the selection of contingency information and causal generalization are discussed.

Interactional synchrony in chimpanzees: Examination through a finger-tapping experiment.

PubMed

Yu, Lira; Tomonaga, Masaki

2015-05-11

Humans often unconsciously coordinate behaviour with that of others in daily life. This interpersonal coordination, including mimicry and interactional synchrony, has been suggested to play a fundamental role in social interaction. If this coordinative behavior is socially adaptive, it may be shared with other highly social animal species. The current study targeted chimpanzees, which phylogenetically are the closest living relatives of humans and live in complex social groups, and examined whether interactional synchrony would emerge in pairs of chimpanzees when auditory information about a partner's movement was provided. A finger-tapping task was introduced via touch panels to elicit repetitive and rhythmic movement from each chimpanzee. We found that one of four chimpanzees produced significant changes in both tapping tempo and timing of the tapping relative to its partner's tap when auditory sounds were provided. Although the current results may have limitations in generalizing to chimpanzees as a species, we suggest that a finger-tapping task is one potential method to investigate interactional synchrony in chimpanzees under a laboratory setup.

A General Method for Targeted Quantitative Cross-Linking Mass Spectrometry.

PubMed

Chavez, Juan D; Eng, Jimmy K; Schweppe, Devin K; Cilia, Michelle; Rivera, Keith; Zhong, Xuefei; Wu, Xia; Allen, Terrence; Khurgel, Moshe; Kumar, Akhilesh; Lampropoulos, Athanasios; Larsson, Mårten; Maity, Shuvadeep; Morozov, Yaroslav; Pathmasiri, Wimal; Perez-Neut, Mathew; Pineyro-Ruiz, Coriness; Polina, Elizabeth; Post, Stephanie; Rider, Mark; Tokmina-Roszyk, Dorota; Tyson, Katherine; Vieira Parrine Sant'Ana, Debora; Bruce, James E

2016-01-01

Chemical cross-linking mass spectrometry (XL-MS) provides protein structural information by identifying covalently linked proximal amino acid residues on protein surfaces. The information gained by this technique is complementary to other structural biology methods such as x-ray crystallography, NMR and cryo-electron microscopy[1]. The extension of traditional quantitative proteomics methods with chemical cross-linking can provide information on the structural dynamics of protein structures and protein complexes. The identification and quantitation of cross-linked peptides remains challenging for the general community, requiring specialized expertise ultimately limiting more widespread adoption of the technique. We describe a general method for targeted quantitative mass spectrometric analysis of cross-linked peptide pairs. We report the adaptation of the widely used, open source software package Skyline, for the analysis of quantitative XL-MS data as a means for data analysis and sharing of methods. We demonstrate the utility and robustness of the method with a cross-laboratory study and present data that is supported by and validates previously published data on quantified cross-linked peptide pairs. This advance provides an easy to use resource so that any lab with access to a LC-MS system capable of performing targeted quantitative analysis can quickly and accurately measure dynamic changes in protein structure and protein interactions.

Stability of the Superconducting d-Wave Pairing Toward the Intersite Coulomb Repulsion in CuO_2 Plane

NASA Astrophysics Data System (ADS)

Val'kov, V. V.; Dzebisashvili, D. M.; Korovushkin, M. M.; Barabanov, A. F.

2018-06-01

Taking into account the real crystalline structure of the CuO_2 plane and the strong spin-fermion coupling, we study the influence of the intersite Coulomb repulsion between holes on the Cooper instability of the spin-polaron quasiparticles in cuprate superconductors. The analysis shows that only the superconducting d-wave pairing is implemented in the whole region of doping, whereas the solutions of the self-consistent equations for the s-wave pairing are absent. It is shown that intersite Coulomb interaction V_1 between the holes located at the nearest oxygen ions does not affect the d-wave pairing, because its Fourier transform V_q vanishes in the kernel of the corresponding integral equation. The intersite Coulomb interaction V_2 of quasiparticles located at the next-nearest oxygen ions does not vanish in the integral equations, however, but it is also shown that the d-wave pairing is robust toward this interaction for physically reasonable values of V_2.

Stability of the Superconducting d-Wave Pairing Toward the Intersite Coulomb Repulsion in CuO_2 Plane

NASA Astrophysics Data System (ADS)

Val'kov, V. V.; Dzebisashvili, D. M.; Korovushkin, M. M.; Barabanov, A. F.

2018-03-01

Taking into account the real crystalline structure of the CuO_2 plane and the strong spin-fermion coupling, we study the influence of the intersite Coulomb repulsion between holes on the Cooper instability of the spin-polaron quasiparticles in cuprate superconductors. The analysis shows that only the superconducting d-wave pairing is implemented in the whole region of doping, whereas the solutions of the self-consistent equations for the s-wave pairing are absent. It is shown that intersite Coulomb interaction V_1 between the holes located at the nearest oxygen ions does not affect the d-wave pairing, because its Fourier transform V_q vanishes in the kernel of the corresponding integral equation. The intersite Coulomb interaction V_2 of quasiparticles located at the next-nearest oxygen ions does not vanish in the integral equations, however, but it is also shown that the d-wave pairing is robust toward this interaction for physically reasonable values of V_2.

Quantitative study of interactions between oxygen lone pair and aromatic rings: substituent effect and the importance of closeness of contact.

PubMed

Gung, Benjamin W; Zou, Yan; Xu, Zhigang; Amicangelo, Jay C; Irwin, Daniel G; Ma, Shengqian; Zhou, Hong-Cai

2008-01-18

Current models describe aromatic rings as polar groups based on the fact that benzene and hexafluorobenzene are known to have large and permanent quadrupole moments. This report describes a quantitative study of the interactions between oxygen lone pair and aromatic rings. We found that even electron-rich aromatic rings and oxygen lone pairs exhibit attractive interactions. Free energies of interactions are determined using the triptycene scaffold and the equilibrium constants were determined by low-temperature 1H NMR spectroscopy. An X-ray structure analysis for one of the model compounds confirms the close proximity between the oxygen and the center of the aromatic ring. Theoretical calculations at the MP2/aug-cc-pVTZ level corroborate the experimental results. The origin of attractive interactions was explored by using aromatic rings with a wide range of substituents. The interactions between an oxygen lone pair and an aromatic ring are attractive at van der Waals' distance even with electron-donating substituents. Electron-withdrawing groups increase the strength of the attractive interactions. The results from this study can be only partly rationalized by using the current models of aromatic system. Electrostatic-based models are consistent with the fact that stronger electron-withdrawing groups lead to stronger attractions, but fail to predict or rationalize the fact that weak attractions even exist between electron-rich arenes and oxygen lone pairs. The conclusion from this study is that aromatic rings cannot be treated as a simple quadrupolar functional group at van der Waals' distance. Dispersion forces and local dipole should also be considered.

Pair-correlations in swimmer suspensions

NASA Astrophysics Data System (ADS)

Nambiar, Sankalp; Subramanian, Ganesh

2017-11-01

Suspensions of rear-actuated swimming microorganisms, such as E.coli, exhibit several interesting phenomena including spontaneous pattern formation above a critical concentration, novel rheological properties, shear-induced concentration banding etc. Explanations based on mean-field theory are only qualitative, since interactions between swimmers are important for typical experimental concentrations. We analytically characterize the hydrodynamic pair-interactions in a quiescent suspension of slender straight swimmers. The pair-correlation, calculated at leading order by integrating the swimmer velocity disturbances along straight trajectories, decays as 1/r2 for r >> L (L being the swimmer size). This allows us to characterize both polar and nematic correlations in an interacting swimmer suspension. In the absence of correlations, the velocity covariance asymptotes from a constant for r << L to a far-field decay of O(1/r2) for r >> L, the latter being characteristic of a suspension of non-interacting point force-dipoles. On including correlations, the slow decay of the pair-orientation correlation leads to an additional contribution to the velocity covariance that diverges logarithmically with system size.

Patterns of mother-infant interaction from 3 to 12 months among dyads with substance abuse and psychiatric problems.

PubMed

Siqveland, Torill S; Haabrekke, Kristin; Wentzel-Larsen, Tore; Moe, Vibeke

2014-11-01

The aim of this study was to investigate the development of mother-infant interaction patterns from 3 to 12 months among three groups of mother-baby pairs recruited during pregnancy: one group from residential substance abuse treatment (n=28), a second group from psychiatric outpatient treatment (n=22), and a third group from well-baby clinics (n=30). The mother-infant interaction at 3 and 12 months was assessed by the Parent-Child Early Relational Assessment (PCERA), which consists of maternal, child and dyadic subscales (Clark, 2006). Linear mixed effects models were used to analyze group differences and the changes in mother-infant interaction from 3 to 12 months. At 3 months, pairwise comparisons showed that the group with psychiatric problems had significantly more difficulties in the mother-infant interaction than the two other groups. The group with substance abuse problems was not significantly different from the two other groups. At 12 months, the mother-infant pairs in the substance abuse group showed significantly more relational disturbances than the non-clinical pairs, as well as a poorer affective quality of interaction than the dyads in the group with psychiatric problems. Analysis of change from 3 to 12 months showed that difficulties in the interaction increased among the mother-baby pairs in the substance abuse group, while improvements were displayed in the two other groups. These results underline that mother-infant pairs at double risk due to maternal substance abuse and other non-optimal factors, are in need for long-term follow up in order to prevent the development of negative interactional patterns. Copyright © 2014 Elsevier Inc. All rights reserved.

Base-Pairing Energies of Protonated Nucleoside Base Pairs of dCyd and m5dCyd: Implications for the Stability of DNA i-Motif Conformations

NASA Astrophysics Data System (ADS)

Yang, Bo; Rodgers, M. T.

2015-08-01

Hypermethylation of cytosine in expanded (CCG)n•(CGG)n trinucleotide repeats results in Fragile X syndrome, the most common cause of inherited mental retardation. The (CCG)n•(CGG)n repeats adopt i-motif conformations that are preferentially stabilized by base-pairing interactions of protonated base pairs of cytosine. Here we investigate the effects of 5-methylation and the sugar moiety on the base-pairing energies (BPEs) of protonated cytosine base pairs by examining protonated nucleoside base pairs of 2'-deoxycytidine (dCyd) and 5-methyl-2'-deoxycytidine (m5dCyd) using threshold collision-induced dissociation techniques. 5-Methylation of a single or both cytosine residues leads to very small change in the BPE. However, the accumulated effect may be dramatic in diseased state trinucleotide repeats where many methylated base pairs may be present. The BPEs of the protonated nucleoside base pairs examined here significantly exceed those of Watson-Crick dGuo•dCyd and neutral dCyd•dCyd base pairs, such that these base-pairing interactions provide the major forces responsible for stabilization of DNA i-motif conformations. Compared with isolated protonated nucleobase pairs of cytosine and 1-methylcytosine, the 2'-deoxyribose sugar produces an effect similar to the 1-methyl substituent, and leads to a slight decrease in the BPE. These results suggest that the base-pairing interactions may be slightly weaker in nucleic acids, but that the extended backbone is likely to exert a relatively small effect on the total BPE. The proton affinity (PA) of m5dCyd is also determined by competitive analysis of the primary dissociation pathways that occur in parallel for the protonated (m5dCyd)H+(dCyd) nucleoside base pair and the absolute PA of dCyd previously reported.

The influence of self-assembling supramolecular structures on the passive membrane transport of ion-paired molecules.

PubMed

Benaouda, F; Brown, M B; Shah, B; Martin, G P; Jones, S A

2012-12-15

Weak ion-ion interactions, such as those associated with ion-pair formation, are difficult to isolate and characterise in the liquid state, but they have the potential to alter significantly the physicochemical behaviour of molecules in solution. The aim of this work was to gain a better understanding of how ion-ion interactions influenced passive membrane transport. The test system was composed of propylene (PG) glycol, water and diclofenac diethylamine (DDEA). Infrared spectroscopy was employed to determine the nature of the DDEA ion-pair interactions and the drug-vehicle association. Passive transport was assessed using homogeneous synthetic membranes. Solution-state analysis demonstrated that the ion-pair was unperturbed by vehicle composition changes, but the solvent-DDEA interactions were modified. DDEA-PG/water hydrogen bonding influenced the ion-pair solubility (X(dev)) and the solvent interactions slowed transport rate in PG-rich vehicles (0.84±0.05 μg cm(-2) h(-1), at ln(X(dev))=0.57). In water-rich co-solvents, the presence of strong water structuring facilitated a significant increase (p<0.05) in transmembrane penetration rate (e.g. 4.33±0.92 μg cm(-2) h(-1), at ln(X(dev))=-0.13). The data demonstrates that weak ion-ion interactions can result in the embedding of polar entities within a stable solvent complex and spontaneous supramolecular assembly should be considered when interpreting transmembrane transport processes of ionic molecules. Copyright © 2012 Elsevier B.V. All rights reserved.

Twitter K-H networks in action: Advancing biomedical literature for drug search.

PubMed

Hamed, Ahmed Abdeen; Wu, Xindong; Erickson, Robert; Fandy, Tamer

2015-08-01

The importance of searching biomedical literature for drug interaction and side-effects is apparent. Current digital libraries (e.g., PubMed) suffer infrequent tagging and metadata annotation updates. Such limitations cause absence of linking literature to new scientific evidence. This demonstrates a great deal of challenges that stand in the way of scientists when searching biomedical repositories. In this paper, we present a network mining approach that provides a bridge for linking and searching drug-related literature. Our contributions here are two fold: (1) an efficient algorithm called HashPairMiner to address the run-time complexity issues demonstrated in its predecessor algorithm: HashnetMiner, and (2) a database of discoveries hosted on the web to facilitate literature search using the results produced by HashPairMiner. Though the K-H network model and the HashPairMiner algorithm are fairly young, their outcome is evidence of the considerable promise they offer to the biomedical science community in general and the drug research community in particular. Copyright © 2015 Elsevier Inc. All rights reserved.

Enzymatically Regulated Peptide Pairing and Catalysis for the Bioanalysis of Extracellular Prometastatic Activities of Functionally Linked Enzymes

NASA Astrophysics Data System (ADS)

Li, Hao; Huang, Yue; Yu, Yue; Li, Tianqi; Li, Genxi; Anzai, Jun-Ichi

2016-05-01

Diseases such as cancer arise from systematical reconfiguration of interactions of exceedingly large numbers of proteins in cell signaling. The study of such complicated molecular mechanisms requires multiplexed detection of the inter-connected activities of several proteins in a disease-associated context. However, the existing methods are generally not well-equipped for this kind of application. Here a method for analyzing functionally linked protein activities is developed based on enzyme controlled pairing between complementary peptide helix strands, which simultaneously enables elaborate regulation of catalytic activity of the paired peptides. This method has been used to detect three different types of protein modification enzymes that participate in the modification of extracellular matrix and the formation of invasion front in tumour. In detecting breast cancer tissue samples using this method, up-regulated activity can be observed for two of the assessed enzymes, while the third enzyme is found to have a subtle fluctuation of activity. These results may point to the application of this method in evaluating prometastatic activities of proteins in tumour.

Personalizing Chinese medicine by integrating molecular features of diseases and herb ingredient information: application to acute myeloid leukemia

PubMed Central

Xie, Duoli; Shi, Tieliu; Wen, Chengping

2017-01-01

Traditional Chinese Medicine (TCM) has been widely used as a complementary medicine in Acute Myeloid Leukemia (AML) treatment. In this study, we proposed a new classification of Chinese Medicines (CMs) by integrating the latest discoveries in disease molecular mechanisms and traditional medicine theory. We screened out a set of chemical compounds on basis of AML differential expression genes and chemical-protein interactions and then mapped them to Traditional Chinese Medicine Integrated Database. 415 CMs contain those compounds and they were categorized into 8 groups according to the Traditional Chinese Pharmacology. Pathway analysis and synthetic lethality gene pairs were applied to analyze the dissimilarity, generality and intergroup relations of different groups. We defined hub CM pairs and alternative CM groups based on the analysis result and finally proposed a formula to form an effective anti-AML prescription which combined the hub CM pairs with alternative CMs according to patients’ molecular features. Our method of formulating CMs based on patients’ stratification provides novel insights into the new usage of conventional CMs and will promote TCM modernization. PMID:28454110

Personalizing Chinese medicine by integrating molecular features of diseases and herb ingredient information: application to acute myeloid leukemia.

PubMed

Huang, Lin; Li, Haichang; Xie, Duoli; Shi, Tieliu; Wen, Chengping

2017-06-27

Traditional Chinese Medicine (TCM) has been widely used as a complementary medicine in Acute Myeloid Leukemia (AML) treatment. In this study, we proposed a new classification of Chinese Medicines (CMs) by integrating the latest discoveries in disease molecular mechanisms and traditional medicine theory. We screened out a set of chemical compounds on basis of AML differential expression genes and chemical-protein interactions and then mapped them to Traditional Chinese Medicine Integrated Database. 415 CMs contain those compounds and they were categorized into 8 groups according to the Traditional Chinese Pharmacology. Pathway analysis and synthetic lethality gene pairs were applied to analyze the dissimilarity, generality and intergroup relations of different groups. We defined hub CM pairs and alternative CM groups based on the analysis result and finally proposed a formula to form an effective anti-AML prescription which combined the hub CM pairs with alternative CMs according to patients' molecular features. Our method of formulating CMs based on patients' stratification provides novel insights into the new usage of conventional CMs and will promote TCM modernization.

Structural studies of CNG repeats.

PubMed

Kiliszek, Agnieszka; Rypniewski, Wojciech

2014-07-01

CNG repeats (where N denotes one of the four natural nucleotides) are abundant in the human genome. Their tendency to undergo expansion can lead to hereditary diseases known as TREDs (trinucleotide repeat expansion disorders). The toxic factor can be protein, if the abnormal gene is expressed, or the gene transcript, or both. The gene transcripts have attracted much attention in the biomedical community, but their molecular structures have only recently been investigated. Model RNA molecules comprising CNG repeats fold into long hairpins whose stems generally conform to an A-type helix, in which the non-canonical N-N pairs are flanked by C-G and G-C pairs. Each homobasic pair is accommodated in the helical context in a unique manner, with consequences for the local helical parameters, solvent structure, electrostatic potential and potential to interact with ligands. The detailed three-dimensional profiles of RNA CNG repeats can be used in screening of compound libraries for potential therapeutics and in structure-based drug design. Here is a brief survey of the CNG structures published to date. © Published by Oxford University Press on behalf of Nucleic Acids Research.

Predicting community composition from pairwise interactions

NASA Astrophysics Data System (ADS)

Friedman, Jonathan; Higgins, Logan; Gore, Jeff

The ability to predict the structure of complex, multispecies communities is crucial for understanding the impact of species extinction and invasion on natural communities, as well as for engineering novel, synthetic communities. Communities are often modeled using phenomenological models, such as the classical generalized Lotka-Volterra (gLV) model. While a lot of our intuition comes from such models, their predictive power has rarely been tested experimentally. To directly assess the predictive power of this approach, we constructed synthetic communities comprised of up to 8 soil bacteria. We measured the outcome of competition between all species pairs, and used these measurements to predict the composition of communities composed of more than 2 species. The pairwise competitions resulted in a diverse set of outcomes, including coexistence, exclusion, and bistability, and displayed evidence for both interference and facilitation. Most pair outcomes could be captured by the gLV framework, and the composition of multispecies communities could be predicted for communities composed solely of such pairs. Our results demonstrate the predictive ability and utility of simple phenomenology, which enables accurate predictions in the absence of mechanistic details.

Double Gamow-Teller Transitions and its Relation to Neutrinoless β β Decay

NASA Astrophysics Data System (ADS)

Shimizu, Noritaka; Menéndez, Javier; Yako, Kentaro

2018-04-01

We study the double Gamow-Teller (DGT) strength distribution of 48Ca with state-of-the-art large-scale nuclear shell model calculations. Our analysis shows that the centroid energy of the DGT giant resonance depends mostly on the isovector pairing interaction, while the resonance width is more sensitive to isoscalar pairing. Pairing correlations are also key in neutrinoless β β (0 ν β β ) decay. We find a simple relation between the centroid energy of the 48Ca DGT giant resonance and the 0 ν β β decay nuclear matrix element. More generally, we observe a very good linear correlation between the DGT transition to the ground state of the final nucleus and the 0 ν β β decay matrix element. The correlation, which originates on the dominant short-range character of both transitions, extends to heavier systems including several β β emitters and also holds in energy-density functional results. Our findings suggest that DGT experiments can be a very valuable tool to obtain information on the value of 0 ν β β decay nuclear matrix elements.

Food reinforcement and delay discounting in zBMI-discordant siblings.

PubMed

Feda, Denise M; Roemmich, James N; Roberts, April; Epstein, Leonard H

2015-02-01

The interaction of food reinforcement and the inability to delay gratification are related to adult energy intake and obesity. This study was designed to test the association of sibling pair differences in relative reinforcing efficacy of food and delay discounting on sibling pair differences in zBMI scores of same-gender zBMI-discordant siblings. We tested main and interactive relationships between delay discounting and relative reinforcing efficacy of food on zBMI discordance in 14 zBMI-discordant biological sibling pairs (6 female pairs) using a discordant sibling study design. Sibling pair differences in relative reinforcing efficacy of food were associated with sibling pair differences in zBMI (p= 0.046); this effect was moderated by delay discounting (p <0.002). Sibling pairs with greater differences in relative reinforcing efficacy and delay discounting had greater differences in zBMI. The combination of greater sibling pair differences in delay discounting and relative reinforcing efficacy is associated with greater discordance in zBMI in adolescent sibling pairs. Copyright © 2014 Elsevier Ltd. All rights reserved.

Food reinforcement and delay discounting in zBMI-discordant siblings ☆

PubMed Central

Feda, Denise M.; Roemmich, James N.; Roberts, April; Epstein, Leonard H.

2014-01-01

Objective The interaction of food reinforcement and the inability to delay gratification are related to adult energy intake and obesity. This study was designed to test the association of sibling pair differences in relative reinforcing efficacy of food and delay discounting on sibling pair differences in zBMI scores of same-gender zBMI-discordant siblings. Design and methods We tested main and interactive relationships between delay discounting and relative reinforcing efficacy of food on zBMI discordance in 14 zBMI-discordant biological sibling pairs (6 female pairs) using a discordant sibling study design. Results Sibling pair differences in relative reinforcing efficacy of food were associated with sibling pair differences in zBMI (p = 0.046); this effect was moderated by delay discounting (p < 0.002). Sibling pairs with greater differences in relative reinforcing efficacy and delay discounting had greater differences in zBMI. Conclusions The combination of greater sibling pair differences in delay discounting and relative reinforcing efficacy is associated with greater discordance in zBMI in adolescent sibling pairs. PMID:25464024

Magnetic field effects on coenzyme B12- and B6-dependent lysine 5,6-aminomutase: switching of the J-resonance through a kinetically competent radical-pair intermediate.

PubMed

Chen, Jun-Ru; Ke, Shyue-Chu

2018-05-09

The environmental magnetic field is beneficial to migratory bird navigation through the radical-pair mechanism. One of the continuing challenges in understanding how magnetic fields may perturb biological processes is that only a very few field-sensitive examples have been explored despite the prevalence of radical pairs in enzymatic reactions. We show that the reaction of adenosylcobalamin- and pyridoxal-5'-phosphate-dependent lysine 5,6-aminomutase proceeds via radical-pair intermediates and is magnetic field dependent. The 5'-deoxyadenosyl radical from adenosylcobalamin abstracts a C5(H) from the substrate to yield a {cob(ii)alamin - substrate} radical pair wherein the large spin-spin interaction (2J = 8000 gauss) locks the radical pair in a triplet state, as evidenced by electron paramagnetic resonance spectroscopy. Application of an external magnetic field in the range of 6500 to 8500 gauss triggers intersystem crossing to the singlet {cob(ii)alamin - substrate} radical-pair state. Spin-conserved H back-transfer from deoxyadenosine to the substrate radical yields a singlet {cob(ii)alamin-5'-deoxyadenosyl} radical pair. Spin-selective recombination to adenosylcobalamin decreased the enzyme catalytic efficiency kcat/Km by 16% at 7600 gauss. As a mechanistic probe, observation of magnetic field effects successfully demonstrates the presence of a kinetically significant radical pair in this enzyme. The study of a pronounced high-field level-crossing characteristic through an immobilized radical pair with a constant exchange interaction deepens our understanding of how a magnetic field may interact with an enzyme.

Testing enhances both encoding and retrieval for both tested and untested items.

PubMed

Cho, Kit W; Neely, James H; Crocco, Stephanie; Vitrano, Deana

2017-07-01

In forward testing effects, taking a test enhances memory for subsequently studied material. These effects have been observed for previously studied and tested items, a potentially item-specific testing effect, and newly studied untested items, a purely generalized testing effect. We directly compared item-specific and generalized forward testing effects using procedures to separate testing benefits due to encoding versus retrieval. Participants studied two lists of Swahili-English word pairs, with the second study list containing "new" pairs intermixed with the previously studied "old" pairs. Participants completed a review phase in which they took a cued-recall test on only the "old" pairs or restudied them. In Experiments 1a, 1b, and 2, the review phase was given either before or after the second study list. Testing benefited memory to the same degree for both "new" and "old" pairs, suggesting that there were no pair-specific benefits of testing. The larger benefit from testing when review was given before rather than after the second study list suggests that the memory enhancement was due to both testing-enhanced encoding and testing-enhanced retrieval. To better equate generalized testing effects for "new" and "old" pairs, Experiment 3 intermixed them in the review phase. A statistically significant pair-specific testing effect for "old" items was now observed. Overall, these results show that forward testing effects are due to both testing-enhanced encoding and retrieval effects and that direct, pair-specific forward testing benefits are considerably smaller than indirect, generalized forward testing benefits.

Non-invasive determination of external forces in vortex-pair-cylinder interactions

NASA Astrophysics Data System (ADS)

Hartmann, D.; Schröder, W.; Shashikanth, B. N.

2012-06-01

Expressions for the conserved linear and angular momenta of a dynamically coupled fluid + solid system are derived. Based on the knowledge of the flow velocity field, these expressions allow the determination of the external forces exerted on a body moving in the fluid such as, e.g., swimming fish. The verification of the derived conserved quantities is done numerically. The interaction of a vortex pair with a circular cylinder in various configurations of motions representing a generic test case for a dynamically coupled fluid + solid system is investigated in a weakly compressible Navier-Stokes setting using a Cartesian cut-cell method, i.e., the moving circular cylinder is represented by cut cells on a moving mesh. The objectives of this study are twofold. The first objective is to show the robustness of the derived expressions for the conserved linear and angular momenta with respect to bounded and discrete data sets. The second objective is to study the coupled dynamics of the vortex pair and a neutrally buoyant cylinder free to move in response to the fluid stresses exerted on its surface. A comparison of the vortex-body interaction with the case of a fixed circular cylinder evidences significant differences in the vortex dynamics. When the cylinder is fixed strong secondary vorticity is generated resulting in a repeating process between the primary vortex pair and the cylinder. In the neutrally buoyant cylinder case, a stable structure consisting of the primary vortex pair and secondary vorticity shear layers stays attached to the moving cylinder. In addition to these fundamental cases, the vortex-pair-cylinder interaction is studied for locomotion at constant speed and locomotion at constant thrust. It is shown that a similar vortex structure like in the neutrally buoyant cylinder case is obtained when the cylinder moves away from the approaching vortex pair at a constant speed smaller than the vortex pair translational velocity. Finally, the idealized symmetric settings are complemented by an asymmetric interaction of a vortex pair and a cylinder. This case is discussed for a fixed and a neutrally buoyant cylinder to show the validity of the derived relations for multi-dimensional body dynamics.

Investigation of the interaction dynamics of a pair of laser-induced bubbles generated at the same time through double-exposure strobe method and numerical simulations

NASA Astrophysics Data System (ADS)

Han, Bing; Liu, Liu; Ni, Xiao-Wu

2017-08-01

In order to understand the interaction dynamics of a pair of laser-induced bubbles, a double-exposure strobe photography experimental setup is build up to study the temporal evolution of the bubble pairs and to measure the transient bubble-interface moving speed. The interaction mechanisms of the bubble pairs are discussed together with the numerical results obtained through OpenFOAM. It is shown that the direction and the velocity of the jetting could be controlled by the relative size and the relative initiation distance of the bubble pair, when the bubbles are generated at the same time, i.e., in-phase. The liquid jet is considered to be a penetrating jet. The jet is originated from the smaller bubble and clearly protruding outside of the bigger bubble. The parameter space of the relative size and the initiation distance of the bubble pair allowing the formation of the penetrating jet are very narrow. It is concluded that the liquid jet induced by the bubble interactions resulted from the collapse and the rebound of the smaller bubble nearby the bigger bubble. This is defined as the "catapult effect." Such a directional liquid transportation is a promising tool as a micro-injector or a micro-pump. The investigation results could be also supplementary to the understandings of the bubble dynamics.

Soft pair excitations and double-log divergences due to carrier interactions in graphene

NASA Astrophysics Data System (ADS)

Lewandowski, Cyprian; Levitov, L. S.

2018-03-01

Interactions between charge carriers in graphene lead to logarithmic renormalization of observables mimicking the behavior known in (3+1)-dimensional quantum electrodynamics (QED). Here we analyze soft electron-hole (e -h ) excitations generated as a result of fast charge dynamics, a direct analog of the signature QED effect—multiple soft photons produced by the QED vacuum shakeup. We show that such excitations are generated in photon absorption, when a photogenerated high-energy e -h pair cascades down in energy and gives rise to multiple soft e -h excitations. This fundamental process is manifested in a double-log divergence in the emission rate of soft pairs and a characteristic power-law divergence in their energy spectrum of the form 1/ω ln(ω/Δ ) . Strong carrier-carrier interactions make pair production a prominent pathway in the photoexcitation cascade.

Structural and thermodynamic consequences of burial of an artificial ion pair in the hydrophobic interior of a protein.

PubMed

Robinson, Aaron C; Castañeda, Carlos A; Schlessman, Jamie L; García-Moreno, E Bertrand

2014-08-12

An artificial charge pair buried in the hydrophobic core of staphylococcal nuclease was engineered by making the V23E and L36K substitutions. Buried individually, Glu-23 and Lys-36 both titrate with pKa values near 7. When buried together their pKa values appear to be normal. The ionizable moieties of the buried Glu-Lys pair are 2.6 Å apart. The interaction between them at pH 7 is worth 5 kcal/mol. Despite this strong interaction, the buried Glu-Lys pair destabilizes the protein significantly because the apparent Coulomb interaction is sufficient to offset the dehydration of only one of the two buried charges. Save for minor reorganization of dipoles and water penetration consistent with the relatively high dielectric constant reported by the buried ion pair, there is no evidence that the presence of two charges in the hydrophobic interior of the protein induces any significant structural reorganization. The successful engineering of an artificial ion pair in a highly hydrophobic environment suggests that buried Glu-Lys pairs in dehydrated environments can be charged and that it is possible to engineer charge clusters that loosely resemble catalytic sites in a scaffold protein with high thermodynamic stability, without the need for specialized structural adaptations.

Structural and thermodynamic consequences of burial of an artificial ion pair in the hydrophobic interior of a protein

PubMed Central

Robinson, Aaron C.; Castañeda, Carlos A.; Schlessman, Jamie L.; García-Moreno E., Bertrand

2014-01-01

An artificial charge pair buried in the hydrophobic core of staphylococcal nuclease was engineered by making the V23E and L36K substitutions. Buried individually, Glu-23 and Lys-36 both titrate with pKa values near 7. When buried together their pKa values appear to be normal. The ionizable moieties of the buried Glu–Lys pair are 2.6 Å apart. The interaction between them at pH 7 is worth 5 kcal/mol. Despite this strong interaction, the buried Glu–Lys pair destabilizes the protein significantly because the apparent Coulomb interaction is sufficient to offset the dehydration of only one of the two buried charges. Save for minor reorganization of dipoles and water penetration consistent with the relatively high dielectric constant reported by the buried ion pair, there is no evidence that the presence of two charges in the hydrophobic interior of the protein induces any significant structural reorganization. The successful engineering of an artificial ion pair in a highly hydrophobic environment suggests that buried Glu–Lys pairs in dehydrated environments can be charged and that it is possible to engineer charge clusters that loosely resemble catalytic sites in a scaffold protein with high thermodynamic stability, without the need for specialized structural adaptations. PMID:25074910

Condensates of p-wave pairs are exact solutions for rotating two-component Bose gases.

PubMed

Papenbrock, T; Reimann, S M; Kavoulakis, G M

2012-02-17

We derive exact analytical results for the wave functions and energies of harmonically trapped two-component Bose-Einstein condensates with weakly repulsive interactions under rotation. The isospin symmetric wave functions are universal and do not depend on the matrix elements of the two-body interaction. The comparison with the results from numerical diagonalization shows that the ground state and low-lying excitations consist of condensates of p-wave pairs for repulsive contact interactions, Coulomb interactions, and the repulsive interactions between aligned dipoles.

DIMA 3.0: Domain Interaction Map.

PubMed

Luo, Qibin; Pagel, Philipp; Vilne, Baiba; Frishman, Dmitrij

2011-01-01

Domain Interaction MAp (DIMA, available at http://webclu.bio.wzw.tum.de/dima) is a database of predicted and known interactions between protein domains. It integrates 5807 structurally known interactions imported from the iPfam and 3did databases and 46,900 domain interactions predicted by four computational methods: domain phylogenetic profiling, domain pair exclusion algorithm correlated mutations and domain interaction prediction in a discriminative way. Additionally predictions are filtered to exclude those domain pairs that are reported as non-interacting by the Negatome database. The DIMA Web site allows to calculate domain interaction networks either for a domain of interest or for entire organisms, and to explore them interactively using the Flash-based Cytoscape Web software.

Massive Stars in Interactive Binaries

NASA Astrophysics Data System (ADS)

St.-Louis, Nicole; Moffat, Anthony F. J.

Massive stars start their lives above a mass of ~8 time solar, finally exploding after a few million years as core-collapse or pair-production supernovae. Above ~15 solar masses, they also spend most of their lives driving especially strong, hot winds due to their extreme luminosities. All of these aspects dominate the ecology of the Universe, from element enrichment to stirring up and ionizing the interstellar medium. But when they occur in close pairs or groups separated by less than a parsec, the interaction of massive stars can lead to various exotic phenomena which would not be seen if there were no binaries. These depend on the actual separation, and going from wie to close including colliding winds (with non-thermal radio emission and Wolf-Rayet dust spirals), cluster dynamics, X-ray binaries, Roche-lobe overflow (with inverse mass-ratios and rapid spin up), collisions, merging, rejuventation and massive blue stragglers, black-hole formation, runaways and gamma-ray bursts. Also, one wonders whether the fact that a massive star is in a binary affects its parameters compared to its isolated equivalent. These proceedings deal with all of these phenomena, plus binary statistics and determination of general physical properties of massive stars, that would not be possible with their single cousins. The 77 articles published in these proceedings, all based on oral talks, vary from broad revies to the lates developments in the field. About a third of the time was spent in open discussion of all participants, both for ~5 minutes after each talk and 8 half-hour long general dialogues, all audio-recorded, transcribed and only moderately edited to yield a real flavour of the meeting. The candid information in these discussions is sometimes more revealing than the article(s) that preceded them and also provide entertaining reading. The book is suitable for researchers and graduate students interested in stellar astrophysics and in various physical processes involved when stars occur in bound pairs, groups or tight clusters.

Interaction of Aircraft Wakes From Laterally Spaced Aircraft

NASA Technical Reports Server (NTRS)

Proctor, Fred H.

2009-01-01

Large Eddy Simulations are used to examine wake interactions from aircraft on closely spaced parallel paths. Two sets of experiments are conducted, with the first set examining wake interactions out of ground effect (OGE) and the second set for in ground effect (IGE). The initial wake field for each aircraft represents a rolled-up wake vortex pair generated by a B-747. Parametric sets include wake interactions from aircraft pairs with lateral separations of 400, 500, 600, and 750 ft. The simulation of a wake from a single aircraft is used as baseline. The study shows that wake vortices from either a pair or a formation of B-747 s that fly with very close lateral spacing, last longer than those from an isolated B-747. For OGE, the inner vortices between the pair of aircraft, ascend, link and quickly dissipate, leaving the outer vortices to decay and descend slowly. For the IGE scenario, the inner vortices ascend and last longer, while the outer vortices decay from ground interaction at a rate similar to that expected from an isolated aircraft. Both OGE and IGE scenarios produce longer-lasting wakes for aircraft with separations less than 600 ft. The results are significant because concepts to increase airport capacity have been proposed that assume either aircraft formations and/or aircraft pairs landing on very closely spaced runways.

Predicting domain-domain interaction based on domain profiles with feature selection and support vector machines

PubMed Central

2010-01-01

Background Protein-protein interaction (PPI) plays essential roles in cellular functions. The cost, time and other limitations associated with the current experimental methods have motivated the development of computational methods for predicting PPIs. As protein interactions generally occur via domains instead of the whole molecules, predicting domain-domain interaction (DDI) is an important step toward PPI prediction. Computational methods developed so far have utilized information from various sources at different levels, from primary sequences, to molecular structures, to evolutionary profiles. Results In this paper, we propose a computational method to predict DDI using support vector machines (SVMs), based on domains represented as interaction profile hidden Markov models (ipHMM) where interacting residues in domains are explicitly modeled according to the three dimensional structural information available at the Protein Data Bank (PDB). Features about the domains are extracted first as the Fisher scores derived from the ipHMM and then selected using singular value decomposition (SVD). Domain pairs are represented by concatenating their selected feature vectors, and classified by a support vector machine trained on these feature vectors. The method is tested by leave-one-out cross validation experiments with a set of interacting protein pairs adopted from the 3DID database. The prediction accuracy has shown significant improvement as compared to InterPreTS (Interaction Prediction through Tertiary Structure), an existing method for PPI prediction that also uses the sequences and complexes of known 3D structure. Conclusions We show that domain-domain interaction prediction can be significantly enhanced by exploiting information inherent in the domain profiles via feature selection based on Fisher scores, singular value decomposition and supervised learning based on support vector machines. Datasets and source code are freely available on the web at http://liao.cis.udel.edu/pub/svdsvm. Implemented in Matlab and supported on Linux and MS Windows. PMID:21034480

Ab initio molecular dynamics simulations of ion-solid interactions in zirconate pyrochlores

DOE PAGES

Xiao, Haiyan Y.; Weber, William J.; Zhang, Yanwen; ...

2015-01-31

In this paper, an ab initio molecular dynamics method is employed to study low energy recoil events in zirconate pyrochlores (A 2Zr 2O 7, A = La, Nd and Sm). It shows that both cations and anions in Nd 2Zr 2O 7 and Sm 2Zr 2O 7 are generally more likely to be displaced than those in La 2Zr 2O 7. The damage end states mainly consist of Frenkel pair defects, and the Frenkel pair formation energies in Nd 2Zr 2O 7 and Sm 2Zr 2O 7 are lower than those in La 2Zr 2O 7. These results suggest thatmore » the order–disorder structural transition more easily occurs in Nd 2Zr 2O 7 and Sm 2Zr 2O 7 resulting in a defect-fluorite structure, which agrees well with experimental observations. Our calculations indicate that oxygen migration from 48f and 8b to 8a sites is dominant under low energy irradiation. A number of new defects, including four types of cation Frenkel pairs and six types of anion Frenkel pairs, are revealed by ab initio molecular dynamics simulations. The present findings may help to advance the fundamental understanding of the irradiation response behavior of zirconate pyrochlores.« less

Local thermodynamics and the generalized Gibbs-Duhem equation in systems with long-range interactions.

PubMed

Latella, Ivan; Pérez-Madrid, Agustín

2013-10-01

The local thermodynamics of a system with long-range interactions in d dimensions is studied using the mean-field approximation. Long-range interactions are introduced through pair interaction potentials that decay as a power law in the interparticle distance. We compute the local entropy, Helmholtz free energy, and grand potential per particle in the microcanonical, canonical, and grand canonical ensembles, respectively. From the local entropy per particle we obtain the local equation of state of the system by using the condition of local thermodynamic equilibrium. This local equation of state has the form of the ideal gas equation of state, but with the density depending on the potential characterizing long-range interactions. By volume integration of the relation between the different thermodynamic potentials at the local level, we find the corresponding equation satisfied by the potentials at the global level. It is shown that the potential energy enters as a thermodynamic variable that modifies the global thermodynamic potentials. As a result, we find a generalized Gibbs-Duhem equation that relates the potential energy to the temperature, pressure, and chemical potential. For the marginal case where the power of the decaying interaction potential is equal to the dimension of the space, the usual Gibbs-Duhem equation is recovered. As examples of the application of this equation, we consider spatially uniform interaction potentials and the self-gravitating gas. We also point out a close relationship with the thermodynamics of small systems.

Spin singlet and spin triplet pairing correlations on shape evolution in s d -shell N =Z Nuclei

NASA Astrophysics Data System (ADS)

Ha, Eunja; Cheoun, Myung-Ki; Sagawa, H.

2018-02-01

We study the shape evolution of N =Z nuclei 24Mg,28Si, and 32S in the axially symmetric deformed Woods-Saxon model, taking into account both T =0 and T =1 pairing interactions. We find the coexistence of T =0 and T =1 superfluidity phases in the large deformation region | β2|>0.3 in these three nuclei. The interplay between the two pairing interactions has an important effect on determining the deformation of the ground states in these nuclei. The self-energy contributions from the pairing correlations to the single particle (s.p.) energies are also examined.

An in vivo library-versus-library selection of optimized protein-protein interactions.

PubMed

Pelletier, J N; Arndt, K M; Plückthun, A; Michnick, S W

1999-07-01

We describe a rapid and efficient in vivo library-versus-library screening strategy for identifying optimally interacting pairs of heterodimerizing polypeptides. Two leucine zipper libraries, semi-randomized at the positions adjacent to the hydrophobic core, were genetically fused to either one of two designed fragments of the enzyme murine dihydrofolate reductase (mDHFR), and cotransformed into Escherichia coli. Interaction between the library polypeptides reconstituted enzymatic activity of mDHFR, allowing bacterial growth. Analysis of the resulting colonies revealed important biases in the zipper sequences relative to the original libraries, which are consistent with selection for stable, heterodimerizing pairs. Using more weakly associating mDHFR fragments, we increased the stringency of selection. We enriched the best-performing leucine zipper pairs by multiple passaging of the pooled, selected colonies in liquid culture, as the best pairs allowed for better bacterial propagation. This competitive growth allowed small differences among the pairs to be amplified, and different sequence positions were enriched at different rates. We applied these selection processes to a library-versus-library sample of 2.0 x 10(6) combinations and selected a novel leucine zipper pair that may be appropriate for use in further in vivo heterodimerization strategies.

Marginal and mindful: deviants in social interactions.

PubMed

Frable, D E; Blackstone, T; Scherbaum, C

1990-07-01

Master status people's behavior, physical appearance, or life circumstance is statistically unusual and centrally defining (e.g., the physically attractive, the obese, the intellectually gifted, the facially scarred, the talented, the athletic, Blacks, gays, the wealthy, rape and incest victims). These individuals were paired with people without such conditions. Each pair was left alone on a pretext and covertly videotaped. Pairs were then separated; each member spontaneously recalled information about her partner and the experimental room and provided a record of her thoughts and feelings during the interaction. As hypothesized, all master status Ss were particularly likely to be mindful in social interactions; they recalled detailed information about the situation and often took their partner's perspective during the interaction. The positive or negative connotations of the master status conditions were irrelevant in predicting Ss cognitions (mindfulness) but were critical in determining Ss behaviors (interaction strategies).

Interactions between nesting pileated woodpeckers and wood ducks

Treesearch

Richard N. Conner; Clifford E. Shackelford; Daniel Saenz; Richard R. Schaefer

2001-01-01

We observed interactions between a nesting pair of pileated woodpeckers (Dryocopus pileatus) and what appeared to be four pairs of wood ducks (Aix sponsa). Wood ducks regularly approached and attempted to enter an active pileated woodpecker nest cavity that contained three fully feathered young pileated woodpeckers. The male...

Relativistic Hamiltonian dynamics for N point particles

NASA Astrophysics Data System (ADS)

King, M. J.

1980-08-01

The theory is quantized canonically to give a relativistic quantum mechanics for N particles. The existence of such a theory has been in doubt since the proof of the No-interaction theorem. However, such a theory does exist and was generalized. This dynamics is expressed in terms of N + 1 pairs of canonical fourvectors (center-of-momentum variables or CMV). A gauge independent reduction due to N + 3 first class kinematic constraints leads to a 6N + 2 dimensional minimum kinematic phase space, K. The kinematics and dynamics of particles with intrinsic spin were also considered. To this end known constraint techniques were generalized to make use of graded Lie algebras. The (Poincare) invariant Hamiltonian is specified in terms of the gauge invarient variables of K. The covariant worldline variables of each particle were found to be gauge dependent. As such they will usually not satisfy a canonical algebra. An exception exists for free particles. The No-interaction theorem therefore is not violated.

Demons and superconductivity

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

Ihm, J.; Cohen, M.L.; Tuan, S.F.

1981-04-01

Model calculations are used to explore the role of demons (acoustic plasmons involving light and heavy mass carriers) in superconductivity. Heavy d electrons and light s and p electrons in a transition metal are used for discussion, but the calculation presented is more general, and the results can be applied to other systems. The analysis is based on the dielectric-function approach and the Bardeen-Cooper-Schrieffer theory. The dielectric function includes intraband and interband s-d scattering, and a tight-binding model is used to examine the role of s-d hybridization. The demon contribution generally reduces the Coulomb interaction between the electrons. Under suitablemore » conditions, the model calculations indicate that the electron-electron interaction via demons can be attractive, but the results also suggest that this mechanism is probably not dominant in transition metals and transition-metal compounds. An attractive interband contribution is found, and it is proposed that this effect may lead to pairing in suitable systems.« less

Triplet p + ip pairing correlations in the doped Kane-Mele-Hubbard model: A quantum Monte Carlo study

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

Ma, Tianxing; Lin, Hai-Qing; Gubernatis, James E.

2015-09-01

By using the constrained-phase quantum Monte Carlo method, we performed a systematic study of the pairing correlations in the ground state of the doped Kane-Mele-Hubbard model on a honeycomb lattice. We find that pairing correlations with d + id symmetry dominate close to half filling, but pairing correlations with p+ip symmetry dominate as hole doping moves the system below three-quarters filling. We correlate these behaviors of the pairing correlations with the topology of the Fermi surfaces of the non-interacting problem. We also find that the effective pairing correlation is enhanced greatly as the interaction increases, and these superconducting correlations aremore » robust against varying the spin-orbit coupling strength. Finally, our numerical results suggest a possible way to realize spin triplet superconductivity in doped honeycomb-like materials or ultracold atoms in optical traps.« less

Distinguishing Mother-Infant Interaction from Stranger-Infant Interaction at 2, 4, and 6 Months of Age

ERIC Educational Resources Information Center

Bigelow, Ann E.; Power, Michelle; Mcquaid, Nancy; Ward, Ashley; Rochat, Philippe

2008-01-01

Observers watched videotaped face-to-face mother-infant and stranger-infant interactions of 12 infants at 2, 4, or 6 months of age. Half of the observers saw each mother paired with her own infant and another infant of the same age (mother tapes) and half saw each infant paired with his or her mother and with a stranger (infant tapes). Observers…

Exact solution of mean-field plus an extended T = 1 nuclear pairing Hamiltonian in the seniority-zero symmetric subspace

NASA Astrophysics Data System (ADS)

Pan, Feng; Ding, Xiaoxue; Launey, Kristina D.; Dai, Lianrong; Draayer, Jerry P.

2018-05-01

An extended pairing Hamiltonian that describes multi-pair interactions among isospin T = 1 and angular momentum J = 0 neutron-neutron, proton-proton, and neutron-proton pairs in a spherical mean field, such as the spherical shell model, is proposed based on the standard T = 1 pairing formalism. The advantage of the model lies in the fact that numerical solutions within the seniority-zero symmetric subspace can be obtained more easily and with less computational time than those calculated from the mean-field plus standard T = 1 pairing model. Thus, large-scale calculations within the seniority-zero symmetric subspace of the model is feasible. As an example of the application, the average neutron-proton interaction in even-even N ∼ Z nuclei that can be suitably described in the f5 pg9 shell is estimated in the present model, with a focus on the role of np-pairing correlations.

Nematic and chiral superconductivity induced by odd-parity fluctuations

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

Wu, Fengcheng; Martin, Ivar

Recent experiments indicate that superconductivity in Bi 2Se 3 intercalated with Cu, Nb, or Sr is nematic with rotational symmetry breaking. Motivated by this observation, we present a model study of nematic and chiral superconductivity induced by odd-parity fluctuations. Additionally, we show that odd-parity fluctuations in the two-component E u representation of D 3d crystal point group can generate attractive interaction in both the even-parity s-wave and odd-parity E-u pairing channels, but repulsive interaction in other odd-parity pairing channels. Coulomb repulsion can suppress s-wave pairing relative to E u pairing, and thus the latter can have a higher critical temperature.more » E u pairing has two distinct phases: a nematic phase and a chiral phase, both of which can be realized in our model. Finally, when s-wave and E u pairings have similar instability temperature, we find an intermediate phase in which both types of pairing coexist.« less

Nematic and chiral superconductivity induced by odd-parity fluctuations

DOE PAGES

Wu, Fengcheng; Martin, Ivar

2017-10-09

Recent experiments indicate that superconductivity in Bi 2Se 3 intercalated with Cu, Nb, or Sr is nematic with rotational symmetry breaking. Motivated by this observation, we present a model study of nematic and chiral superconductivity induced by odd-parity fluctuations. Additionally, we show that odd-parity fluctuations in the two-component E u representation of D 3d crystal point group can generate attractive interaction in both the even-parity s-wave and odd-parity E-u pairing channels, but repulsive interaction in other odd-parity pairing channels. Coulomb repulsion can suppress s-wave pairing relative to E u pairing, and thus the latter can have a higher critical temperature.more » E u pairing has two distinct phases: a nematic phase and a chiral phase, both of which can be realized in our model. Finally, when s-wave and E u pairings have similar instability temperature, we find an intermediate phase in which both types of pairing coexist.« less

Effect of Fibonacci modulation on superconductivity

NASA Astrophysics Data System (ADS)

Gupta, Sanjay; Sil, Shreekantha; Bhattacharyya, Bibhas

2006-02-01

We have studied finite-sized single band models with short-range pairing interactions between electrons in the presence of diagonal Fibonacci modulation in one dimension. Two models, namely the attractive Hubbard model and the Penson-Kolb model, have been investigated at half-filling at zero temperature by solving the Bogoliubov-de Gennes equations in real space within a mean-field approximation. The competition between 'disorder' and the pairing interaction leads to a suppression of superconductivity (of usual pairs with zero centre-of-mass momenta) in the strong-coupling limit while an enhancement of the pairing correlation is observed in the weak-coupling regime for both models. However, the dissimilarity of the pairing mechanisms in these two models brings about notable differences in the results. The extent to which the bond-ordered wave and the η-paired (of pairs with centre-of-mass momenta = π) phases of the Penson-Kolb model are affected by the disorder has also been studied in the present calculation. Some finite size effects are also identified.

Type-I and type-II topological nodal superconductors with s -wave interaction

NASA Astrophysics Data System (ADS)

Huang, Beibing; Yang, Xiaosen; Xu, Ning; Gong, Ming

2018-01-01

Topological nodal superconductors with protected gapless points in momentum space are generally realized based on unconventional pairings. In this work we propose a minimal model to realize these topological nodal phases with only s -wave interaction. In our model the linear and quadratic spin-orbit couplings along the two orthogonal directions introduce anisotropic effective unconventional pairings in momentum space. This model may support different nodal superconducting phases characterized by either an integer winding number in BDI class or a Z2 index in D class at the particle-hole invariant axes. In the vicinity of the nodal points the effective Hamiltonian can be described by either type-I or type-II Dirac equations, and the Lifshitz transition from type-I nodal phases to type-II nodal phases can be driven by external in-plane magnetic fields. We show that these nodal phases are robust against weak impurities, which only slightly renormalizes the momentum-independent parameters in the impurity-averaged Hamiltonian, thus these phases are possible to be realized in experiments with real semi-Dirac materials. The smoking-gun evidences to verify these phases based on scanning tunneling spectroscopy method are also briefly discussed.

Mobility-based correction for accurate determination of binding constants by capillary electrophoresis-frontal analysis.

PubMed

Qian, Cheng; Kovalchik, Kevin A; MacLennan, Matthew S; Huang, Xiaohua; Chen, David D Y

2017-06-01

Capillary electrophoresis frontal analysis (CE-FA) can be used to determine binding affinity of molecular interactions. However, its current data processing method mandate specific requirement on the mobilities of the binding pair in order to obtain accurate binding constants. This work shows that significant errors are resulted when the mobilities of the interacting species do not meet these requirements. Therefore, the applicability of CE-FA in many real word applications becomes questionable. An electrophoretic mobility-based correction method is developed in this work based on the flux of each species. A simulation program and a pair of model compounds are used to verify the new equations and evaluate the effectiveness of this method. Ibuprofen and hydroxypropyl-β-cyclodextrinare used to demonstrate the differences in the obtained binding constant by CE-FA when different calculation methods are used, and the results are compared with those obtained by affinity capillary electrophoresis (ACE). The results suggest that CE-FA, with the mobility-based correction method, can be a generally applicable method for a much wider range of applications. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Simple Physics-Based Analytical Formulas for the Potentials of Mean Force of the Interaction of Amino Acid Side Chains in Water. VII. Charged-Hydrophobic/Polar and Polar-Hydrophobic/Polar Side Chains.

PubMed

Makowski, Mariusz; Liwo, Adam; Scheraga, Harold A

2017-01-19

The physics-based potentials of side-chain-side-chain interactions corresponding to pairs composed of charged and polar, polar and polar, charged and hydrophobic, and hydrophobic and hydrophobic side chains have been determined. A total of 144 four-dimensional potentials of mean force (PMFs) of all possible pairs of molecules modeling these pairs were determined by umbrella-sampling molecular dynamics simulations in explicit water as functions of distance and orientation, and the analytical expressions were then fitted to the PMFs. Depending on the type of interacting sites, the analytical approximation to the PMF is a sum of terms corresponding to van der Waals interactions and cavity-creation involving the nonpolar sections of the side chains and van der Waals, cavity-creation, and electrostatic (charge-dipole or dipole-dipole) interaction energies and polarization energies involving the charged or polar sections of the side chains. The model used in this work reproduces all features of the interacting pairs. The UNited RESidue force field with the new side-chain-side-chain interaction potentials was preliminarily tested with the N-terminal part of the B-domain of staphylococcal protein A (PDBL 1BDD ; a three-α-helix bundle) and UPF0291 protein YnzC from Bacillus subtilis (PDB: 2HEP ; an α-helical hairpin).

Superconductivity mediated by quantum critical antiferromagnetic fluctuations: The rise and fall of hot spots

NASA Astrophysics Data System (ADS)

Wang, Xiaoyu; Schattner, Yoni; Berg, Erez; Fernandes, Rafael M.

2017-05-01

In several unconventional superconductors, the highest superconducting transition temperature Tc is found in a region of the phase diagram where the antiferromagnetic transition temperature extrapolates to zero, signaling a putative quantum critical point. The elucidation of the interplay between these two phenomena—high-Tc superconductivity and magnetic quantum criticality—remains an important piece of the complex puzzle of unconventional superconductivity. In this paper, we combine sign-problem-free quantum Monte Carlo simulations and field-theoretical analytical calculations to unveil the microscopic mechanism responsible for the superconducting instability of a general low-energy model, called the spin-fermion model. In this approach, low-energy electronic states interact with each other via the exchange of quantum critical magnetic fluctuations. We find that even in the regime of moderately strong interactions, both the superconducting transition temperature and the pairing susceptibility are governed not by the properties of the entire Fermi surface, but instead by the properties of small portions of the Fermi surface called hot spots. Moreover, Tc increases with increasing interaction strength, until it starts to saturate at the crossover from hot-spots-dominated to Fermi-surface-dominated pairing. Our work provides not only invaluable insights into the system parameters that most strongly affect Tc, but also important benchmarks to assess the origin of superconductivity in both microscopic models and actual materials.

Biomechanical Constraints Underlying Motor Primitives Derived from the Musculoskeletal Anatomy of the Human Arm.

PubMed

Gritsenko, Valeriya; Hardesty, Russell L; Boots, Mathew T; Yakovenko, Sergiy

2016-01-01

Neural control of movement can only be realized though the interaction between the mechanical properties of the limb and the environment. Thus, a fundamental question is whether anatomy has evolved to simplify neural control by shaping these interactions in a beneficial way. This inductive data-driven study analyzed the patterns of muscle actions across multiple joints using the musculoskeletal model of the human upper limb. This model was used to calculate muscle lengths across the full range of motion of the arm and examined the correlations between these values between all pairs of muscles. Musculoskeletal coupling was quantified using hierarchical clustering analysis. Muscle lengths between multiple pairs of muscles across multiple postures were highly correlated. These correlations broadly formed two proximal and distal groups, where proximal muscles of the arm were correlated with each other and distal muscles of the arm and hand were correlated with each other, but not between groups. Using hierarchical clustering, between 11 and 14 reliable muscle groups were identified. This shows that musculoskeletal anatomy does indeed shape the mechanical interactions by grouping muscles into functional clusters that generally match the functional repertoire of the human arm. Together, these results support the idea that the structure of the musculoskeletal system is tuned to solve movement complexity problem by reducing the dimensionality of available solutions.

Model for an RNA tertiary interaction from the structure of an intermolecular complex between a GAAA tetraloop and an RNA helix.

PubMed

Pley, H W; Flaherty, K M; McKay, D B

1994-11-03

In large structured RNAs, RNA hairpins in which the strands of the duplex stem are connected by a tetraloop of the consensus sequence 5'-GNRA (where N is any nucleotide, and R is either G or A) are unusually frequent. In group I introns there is a covariation in sequence between nucleotides in the third and fourth positions of the loop with specific distant base pairs in putative RNA duplex stems: GNAA loops correlate with successive 5'-C-C.G-C base pairs in stems, whereas GNGA loops correlate with 5'-C-U.G-A. This has led to the suggestion that GNRA tetraloops may be involved in specific long-range tertiary interactions, with each A in position 3 or 4 of the loop interacting with a C-G base pair in the duplex, and G in position 3 interacting with a U-A base pair. This idea is supported experimentally for the GAAA loop of the P5b extension of the group I intron of Tetrahymena thermophila and the L9 GUGA terminal loop of the td intron of bacteriophage T4 (ref. 4). NMR has revealed the overall structure of the tetraloop for 12-nucleotide hairpins with GCAA and GAAA loops and models have been proposed for the interaction of GNRA tetraloops with base pairs in the minor groove of A-form RNA. Here we describe the crystal structure of an intermolecular complex between a GAAA tetraloop and an RNA helix. The interactions we observe correlate with the specificity of GNRA tetraloops inferred from phylogenetic studies, suggesting that this complex is a legitimate model for intramolecular tertiary interactions mediated by GNRA tetraloops in large structured RNAs.

The N-terminal cysteine pair of yeast sulfhydryl oxidase Erv1p is essential for in vivo activity and interacts with the primary redox centre.

PubMed

Hofhaus, Götz; Lee, Jeung-Eun; Tews, Ivo; Rosenberg, Beate; Lisowsky, Thomas

2003-04-01

Yeast Erv1p is a ubiquitous FAD-dependent sulfhydryl oxidase, located in the intermembrane space of mitochondria. The dimeric enzyme is essential for survival of the cell. Besides the redox-active CXXC motif close to the FAD, Erv1p harbours two additional cysteine pairs. Site-directed mutagenesis has identified all three cysteine pairs as essential for normal function. The C-terminal cysteine pair is of structural importance as it contributes to the correct arrangement of the FAD-binding fold. Variations in dimer formation and unique colour changes of mutant proteins argue in favour of an interaction between the N-terminal cysteine pair with the redox centre of the partner monomer.

Applicability of effective pair potentials for active Brownian particles.

PubMed

Rein, Markus; Speck, Thomas

2016-09-01

We have performed a case study investigating a recently proposed scheme to obtain an effective pair potential for active Brownian particles (Farage et al., Phys. Rev. E 91, 042310 (2015)). Applying this scheme to the Lennard-Jones potential, numerical simulations of active Brownian particles are compared to simulations of passive Brownian particles interacting by the effective pair potential. Analyzing the static pair correlations, our results indicate a limited range of activity parameters (speed and orientational correlation time) for which we obtain quantitative, or even qualitative, agreement. Moreover, we find a qualitatively different behavior for the virial pressure even for small propulsion speeds. Combining these findings we conclude that beyond linear response active particles exhibit genuine non-equilibrium properties that cannot be captured by effective pair interaction alone.

Consequences of plant invasions on compartmentalization and species’ roles in plant–pollinator networks

PubMed Central

Albrecht, Matthias; Padrón, Benigno; Bartomeus, Ignasi; Traveset, Anna

2014-01-01

Compartmentalization—the organization of ecological interaction networks into subsets of species that do not interact with other subsets (true compartments) or interact more frequently among themselves than with other species (modules)—has been identified as a key property for the functioning, stability and evolution of ecological communities. Invasions by entomophilous invasive plants may profoundly alter the way interaction networks are compartmentalized. We analysed a comprehensive dataset of 40 paired plant–pollinator networks (invaded versus uninvaded) to test this hypothesis. We show that invasive plants have higher generalization levels with respect to their pollinators than natives. The consequences for network topology are that—rather than displacing native species from the network—plant invaders attracting pollinators into invaded modules tend to play new important topological roles (i.e. network hubs, module hubs and connectors) and cause role shifts in native species, creating larger modules that are more connected among each other. While the number of true compartments was lower in invaded compared with uninvaded networks, the effect of invasion on modularity was contingent on the study system. Interestingly, the generalization level of the invasive plants partially explains this pattern, with more generalized invaders contributing to a lower modularity. Our findings indicate that the altered interaction structure of invaded networks makes them more robust against simulated random secondary species extinctions, but more vulnerable when the typically highly connected invasive plants go extinct first. The consequences and pathways by which biological invasions alter the interaction structure of plant–pollinator communities highlighted in this study may have important dynamical and functional implications, for example, by influencing multi-species reciprocal selection regimes and coevolutionary processes. PMID:24943368

Search for pair production of strongly interacting particles decaying to pairs of jets in pp collisions at √s=1.96 TeV.

PubMed

Aaltonen, T; Albin, E; Amerio, S; Amidei, D; Anastassov, A; Annovi, A; Antos, J; Apollinari, G; Appel, J A; Arisawa, T; Artikov, A; Asaadi, J; Ashmanskas, W; Auerbach, B; Aurisano, A; Azfar, F; Badgett, W; Bae, T; Barbaro-Galtieri, A; Barnes, V E; Barnett, B A; Barria, P; Bartos, P; Bauce, M; Bedeschi, F; Behari, S; Bellettini, G; Bellinger, J; Benjamin, D; Beretvas, A; Bhatti, A; Bland, K R; Blumenfeld, B; Bocci, A; Bodek, A; Bortoletto, D; Boudreau, J; Boveia, A; Brigliadori, L; Bromberg, C; Brucken, E; Budagov, J; Budd, H S; Burkett, K; Busetto, G; Bussey, P; Butti, P; Buzatu, A; Calamba, A; Camarda, S; Campanelli, M; Canelli, F; Carls, B; Carlsmith, D; Carosi, R; Carrillo, S; Casal, B; Casarsa, M; Castro, A; Catastini, P; Cauz, D; Cavaliere, V; Cavalli-Sforza, M; Cerri, A; Cerrito, L; Chen, Y C; Chertok, M; Chiarelli, G; Chlachidze, G; Cho, K; Chokheli, D; Ciocci, M A; Clark, A; Clarke, C; Convery, M E; Conway, J; Corbo, M; Cordelli, M; Cox, C A; Cox, D J; Cremonesi, M; Cruz, D; Cuevas, J; Culbertson, R; d'Ascenzo, N; Datta, M; De Barbaro, P; Demortier, L; Deninno, M; Devoto, F; d'Errico, M; Di Canto, A; Di Ruzza, B; Dittmann, J R; D'Onofrio, M; Donati, S; Dorigo, M; Driutti, A; Ebina, K; Edgar, R; Elagin, A; Erbacher, R; Errede, S; Esham, B; Eusebi, R; Farrington, S; Fernández Ramos, J P; Field, R; Flanagan, G; Forrest, R; Franklin, M; Freeman, J C; Frisch, H; Funakoshi, Y; Garfinkel, A F; Garosi, P; Gerberich, H; Gerchtein, E; Giagu, S; Giakoumopoulou, V; Gibson, K; Ginsburg, C M; Giokaris, N; Giromini, P; Giurgiu, G; Glagolev, V; Glenzinski, D; Gold, M; Goldin, D; Golossanov, A; Gomez, G; Gomez-Ceballos, G; Goncharov, M; González López, O; Gorelov, I; Goshaw, A T; Goulianos, K; Gramellini, E; Grinstein, S; Grosso-Pilcher, C; Group, R C; Guimaraes da Costa, J; Hahn, S R; Han, J Y; Happacher, F; Hara, K; Hare, M; Harr, R F; Harrington-Taber, T; Hatakeyama, K; Hays, C; Heinrich, J; Herndon, M; Hocker, A; Hong, Z; Hopkins, W; Hou, S; Hughes, R E; Husemann, U; Hussein, M; Huston, J; Introzzi, G; Iori, M; Ivanov, A; James, E; Jang, D; Jayatilaka, B; Jeon, E J; Jindariani, S; Jones, M; Joo, K K; Jun, S Y; Junk, T R; Kambeitz, M; Kamon, T; Karchin, P E; Kasmi, A; Kato, Y; Ketchum, W; Keung, J; Kilminster, B; Kim, D H; Kim, H S; Kim, J E; Kim, M J; Kim, S B; Kim, S H; Kim, Y K; Kim, Y J; Kimura, N; Kirby, M; Knoepfel, K; Kondo, K; Kong, D J; Konigsberg, J; Kotwal, A V; Kreps, M; Kroll, J; Kruse, M; Kuhr, T; Kurata, M; Laasanen, A T; Lammel, S; Lancaster, M; Lannon, K; Latino, G; Lee, H S; Lee, J S; Leo, S; Leone, S; Lewis, J D; Limosani, A; Lipeles, E; Liu, H; Liu, Q; Liu, T; Lockwitz, S; Loginov, A; Lucchesi, D; Lueck, J; Lujan, P; Lukens, P; Lungu, G; Lys, J; Lysak, R; Madrak, R; Maestro, P; Malik, S; Manca, G; Manousakis-Katsikakis, A; Margaroli, F; Marino, P; Martínez, M; Matera, K; Mattson, M E; Mazzacane, A; Mazzanti, P; McNulty, R; Mehta, A; Mehtala, P; Mesropian, C; Miao, T; Mietlicki, D; Mitra, A; Miyake, H; Moed, S; Moggi, N; Moon, C S; Moore, R; Morello, M J; Mukherjee, A; Muller, Th; Murat, P; Mussini, M; Nachtman, J; Nagai, Y; Naganoma, J; Nakano, I; Napier, A; Nett, J; Neu, C; Nigmanov, T; Nodulman, L; Noh, S Y; Norniella, O; Oakes, L; Oh, S H; Oh, Y D; Oksuzian, I; Okusawa, T; Orava, R; Ortolan, L; Pagliarone, C; Palencia, E; Palni, P; Papadimitriou, V; Parker, W; Pauletta, G; Paulini, M; Paus, C; Phillips, T J; Piacentino, G; Pianori, E; Pilot, J; Pitts, K; Plager, C; Pondrom, L; Poprocki, S; Potamianos, K; Prokoshin, F; Pranko, A; Ptohos, F; Punzi, G; Ranjan, N; Redondo Fernández, I; Renton, P; Rescigno, M; Riddick, T; Rimondi, F; Ristori, L; Robson, A; Rodriguez, T; Rolli, S; Ronzani, M; Roser, R; Rosner, J L; Ruffini, F; Ruiz, A; Russ, J; Rusu, V; Safonov, A; Sakumoto, W K; Sakurai, Y; Santi, L; Sato, K; Saveliev, V; Savoy-Navarro, A; Schlabach, P; Schmidt, E E; Schwarz, T; Scodellaro, L; Scuri, F; Seidel, S; Seiya, Y; Semenov, A; Sforza, F; Shalhout, S Z; Shears, T; Shepard, P F; Shimojima, M; Shochet, M; Shreyber-Tecker, I; Simonenko, A; Sinervo, P; Sliwa, K; Smith, J R; Snider, F D; Sorin, V; Song, H; Stancari, M; St Denis, R; Stelzer, B; Stelzer-Chilton, O; Stentz, D; Strologas, J; Sudo, Y; Sukhanov, A; Suslov, I; Takemasa, K; Takeuchi, Y; Tang, J; Tecchio, M; Teng, P K; Thom, J; Thomson, E; Thukral, V; Toback, D; Tokar, S; Tollefson, K; Tomura, T; Tonelli, D; Torre, S; Torretta, D; Totaro, P; Trovato, M; Ukegawa, F; Uozumi, S; Vázquez, F; Velev, G; Vellidis, C; Vernieri, C; Vidal, M; Vilar, R; Vizán, J; Vogel, M; Volpi, G; Wagner, P; Wallny, R; Wang, S M; Warburton, A; Waters, D; Wester, W C; Whiteson, D; Wicklund, A B; Wilbur, S; Williams, H H; Wilson, J S; Wilson, P; Winer, B L; Wittich, P; Wolbers, S; Wolfe, H; Wright, T; Wu, X; Wu, Z; Yamamoto, K; Yamato, D; Yang, T; Yang, U K; Yang, Y C; Yao, W-M; Yeh, G P; Yi, K; Yoh, J; Yorita, K; Yoshida, T; Yu, G B; Yu, I; Zanetti, A M; Zeng, Y; Zhou, C; Zucchelli, S

2013-07-19

We present a search for the pair production of a narrow nonstandard-model strongly interacting particle that decays to a pair of quarks or gluons, leading to a final state with four hadronic jets. We consider both nonresonant production via an intermediate gluon as well as resonant production via a distinct nonstandard-model intermediate strongly interacting particle. We use data collected by the CDF experiment in proton-antiproton collisions at √[s]=1.96 TeV corresponding to an integrated luminosity of 6.6 fb(-1). We find the data to be consistent with nonresonant production. We report limits on σ(pp[over ¯]→jjjj) as a function of the masses of the hypothetical intermediate particles. Upper limits on the production cross sections for nonstandard-model particles in several resonant and nonresonant processes are also derived.

Evidence of Antiblockade in an Ultracold Rydberg Gas

NASA Astrophysics Data System (ADS)

Amthor, Thomas; Giese, Christian; Hofmann, Christoph S.; Weidemüller, Matthias

2010-01-01

We present the experimental observation of the antiblockade in an ultracold Rydberg gas recently proposed by Ates et al. [Phys. Rev. Lett. 98, 023002 (2007)PRLTAO0031-900710.1103/PhysRevLett.98.023002]. Our approach allows the control of the pair distribution in the gas and is based on a strong coupling of one transition in an atomic three-level system, while introducing specific detunings of the other transition. When the coupling energy matches the interaction energy of the Rydberg long-range interactions, the otherwise blocked excitation of close pairs becomes possible. A time-resolved spectroscopic measurement of the Penning ionization signal is used to identify slight variations in the Rydberg pair distribution of a random arrangement of atoms. A model based on a pair interaction Hamiltonian is presented which well reproduces our experimental observations and allows one to deduce the distribution of nearest-neighbor distances.

Search for Pair Production of Strongly Interacting Particles Decaying to Pairs of Jets in pp̄ Collisions at √s=1.96 TeV

DOE PAGES

Aaltonen, T.; Albin, E.; Amerio, S.; ...

2013-07-18

We present a search for the pair production of a narrow nonstandard-model strongly interacting particle that decays to a pair of quarks or gluons, leading to a final state with four hadronic jets. We consider both nonresonant production via an intermediate gluon as well as resonant production via a distinct nonstandard-model intermediate strongly interacting particle. We use data collected by the CDF experiment in proton-antiproton collisions at √s=1.96 TeV corresponding to an integrated luminosity of 6.6 fb⁻¹. We find the data to be consistent with nonresonant production. We report limits on σ(pp̄→jjjj) as a function of the masses of themore » hypothetical intermediate particles. Upper limits on the production cross sections for nonstandard-model particles in several resonant and nonresonant processes are also derived.« less

Interspecific competition among Hawaiian forest birds

USGS Publications Warehouse

Mountainspring, S.; Scott, J.M.

1985-01-01

The object of this study was to determine whether interspecific competition modified local geographic distribution, after taking into account the effect of habitat structure. The tendencies for 14 passerine birds to have positive or negative associations were examined, using 7861 sample points in seven native forests on the islands of Hawaii, Maui, and Kauai. All birds were at least partly insectivorous and were fairly common in forested areas, although some fed chiefly on nectar or fruit. Species-pairs were classified as primary or secondary potential competitors based on general dietary similarity. To evaluate the association between species and to account for the effect of individual species habitat preferences, partial correlations were computed for each species-pair in a study area from the simple correlations between the species and 26 habitat variables plus two quadratic terms to represent nonlinearity. The partial correlations represented a short-term ('instantaneous') assessment of the strength of competitive interactions, and did not reflect the accumulation of competitive displacement through time. Of 170 partial correlations in the analysis, only 10 indicated significant negative association. The general pattern was of positive association (76 significantly positive partials), which probably resulted from flocking and from attraction of birds to areas of resource superabundance. Two species showed consistent patterns of negative partial correlations over several adjacent study areas, the Japanese White-eye/Iiwi in montane Hawaii, and the Japanese White-eye/Elepaio in windward Hawaii; both patterns could be reasonably attributed to direct competition. Species-pairs were grouped by the native or exotic status of the component species. Native/exotic pairs had a significantly greater proportion of negative partial correlations (37%) than either native/native pairs (8%) or exotic/exotic pairs (0%). This pattern was consistent across the seven study areas and appeared to reflect the occurrence of interspecific competition along a broad and diffuse ecological 'front' between a co-evolved native avifauna and recently introduced exotic species. The role of competition in the pattern was corroborated by the significantly higher proportion of negative partial correlations among species-pairs of primary potential competitors than among those of secondary potential competitors. Our results suggested that 47% of the primary potential competitors among native/exotic species-pairs may experience at least small depressions in local population density due to competition. Although the negative correlations were for the most part small (average negative r = 0.06), one species could eventually replace another as spatial displacement accumulated through time. The Japanese White-eye appeared to have a principal role in native/exotic interactions, with 62% of the partial correlations between it and native primary potential competitor species being negative. Noteworthy implications were that (1) it was important to account for the habitat responses of individual species when studying the role of interspecific competition in modifying small-scale geographic distribution; (2) competition was frequently sporadic in its geographic occurrence and in the species affected, thus supporting Wiens' (1977) theory of competition; and (3) as a consequence, the role of interspecific competition in modifying distribution may be difficult to detect statistically with small data sets.

A study of photon interaction in some building materials: High-volume admixture of blast furnace slag into Portland cement

NASA Astrophysics Data System (ADS)

Kurudirek, Murat; Türkmen, İbrahim; Özdemir, Yüksel

2009-09-01

Total mass attenuation coefficients, mean free paths (MFP), half-value (HVT) and tenth-value (TVT) thicknesses of Portland cement and three mixtures have been calculated in function of the energy from 1 keV to 100 GeV. Both in the low- and high-energy region there were significant variations in those parameters where photoelectric process and pair production partially dominates, respectively. In general, the attenuation parameters were found to vary with chemical composition, density of given material and photon energy.

Classical integrable many-body systems disconnected with semi-simple Lie algebras

NASA Astrophysics Data System (ADS)

Inozemtsev, V. I.

2017-05-01

The review of the results in the theory of integrable many-body systems disconnected with semisimple Lie algebras is done. The one-dimensional systems of light Calogero-Sutherland-Moser particles interacting with one particle of infinite mass located at the origin are described in detail. In some cases the exact solutions of the equations of motion are obtained. The general theory of integration of the equations of motion needs the methods of algebraic geometry. The Lax pairs with spectral parameter are constructed for this purpose. The theory still contains many unsolved problems.

Spinning geodesic Witten diagrams

DOE PAGES

Dyer, Ethan; Freedman, Daniel Z.; Sully, James

2017-11-10

We present an expression for the four-point conformal blocks of symmetric traceless operators of arbitrary spin as an integral over a pair of geodesics in Anti-de Sitter space, generalizing the geodesic Witten diagram formalism of Hijano et al. to arbitrary spin. As an intermediate step in the derivation, we identify a convenient basis of bulk threepoint interaction vertices which give rise to all possible boundary three point structures. Lastly, we highlight a direct connection between the representation of the conformal block as geodesic Witten diagram and the shadow operator formalism.

Direct and inverted nematic dispersions for soft matter photonics.

PubMed

Muševič, I; Skarabot, M; Humar, M

2011-07-20

General properties and recent developments in the field of nematic colloids and emulsions are discussed. The origin and nature of pair colloidal interactions in the nematic colloids are explained and an overview of the stable colloidal 2D crystalline structures and superstructures discovered so far is given. The nature and role of topological defects in the nematic colloids is discussed, with an emphasis on recently discovered entangled colloidal structures. Applications of inverted nematic emulsions and binding force mechanisms in nematic colloids for soft matter photonic devices are discussed.

Minor Allele Frequency Changes the Nature of Genotype by Environment Interactions.

PubMed

Verhulst, Brad; Neale, Michael C

2016-09-01

In the classical twin study, phenotypic variation is often partitioned into additive genetic (A), common (C) and specific environment (E) components. From genetical theory, the outcome of genotype by environment interaction is expected to inflate A when the interacting factor is shared (i.e., C) between the members of a twin pair. We show that estimates of both A and C can be inflated. When the shared interacting factor changes the size of the difference between homozygotes' means, the expected sibling or DZ twin correlation is .5 if and only if the minor allele frequency (MAF) is .5; otherwise the expected DZ correlation is greater than this value, consistent (and confounded) with some additional effect of C. This result is considered in the light of the distribution of minor allele frequencies for polygenic traits. Also discussed is whether such interactions take place at the locus level or affect an aggregated biological structure or system. Interactions with structures or endophenotypes that result from the aggregated effects of many loci will generally emerge as part of the A estimate.

Oligomerisation status and evolutionary conservation of interfaces of protein structural domain superfamilies.

PubMed

Sukhwal, Anshul; Sowdhamini, Ramanathan

2013-07-01

Protein-protein interactions are important in carrying out many biological processes and functions. These interactions may be either permanent or of temporary nature. Several studies have employed tools like solvent accessibility and graph theory to identify these interactions, but still more studies need to be performed to quantify and validate them. Although we now have many databases available with predicted and experimental results on protein-protein interactions, we still do not have many databases which focus on providing structural details of the interacting complexes, their oligomerisation state and homologues. In this work, protein-protein interactions have been thoroughly investigated within the structural regime and quantified for their strength using calculated pseudoenergies. The PPCheck server, an in-house webserver, has been used for calculating the pseudoenergies like van der Waals, hydrogen bonds and electrostatic energy based on distances between atoms of amino acids from two interacting proteins. PPCheck can be visited at . Based on statistical data, as obtained by studying established protein-protein interacting complexes from earlier studies, we came to a conclusion that an average protein-protein interface consisted of about 51 to 150 amino acid residues and the generalized energy per residue ranged from -2 kJ mol(-1) to -6 kJ mol(-1). We found that some of the proteins have an exceptionally higher number of amino acids at the interface and it was purely because of their elaborate interface or extended topology i.e. some of their secondary structure regions or loops were either inter-mixing or running parallel to one another or they were taking part in domain swapping. Residue networks were prepared for all the amino acids of the interacting proteins involved in different types of interactions (like van der Waals, hydrogen-bonding, electrostatic or intramolecular interactions) and were analysed between the query domain-interacting partner pair and its remote homologue-interacting partner pair. We found that, in exceptional cases, homologous proteins belonging to the same superfamily, but with remote sequence similarity, can share similar interfaces.

Interactions in ion pairs of protic ionic liquids: Comparison with aprotic ionic liquids

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

Tsuzuki, Seiji, E-mail: s.tsuzuki@aist.go.jp; Shinoda, Wataru; Miran, Md. Shah

2013-11-07

The stabilization energies for the formation (E{sub form}) of 11 ion pairs of protic and aprotic ionic liquids were studied by MP2/6-311G{sup **} level ab initio calculations to elucidate the difference between the interactions of ions in protic ionic liquids and those in aprotic ionic liquids. The interactions in the ion pairs of protic ionic liquids (diethylmethylammonium [dema] and dimethylpropylammonium [dmpa] based ionic liquids) are stronger than those of aprotic ionic liquids (ethyltrimethylammonium [etma] based ionic liquids). The E{sub form} for the [dema][CF{sub 3}SO{sub 3}] and [dmpa][CF{sub 3}SO{sub 3}] complexes (−95.6 and −96.4 kcal/mol, respectively) are significantly larger (more negative)more » than that for the [etma][CF{sub 3}SO{sub 3}] complex (−81.0 kcal/mol). The same trend was observed for the calculations of ion pairs of the three cations with the Cl{sup −}, BF{sub 4}{sup −}, TFSA{sup −} anions. The anion has contact with the N–H bond of the dema{sup +} or dmpa{sup +} cations in the most stable geometries of the dema{sup +} and dmpa{sup +} complexes. The optimized geometries, in which the anions locate on the counter side of the cations, are 11.0–18.0 kcal/mol less stable, which shows that the interactions in the ions pairs of protic ionic liquids have strong directionality. The E{sub form} for the less stable geometries for the dema{sup +} and dmpa{sup +} complexes are close to those for the most stable etma{sup +} complexes. The electrostatic interaction, which is the major source of the attraction in the ion pairs, is responsible for the directionality of the interactions and determining the magnitude of the interaction energy. Molecular dynamic simulations of the [dema][TFSA] and [dmpa][TFSA] ionic liquids show that the N–H bonds of the cations have contact with the negatively charged (oxygen and nitrogen) atoms of TFSA{sup −} anion, while the strong directionality of the interactions was not suggested from the simulation of the [etma][CF{sub 3}SO{sub 3}] ionic liquid.« less

Non-axisymmetric viscous lower-branch modes in axisymmetric supersonic flows

NASA Technical Reports Server (NTRS)

Duck, Peter W.; Hall, Philip

1990-01-01

A previous paper by Duck and Hall (1989) considered the weakly nonlinear interaction of a pair of axisymmetric lower-branch Tollmien-Schlichting instabilities in cylindrical supersonic flows. Here, the possibility that nonaxisymmetric modes might also exist is investigated. In fact, it is found that such modes do exist and, on the basis of linear theory, it appears that these modes are the most important. The nonaxisymmetric modes are found to exist for flows around cylinders with nondimensional radius a less than some critical value a(c). This critical value a(c) is found to increase monotonically with the azimuthal wavenumber n of the disturbance, and it is found that unstable modes always occur in pairs. It is shown that, in general, instability in the form of lower-branch Tollmien-Schlichting waves will occur first for nonaxisymmetric modes and that, in the unstable regime, the largest growth rates correspond to the latter modes.

Nonaxisymmetric viscous lower branch modes in axisymmetric supersonic flows

NASA Technical Reports Server (NTRS)

Duck, Peter W.; Hall, Philip

1988-01-01

In a previous paper, the weakly nonlinear interaction of a pair of axisymmetric lower branch Tollmien-Schlichting instabilities in cylindrical supersonic flows was considered. Here the possibility that nonaxisymmetric modes might also exist is investigated. In fact, it is found that such modes do exist and, on the basis of linear theory, it appears that these modes are the most important. The nonaxisymmetric modes are found to exist for flows around cylinders with nondimensional radius alpha less than some critical value alpha sub c. This critical value alpha sub c is found to increase monotonically with the azimuthal wavenumber nu of the disturbance and it is found that unstable modes always occur in pairs. It is also shown that, in general, instability in the form of lower branch Tollmien-Schlichting waves will occur first for nonaxisymmetric modes and that in the unstable regime the largest growth rates correspond to the latter modes.

Learning Gains from a Recurring "Teach and Question" Homework Assignment in a General Biology Course: Using Reciprocal Peer Tutoring Outside Class.

PubMed

Bailey, E G; Baek, D; Meiling, J; Morris, C; Nelson, N; Rice, N S; Rose, S; Stockdale, P

2018-06-01

Providing students with one-on-one interaction with instructors is a big challenge in large courses. One solution is to have students interact with their peers during class. Reciprocal peer tutoring (RPT) is a more involved interaction that requires peers to alternate the roles of "teacher" and "student." Theoretically, advantages for peer tutoring include the verbalization and questioning of information and the scaffolded exploration of material through social and cognitive interaction. Studies on RPT vary in their execution, but most require elaborate planning and take up valuable class time. We tested the effectiveness of a "teach and question" (TQ) assignment that required student pairs to engage in RPT regularly outside class. A quasi-experimental design was implemented: one section of a general biology course completed TQ assignments, while another section completed a substitute assignment requiring individuals to review course material. The TQ section outperformed the other section by ∼6% on exams. Session recordings were coded to investigate correlation between TQ quality and student performance. Asking more questions was the characteristic that best predicted exam performance, and this was more predictive than most aspects of the course. We propose the TQ as an easy assignment to implement with large performance gains.

Discovery of a transparent sightline at ρ ≲ 20 kpc from an interacting pair of galaxies

NASA Astrophysics Data System (ADS)

Johnson, Sean D.; Chen, Hsiao-Wen; Mulchaey, John S.; Tripp, Todd M.; Prochaska, J. Xavier; Werk, Jessica K.

2014-03-01

We report the discovery of a transparent sightline at projected distances of ρ ≲ 20 kpc to an interacting pair of mature galaxies at z = 0.12. The sightline of the UV-bright quasar PG 1522+101 at zem = 1.328 passes at ρ = 11.5 kpc from the higher mass galaxy (M* = 1010.6 M⊙) and ρ = 20.4 kpc from the lower mass one (M* = 1010.0 M⊙). The two galaxies are separated by 9 kpc in projected distance and 30 km s-1 in line-of-sight velocity. Deep optical images reveal tidal features indicative of close interactions. Despite the small projected distances, the quasar sightline shows little absorption associated with the galaxy pair with a total H I column density no greater than log N({H I})/cm^{-2}=13.65. This limiting H I column density is already two orders of magnitude less than what is expected from previous halo gas studies. In addition, we detect no heavy-element absorption features associated with the galaxy pair with 3σ limits of log N({Mg II})/cm^{-2} < 12.2 and log N({O VI})/cm^{-2} < 13.7. The probability of seeing such little absorption in a sightline passing at a small projected distance from two non-interacting galaxies is 0.2 per cent. The absence of strong absorbers near the close galaxy pair suggests that the cool gas reservoirs of the galaxies have been significantly depleted by the galaxy interaction. These observations therefore underscore the potential impact of galaxy interactions on the gaseous haloes around galaxies.

Transition from Sign-Reversed to Sign-Preserved Cooper-Pairing Symmetry in Sulfur-Doped Iron Selenide Superconductors.

PubMed

Wang, Qisi; Park, J T; Feng, Yu; Shen, Yao; Hao, Yiqing; Pan, Bingying; Lynn, J W; Ivanov, A; Chi, Songxue; Matsuda, M; Cao, Huibo; Birgeneau, R J; Efremov, D V; Zhao, Jun

2016-05-13

An essential step toward elucidating the mechanism of superconductivity is to determine the sign or phase of the superconducting order parameter, as it is closely related to the pairing interaction. In conventional superconductors, the electron-phonon interaction induces attraction between electrons near the Fermi energy and results in a sign-preserved s-wave pairing. For high-temperature superconductors, including cuprates and iron-based superconductors, prevalent weak coupling theories suggest that the electron pairing is mediated by spin fluctuations which lead to repulsive interactions, and therefore that a sign-reversed pairing with an s_{±} or d-wave symmetry is favored. Here, by using magnetic neutron scattering, a phase sensitive probe of the superconducting gap, we report the observation of a transition from the sign-reversed to sign-preserved Cooper-pairing symmetry with insignificant changes in T_{c} in the S-doped iron selenide superconductors K_{x}Fe_{2-y}(Se_{1-z}S_{z})_{2}. We show that a rather sharp magnetic resonant mode well below the superconducting gap (2Δ) in the undoped sample (z=0) is replaced by a broad hump structure above 2Δ under 50% S doping. These results cannot be readily explained by simple spin fluctuation-exchange pairing theories and, therefore, multiple pairing channels are required to describe superconductivity in this system. Our findings may also yield a simple explanation for the sometimes contradictory data on the sign of the superconducting order parameter in iron-based materials.

Analyses of interactions among pair-rule genes and the gap gene Krüppel in Bombyx segmentation.

PubMed

Nakao, Hajime

2015-09-01

In the short-germ insect Tribolium, a pair-rule gene circuit consisting of the Tribolium homologs of even-skipped, runt, and odd-skipped (Tc-eve, Tc-run and Tc-odd, respectively) has been implicated in segment formation. To examine the application of the model to other taxa, I studied the expression and function of pair-rule genes in Bombyx mori, together with a Bombyx homolog of Krüppel (Bm-Kr), a known gap gene. Knockdown embryos of Bombyx homologs of eve, run and odd (Bm-eve, Bm-run and Bm-odd) exhibited asegmental phenotypes similar to those of Tribolium knockdowns. However, pair-rule gene interactions were similar to those of both Tribolium and Drosophila, which, different from Tribolium, shows a hierarchical segmentation mode. Additionally, the Bm-odd expression pattern shares characteristics with those of Drosophila pair-rule genes that receive upstream regulatory input. On the other hand, Bm-Kr knockdowns exhibited a large posterior segment deletion as observed in short-germ insects. However, a detailed analysis of these embryos indicated that Bm-Kr modulates expression of pair-rule genes like in Drosophila, although the mechanisms appear to be different. This suggested hierarchical interactions between Bm-Kr and pair-rule genes. Based on these results, I concluded that the pair-rule gene circuit model that describes Tribolium development is not applicable to Bombyx. Copyright © 2015 Elsevier Inc. All rights reserved.

Atom-Pair Kinetics with Strong Electric-Dipole Interactions.

PubMed

Thaicharoen, N; Gonçalves, L F; Raithel, G

2016-05-27

Rydberg-atom ensembles are switched from a weakly to a strongly interacting regime via adiabatic transformation of the atoms from an approximately nonpolar into a highly dipolar quantum state. The resultant electric dipole-dipole forces are probed using a device akin to a field ion microscope. Ion imaging and pair-correlation analysis reveal the kinetics of the interacting atoms. Dumbbell-shaped pair-correlation images demonstrate the anisotropy of the binary dipolar force. The dipolar C_{3} coefficient, derived from the time dependence of the images, agrees with the value calculated from the permanent electric-dipole moment of the atoms. The results indicate many-body dynamics akin to disorder-induced heating in strongly coupled particle systems.

Evaluating effective pair and multisite interactions for Ni-Mo system

NASA Astrophysics Data System (ADS)

Banerjee, Rumu H.; Arya, A.; Banerjee, S.

2018-04-01

Cluster expansion (CE) method was used to calculate the energies of various Ni-Mo phases. The clusters comprising of few nearest neighbours can describe any phase of Ni-Mo system by suitable choice of effective pair and multisite interaction parameters (ECI). The ECIs were evaluated in present study by fitting the ground state energies obtained by first principle calculations. The ECIs evaluated for Ni-Mo system were mostly pair clusters followed by triplets and quadruplet clusters with cluster diameters in the range 2.54 - 10.20 Å. The ECI values diminished for multi-body (triplets and quadruplets) clusters as compared to 2-point or pair clusters indicating a good convergence of CE model. With these ECIs the predicted energies of all the Ni-Mo structures across the Mo concentration range 0-100 at% were obtained. The quantitative error in the energies calculated by CE approach and first principle is very small (< 0.026 meV/atom). The appreciable values of 2-point ECIs upto 4th nearest neighbour reveal that two body interactions are dominant in the case of Ni-Mo system. These ECIs are compared with the reported values of compositional dependent effective pair interactions evaluated by first principle as well as by Monte Carlo method.

Electrophysiological correlates of implicit valenced self-processing in high vs. low self-esteem individuals.

PubMed

Grundy, John G; Benarroch, Miriam F F; Lebarr, A Nicole; Shedden, Judith M

2015-01-01

We provide the first high-temporal resolution account of the self-esteem implicit association test (IAT; Greenwald & Farnham, 2000) to highlight important similarities and differences between the cognitive processes corresponding to implicit valenced self-processing in high vs. low self-esteem individuals. We divided individuals into high and low self-esteem groups based on the Rosenberg self-esteem scale (Rosenberg, 1965) and administered the self-esteem IAT while recording electroencephalographic data. We show that the P2 captured group (high vs. low self-esteem) differences, the N250 and the late parietal positivity (LPP) captured differences corresponding to category pairing (self/positive vs. self/negative pairing), and the N1, P2, and P300-400 components captured interactions between self-esteem groups and whether the self was paired with positive or negative categories in the IAT. Overall, both high and low self-esteem groups were sensitive to the distinction between positive and negative information in relation to the self (me/negative generally displayed larger event-related potential amplitudes than me/positive), but for high self-esteem individuals, this difference was generally larger, earlier, and most pronounced over left-hemisphere electrodes. These electrophysiological differences may reflect differences in attentional resources devoted to teasing apart these two oppositely valenced associations. High self-esteem individuals appear to devote more automatic (early) attentional resources to strengthen the distinction between positively or negatively valenced information in relation to the self.

ReLiance: a machine learning and literature-based prioritization of receptor—ligand pairings

PubMed Central

Iacucci, Ernesto; Tranchevent, Léon-Charles; Popovic, Dusan; Pavlopoulos, Georgios A.; De Moor, Bart; Schneider, Reinhard; Moreau, Yves

2012-01-01

Motivation: The prediction of receptor—ligand pairings is an important area of research as intercellular communications are mediated by the successful interaction of these key proteins. As the exhaustive assaying of receptor—ligand pairs is impractical, a computational approach to predict pairings is necessary. We propose a workflow to carry out this interaction prediction task, using a text mining approach in conjunction with a state of the art prediction method, as well as a widely accessible and comprehensive dataset. Among several modern classifiers, random forests have been found to be the best at this prediction task. The training of this classifier was carried out using an experimentally validated dataset of Database of Ligand-Receptor Partners (DLRP) receptor—ligand pairs. New examples, co-cited with the training receptors and ligands, are then classified using the trained classifier. After applying our method, we find that we are able to successfully predict receptor—ligand pairs within the GPCR family with a balanced accuracy of 0.96. Upon further inspection, we find several supported interactions that were not present in the Database of Interacting Proteins (DIPdatabase). We have measured the balanced accuracy of our method resulting in high quality predictions stored in the available database ReLiance. Availability: http://homes.esat.kuleuven.be/~bioiuser/ReLianceDB/index.php Contact: yves.moreau@esat.kuleuven.be; ernesto.iacucci@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:22962483

Dynamical Bayesian inference of time-evolving interactions: From a pair of coupled oscillators to networks of oscillators

NASA Astrophysics Data System (ADS)

Duggento, Andrea; Stankovski, Tomislav; McClintock, Peter V. E.; Stefanovska, Aneta

2012-12-01

Living systems have time-evolving interactions that, until recently, could not be identified accurately from recorded time series in the presence of noise. Stankovski [Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.109.024101 109, 024101 (2012)] introduced a method based on dynamical Bayesian inference that facilitates the simultaneous detection of time-varying synchronization, directionality of influence, and coupling functions. It can distinguish unsynchronized dynamics from noise-induced phase slips. The method is based on phase dynamics, with Bayesian inference of the time-evolving parameters being achieved by shaping the prior densities to incorporate knowledge of previous samples. We now present the method in detail using numerically generated data, data from an analog electronic circuit, and cardiorespiratory data. We also generalize the method to encompass networks of interacting oscillators and thus demonstrate its applicability to small-scale networks.

Transferable Pseudo-Classical Electrons for Aufbau of Atomic Ions

PubMed Central

Ekesan, Solen; Kale, Seyit; Herzfeld, Judith

2014-01-01

Generalizing the LEWIS reactive force field from electron pairs to single electrons, we present LEWIS• in which explicit valence electrons interact with each other and with nuclear cores via pairwise interactions. The valence electrons are independently mobile particles, following classical equations of motion according to potentials modified from Coulombic as required to capture quantum characteristics. As proof of principle, the aufbau of atomic ions is described for diverse main group elements from the first three rows of the periodic table, using a single potential for interactions between electrons of like spin and another for electrons of unlike spin. The electrons of each spin are found to distribute themselves in a fashion akin to the major lobes of the hybrid atomic orbitals, suggesting a pointillist description of the electron density. The broader validity of the LEWIS• force field is illustrated by predicting the vibrational frequencies of diatomic and triatomic hydrogen species. PMID:24752384

Transferable pseudoclassical electrons for aufbau of atomic ions.

PubMed

Ekesan, Solen; Kale, Seyit; Herzfeld, Judith

2014-06-05

Generalizing the LEWIS reactive force field from electron pairs to single electrons, we present LEWIS• in which explicit valence electrons interact with each other and with nuclear cores via pairwise interactions. The valence electrons are independently mobile particles, following classical equations of motion according to potentials modified from Coulombic as required to capture quantum characteristics. As proof of principle, the aufbau of atomic ions is described for diverse main group elements from the first three rows of the periodic table, using a single potential for interactions between electrons of like spin and another for electrons of unlike spin. The electrons of each spin are found to distribute themselves in a fashion akin to the major lobes of the hybrid atomic orbitals, suggesting a pointillist description of the electron density. The broader validity of the LEWIS• force field is illustrated by predicting the vibrational frequencies of diatomic and triatomic hydrogen species. Copyright © 2014 Wiley Periodicals, Inc.

The role of wine polysaccharides on salivary protein-tannin interaction: A molecular approach.

PubMed

Brandão, Elsa; Silva, Mafalda Santos; García-Estévez, Ignacio; Williams, Pascale; Mateus, Nuno; Doco, Thierry; de Freitas, Victor; Soares, Susana

2017-12-01

Polysaccharides are described to inhibit aggregation between food polyphenols and salivary proteins (SP) and may hence lead to astringency modulation. In this work, the effect of two wine polysaccharides (arabinogalactan proteins-AGPs and rhamnogalacturonan II- RGII) on SP-polyphenol interaction was evaluated. In general, both polysaccharides were effective to inhibit or reduce SP-polyphenol interaction and aggregation. They can act by two different mechanisms (ternary or competitive) depending on the SP-tannin pair. In the case of salivary P-B peptide, AGPs and RGII seem to act by a ternary mechanism, in which they surround this complex, enhancing its solubility. Concerning acidic proline-rich proteins (aPRPs), it was possible to observe both mechanisms, depending on the tannin and the polysaccharide involved. Overall, this work point out for a specific property of wine polysaccharides important to modulate this and other beverages and food astringency perception. Copyright © 2017 Elsevier Ltd. All rights reserved.

Detection of back-to-back proton pairs in charged-current neutrino interactions with the ArgoNeuT detector in the NuMI low energy beam line

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

Acciarri, R.; Adams, C.; Asaadi, J.

2014-07-01

Short range nucleon-nucleon correlations in nuclei (NN SRC) carry important information on nuclear structure and dynamics. NN SRC have been extensively probed through two-nucleon knock- out reactions in both pion and electron scattering experiments. We report here on the detection of two-nucleon knock-out events from neutrino interactions and discuss their topological features as possibly involving NN SRC content in the target argon nuclei. The ArgoNeuT detector in the Main Injector neutrino beam at Fermilab has recorded a sample of 30 fully reconstructed charged current events where the leading muon is accompanied by a pair of protons at the interaction vertex,more » 19 of which have both protons above the Fermi momentum of the Ar nucleus. Out of these 19 events, four are found with the two protons in a strictly back-to-back high momenta configuration directly observed in the final state and can be associated to nucleon Resonance pionless mechanisms involving a pre-existing short range correlated np pair in the nucleus. Another fraction (four events) of the remaining 15 events have a reconstructed back-to-back configuration of a np pair in the initial state, a signature compatible with one-body Quasi Elastic interaction on a neutron in a SRC pair. The detection of these two subsamples of the collected (mu- + 2p) events suggests that mechanisms directly involving nucleon-nucleon SRC pairs in the nucleus are active and can be efficiently explored in neutrino-argon interactions with the LAr TPC technology.« less

Common Coupled Fixed Point Theorems for Two Hybrid Pairs of Mappings under φ-ψ Contraction

PubMed Central

Handa, Amrish

2014-01-01

We introduce the concept of (EA) property and occasional w-compatibility for hybrid pair F : X × X → 2X and f : X → X. We also introduce common (EA) property for two hybrid pairs F, G : X → 2X and f, g : X → X. We establish some common coupled fixed point theorems for two hybrid pairs of mappings under φ-ψ contraction on noncomplete metric spaces. An example is also given to validate our results. We improve, extend and generalize several known results. The results of this paper generalize the common fixed point theorems for hybrid pairs of mappings and essentially contain fixed point theorems for hybrid pair of mappings. PMID:27340688

Spin relaxation of radicals in cryptochrome and its role in avian magnetoreception

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

Worster, Susannah; Kattnig, Daniel R.; Hore, P. J., E-mail: peter.hore@chem.ox.ac.uk

2016-07-21

Long-lived spin coherence and rotationally ordered radical pairs have previously been identified as key requirements for the radical pair mechanism of the avian magnetic compass sense. Both criteria are hard to meet in a biological environment, where thermal motion of the radicals creates dynamic disorder and drives efficient spin relaxation. This has long been cited as a major stumbling block of the radical pair hypothesis. Here we combine Redfield relaxation theory with analytical solutions to a rotational diffusion equation to assess the impact of restricted rotational motion of the radicals on the operation of the compass. The effects of suchmore » motions are first investigated generally in small, model systems and are then critically examined in the magnetically sensitive flavin-tryptophan radical pair that is formed photochemically in the proposed magnetoreceptor protein, cryptochrome. We conclude that relaxation is slowest when rotational motion of the radicals within the protein is fast and highly constrained; that in a regime of slow relaxation, the motional averaging of hyperfine interactions has the potential to improve the sensitivity of the compass; and that consideration of motional effects can significantly alter the design criteria for an optimal compass. In addition, we demonstrate that motion of the flavin radical is likely to be compatible with its role as a component of a functioning radical-pair compass, whereas the motion of the tryptophan radical is less ideal, unless it is particularly fast.« less

Chronic exposure to low doses bisphenol A interferes with pair-bonding and exploration in female Mongolian gerbils.

PubMed

Razzoli, M; Valsecchi, P; Palanza, P

2005-04-15

Estrogenic endocrine disruptors, synthetic or naturally occurring substances found in the environment, can interfere with the vertebrate endocrine system and, mimicking estrogens, interact with the neuroendocrine substrates of behavior. Since species vary in their sensitivity to steroids, it is of great interest to widen the range of species included in the researches on neurobehavioral effects of estrogenic endocrine disruptors. We examined socio-sexual and exploratory behavior of Mongolian gerbil females (Meriones unguiculatus), a monogamous rodent, in response to chronic exposure to the estrogenic endocrine disruptor bisphenol A. Paired females were daily administered with one of the following treatments: bisphenol A (2 or 20 microg/kg body weight/day); 17alpha-ethynil estradiol (0.04 microg/kg body weight/day 17alphaE); oil (vehicle). Females were treated for 3 weeks after pairing. Starting on day of pairing, social interactions within pairs were daily recorded. Three weeks after pairing, females were individually tested in a free exploratory paradigm. Bisphenol A and 17alphaE affected male-female social interactions by increasing social investigation. Bisphenol A reduced several exploratory parameters, indicating a decreased exploratory propensity of females. These results highlight the sensitivity of adult female gerbils to bisphenol A during the hormonally sensitive period of pair formation, also considering that the bisphenol A doses tested are well below the suggested human tolerable daily intake.

Cooperative Interactions in Peer Tutoring: Patterns and Sequences in Paired Writing

ERIC Educational Resources Information Center

Duran, David

2010-01-01

The research analyzes the interaction of 24 students (12 pairs) of secondary students when using peer tutoring techniques to learn Catalan. Students worked together in a program to produce an authentic writing experience. Significant increases were observed in pre- and posttest Catalan attainment scores of students. An analysis of the…

Relationship of Sibling Structure and Interaction to Categorization Ability. Final Report.

ERIC Educational Resources Information Center

Cicirelli, Victor G.; And Others

This study identified behaviors of sibling pairs interacting on a cognitive task and related these behaviors to sibling structure variables (age and sex of each sibling and age spacing between them) and to measure of cognitive abilities of the younger sibling. Subjects were 160 sibling pairs randomly selected from appropriate subpopulations of…

Paired and Interacting Galaxies: International Astronomical Union Colloquium No. 124

NASA Technical Reports Server (NTRS)

Sulentic, Jack W. (Editor); Keel, William C. (Editor); Telesco, C. M. (Editor)

1990-01-01

The proceedings of the International Astronomical Union Colloquium No. 124, held at the University of Alabama at Tuscaloosa, on December 4 to 7, are given. The purpose of the conference was to describe the current state of theoretical and observational knowledge of interacting galaxies, with particular emphasis on galaxies in pairs.

Neural Correlates of Appetitive-Aversive Interactions in Pavlovian Fear Conditioning

ERIC Educational Resources Information Center

Nasser, Helen M.; McNally, Gavan P.

2013-01-01

We used Pavlovian counterconditioning in rats to identify the neural mechanisms for appetitive-aversive motivational interactions. In Stage I, rats were trained on conditioned stimulus (CS)-food (unconditioned stimulus [US]) pairings. In Stage II, this appetitive CS was transformed into a fear CS via pairings with footshock. The development of…

Universality of the Berezinskii-Kosterlitz-Thouless type of phase transition in the dipolar XY-model

NASA Astrophysics Data System (ADS)

Vasiliev, A. Yu; Tarkhov, A. E.; Menshikov, L. I.; Fedichev, P. O.; Fischer, Uwe R.

2014-05-01

We investigate the nature of the phase transition occurring in a planar XY-model spin system with dipole-dipole interactions. It is demonstrated that a Berezinskii-Kosterlitz-Thouless (BKT) type of phase transition always takes place at a finite temperature separating the ordered (ferro) and the disordered (para) phases. The low-temperature phase corresponds to an ordered state with thermal fluctuations, composed of a ‘gas’ of bound vortex-antivortex pairs, which would, when considered isolated, be characterized by a constant vortex-antivortex attraction force which is due to the dipolar interaction term in the Hamiltonian. Using a topological charge model, we show that small bound pairs are easily polarized, and screen the vortex-antivortex interaction in sufficiently large pairs. Screening changes the linear attraction potential of vortices to a logarithmic one, and leads to the familiar pair dissociation mechanism of the BKT type phase transition. The topological charge model is confirmed by numerical simulations, in which we demonstrate that the transition temperature slightly increases when compared with the BKT result for short-range interactions.

Cytonuclear interactions affect adaptive traits of the annual plant Arabidopsis thaliana in the field

PubMed Central

Roux, Fabrice; Mary-Huard, Tristan; Barillot, Elise; Wenes, Estelle; Botran, Lucy; Durand, Stéphanie; Villoutreix, Romain; Martin-Magniette, Marie-Laure; Camilleri, Christine; Budar, Françoise

2016-01-01

Although the contribution of cytonuclear interactions to plant fitness variation is relatively well documented at the interspecific level, the prevalence of cytonuclear interactions at the intraspecific level remains poorly investigated. In this study, we set up a field experiment to explore the range of effects that cytonuclear interactions have on fitness-related traits in Arabidopsis thaliana. To do so, we created a unique series of 56 cytolines resulting from cytoplasmic substitutions among eight natural accessions reflecting within-species genetic diversity. An assessment of these cytolines and their parental lines scored for 28 adaptive whole-organism phenotypes showed that a large proportion of phenotypic traits (23 of 28) were affected by cytonuclear interactions. The effects of these interactions varied from slight but frequent across cytolines to strong in some specific parental pairs. Two parental pairs accounted for half of the significant pairwise interactions. In one parental pair, Ct-1/Sha, we observed symmetrical phenotypic responses between the two nuclear backgrounds when combined with specific cytoplasms, suggesting nuclear differentiation at loci involved in cytonuclear epistasis. In contrast, asymmetrical phenotypic responses were observed in another parental pair, Cvi-0/Sha. In the Cvi-0 nuclear background, fecundity and phenology-related traits were strongly affected by the Sha cytoplasm, leading to a modified reproductive strategy without penalizing total seed production. These results indicate that natural variation in cytoplasmic and nuclear genomes interact to shape integrative traits that contribute to adaptation, thereby suggesting that cytonuclear interactions can play a major role in the evolutionary dynamics of A. thaliana. PMID:26979961

Core drug-drug interaction alerts for inclusion in pediatric electronic health records with computerized prescriber order entry.

PubMed

Harper, Marvin B; Longhurst, Christopher A; McGuire, Troy L; Tarrago, Rod; Desai, Bimal R; Patterson, Al

2014-03-01

The study aims to develop a core set of pediatric drug-drug interaction (DDI) pairs for which electronic alerts should be presented to prescribers during the ordering process. A clinical decision support working group composed of Children's Hospital Association (CHA) members was developed. CHA Pharmacists and Chief Medical Information Officers participated. Consensus was reached on a core set of 19 DDI pairs that should be presented to pediatric prescribers during the order process. We have provided a core list of 19 high value drug pairs for electronic drug-drug interaction alerts to be recommended for inclusion as high value alerts in prescriber order entry software used with a pediatric patient population. We believe this list represents the most important pediatric drug interactions for practical implementation within computerized prescriber order entry systems.

Role of 6-Mercaptopurine in the potential therapeutic targets DNA base pairs and G-quadruplex DNA: insights from quantum chemical and molecular dynamics simulations.

PubMed

Radhika, R; Shankar, R; Vijayakumar, S; Kolandaivel, P

2018-05-01

The theoretical studies on DNA with the anticancer drug 6-Mercaptopurine (6-MP) are investigated using theoretical methods to shed light on drug designing. Among the DNA base pairs considered, 6-MP is stacked with GC with the highest interaction energy of -46.19 kcal/mol. Structural parameters revealed that structure of the DNA base pairs is deviated from the planarity of the equilibrium position due to the formation of hydrogen bonds and stacking interactions with 6-MP. These deviations are verified through the systematic comparison between X-H bond contraction and elongation and the associated blue shift and red shift values by both NBO analysis and vibrational analysis. Bent's rule is verified for the C-H bond contraction in the 6-MP interacted base pairs. The AIM results disclose that the higher values of electron density (ρ) and Laplacian of electron density (∇ 2 ρ) indicate the increased overlap between the orbitals that represent the strong interaction and positive values of the total electron density show the closed-shell interaction. The relative sensitivity of the chemical shift values for the DNA base pairs with 6-MP is investigated to confirm the hydrogen bond strength. Molecular dynamics simulation studies of G-quadruplex DNA d(TGGGGT) 4 with 6-MP revealed that the incorporation of 6-MP appears to cause local distortions and destabilize the G-quadruplex DNA.

Rigid body formulation in a finite element context with contact interaction

NASA Astrophysics Data System (ADS)

Refachinho de Campos, Paulo R.; Gay Neto, Alfredo

2018-03-01

The present work proposes a formulation to employ rigid bodies together with flexible bodies in the context of a nonlinear finite element solver, with contact interactions. Inertial contributions due to distribution of mass of a rigid body are fully developed, considering a general pole position associated with a single node, representing a rigid body element. Additionally, a mechanical constraint is proposed to connect a rigid region composed by several nodes, which is useful for linking rigid/flexible bodies in a finite element environment. Rodrigues rotation parameters are used to describe finite rotations, by an updated Lagrangian description. In addition, the contact formulation entitled master-surface to master-surface is employed in conjunction with the rigid body element and flexible bodies, aiming to consider their interaction in a rigid-flexible multibody environment. New surface parameterizations are presented to establish contact pairs, permitting pointwise interaction in a frictional scenario. Numerical examples are provided to show robustness and applicability of the methods.

Generalized Bose-Einstein Condensation in Superconductivity

NASA Astrophysics Data System (ADS)

de Llano, Manuel

2011-03-01

Unification of the BCS and the Bose-Einstein condensation (BEC) theories is surveyed in detail via a generalized BEC (GBEC) finite-temperature statistical formalism. Its major difference with BCS theory is that it can be diagonalized exactly. Under specified conditions it yields the precise BCS gap equation for all temperatures as well as the precise BCS zero-temperature condensation energy for all couplings, thereby suggesting that a BCS condensate is a BE condensate in a ternary mixture of kinematically independent unpaired electrons coexisting with equally proportioned weakly-bound two-electron and two-hole Cooper pairs. Without abandoning the electron-phonon mechanism in moderately weak coupling it suffices, in principle, to reproduce the unusually high values of Tc (in units of the Fermi temperature TF) of 0.01-0.05 empirically reported in the so-called "exotic" superconductors of the Uemura plot, including cuprates, in contrast to the low values of Tc/TF ≤ 10-3 roughly reproduced by BCS theory for conventional (mostly elemental) superconductors. Replacing the characteristic phonon-exchange Debye temperature by a characteristic magnon-exchange one more than twice in size can lead to a simple interaction model associated with spin-fluctuation-mediated pairing.

Generalized Bose-Einstein Condensation in Superconductivity

NASA Astrophysics Data System (ADS)

de Llano, Manuel

Unification of the BCS and the Bose-Einstein condensation (BEC) theories is surveyed in detail via a generalized BEC (GBEC) finite-temperature statistical formalism. Its major difference with BCS theory is that it can be diagonalized exactly. Under specified conditions it yields the precise BCS gap equation for all temperatures as well as the precise BCS zero-temperature condensation energy for all couplings, thereby suggesting that a BCS condensate is a BE condensate in a ternary mixture of kinematically independent unpaired electrons coexisting with equally proportioned weakly-bound two-electron and two-hole Cooper pairs. Without abandoning the electron-phonon mechanism in moderately weak coupling it suffices, in principle, to reproduce the unusually high values of Tc (in units of the Fermi temperature TF) of 0.01-0.05 empirically reported in the so-called "exotic" superconductors of the Uemura plot, including cuprates, in contrast to the low values of Tc/TF ≤ 10-3 roughly reproduced by BCS theory for conventional (mostly elemental) superconductors. Replacing the characteristic phonon-exchange Debye temperature by a characteristic magnon-exchange one more than twice in size can lead to a simple interaction model associated with spin-fluctuation-mediated pairing.

Darboux transformation of the coupled nonisospectral Gross-Pitaevskii system and its multi-component generalization

NASA Astrophysics Data System (ADS)

Xu, Tao; Chen, Yong

2018-04-01

In this paper, we extend the one-component Gross-Pitaevskii (GP) equation to the two-component coupled GP system including damping term, linear and parabolic density profiles. The Lax pair with nonisospectral parameter and infinitely-many conservation laws of this coupled GP system are presented. Actually, the Darboux transformation (DT) for this kind of nonautonomous system is essentially different from the autonomous case. Consequently, we construct the DT of the coupled GP equations, besides, nonautonomous multi-solitons, one-breather and the first-order rogue wave are also obtained. Various kinds of one-soliton solution are constructed, which include stationary one-soliton and nonautonomous one-soliton propagating along the negative (positive) direction of x-axis. The interaction of two solitons and two-soliton bound state are demonstrated respectively. We get the nonautonomous one-breather on a curved background and this background is completely controlled by the parameter β. Using a limiting process, the nonautonomous first-order rogue wave can be obtained. Furthermore, some dynamic structures of these analytical solutions are discussed in detail. In addition, the multi-component generalization of GP equations are given, then the corresponding Lax pair and DT are also constructed.

Thermodynamic stability of Hoogsteen and Watson-Crick base pairs in the presence of histone H3-mimicking peptide.

PubMed

Pramanik, Smritimoy; Nakamura, Kaori; Usui, Kenji; Nakano, Shu-ichi; Saxena, Sarika; Matsui, Jun; Miyoshi, Daisuke; Sugimoto, Naoki

2011-03-14

We found that Hoogsteen base pairs were stabilized by molecular crowding and a histone H3-mimicking peptide, which was not observed for Watson-Crick base pairs. Our findings demonstrate that the type of DNA base pair is critical for the interaction between DNA and histones.

Vortex/boundary layer interactions

NASA Technical Reports Server (NTRS)

Cutler, A. D.; Bradshaw, P.

1989-01-01

Detailed and high quality measurements with hot-wires and pressure probes are presented for two different interactions between a vortex pair with common flow down and a turbulent boundary layer. The interactions studied have larger values of the vortex circulation parameter than those studied previously. The results indicate that the boundary layer under the vortex pair is thinned by lateral divergence and that boundary layer fluid is entrained into the vortex. The effect of the interaction on the vortex core (other than the inviscid effect of the image vortices behind the surface) is small.

Effective cluster interactions at alloy surfaces and charge self-consistency: Surface segregation in Ni-10 at. % Al and Cu-Ni

NASA Astrophysics Data System (ADS)

Schulthess, T.; Monnier, R.; Crampin, S.

1994-12-01

First-principles results are presented for the effective cluster interactions at the surface of a random Ni-10 at. % Al alloy. The derivation is based on an extension of the generalized perturbation method to semi-infinite inhomogeneous binary alloys, using a layer version of the Korringa-Kohn-Rostocker multiple-scattering approach in conjunction with the single-site coherent potential approximation to compute the self-consistent electronic structure of the system. When applied to the bulk, the method yields effective pair interactions that have the full point-group symmetry of the lattice to a very high level of numerical accuracy, despite the fact that intra- and interlayer couplings (scattering-path operators) are treated differently, and which are in perfect agreement with those of a recent three-dimensional treatment. Besides the pair terms, a selected class of triplet and quadruplet interactions are calculated, as well as the point interactions induced by the presence of the surface. The value of the latter in the first lattice plane is strongly exaggerated in our approach, leading to a complete segregation of the minority species to the surface. Using a value corresponding to the difference in the surface energies of the pure components for this term leads to the observed Al concentration of ~=25% at the surface. Possible reasons for the shortcomings of the theory are analyzed, and test calculations for the well studied Cu-Ni system show that the free energy of the semi-infinite alloy cannot be approximated by the sum over the single-particle band energies, once charge self-consistency is enforced at the surface.

Coherent vs. incoherent pairing in 2D systems near magnetic instability

NASA Astrophysics Data System (ADS)

Abanov, Ar.; Chubukov, A. V.; Finkel'stein, A. M.

2001-05-01

We study the superconductivity in 2D fermionic systems near antiferromagnetic instability, assuming that the pairing is mediated by spin fluctuations. This pairing involves fully incoherent fermions and diffusive spin excitations. We show that the competition between fermionic incoherence and strong pairing interaction yields the pairing instability temperature Tins which increases and saturates as the magnetic correlation length ξ → ∞. We argue that in this quantum-critical regime the pairing problem is qualitatively different from the BCS one.

Evolutionary games with coordination and self-dependent interactions

NASA Astrophysics Data System (ADS)

Király, Balázs; Szabó, György

2017-01-01

Multistrategy evolutionary games are studied on a square lattice when the pair interactions are composed of coordinations between strategy pairs and an additional term with self-dependent payoff. We describe a method for determining the strength of each elementary coordination component in n -strategy potential games. Using analytical and numerical methods, the presence and absence of Ising-type order-disorder phase transitions are studied when a single pair coordination is extended by some types of self-dependent elementary games. We also introduce noise-dependent three-strategy equivalents of the n -strategy elementary coordination games.

Evolutionary games combining two or three pair coordinations on a square lattice

NASA Astrophysics Data System (ADS)

Király, Balázs; Szabó, György

2017-10-01

We study multiagent logit-rule-driven evolutionary games on a square lattice whose pair interactions are composed of a maximal number of nonoverlapping elementary coordination games describing Ising-type interactions between just two of the available strategies. Using Monte Carlo simulations we investigate the macroscopic noise-level-dependent behavior of the two- and three-pair games and the critical properties of the continuous phase transtitions these systems exhibit. The four-strategy game is shown to be equivalent to a system that consists of two independent and identical Ising models.

Evolutionary games combining two or three pair coordinations on a square lattice.

PubMed

Király, Balázs; Szabó, György

2017-10-01

We study multiagent logit-rule-driven evolutionary games on a square lattice whose pair interactions are composed of a maximal number of nonoverlapping elementary coordination games describing Ising-type interactions between just two of the available strategies. Using Monte Carlo simulations we investigate the macroscopic noise-level-dependent behavior of the two- and three-pair games and the critical properties of the continuous phase transtitions these systems exhibit. The four-strategy game is shown to be equivalent to a system that consists of two independent and identical Ising models.

Competition in saccade target selection reveals attentional guidance by simultaneously active working memory representations.

PubMed

Beck, Valerie M; Hollingworth, Andrew

2017-02-01

The content of visual working memory (VWM) guides attention, but whether this interaction is limited to a single VWM representation or functional for multiple VWM representations is under debate. To test this issue, we developed a gaze-contingent search paradigm to directly manipulate selection history and examine the competition between multiple cue-matching saccade target objects. Participants first saw a dual-color cue followed by two pairs of colored objects presented sequentially. For each pair, participants selectively fixated an object that matched one of the cued colors. Critically, for the second pair, the cued color from the first pair was presented either with a new distractor color or with the second cued color. In the latter case, if two cued colors in VWM interact with selection simultaneously, we expected the second cued color object to generate substantial competition for selection, even though the first cued color was used to guide attention in the immediately previous pair. Indeed, in the second pair, selection probability of the first cued color was substantially reduced in the presence of the second cued color. This competition between cue-matching objects provides strong evidence that both VWM representations interacted simultaneously with selection. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Discovering Implicit Entity Relation with the Gene-Citation-Gene Network

PubMed Central

Song, Min; Han, Nam-Gi; Kim, Yong-Hwan; Ding, Ying; Chambers, Tamy

2013-01-01

In this paper, we apply the entitymetrics model to our constructed Gene-Citation-Gene (GCG) network. Based on the premise there is a hidden, but plausible, relationship between an entity in one article and an entity in its citing article, we constructed a GCG network of gene pairs implicitly connected through citation. We compare the performance of this GCG network to a gene-gene (GG) network constructed over the same corpus but which uses gene pairs explicitly connected through traditional co-occurrence. Using 331,411 MEDLINE abstracts collected from 18,323 seed articles and their references, we identify 25 gene pairs. A comparison of these pairs with interactions found in BioGRID reveal that 96% of the gene pairs in the GCG network have known interactions. We measure network performance using degree, weighted degree, closeness, betweenness centrality and PageRank. Combining all measures, we find the GCG network has more gene pairs, but a lower matching rate than the GG network. However, combining top ranked genes in both networks produces a matching rate of 35.53%. By visualizing both the GG and GCG networks, we find that cancer is the most dominant disease associated with the genes in both networks. Overall, the study indicates that the GCG network can be useful for detecting gene interaction in an implicit manner. PMID:24358368

Node similarity within subgraphs of protein interaction networks

NASA Astrophysics Data System (ADS)

Penner, Orion; Sood, Vishal; Musso, Gabriel; Baskerville, Kim; Grassberger, Peter; Paczuski, Maya

2008-06-01

We propose a biologically motivated quantity, twinness, to evaluate local similarity between nodes in a network. The twinness of a pair of nodes is the number of connected, labeled subgraphs of size n in which the two nodes possess identical neighbours. The graph animal algorithm is used to estimate twinness for each pair of nodes (for subgraph sizes n=4 to n=12) in four different protein interaction networks (PINs). These include an Escherichia coli PIN and three Saccharomyces cerevisiae PINs - each obtained using state-of-the-art high-throughput methods. In almost all cases, the average twinness of node pairs is vastly higher than that expected from a null model obtained by switching links. For all n, we observe a difference in the ratio of type A twins (which are unlinked pairs) to type B twins (which are linked pairs) distinguishing the prokaryote E. coli from the eukaryote S. cerevisiae. Interaction similarity is expected due to gene duplication, and whole genome duplication paralogues in S. cerevisiae have been reported to co-cluster into the same complexes. Indeed, we find that these paralogous proteins are over-represented as twins compared to pairs chosen at random. These results indicate that twinness can detect ancestral relationships from currently available PIN data.

Distinct neuronal interactions in anterior inferotemporal areas of macaque monkeys during retrieval of object association memory.

PubMed

Hirabayashi, Toshiyuki; Tamura, Keita; Takeuchi, Daigo; Takeda, Masaki; Koyano, Kenji W; Miyashita, Yasushi

2014-07-09

In macaque monkeys, the anterior inferotemporal cortex, a region crucial for object memory processing, is composed of two adjacent, hierarchically distinct areas, TE and 36, for which different functional roles and neuronal responses in object memory tasks have been characterized. However, it remains unknown how the neuronal interactions differ between these areas during memory retrieval. Here, we conducted simultaneous recordings from multiple single-units in each of these areas while monkeys performed an object association memory task and examined the inter-area differences in neuronal interactions during the delay period. Although memory neurons showing sustained activity for the presented cue stimulus, cue-holding (CH) neurons, interacted with each other in both areas, only those neurons in area 36 interacted with another type of memory neurons coding for the to-be-recalled paired associate (pair-recall neurons) during memory retrieval. Furthermore, pairs of CH neurons in area TE showed functional coupling in response to each individual object during memory retention, whereas the same class of neuron pairs in area 36 exhibited a comparable strength of coupling in response to both associated objects. These results suggest predominant neuronal interactions in area 36 during the mnemonic processing, which may underlie the pivotal role of this brain area in both storage and retrieval of object association memory. Copyright © 2014 the authors 0270-6474/14/349377-12$15.00/0.

Computational prediction of host-pathogen protein-protein interactions.

PubMed

Dyer, Matthew D; Murali, T M; Sobral, Bruno W

2007-07-01

Infectious diseases such as malaria result in millions of deaths each year. An important aspect of any host-pathogen system is the mechanism by which a pathogen can infect its host. One method of infection is via protein-protein interactions (PPIs) where pathogen proteins target host proteins. Developing computational methods that identify which PPIs enable a pathogen to infect a host has great implications in identifying potential targets for therapeutics. We present a method that integrates known intra-species PPIs with protein-domain profiles to predict PPIs between host and pathogen proteins. Given a set of intra-species PPIs, we identify the functional domains in each of the interacting proteins. For every pair of functional domains, we use Bayesian statistics to assess the probability that two proteins with that pair of domains will interact. We apply our method to the Homo sapiens-Plasmodium falciparum host-pathogen system. Our system predicts 516 PPIs between proteins from these two organisms. We show that pairs of human proteins we predict to interact with the same Plasmodium protein are close to each other in the human PPI network and that Plasmodium pairs predicted to interact with same human protein are co-expressed in DNA microarray datasets measured during various stages of the Plasmodium life cycle. Finally, we identify functionally enriched sub-networks spanned by the predicted interactions and discuss the plausibility of our predictions. Supplementary data are available at http://staff.vbi.vt.edu/dyermd/publications/dyer2007a.html. Supplementary data are available at Bioinformatics online.

Ionic and Covalent Stabilization of Intermediates and Transition States in Catalysis by Solid Acids

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

Deshlahra, Prashant; Carr, Robert T.; Iglesia, Enrique

Reactivity descriptors describe catalyst properties that determine the stability of kinetically relevant transition states and adsorbed intermediates. Theoretical descriptors, such as deprotonation energies (DPE), rigorously account for Brønsted acid strength for catalytic solids with known structure. Here, mechanistic interpretations of methanol dehydration turnover rates are used to assess how charge reorganization (covalency) and electrostatic interactions determine DPE and how such interactions are recovered when intermediates and transition states interact with the conjugate anion in W and Mo polyoxometalate (POM) clusters and gaseous mineral acids. Turnover rates are lower and kinetically relevant species are less stable on Mo than W POMmore » clusters with similar acid strength, and such species are more stable on mineral acids than that predicted from W-POM DPE–reactivity trends, indicating that DPE and acid strength are essential but incomplete reactivity descriptors. Born–Haber thermochemical cycles indicate that these differences reflect more effective charge reorganization upon deprotonation of Mo than W POM clusters and the much weaker reorganization in mineral acids. Such covalency is disrupted upon deprotonation but cannot be recovered fully upon formation of ion pairs at transition states. Predictive descriptors of reactivity for general classes of acids thus require separate assessments of the covalent and ionic DPE components. Here, we describe methods to estimate electrostatic interactions, which, taken together with energies derived from density functional theory, give the covalent and ionic energy components of protons, intermediates, and transition states. In doing so, we provide a framework to predict the reactive properties of protons for chemical reactions mediated by ion-pair transition states.« less

Molecular dynamics studies on troponin (TnI-TnT-TnC) complexes: insight into the regulation of muscle contraction.

PubMed

Varughese, Jayson F; Chalovich, Joseph M; Li, Yumin

2010-10-01

Mutations of any subunit of the troponin complex may lead to serious disorders. Rational approaches to managing these disorders require knowledge of the complex interactions among the three subunits that are required for proper function. Molecular dynamics (MD) simulations were performed for both skeletal (sTn) and cardiac (cTn) troponin. The interactions and correlated motions among the three components of the troponin complex were analyzed using both Molecular Mechanics-Generalized Born Surface Area (MMGBSA) and cross-correlation techniques. The TnTH2 helix was strongly positively correlated with the two long helices of TnI. The C domain of TnC was positively correlated with TnI and TnT. The N domain of TnC was negatively correlated with TnI and TnT in cTn, but not in sTn. The two C-domain calcium-binding sites of TnC were dynamically correlated. The two regulatory N-domain calcium-binding sites of TnC were dynamically correlated, even though the calcium-binding site I is dysfunctional. The strong interaction residue pairs and the strong dynamically correlated residues pairs among the three components of troponin complexes were identified. These correlated motions are consistent with the idea that there is a high degree of cooperativity among the components of the regulatory complex in response to Ca(2+) and other effectors. This approach may give insight into the mechanism by which mutations of troponin cause disease. It is interesting that some observed disease causing mutations fall within regions of troponin that are strongly correlated or interacted.

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

Isobe, Hiroki; Fu, Liang

Here, we study the pairing symmetry of the interlayer paired state of composite fermions in quantum Hall bilayers. Based on the Halperin-Lee-Read (HLR) theory, the effect of the long-range Coulomb interaction and the internal Chern-Simons gauge fluctuation is analyzed with the random-phase approximation beyond the leading order contribution in small momentum expansion, and we observe that the interlayer paired states with a relative angular momentummore » $l=+1$ are energetically favored for filling ν=$$\\frac{1}2$$+$$\\frac{1}2$$ and $$\\frac{1}4$$+$$\\frac{1}4$$. The degeneracy between states with $±l$ is lifted by the interlayer density-current interaction arising from the interplay of the long-range Coulomb interaction and the Chern-Simons term in the HLR theory.« less

New Patterns of Activity in a Pair of Interacting Excitatory-Inhibitory Neural Fields

NASA Astrophysics Data System (ADS)

Folias, S. E.; Ermentrout, G. B.

2011-11-01

In this Letter, we study stationary bump solutions in a pair of interacting excitatory-inhibitory (E-I) neural fields in one dimension. We demonstrate the existence of localized bump solutions of persistent activity that can be maintained by the pair of interacting layers when a stationary bump is not supported by either layer in isolation—a scenario which may be relevant as a mechanism for the persistent activity associated with working memory in the prefrontal cortex and may explain why bumps are not seen in in vitro slice preparations. Furthermore, we describe a new type of stationary bump solution arising from a pitchfork bifurcation which produces a stationary bump in each layer with a spatial offset that increases with the bifurcation parameter.

Spatial Imaging of Strongly Interacting Rydberg Atoms

NASA Astrophysics Data System (ADS)

Thaicharoen, Nithiwadee

The strong interactions between Rydberg excitations can result in spatial correlations between the excitations. The ability to control the interaction strength and the correlations between Rydberg atoms is applicable in future technological implementations of quantum computation. In this thesis, I investigates how both the character of the Rydberg-Rydberg interactions and the details of the excitation process affect the nature of the spatial correlations and the evolution of those correlations in time. I first describes the experimental apparatus and methods used to perform high-magnification Rydberg-atom imaging, as well as three experiments in which these methods play an important role. The obtained Rydberg-atom positions reveal the correlations in the many-body Rydberg-atom system and their time dependence with sub-micron spatial resolution. In the first experiment, atoms are excited to a Rydberg state that experiences a repulsive van der Waals interaction. The Rydberg excitations are prepared with a well-defined initial separation, and the effect of van der Waals forces is observed by tracking the interatomic distance between the Rydberg atoms. The atom trajectories and thereby the interaction coefficient C6 are extracted from the pair correlation functions of the Rydberg atom positions. In the second experiment, the Rydberg atoms are prepared in a highly dipolar state by using adiabatic state transformation. The atom-pair kinetics that follow from the strong dipole-dipole interactions are observed. The pair correlation results provide the first direct visualization of the electric-dipole interaction and clearly exhibit its anisotropic nature. In both the first and the second experiment, results of semi-classical simulations of the atom-pair trajectories agree well with the experimental data. In the analysis, I use energy conservation and measurements of the initial positions and the terminal velocities of the atom pairs to extract the C6 and C 3 interaction coefficients. The final experiment demonstrates the ability to enhance or suppress the degree of spatial correlation in a system of Rydberg excitations, using a rotary-echo excitation process in concert with particular excitation laser detunings. The work in this thesis demonstrates an ability to control long-range interactions between Rydberg atoms, which paves the way towards preparing and studying increasingly complex many-body systems.

Unidirectional adaptation in tempo in pairs of chimpanzees during simultaneous tapping movement: an examination under face-to-face setup.

PubMed

Yu, Lira; Tomonaga, Masaki

2016-04-01

Many studies have reported a spontaneous nature to synchronized movement in humans and in non-human primates. However, it is not yet clear whether individuals mutually adapt their movement to each other or whether one individual significantly changes to synchronize with the other. In the current study, we examined a directionality of the tempo adaptation to understand an introductive process of interactional synchrony in pairs of chimpanzees. Four pairs, consisting of five female chimpanzees, produced a finger-tapping movement under a face-to-face experimental setup where both auditory and visual cues of the partner's movement were available. Two test conditions were prepared: alone and paired. An analysis of the tapping tempo depending on condition showed that only one chimpanzee in each pair significantly changed their tapping tempo in the direction of the partner's tapping tempo in the paired condition compared with the alone condition. The current study demonstrated that unidirectional adaptation in tempo occurs in pairs of chimpanzees when they simultaneously produce the tapping movement under auditory and visual interaction.

Dopamine and opioid systems interact within the nucleus accumbens to maintain monogamous pair bonds

PubMed Central

Resendez, Shanna L; Keyes, Piper C; Day, Jeremy J; Hambro, Caely; Austin, Curtis J; Maina, Francis K; Eidson, Lori N; Porter-Stransky, Kirsten A; Nevárez, Natalie; McLean, J William; Kuhnmuench, Morgan A; Murphy, Anne Z; Mathews, Tiffany A; Aragona, Brandon J

2016-01-01

Prairie vole breeder pairs form monogamous pair bonds, which are maintained through the expression of selective aggression toward novel conspecifics. Here, we utilize behavioral and anatomical techniques to extend the current understanding of neural mechanisms that mediate pair bond maintenance. For both sexes, we show that pair bonding up-regulates mRNA expression for genes encoding D1-like dopamine (DA) receptors and dynorphin as well as enhances stimulated DA release within the nucleus accumbens (NAc). We next show that D1-like receptor regulation of selective aggression is mediated through downstream activation of kappa-opioid receptors (KORs) and that activation of these receptors mediates social avoidance. Finally, we also identified sex-specific alterations in KOR binding density within the NAc shell of paired males and demonstrate that this alteration contributes to the neuroprotective effect of pair bonding against drug reward. Together, these findings suggest motivational and valence processing systems interact to mediate the maintenance of social bonds. DOI: http://dx.doi.org/10.7554/eLife.15325.001 PMID:27371827

Intracortical pathways mediate nonlinear fast oscillation (>200 Hz) interactions within rat barrel cortex.

PubMed

Staba, Richard J; Ard, Tyler D; Benison, Alexander M; Barth, Daniel S

2005-05-01

Whisker evoked fast oscillations (FOs; >200 Hz) within the rodent posteromedial barrel subfield are thought to reflect very rapid integration of multiwhisker stimuli, yet the pathways mediating FO interactions remain unclear and may involve interactions within thalamus and/or cortex. In the present study using anesthetized rats, a cortical incision was made between sites representing the stimulated whiskers to determine how intracortical networks contributed to patterns of FOs. With cortex intact, simultaneous stimulation of a pair of whiskers aligned in a row evoked supralinear responses between sites separated by several millimeters. In contrast, stimulation of a nonadjacent pair of whiskers within an arc evoked FOs with no evidence for nonlinear interactions. However, stimulation of an adjacent pair of whiskers in an arc did evoke supralinear responses. After a cortical cut, supralinear interactions associated with FOs within a row were lost. These data indicate a distinct bias for stronger long-range connectivity that extends along barrel rows and that horizontal intracortical pathways exclusively mediate FO-related integration of tactile information.

Verbal play as a discourse resource in the social interactions of older and younger communication pairs.

PubMed

Shune, Samantha; Duff, Melissa Collins

2014-01-01

Verbal play, or the playful manipulation of elements of language, is a pervasive component of social interaction, serving important interpersonal functions. We analyzed verbal play in the interactional discourse of ten healthy younger pairs and ten healthy older pairs as they completed a collaborative referencing task. A total of 1,893 verbal play episodes were coded. While there were no group differences in verbal play frequency, age-related differences in the quality and function of these episodes emerged. While older participants engaged in more complex, extended, and reciprocal episodes that supported the social nature of communicative interactions (e.g., teasing), younger participants were more likely to engage in verbal play episodes for the purpose of successful task completion. Despite these age-related variations in the deployment of verbal play, verbal play is a robust interactional discourse resource in healthy aging, highlighting an element of human cognition that does not appear to decline with age.

Verbal play as a discourse resource in the social interactions of older and younger communication pairs

PubMed Central

Shune, Samantha; Duff, Melissa Collins

2014-01-01

Verbal play, or the playful manipulation of elements of language, is a pervasive component of social interaction, serving important interpersonal functions. We analyzed verbal play in the interactional discourse of ten healthy younger pairs and ten healthy older pairs as they completed a collaborative referencing task. A total of 1,893 verbal play episodes were coded. While there were no group differences in verbal play frequency, age-related differences in the quality and function of these episodes emerged. While older participants engaged in more complex, extended, and reciprocal episodes that supported the social nature of communicative interactions (e.g., teasing), younger participants were more likely to engage in verbal play episodes for the purpose of successful task completion. Despite these age-related variations in the deployment of verbal play, verbal play is a robust interactional discourse resource in healthy aging, highlighting an element of human cognition that does not appear to decline with age. PMID:25485072

Ecology of dark matter haloes - II. Effects of interactions on the alignment of halo pairs

NASA Astrophysics Data System (ADS)

L'Huillier, Benjamin; Park, Changbom; Kim, Juhan

2017-04-01

We use the Horizon Run 4 cosmological N-body simulation to study the effects of distant and close interactions on the alignments of the shapes, spins and orbits of targets haloes with their neighbours, and their dependence on the local density environment and neighbour separation. Interacting targets have a significantly lower spin and higher sphericity and oblateness than all targets. Interacting pairs initially have antiparallel spins, but the spins develop parallel alignment as time goes on. Neighbours tend to evolve in the plane of rotation of the target, and in the direction of the major axis of prolate haloes. Moreover, interactions are preferentially radial, while pairs with non-radial orbits are preferentially prograde. The alignment signals are stronger at high mass and for close separations, and independent of the large-scale density. Positive alignment signals are found at redshifts up to 4, and increase with decreasing redshifts. Moreover, the orbits tend to become prograde at low redshift, while no alignment is found at high redshift (z = 4).

Majorana Kramers pairs in Rashba double nanowires with interactions and disorder

NASA Astrophysics Data System (ADS)

Thakurathi, Manisha; Simon, Pascal; Mandal, Ipsita; Klinovaja, Jelena; Loss, Daniel

2018-01-01

We analyze the effects of electron-electron interactions and disorder on a Rashba double-nanowire setup coupled to an s -wave superconductor, which has been recently proposed as a versatile platform to generate Kramers pairs of Majorana bound states in the absence of magnetic fields. We identify the regime of parameters for which these Kramers pairs are stable against interaction and disorder effects. We use bosonization, perturbative renormalization group, and replica techniques to derive the flow equations for various parameters of the model and evaluate the corresponding phase diagram with topological and disorder-dominated phases. We confirm aforementioned results by considering a more microscopic approach, which starts from the tunneling Hamiltonian between the three-dimensional s -wave superconductor and the nanowires. We find again that the interaction drives the system into the topological phase and, as the strength of the source term coming from the tunneling Hamiltonian increases, strong electron-electron interactions are required to reach the topological phase.

Interaction, coalescence, and collapse of localized patterns in a quasi-one-dimensional system of interacting particles

NASA Astrophysics Data System (ADS)

Dessup, Tommy; Coste, Christophe; Saint Jean, Michel

2017-01-01

We study the path toward equilibrium of pairs of solitary wave envelopes (bubbles) that modulate a regular zigzag pattern in an annular channel. We evidence that bubble pairs are metastable states, which spontaneously evolve toward a stable single bubble. We exhibit the concept of topological frustration of a bubble pair. A configuration is frustrated when the particles between the two bubbles are not organized in a modulated staggered row. For a nonfrustrated (NF) bubble pair configuration, the bubbles interaction is attractive, whereas it is repulsive for a frustrated (F) configuration. We describe a model of interacting solitary wave that provides all qualitative characteristics of the interaction force: It is attractive for NF systems and repulsive for F systems and decreases exponentially with the bubbles distance. Moreover, for NF systems, the bubbles come closer and eventually merge as a single bubble, in a coalescence process. We also evidence a collapse process, in which one bubble shrinks in favor of the other one, overcoming an energetic barrier in phase space. This process is relevant for both NF systems and F systems. In NF systems, the coalescence prevails at low temperature, whereas thermally activated jumps make the collapse prevail at high temperature. In F systems, the path toward equilibrium involves a collapse process regardless of the temperature.

Statistical models for detecting differential chromatin interactions mediated by a protein.

PubMed

Niu, Liang; Li, Guoliang; Lin, Shili

2014-01-01

Chromatin interactions mediated by a protein of interest are of great scientific interest. Recent studies show that protein-mediated chromatin interactions can have different intensities in different types of cells or in different developmental stages of a cell. Such differences can be associated with a disease or with the development of a cell. Thus, it is of great importance to detect protein-mediated chromatin interactions with different intensities in different cells. A recent molecular technique, Chromatin Interaction Analysis by Paired-End Tag Sequencing (ChIA-PET), which uses formaldehyde cross-linking and paired-end sequencing, is able to detect genome-wide chromatin interactions mediated by a protein of interest. Here we proposed two models (One-Step Model and Two-Step Model) for two sample ChIA-PET count data (one biological replicate in each sample) to identify differential chromatin interactions mediated by a protein of interest. Both models incorporate the data dependency and the extent to which a fragment pair is related to a pair of DNA loci of interest to make accurate identifications. The One-Step Model makes use of the data more efficiently but is more computationally intensive. An extensive simulation study showed that the models can detect those differentially interacted chromatins and there is a good agreement between each classification result and the truth. Application of the method to a two-sample ChIA-PET data set illustrates its utility. The two models are implemented as an R package MDM (available at http://www.stat.osu.edu/~statgen/SOFTWARE/MDM).

Statistical Models for Detecting Differential Chromatin Interactions Mediated by a Protein

PubMed Central

Niu, Liang; Li, Guoliang; Lin, Shili

2014-01-01

Chromatin interactions mediated by a protein of interest are of great scientific interest. Recent studies show that protein-mediated chromatin interactions can have different intensities in different types of cells or in different developmental stages of a cell. Such differences can be associated with a disease or with the development of a cell. Thus, it is of great importance to detect protein-mediated chromatin interactions with different intensities in different cells. A recent molecular technique, Chromatin Interaction Analysis by Paired-End Tag Sequencing (ChIA-PET), which uses formaldehyde cross-linking and paired-end sequencing, is able to detect genome-wide chromatin interactions mediated by a protein of interest. Here we proposed two models (One-Step Model and Two-Step Model) for two sample ChIA-PET count data (one biological replicate in each sample) to identify differential chromatin interactions mediated by a protein of interest. Both models incorporate the data dependency and the extent to which a fragment pair is related to a pair of DNA loci of interest to make accurate identifications. The One-Step Model makes use of the data more efficiently but is more computationally intensive. An extensive simulation study showed that the models can detect those differentially interacted chromatins and there is a good agreement between each classification result and the truth. Application of the method to a two-sample ChIA-PET data set illustrates its utility. The two models are implemented as an R package MDM (available at http://www.stat.osu.edu/~statgen/SOFTWARE/MDM). PMID:24835279

Pairing in a dry Fermi sea

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

Maier, Thomas A.; Staar, Peter; Mishra, V.

In the traditional Bardeen–Cooper–Schrieffer theory of superconductivity, the amplitude for the propagation of a pair of electrons with momentum k and -k has a log singularity as the temperature decreases. This so-called Cooper instability arises from the presence of an electron Fermi sea. It means that an attractive interaction, no matter how weak, will eventually lead to a pairing instability. However, in the pseudogap regime of the cuprate superconductors, where parts of the Fermi surface are destroyed, this log singularity is suppressed, raising the question of how pairing occurs in the absence of a Fermi sea. In this paper, wemore » report Hubbard model numerical results and the analysis of angular-resolved photoemission experiments on a cuprate superconductor. Finally, in contrast to the traditional theory, we find that in the pseudogap regime the pairing instability arises from an increase in the strength of the spin–fluctuation pairing interaction as the temperature decreases rather than the Cooper log instability.« less

Pairing in a dry Fermi sea

DOE PAGES

Maier, Thomas A.; Staar, Peter; Mishra, V.; ...

2016-06-17

In the traditional Bardeen–Cooper–Schrieffer theory of superconductivity, the amplitude for the propagation of a pair of electrons with momentum k and -k has a log singularity as the temperature decreases. This so-called Cooper instability arises from the presence of an electron Fermi sea. It means that an attractive interaction, no matter how weak, will eventually lead to a pairing instability. However, in the pseudogap regime of the cuprate superconductors, where parts of the Fermi surface are destroyed, this log singularity is suppressed, raising the question of how pairing occurs in the absence of a Fermi sea. In this paper, wemore » report Hubbard model numerical results and the analysis of angular-resolved photoemission experiments on a cuprate superconductor. Finally, in contrast to the traditional theory, we find that in the pseudogap regime the pairing instability arises from an increase in the strength of the spin–fluctuation pairing interaction as the temperature decreases rather than the Cooper log instability.« less

Binding in pair potentials of liquid simple metals from nonlocality in electronic kinetic energy

NASA Technical Reports Server (NTRS)

Perrot, F.; March, N. H.

1990-01-01

The paper presents an explicit expression for the pair potential in liquid simple metals from low-order density-gradient theory when the superposition of single-center displaced charges is employed. Numerical results are presented for the gradient expansion pair interaction in liquid Na and Be. The low-order density-gradient equation for the pair potential is presented.

Fourier decomposition of payoff matrix for symmetric three-strategy games.

PubMed

Szabó, György; Bodó, Kinga S; Allen, Benjamin; Nowak, Martin A

2014-10-01

In spatial evolutionary games the payoff matrices are used to describe pair interactions among neighboring players located on a lattice. Now we introduce a way how the payoff matrices can be built up as a sum of payoff components reflecting basic symmetries. For the two-strategy games this decomposition reproduces interactions characteristic to the Ising model. For the three-strategy symmetric games the Fourier components can be classified into four types representing games with self-dependent and cross-dependent payoffs, variants of three-strategy coordinations, and the rock-scissors-paper (RSP) game. In the absence of the RSP component the game is a potential game. The resultant potential matrix has been evaluated. The general features of these systems are analyzed when the game is expressed by the linear combinations of these components.

Exact solution of CKP equation and formation and interaction of two solitons in pair-ion-electron plasma

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

Batool, Nazia; Jahangir, R.; National Center of Physics

In the present investigation, cylindrical Kadomstev-Petviashvili (CKP) equation is derived in pair-ion-electron plasmas to study the propagation and interaction of two solitons. Using a novel gauge transformation, two soliton solutions of CKP equation are found analytically by using Hirota's method and to the best of our knowledge have been used in plasma physics for the first time. Interestingly, it is observed that unlike the planar Kadomstev-Petviashvili (KP) equation, the CKP equation admits horseshoe-like solitary structures. Another non-trivial feature of CKP solitary solution is that the interaction parameter gets modified by the plasma parameters contrary to the one obtained for Korteweg–demore » Vries equation. The importance of the present investigation to understand the formation and interaction of solitons in laboratory produced pair plasmas is also highlighted.« less

Accurate prediction of protein–protein interactions from sequence alignments using a Bayesian method

PubMed Central

Burger, Lukas; van Nimwegen, Erik

2008-01-01

Accurate and large-scale prediction of protein–protein interactions directly from amino-acid sequences is one of the great challenges in computational biology. Here we present a new Bayesian network method that predicts interaction partners using only multiple alignments of amino-acid sequences of interacting protein domains, without tunable parameters, and without the need for any training examples. We first apply the method to bacterial two-component systems and comprehensively reconstruct two-component signaling networks across all sequenced bacteria. Comparisons of our predictions with known interactions show that our method infers interaction partners genome-wide with high accuracy. To demonstrate the general applicability of our method we show that it also accurately predicts interaction partners in a recent dataset of polyketide synthases. Analysis of the predicted genome-wide two-component signaling networks shows that cognates (interacting kinase/regulator pairs, which lie adjacent on the genome) and orphans (which lie isolated) form two relatively independent components of the signaling network in each genome. In addition, while most genes are predicted to have only a small number of interaction partners, we find that 10% of orphans form a separate class of ‘hub' nodes that distribute and integrate signals to and from up to tens of different interaction partners. PMID:18277381

The genetic links between the big five personality traits and general interest domains.

PubMed

Kandler, Christian; Bleidorn, Wiebke; Riemann, Rainer; Angleitner, Alois; Spinath, Frank M

2011-12-01

This is the first genetically informative study in which multiple informants were used to quantify the genetic and environmental sources of individual differences in general interests as well as the phenotypic and genetic links between general interests and Big Five personality traits. Self-reports and two peer ratings from 844 individuals, including 225 monozygotic and 113 dizygotic complete twin pairs, were collected. Multiple-rater scores (composites) revealed that the averaged levels of genetic and environmental effects on seven broad interest domains were similar to those on personality traits. Multivariate analyses showed that about 35% of the genetic and 9% of the environmental variance in interests were explained by personality domains, in particular by Openness. The findings suggest that interests cannot easily be considered as a byproduct of the interactions between personality genotypes and the environmental influences but rather as an internal regulation of behavior with an own genetic basis.

Practical sliced configuration spaces for curved planar pairs

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

Sacks, E.

1999-01-01

In this article, the author presents a practical configuration-space computation algorithm for pairs of curved planar parts, based on the general algorithm developed by Bajaj and the author. The general algorithm advances the theoretical understanding of configuration-space computation, but is too slow and fragile for some applications. The new algorithm solves these problems by restricting the analysis to parts bounded by line segments and circular arcs, whereas the general algorithm handles rational parametric curves. The trade-off is worthwhile, because the restricted class handles most robotics and mechanical engineering applications. The algorithm reduces run time by a factor of 60 onmore » nine representative engineering pairs, and by a factor of 9 on two human-knee pairs. It also handles common special pairs by specialized methods. A survey of 2,500 mechanisms shows that these methods cover 90% of pairs and yield an additional factor of 10 reduction in average run time. The theme of this article is that application requirements, as well as intrinsic theoretical interest, should drive configuration-space research.« less

Helical peptides with three pairs of Asp-Arg and Glu-Arg residues in different orientations and spacings.

PubMed Central

Huyghues-Despointes, B. M.; Scholtz, J. M.; Baldwin, R. L.

1993-01-01

The helix-stabilizing effects of repeating pairs of Asp-Arg and Glu-Arg residues have been characterized using a peptide system of the same design used earlier to study Glu-Lys (Marqusee, S. & Baldwin, R.L., 1987, Proc. Natl. Acad. Sci. USA 84, 8898-8902) and Asp-Lys ion pairs (Marqusee, S. & Baldwin, R.L., 1990, In Protein Folding [Gierasch, L.M. & King, J., Eds.], pp. 85-94, AAAS, Washington, D.C.). The consequences of breaking ion pair and charge-helix dipole interactions by titration to pH 2 have been compared with the results of screening these interactions with NaCl at pH 7.0 and pH 2.5. The four peptides in each set contain three pairs of acidic (A) and basic (B) residues spaced either i, i + 4 or i, i + 3 apart. In one peptide of each kind the pairwise order of residues is AB, with the charges oriented favorably to the helix macrodipole, and in the other peptide the order is BA. The results are as follows: (1) Remarkably, both Asp-Arg and Glu-Arg peptides show the same pattern of helix stabilization at pH 7.0 found earlier for Glu-Lys and Asp-Lys peptides: i + 4 AB > i + 4 BA approximately i + 3 AB > i + 3 BA. (2) The ion pairs and charge-helix dipole interactions cannot be cleanly separated, but the results suggest that both interactions make important contributions to helix stability.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:8443591

How Mg2+ ion and water network affect the stability and structure of non-Watson-Crick base pairs in E. coli loop E of 5S rRNA: a molecular dynamics and reference interaction site model (RISM) study.

PubMed

Shanker, Sudhanshu; Bandyopadhyay, Pradipta

2017-08-01

The non-Watson-Crick (non-WC) base pairs of Escherichia coli loop E of 5S rRNA are stabilized by Mg 2+ ions through water-mediated interaction. It is important to know the synergic role of Mg 2+ and the water network surrounding Mg 2+ in stabilizing the non-WC base pairs of RNA. For this purpose, free energy change of the system is calculated using molecular dynamics (MD) simulation as Mg 2+ is pulled from RNA, which causes disturbance of the water network. It was found that Mg 2+ remains hexahydrated unless it is close to or far from RNA. In the pentahydrated form, Mg 2+ interacts directly with RNA. Water network has been identified by two complimentary methods; MD followed by a density-based clustering algorithm and three-dimensional-reference interaction site model. These two methods gave similar results. Identification of water network around Mg 2+ and non-WC base pairs gives a clue to the strong effect of water network on the stability of this RNA. Based on sequence analysis of all Eubacteria 5s rRNA, we propose that hexahydrated Mg 2+ is an integral part of this RNA and geometry of base pairs surrounding it adjust to accommodate the [Formula: see text]. Overall the findings from this work can help in understanding the basis of the complex structure and stability of RNA with non-WC base pairs.

Strong contributions from vertical triads to helix-partner preferences in parallel coiled coils.

PubMed

Steinkruger, Jay D; Bartlett, Gail J; Woolfson, Derek N; Gellman, Samuel H

2012-09-26

Pairing preferences in heterodimeric coiled coils are determined by complementarities among side chains that pack against one another at the helix-helix interface. However, relationships between dimer stability and interfacial residue identity are not fully understood. In the context of the "knobs-into-holes" (KIH) packing pattern, one can identify two classes of interactions between side chains from different helices: "lateral", in which a line connecting the adjacent side chains is perpendicular to the helix axes, and "vertical", in which the connecting line is parallel to the helix axes. We have previously analyzed vertical interactions in antiparallel coiled coils and found that one type of triad constellation (a'-a-a') exerts a strong effect on pairing preferences, while the other type of triad (d'-d-d') has relatively little impact on pairing tendencies. Here, we ask whether vertical interactions (d'-a-d') influence pairing in parallel coiled-coil dimers. Our results indicate that vertical interactions can exert a substantial impact on pairing specificity, and that the influence of the d'-a-d' triad depends on the lateral a' contact within the local KIH motif. Structure-informed bioinformatic analyses of protein sequences reveal trends consistent with the thermodynamic data derived from our experimental model system in suggesting that heterotriads involving Leu and Ile are preferred over homotriads involving Leu and Ile.

A flexible algorithm for calculating pair interactions on SIMD architectures

NASA Astrophysics Data System (ADS)

Páll, Szilárd; Hess, Berk

2013-12-01

Calculating interactions or correlations between pairs of particles is typically the most time-consuming task in particle simulation or correlation analysis. Straightforward implementations using a double loop over particle pairs have traditionally worked well, especially since compilers usually do a good job of unrolling the inner loop. In order to reach high performance on modern CPU and accelerator architectures, single-instruction multiple-data (SIMD) parallelization has become essential. Avoiding memory bottlenecks is also increasingly important and requires reducing the ratio of memory to arithmetic operations. Moreover, when pairs only interact within a certain cut-off distance, good SIMD utilization can only be achieved by reordering input and output data, which quickly becomes a limiting factor. Here we present an algorithm for SIMD parallelization based on grouping a fixed number of particles, e.g. 2, 4, or 8, into spatial clusters. Calculating all interactions between particles in a pair of such clusters improves data reuse compared to the traditional scheme and results in a more efficient SIMD parallelization. Adjusting the cluster size allows the algorithm to map to SIMD units of various widths. This flexibility not only enables fast and efficient implementation on current CPUs and accelerator architectures like GPUs or Intel MIC, but it also makes the algorithm future-proof. We present the algorithm with an application to molecular dynamics simulations, where we can also make use of the effective buffering the method introduces.

A femtoscopic correlation analysis tool using the Schrödinger equation (CATS)

NASA Astrophysics Data System (ADS)

Mihaylov, D. L.; Mantovani Sarti, V.; Arnold, O. W.; Fabbietti, L.; Hohlweger, B.; Mathis, A. M.

2018-05-01

We present a new analysis framework called "Correlation Analysis Tool using the Schrödinger equation" (CATS) which computes the two-particle femtoscopy correlation function C( k), with k being the relative momentum for the particle pair. Any local interaction potential and emission source function can be used as an input and the wave function is evaluated exactly. In this paper we present a study on the sensitivity of C( k) to the interaction potential for different particle pairs: p-p, p-Λ, K^-p, K^+-p, p-Ξ ^- and Λ- Λ. For the p-p Argonne v_{18} and Reid Soft-Core potentials have been tested. For the other pair systems we present results based on strong potentials obtained from effective Lagrangians such as χ EFT for p-Λ, Jülich models for K(\\bar{K})-N and Nijmegen models for Λ-Λ. For the p-Ξ^- pairs we employ the latest lattice results from the HAL QCD collaboration. Our detailed study of different interacting particle pairs as a function of the source size and different potentials shows that femtoscopic measurements can be exploited in order to constrain the final state interactions among hadrons. In particular, small collision systems of the order of 1 fm, as produced in pp collisions at the LHC, seem to provide a suitable environment for quantitative studies of this kind.

Pairing of one-dimensional Bose-Fermi mixtures with unequal masses

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

Rizzi, Matteo; Max Planck Institut fuer QuantenOptik, Hans Kopfermann Strasse 1, D-85748 Garching; Imambekov, Adilet

We have considered one-dimensional Bose-Fermi mixture with equal densities and unequal masses using numerical density matrix renormalization group. For the mass ratio of K-Rb mixture and attraction between bosons and fermions, we determined the phase diagram. For weak boson-boson interactions, there is a direct transition between two-component Luttinger liquid and collapsed phases as the boson-fermion attraction is increased. For strong enough boson-boson interactions, we find an intermediate 'paired' phase, which is a single-component Luttinger liquid of composite particles. We investigated correlation functions of such a 'paired' phase, studied the stability of 'paired' phase to density imbalance, and discussed various experimentalmore » techniques which can be used to detect it.« less

Morphologies and ages of star cluster pairs and multiplets in the Small Magellanic Cloud

NASA Astrophysics Data System (ADS)

de Oliveira, M. R.; Dutra, C. M.; Bica, E.; Dottori, H.

2000-10-01

An isophotal atlas of 75 star cluster pairs and multiplets in the Small Magellanic Cloud is presented, comprising 176 objects. They are concentrated in the SMC main body. The isophotal contours were made from Digitized Sky Survey* images and showed relevant structural features possibly related to interactions in about 25% of the sample. Previous N-body simulations indicate that such shapes could be due to tidal tails, bridges or common envelopes. The diameter ratio between the members of a pair is preferentially in the range 1 - 2, with a peak at 1. The projected separation is in the range ~ 3 - 22 pc with a pronounced peak at ~ 13 pc. For 91 objects it was possible to derive ages from Colour-Magnitude Diagrams using the OGLE-II photometric survey. The cluster multiplets in general occur in OB stellar associations and/or HII region complexes. This indicates a common origin and suggests that multiplets coalesce into pairs or single clusters in a short time scale. Pairs in the SMC appear to be mostly coeval and consequently captures are a rare phenomenon. We find evidence that star cluster pairs and multiplets may have had an important role in the dynamical history of clusters presently seen as large single objects. The images in this study are based on photographic data obtained using the UK Schmidt Telescope, which was operated by the Royal Observatory Edinburgh, with funding from the UK Science and Engineering Research Council, until 1988 June, and thereafter by the Anglo-Australian Observatory. Original plate material is copyright by the Royal Observatory Edinburgh and the Anglo-Australian Observatory. The plates were processed into the present compressed digital form with their permission. The Digitized Sky Survey was produced at the Space Telescope Science Institute under US Government grant NAG W-2166.

Calix[4]pyrrole: A New Ion-Pair Receptor As Demonstrated by Liquid-Liquid Extraction

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

Wintergerst, Mr. Matthieu; Levitskaia, Tatiana G.; Moyer, Bruce A

Solvent-extraction studies provide confirming evidence that meso-octamethylcalix[4]pyrrole acts as an ion-pair receptor for cesium chloride and cesium bromide in nitrobenzene solution. The stoichiometry of the interaction under extraction conditions from water to nitrobenzene was determined from plots of the cesium distribution ratios vs cesium salt and receptor concentration, indicating the formation of an ionpaired 1:1:1 cesium:calix[4]pyrrole:halide complex. The extraction results were modeled to evaluate the equilibria inherent to the solvent-extraction system, with either chloride or bromide. The binding energy between the halide anion and the calix[4]pyrrole was found to be about 7 kJ/mol larger for cesium chloride than for themore » cesium bromide. The ion-pairing free energies between the calix[4]pyrrole-halide complex and the cesium cation are nearly the same within experimental uncertainty for either halide, consistent with a structural model in which the Cs+ cation resides in the calix bowl. These results are unexpected since nitrobenzene is a polar solvent that generally leads to dissociated complexes in the organic phase when used as a diluent in extraction studies of univalent ions. Control studies involving nitrate revealed no evidence of ion pairing for CsNO3 under conditions identical to those where it is observed for CsCl and CsBr.« less

Unsupervised visual discrimination learning of complex stimuli: Accuracy, bias and generalization.

PubMed

Montefusco-Siegmund, Rodrigo; Toro, Mauricio; Maldonado, Pedro E; Aylwin, María de la L

2018-07-01

Through same-different judgements, we can discriminate an immense variety of stimuli and consequently, they are critical in our everyday interaction with the environment. The quality of the judgements depends on familiarity with stimuli. A way to improve the discrimination is through learning, but to this day, we lack direct evidence of how learning shapes the same-different judgments with complex stimuli. We studied unsupervised visual discrimination learning in 42 participants, as they performed same-different judgments with two types of unfamiliar complex stimuli in the absence of labeling or individuation. Across nine daily training sessions with equiprobable same and different stimuli pairs, participants increased the sensitivity and the criterion by reducing the errors with both same and different pairs. With practice, there was a superior performance for different pairs and a bias for different response. To evaluate the process underlying this bias, we manipulated the proportion of same and different pairs, which resulted in an additional proportion-induced bias, suggesting that the bias observed with equal proportions was a stimulus processing bias. Overall, these results suggest that unsupervised discrimination learning occurs through changes in the stimulus processing that increase the sensory evidence and/or the precision of the working memory. Finally, the acquired discrimination ability was fully transferred to novel exemplars of the practiced stimuli category, in agreement with the acquisition of a category specific perceptual expertise. Copyright © 2018 Elsevier Ltd. All rights reserved.

Performance of Language-Coordinated Collective Systems: A Study of Wine Recognition and Description

PubMed Central

Zubek, Julian; Denkiewicz, Michał; Dębska, Agnieszka; Radkowska, Alicja; Komorowska-Mach, Joanna; Litwin, Piotr; Stępień, Magdalena; Kucińska, Adrianna; Sitarska, Ewa; Komorowska, Krystyna; Fusaroli, Riccardo; Tylén, Kristian; Rączaszek-Leonardi, Joanna

2016-01-01

Most of our perceptions of and engagements with the world are shaped by our immersion in social interactions, cultural traditions, tools and linguistic categories. In this study we experimentally investigate the impact of two types of language-based coordination on the recognition and description of complex sensory stimuli: that of red wine. Participants were asked to taste, remember and successively recognize samples of wines within a larger set in a two-by-two experimental design: (1) either individually or in pairs, and (2) with or without the support of a sommelier card—a cultural linguistic tool designed for wine description. Both effectiveness of recognition and the kinds of errors in the four conditions were analyzed. While our experimental manipulations did not impact recognition accuracy, bias-variance decomposition of error revealed non-trivial differences in how participants solved the task. Pairs generally displayed reduced bias and increased variance compared to individuals, however the variance dropped significantly when they used the sommelier card. The effect of sommelier card reducing the variance was observed only in pairs, individuals did not seem to benefit from the cultural linguistic tool. Analysis of descriptions generated with the aid of sommelier cards shows that pairs were more coherent and discriminative than individuals. The findings are discussed in terms of global properties and dynamics of collective systems when constrained by different types of cultural practices. PMID:27729875

Polarized light modulates light-dependent magnetic compass orientation in birds

PubMed Central

Muheim, Rachel; Sjöberg, Sissel; Pinzon-Rodriguez, Atticus

2016-01-01

Magnetoreception of the light-dependent magnetic compass in birds is suggested to be mediated by a radical-pair mechanism taking place in the avian retina. Biophysical models on magnetic field effects on radical pairs generally assume that the light activating the magnetoreceptor molecules is nondirectional and unpolarized, and that light absorption is isotropic. However, natural skylight enters the avian retina unidirectionally, through the cornea and the lens, and is often partially polarized. In addition, cryptochromes, the putative magnetoreceptor molecules, absorb light anisotropically, i.e., they preferentially absorb light of a specific direction and polarization, implying that the light-dependent magnetic compass is intrinsically polarization sensitive. To test putative interactions between the avian magnetic compass and polarized light, we developed a spatial orientation assay and trained zebra finches to magnetic and/or overhead polarized light cues in a four-arm “plus” maze. The birds did not use overhead polarized light near the zenith for sky compass orientation. Instead, overhead polarized light modulated light-dependent magnetic compass orientation, i.e., how the birds perceive the magnetic field. Birds were well oriented when tested with the polarized light axis aligned parallel to the magnetic field. When the polarized light axis was aligned perpendicular to the magnetic field, the birds became disoriented. These findings are the first behavioral evidence to our knowledge for a direct interaction between polarized light and the light-dependent magnetic compass in an animal. They reveal a fundamentally new property of the radical pair-based magnetoreceptor with key implications for how birds and other animals perceive the Earth’s magnetic field. PMID:26811473

Polarized light modulates light-dependent magnetic compass orientation in birds.

PubMed

Muheim, Rachel; Sjöberg, Sissel; Pinzon-Rodriguez, Atticus

2016-02-09

Magnetoreception of the light-dependent magnetic compass in birds is suggested to be mediated by a radical-pair mechanism taking place in the avian retina. Biophysical models on magnetic field effects on radical pairs generally assume that the light activating the magnetoreceptor molecules is nondirectional and unpolarized, and that light absorption is isotropic. However, natural skylight enters the avian retina unidirectionally, through the cornea and the lens, and is often partially polarized. In addition, cryptochromes, the putative magnetoreceptor molecules, absorb light anisotropically, i.e., they preferentially absorb light of a specific direction and polarization, implying that the light-dependent magnetic compass is intrinsically polarization sensitive. To test putative interactions between the avian magnetic compass and polarized light, we developed a spatial orientation assay and trained zebra finches to magnetic and/or overhead polarized light cues in a four-arm "plus" maze. The birds did not use overhead polarized light near the zenith for sky compass orientation. Instead, overhead polarized light modulated light-dependent magnetic compass orientation, i.e., how the birds perceive the magnetic field. Birds were well oriented when tested with the polarized light axis aligned parallel to the magnetic field. When the polarized light axis was aligned perpendicular to the magnetic field, the birds became disoriented. These findings are the first behavioral evidence to our knowledge for a direct interaction between polarized light and the light-dependent magnetic compass in an animal. They reveal a fundamentally new property of the radical pair-based magnetoreceptor with key implications for how birds and other animals perceive the Earth's magnetic field.

Effects of monoterpenoids, acting alone or in pairs, on seed germination and subsequent seedling growth.

PubMed

Vokou, Despina; Douvli, Panagiota; Blionis, George J; Halley, John M

2003-10-01

We compared the potential allelopathic activity of 47 monoterpenoids of different chemical groups, by estimating their effect on seed germination and subsequent growth of Lactuca sativa seedlings. Apart from individual compounds, eleven pairs at different proportions were also tested. As a group, the hydrocarbons, except for (+)-3-carene, were the least inhibitory. Of the oxygenated compounds, the least inhibitory were the acetates; whenever the free hydroxyl group of an alcohol turned into a carboxyl group, the activity of the resulting ester was markedly lower (against both germination and seedling growth). Twenty-four compounds were extremely active against seedling growth (inhibiting it by more than 85%), but only five against seed germination. The compounds that were most active against both processes belonged to the groups of ketones and alcohols; they were terpinen-4-ol, dihydrocarvone, and two carvone stereoisomers. We used a model to investigate whether compounds acted independently when applied in pairs. The combined effect varied. In half of the cases, it followed the pattern expected under the assumption of independence; in the rest, either synergistic or antagonistic interactions were found in both germination and elongation. However, even in cases of synergistic interactions, the level of inhibition was not comparable to that of a single extremely active compound, unless such a compound already participated in the combination. The specific structural factors that operate and determine the activity of monoterpenoids still remain rather obscure. The same holds true for the combined effect; its character cannot in general be predicted on the basis of individual compounds acting alone.

SPATIAL DISTRIBUTION OF PAIR PRODUCTION OVER THE PULSAR POLAR CAP

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

Belyaev, Mikhail A.; Parfrey, Kyle, E-mail: mbelyaev@berkeley.edu

2016-10-20

Using an analytic, axisymmetric approach that includes general relativity, coupled to a condition for pair production deduced from simulations, we derive general results about the spatial distribution of pair-producing field lines over the pulsar polar cap. In particular, we show that pair production on magnetic field lines operates over only a fraction of the polar cap for an aligned rotator for general magnetic field configurations, assuming the magnetic field varies spatially on a scale that is larger than the size of the polar cap. We compare our result to force-free simulations of a pulsar with a dipole surface field andmore » find excellent agreement. Our work has implications for first-principles simulations of pulsar magnetospheres and for explaining observations of pulsed radio and high-energy emission.« less

``Glue" approximation for the pairing interaction in the Hubbard model with next nearest neighbor hopping

NASA Astrophysics Data System (ADS)

Khatami, Ehsan; Macridin, Alexandru; Jarrell, Mark

2008-03-01

Recently, several authors have employed the ``glue" approximation for the Cuprates in which the full pairing vertex is approximated by the spin susceptibility. We study this approximation using Quantum Monte Carlo Dynamical Cluster Approximation methods on a 2D Hubbard model. By considering a reasonable finite value for the next nearest neighbor hopping, we find that this ``glue" approximation, in the current form, does not capture the correct pairing symmetry. Here, d-wave is not the leading pairing symmetry while it is the dominant symmetry using the ``exact" QMC results. We argue that the sensitivity of this approximation to the band structure changes leads to this inconsistency and that this form of interaction may not be the appropriate description of the pairing mechanism in Cuprates. We suggest improvements to this approximation which help to capture the the essential features of the QMC data.

Pairing in exotic neutron-rich nuclei near the drip line and in the crust of neutron stars

NASA Astrophysics Data System (ADS)

Pastore, A.; Margueron, J.; Schuck, P.; Viñas, X.

2013-09-01

Exotic and drip-line nuclei as well as nuclei immersed in a low-density gas of neutrons in the inner crust of neutron stars are systematically investigated with respect to their neutron pairing properties. This is done using Skyrme density-functional and different pairing forces such as a density-dependent contact interaction and a separable form of a finite-range Gogny interaction. Hartree-Fock-Bogoliubov (HFB) and Bardeen-Cooper-Schrieffer (BCS) theories are compared. It is found that neutron pairing is reduced towards the drip line while overcast by strong shell effects. Furthermore, resonances in the continuum can have an important effect counterbalancing the tendency of reduction and leading to a persistence of pairing at the drip line. It is also shown that in these systems the difference between HFB and BCS approaches can be quantitatively large.

Quantitative analysis of harmonic convergence in mosquito auditory interactions

PubMed Central

Aldersley, Andrew; Champneys, Alan; Robert, Daniel

2016-01-01

This article analyses the hearing and behaviour of mosquitoes in the context of inter-individual acoustic interactions. The acoustic interactions of tethered live pairs of Aedes aegypti mosquitoes, from same and opposite sex mosquitoes of the species, are recorded on independent and unique audio channels, together with the response of tethered individual mosquitoes to playbacks of pre-recorded flight tones of lone or paired individuals. A time-dependent representation of each mosquito's non-stationary wing beat frequency signature is constructed, based on Hilbert spectral analysis. A range of algorithmic tools is developed to automatically analyse these data, and used to perform a robust quantitative identification of the ‘harmonic convergence’ phenomenon. The results suggest that harmonic convergence is an active phenomenon, which does not occur by chance. It occurs for live pairs, as well as for lone individuals responding to playback recordings, whether from the same or opposite sex. Male–female behaviour is dominated by frequency convergence at a wider range of harmonic combinations than previously reported, and requires participation from both partners in the duet. New evidence is found to show that male–male interactions are more varied than strict frequency avoidance. Rather, they can be divided into two groups: convergent pairs, typified by tightly bound wing beat frequencies, and divergent pairs, that remain widely spaced in the frequency domain. Overall, the results reveal that mosquito acoustic interaction is a delicate and intricate time-dependent active process that involves both individuals, takes place at many different frequencies, and which merits further enquiry. PMID:27053654

Particle dynamics and pair production in tightly focused standing wave

NASA Astrophysics Data System (ADS)

Jirka, M.; Klimo, O.; Vranić, M.; Weber, S.; Korn, G.

2017-05-01

With the advent of 10 PW laser facilities, new regimes of laser-matter interaction are opening since effects of quantum electrodynamics, such as electron-positron pair production and cascade development, start to be important. The dynamics of light charged particles, such as electrons and positrons, is affected by the radiation reaction force. This effect can strongly influence the interaction of intense laser pulses with matter since it lowers the energy of emitting particles and transforms their energy to the gamma radiation. Consequently, electron-positron pairs can be generated via Breit-Wheeler process. To study this new regime of interaction, numerical simulations are required. With their help it is possible to predict and study quantum effects which may occur in future experiments at modern laser facilities. In this work we present results of electron interaction with an intense standing wave formed by two colliding laser pulses. Due to the necessity to achieve ultra intense laser field, the laser beam has to be focused to a μm-diameter spot. Since the paraxial approximation is not valid for tight focusing, the appropriate model describing the tightly focused laser beam has to be employed. In tightly focused laser beam the longitudinal component of the electromagnetic field becomes significant and together with the ponderomotive force they affect the dynamics of interacting electrons and also newly generated Breit-Wheeler electron-positron pairs. Using the Particle-In-Cell code we study electron dynamics, gamma radiation and pair production in such a configuration for linear polarization and different types of targets.

Juvenile social experience affects pairing success at adulthood: congruence with the loser effect?

PubMed

Mariette, Mylene M; Cathaud, Charlène; Chambon, Rémi; Vignal, Clémentine

2013-09-22

Social interactions with adults are often critical for the development of mating behaviours. However, the potential role of other primary social partners such as juvenile counterparts is rarely considered. Most interestingly, it is not known whether interactions with juvenile females improve males' courtship and whether, similar to the winner and loser effects in a fighting context--outcome of these interactions shapes males' behaviour in future encounters. We investigated the combined effects of male quality and juvenile social experience on pairing success at adulthood in zebra finches (Taeniopygia guttata). We manipulated brood size to alter male quality and then placed males in either same- or mixed-sex juvenile dyads until adulthood. We found that males from reduced broods obtained more copulations and males from mixed-sex dyads had more complete courtships. Furthermore, independent of their quality, males that failed to pair with juvenile females, but not juvenile males, had a lower pairing success at adulthood. Our study shows that negative social experience with peers during adolescence may be a potent determinant of pairing success that can override the effects of early environmental conditions on male attractiveness and thereby supports the occurrence of an analogous process to the loser effect in a mating context.

EEG correlates of social interaction at distance

PubMed Central

Giroldini, William; Pederzoli, Luciano; Bilucaglia, Marco; Caini, Patrizio; Ferrini, Alessandro; Melloni, Simone; Prati, Elena; Tressoldi, Patrizio

2016-01-01

This study investigated EEG correlates of social interaction at distance between twenty-five pairs of participants who were not connected by any traditional channels of communication. Each session involved the application of 128 stimulations separated by intervals of random duration ranging from 4 to 6 seconds. One of the pair received a one-second stimulation from a light signal produced by an arrangement of red LEDs, and a simultaneous 500 Hz sinusoidal audio signal of the same length. The other member of the pair sat in an isolated sound-proof room, such that any sensory interaction between the pair was impossible. An analysis of the Event-Related Potentials associated with sensory stimulation using traditional averaging methods showed a distinct peak at approximately 300 ms, but only in the EEG activity of subjects who were directly stimulated. However, when a new algorithm was applied to the EEG activity based on the correlation between signals from all active electrodes, a weak but robust response was also detected in the EEG activity of the passive member of the pair, particularly within 9 – 10 Hz in the Alpha range. Using the Bootstrap method and the Monte Carlo emulation, this signal was found to be statistically significant. PMID:26966513

Properties of isoscalar-pair condensates

DOE PAGES

Van Isacker, P.; Macchiavelli, A. O.; Fallon, P.; ...

2016-08-17

In this work, it is pointed out that the ground state of $n$ neutrons and n protons in a single-$j$ shell, interacting through an isoscalar ($T=0$) pairing force, is not paired, $J=0$, but rather spin aligned, $J=n$. This observation is explained in the context of a model of isoscalar $P(J=1)$ pairs, which is mapped onto a system of $p$ bosons, leading to an approximate analytic solution of the isoscalar-pairing limit in $jj$ coupling.

Use of decimal assay for additivity to demonstrate synergy in pair combinations of econazole, nikkomycin Z, and ibuprofen against Candida albicans in vitro.

PubMed Central

Tariq, V N; Scott, E M; McCain, N E

1995-01-01

Interactions between six compounds (econazole, miconazole, amphotericin B, nystatin, nikkomycin Z, and ibuprofen) were investigated for their antifungal activities against Candida albicans by using pair combinations in an in vitro decimal assay for additivity based on disk diffusion. Additive interactions were observed between miconazole and econazole, amphotericin B and nystatin, and amphotericin B and ibuprofen, while an antagonistic interaction was observed between econazole and amphotericin B. Synergistic interactions were recorded for the combinations of econazole and ibuprofen, econazole and nikkomycin Z, and ibuprofen and nikkomycin Z. PMID:8592989

Live interaction distinctively shapes social gaze dynamics in rhesus macaques.

PubMed

Dal Monte, Olga; Piva, Matthew; Morris, Jason A; Chang, Steve W C

2016-10-01

The dynamic interaction of gaze between individuals is a hallmark of social cognition. However, very few studies have examined social gaze dynamics after mutual eye contact during real-time interactions. We used a highly quantifiable paradigm to assess social gaze dynamics between pairs of monkeys and modeled these dynamics using an exponential decay function to investigate sustained attention after mutual eye contact. When monkeys were interacting with real partners compared with static images and movies of the same monkeys, we found a significant increase in the proportion of fixations to the eyes and a smaller dispersion of fixations around the eyes, indicating enhanced focal attention to the eye region. Notably, dominance and familiarity between the interacting pairs induced separable components of gaze dynamics that were unique to live interactions. Gaze dynamics of dominant monkeys after mutual eye contact were associated with a greater number of fixations to the eyes, whereas those of familiar pairs were associated with a faster rate of decrease in this eye-directed attention. Our findings endorse the notion that certain key aspects of social cognition are only captured during interactive social contexts and dependent on the elapsed time relative to socially meaningful events. Copyright © 2016 the American Physiological Society.

Live interaction distinctively shapes social gaze dynamics in rhesus macaques

PubMed Central

Piva, Matthew; Morris, Jason A.; Chang, Steve W. C.

2016-01-01

The dynamic interaction of gaze between individuals is a hallmark of social cognition. However, very few studies have examined social gaze dynamics after mutual eye contact during real-time interactions. We used a highly quantifiable paradigm to assess social gaze dynamics between pairs of monkeys and modeled these dynamics using an exponential decay function to investigate sustained attention after mutual eye contact. When monkeys were interacting with real partners compared with static images and movies of the same monkeys, we found a significant increase in the proportion of fixations to the eyes and a smaller dispersion of fixations around the eyes, indicating enhanced focal attention to the eye region. Notably, dominance and familiarity between the interacting pairs induced separable components of gaze dynamics that were unique to live interactions. Gaze dynamics of dominant monkeys after mutual eye contact were associated with a greater number of fixations to the eyes, whereas those of familiar pairs were associated with a faster rate of decrease in this eye-directed attention. Our findings endorse the notion that certain key aspects of social cognition are only captured during interactive social contexts and dependent on the elapsed time relative to socially meaningful events. PMID:27486105

The Effects of L2 Proficiency Differences in Pairs on Idea Units in a Collaborative Text Reconstruction Task

ERIC Educational Resources Information Center

Shin, Sun-Young; Lidster, Ryan; Sabraw, Stacy; Yeager, Rebecca

2016-01-01

Collaborative text reconstruction tasks such as dictogloss have been suggested as effective second language (L2) learning tasks that promote meaningful interaction between learners and their awareness of L2 target grammatical structures. However, it should be noted that the effect of pair interaction on the final product may differ depending on…

Synthetic Superconductivity in Single-Layer Crystals

NASA Astrophysics Data System (ADS)

Levitov, Leonid; Borgnia, Dan; Lee, Patrick

2015-03-01

Electronic states in atomically thin 2D crystals are fully exposed and can couple to extrinsic degrees of freedom via long-range Coulomb interactions. Novel many-body effects in such systems can be engineered by embedding them in a polar environment. Superconducting pairing interaction induced in this way can enhance the intrinsic electron-phonon pairing mechanism. We take on this notion, which was around since the 60's (''excitonic superconductivity''), and consider synthetic superconductivity (SSC) induced in 2D crystals by a polar environment. One interesting aspect of this scenario is that Coulomb repulsion acts as superconductivity friend rather than a foe. Such repulsion-to-attraction transmutation allows to access strong-coupling superconductivity regime even when intrinsic pairing interaction is weak. We analyze pairing interaction in 2D crystals placed atop a highly polarizable dielectric with dispersive permittivity ɛ (ω) and predict that by optimizing system parameters a substantial enhancement can be achieved. We also argue that the SSC mechanism can be responsible, at least in part, for 100 K superconductivity recently observed in FeSe monolayers grown on SrTiO3 substrate, with Tc more than 10 times larger than in bulk 3D FeSe crystals, arxiv:1406.3435.

Genetic basis of hybrid male sterility among three closely related species of Drosophila.

PubMed

Mishra, Paras Kumar; Singh, B N

2005-05-01

The genetic basis of hybrid male sterility among three closely related species, Drosophila bipectinata, D. parabipectinata and D. malerkotliana has been investigated by using backcross analysis methods. The role of Y chromosome, major hybrid sterility (MHS) genes (genetic factors) and cytoplasm (non-genetic factor) have been studied in the hybrids of these three species. In the species pair, bipectinata--parabipectinata, Y chromosome introgression of parabipectinata in the genomic background of bipectinata and the reciprocal Y chromosome introgression were unsuccessful as all males in second backcross generation were sterile. Neither MHS genes nor cytoplasm was found important for sterility. This suggests the involvement of X-Y, X-autosomes or polygenic interactions in hybrid male sterility. In bipectinata--malerkotliana and parabipectinata--malerkotliana species pairs, Y chromosome substitution in reciprocal crosses did not affect male fertility. Backcross analyses also show no involvement of MHS genes or cytoplasm in hybrid male sterility in these two species pairs. Therefore, X- autosome interaction or polygenic interaction is supposed to be involved in hybrid male sterility in these two species pairs. These findings also provide evidence that even in closely related species, genetic interactions underlying hybrid male sterility may vary.

Type 2 diabetes susceptibility genes on chromosome 1q21-24.

PubMed

Hasstedt, S J; Chu, W S; Das, S K; Wang, H; Elbein, S C

2008-03-01

Type 2 diabetes (T2D) has been linked to chromosome 1q21-24 in multiple samples, including a Utah family sample. Variants in 13 of the numerous candidate genes in the 1q region were tested for association with T2D in a Utah case-control sample. The most promising, 19 variants in 6 candidates, were genotyped on the Utah family sample. Herein, we tested the 19 variants individually and in pairs for an effect on T2D risk in family members using a logistic regression model that accounted for gender, age, and BMI and attributed residual genetic effects to a polygenic component. Seven variants increased risk significantly through 5 pairs of interactions. The significant variant pairs were apolipoprotein A-II (APOA2) rs6413453 interacting with calsequestrin 1 (CASQ1) rs617698, dual specificity phosphatase 12 (DUSP12) rs1503814, and retinoid X receptor gamma (RXRG) rs10918169, a poly-T insertion-deletion polymorphism in liver pyruvate kinase (PKLR) interacting with APOA2 rs12143180, and DUSP12 rs1027702 interacting with RXRG rs10918169. Genotypes of these 5 variant pairs accounted for 25.8% of the genetic variance in T2D in these pedigrees.

Pairing in half-filled Landau level

NASA Astrophysics Data System (ADS)

Wang, Zhiqiang; Mandal, Ipsita; Chung, Suk Bum; Chakravarty, Sudip

2015-03-01

Pairing of composite fermions in half-filled Landau level state is reexamined by solving the BCS gap equation with full frequency dependent current-current interactions. Our results show that there can be a continuous transition from the Halperin-Lee-Read state to a chiral odd angular momentum Cooper pair state for short-range contact interaction. This is at odds with the previously established conclusion of first order pairing transition, in which the low frequency effective interaction was assumed for the entire frequency range. We find that even if the low frequency effective interaction is repulsive, it is compensated by the high frequency regime, which is attractive. We construct the phase diagrams and show that l = 1 angular momentum channel is quite different from higher angular momentum channel l >= 3 . Remarkably, the full frequency dependent analysis applied to the bilayer Hall system with a total filling fraction ν =1/2 +1/2 is quantitatively changed from the previously established results but not qualitatively. This work was supported by US NSF under the Grant DMR-1004520, the funds from the David S. Saxon Presidential Chair at UCLA(37952), and by the Institute for Basic Science in Korea through the Young Scientist grant (5199-2014003).

Monoamine oxidase A genotype, childhood trauma, and subclinical atherosclerosis: a twin study.

PubMed

Zhao, Jinying; Bremner, James D; Goldberg, Jack; Quyyumi, Arshed A; Vaccarino, Viola

2013-06-01

A functional promoter polymorphism in the monoamine oxidase A (MAOA) gene has been implicated in neuropsychiatric disorders and also moderates the association between early-life stress and mental disorders, which often co-occur with cardiovascular disease. No study has examined the relationship between MAOA genotype, childhood trauma, and subclinical atherosclerosis. The objective of this investigation was to examine whether childhood trauma moderates the association between MAOA genotype and subclinical atherosclerosis. A sample including 289 middle-aged male twin pairs was studied. Subclinical atherosclerosis was assessed by brachial flow-mediated dilation (FMD) using ultrasound. Childhood trauma, before age 18 years, was measured with the Early Trauma Inventory and included physical, emotional, and sexual abuse as well as general trauma. Generalized estimating equation models were used to test the main and interactive effects of the MAOA genotype and each domain of childhood trauma on FMD, adjusting for known risk factors. General trauma was the most prevalent childhood trauma (28.4%), followed by physical abuse (25.0%), emotional abuse (19.4%), and sexual abuse (11.6%). MAOA genotype was not associated with any domain of childhood trauma. There was no significant evidence for a main effect for the MAOA genotype (β = .02, p = .82) or childhood trauma (.005 < β < .10, p > .54) FMD. However, a significant interaction was observed between MAOA genotype and physical (β interaction = .37, p = .026) or emotional abuse (β interaction = .43, p = .025) on subclinical atherosclerosis. Childhood trauma modulates the impact of MAOA variant on subclinical atherosclerosis, independent of traditional cardiovascular risk factors.

d +i d chiral superconductivity in a triangular lattice from trigonal bipyramidal complexes

NASA Astrophysics Data System (ADS)

Lu, Chen; Zhang, Li-Da; Wu, Xianxin; Yang, Fan; Hu, Jiangping

2018-04-01

We model the newly predicted high-Tc superconducting candidates constructed by corner-shared trigonal bipyramidal complexes with an effective three-orbital tight-binding Hamiltonian and investigate the pairing symmetry of their superconducting states driven by electron-electron interactions. Our combined weak- and strong-coupling-based calculations consistently identify the chiral d +i d superconductivity as the leading pairing symmetry in a wide doping range with realistic interaction parameters. This pairing state has a nontrivial topological Chern number and can host gapless chiral edge modes, and the vortex cores under magnetic field can carry Majorana zero modes.

Sample size considerations for paired experimental design with incomplete observations of continuous outcomes.

PubMed

Zhu, Hong; Xu, Xiaohan; Ahn, Chul

2017-01-01

Paired experimental design is widely used in clinical and health behavioral studies, where each study unit contributes a pair of observations. Investigators often encounter incomplete observations of paired outcomes in the data collected. Some study units contribute complete pairs of observations, while the others contribute either pre- or post-intervention observations. Statistical inference for paired experimental design with incomplete observations of continuous outcomes has been extensively studied in literature. However, sample size method for such study design is sparsely available. We derive a closed-form sample size formula based on the generalized estimating equation approach by treating the incomplete observations as missing data in a linear model. The proposed method properly accounts for the impact of mixed structure of observed data: a combination of paired and unpaired outcomes. The sample size formula is flexible to accommodate different missing patterns, magnitude of missingness, and correlation parameter values. We demonstrate that under complete observations, the proposed generalized estimating equation sample size estimate is the same as that based on the paired t-test. In the presence of missing data, the proposed method would lead to a more accurate sample size estimate comparing with the crude adjustment. Simulation studies are conducted to evaluate the finite-sample performance of the generalized estimating equation sample size formula. A real application example is presented for illustration.

Modified nucleotides reveal the indirect role of the central base pairs in stabilizing the lac repressor-operator complex.

PubMed Central

Zhang, X; Gottlieb, P A

1995-01-01

Guanine residues in the lac operator were replaced by 2-aminopurine or purine analogues, pairing the modified nucleotides with C. The observed equilibrium dissociation constants for lac repressor binding to substituted operators were measured in 10 mM Tris, 150 mM KCl, 0.1 mM EDTA, 0.1 mM DTE, pH 7.6 at 25 degrees C. These measurements revealed five positions that destabilized the complex when substituted with either analogue. Two positions, which are related by a 2-fold symmetry, are in the major groove of the operator thought to directly interact with the protein. Three sites were in the central region of the operator. A purine analogue at a sixth site perturbed the local DNA structure and destabilized the complex. Alkylation interference experiments of the 2-aminopurine substituted operators demonstrated that, of the five affected, two substitutions displayed altered phosphate interference patterns at the phosphate adjacent to the substituted base. For these operators, complex formation was measured in different concentrations of KCl to assess the contribution of counterion release to the bimolecular process. The results indicated that both complexes were similar to wild-type, although minor changes were observed. The Kobs of the complex was then measured when 2-aminopurine or purine analogues were paired with uracil nucleotide, a base pair that serves to stabilize the DNA. The introduction of the new base pairs revealed two effects on the bimolecular interaction. For those operator sites that are thought to perturb the interaction directly, the affinity of the complex was weakened to levels observed for the singly-substituted operators. In contrast, the nucleotides of 2-aminopurine paired with uracil positioned in the central region of the operator served to enhance the stability of the complex. The purine-uracil base pair substitution on the other hand had a significant destabilizing effect on the interaction. We propose that the central base pairs modulate binding of the complex by altering the intrinsic properties of the DNA. Two specific attributes are required to achieve the lowest free energy of interaction. The DNA must have two interstrand hydrogen bonds to stabilize the duplex and it must have properties associated with directional bending or unwinding. This analysis does not rule out contributions by direct interactions between the protein and the central region of the operator but underscores how indirect effects play a major role in complex formation in this system. Images PMID:7784203

Collisionless magnetic reconnection in curved spacetime and the effect of black hole rotation

NASA Astrophysics Data System (ADS)

Comisso, Luca; Asenjo, Felipe A.

2018-02-01

Magnetic reconnection in curved spacetime is studied by adopting a general-relativistic magnetohydrodynamic model that retains collisionless effects for both electron-ion and pair plasmas. A simple generalization of the standard Sweet-Parker model allows us to obtain the first-order effects of the gravitational field of a rotating black hole. It is shown that the black hole rotation acts to increase the length of azimuthal reconnection layers, thus leading to a decrease of the reconnection rate. However, when coupled to collisionless thermal-inertial effects, the net reconnection rate is enhanced with respect to what would happen in a purely collisional plasma due to a broadening of the reconnection layer. These findings identify an underlying interaction between gravity and collisionless magnetic reconnection in the vicinity of compact objects.

Integrable multi-component generalization of a modified short pulse equation

NASA Astrophysics Data System (ADS)

Matsuno, Yoshimasa

2016-11-01

We propose a multi-component generalization of the modified short pulse (SP) equation which was derived recently as a reduction of Feng's two-component SP equation. Above all, we address the two-component system in depth. We obtain the Lax pair, an infinite number of conservation laws and multisoliton solutions for the system, demonstrating its integrability. Subsequently, we show that the two-component system exhibits cusp solitons and breathers for which the detailed analysis is performed. Specifically, we explore the interaction process of two cusp solitons and derive the formula for the phase shift. While cusp solitons are singular solutions, smooth breather solutions are shown to exist, provided that the parameters characterizing the solutions satisfy certain conditions. Last, we discuss the relation between the proposed system and existing two-component SP equations.

Effects of interlayer Sn-Sn lone pair interaction on the band gap of bulk and nanosheet SnO

NASA Astrophysics Data System (ADS)

Umezawa, Naoto; Zhou, Wei

2015-03-01

Effects of interlayer lone-pair interactions on the electronic structure of SnO are firstly explored by the density-functional theory. Our comprehensive study reveals that the band gap of SnO opens as increase in the interlayer Sn-Sn distance. The effect is rationalized by the character of band edges which consists of bonding and anti-bonding states from interlayer lone pair interactions. The band edges for several nanosheets and strained double-layer SnO are estimated. We conclude that the double-layer SnO is a promising material for visible-light driven photocatalyst for hydrogen evolution. This work is supported by the Japan Science and Technology Agency (JST) Precursory Research for Embryonic Science and Technology (PRESTO) program.

Nonlinear interaction between a pair of oblique modes in a supersonic mixing layer: Long-wave limit

NASA Technical Reports Server (NTRS)

Balsa, Thomas F.; Gartside, James

1995-01-01

The nonlinear interaction between a pair of symmetric, oblique, and spatial instability modes is studied in the long-wave limit using asymptotic methods. The base flow is taken to be a supersonic mixing layer whose Mach number is such that the corresponding vortex sheet is marginally stable according to Miles' criterion. It is shown that the amplitude of the mode obeys a nonlinear integro-differential equation. Numerical solutions of this equation show that, when the obliqueness angle is less than pi/4, the effect of the nonlinearity is to enhance the growth rate of the instability. The solution terminates in a singularity at a finite streamwise location. This result is reminiscent of that obtained in the vicinity of the neutral point by other authors in several different types of flows. On the other hand, when the obliqueness angle is more than pi/4, the streamwise development of the amplitude is characterized by a series of modulations. This arises from the fact that the nonlinear term in the amplitude equation may be either stabilizing or destabilizing, depending on the value of the streamwise coordinate. However, even in this case the amplitude of the disturbance increases, though not as rapidly as in the case for which the angle is less than pi/4. Quite generally then, the nonlinear interaction between two oblique modes in a supersonic mixing layer enhances the growth of the disturbance.

Enthalpic Breakdown of Water Structure on Protein Active-Site Surfaces

PubMed Central

Haider, Kamran; Wickstrom, Lauren; Ramsey, Steven; Gilson, Michael K.; Kurtzman, Tom

2016-01-01

The principles underlying water reorganization around simple non-polar solutes are well understood and provide the framework for classical hydrophobic effect, whereby water molecules structure themselves around solutes so that they maintain favorable energetic contacts with both the solute and with other water molecules. However, for certain solute surface topographies, water molecules, due to their geometry and size, are unable to simultaneously maintain favorable energetic contacts with both the surface and neighboring water molecules. In this study, we analyze the solvation of ligand-binding sites for six structurally diverse proteins using hydration site analysis and measures of local water structure, in order to identify surfaces at which water molecules are unable to structure themselves in a way that maintains favorable enthalpy relative to bulk water. These surfaces are characterized by a high degree of enclosure, weak solute-water interactions, and surface constraints that induce unfavorable pair interactions between neighboring water molecules. Additionally, we find that the solvation of charged side-chains in an active site generally results in favorable enthalpy but can also lead to pair interactions between neighboring water molecules that are significantly unfavorable relative to bulk water. We find that frustrated local structure can occur not only in apolar and weakly polar pockets, where overall enthalpy tends to be unfavorable, but also in charged pockets, where overall water enthalpy tends to be favorable. The characterization of local water structure in these terms may prove useful for evaluating the displacement of water from diverse protein active-site environments. PMID:27169482

Cosmological BCS mechanism and the big bang singularity

NASA Astrophysics Data System (ADS)

Alexander, Stephon; Biswas, Tirthabir

2009-07-01

We provide a novel mechanism that resolves the big bang singularity present in Friedman-Lemaitre-Robertson-Walker space-times without the need for ghost fields. Building on the fact that a four-fermion interaction arises in general relativity when fermions are covariantly coupled, we show that at early times the decrease in scale factor enhances the correlation between pairs of fermions. This enhancement leads to a BCS-like condensation of the fermions and opens a gap dynamically driving the Hubble parameter H to zero and results in a nonsingular bounce, at least in some special cases.

Development Genetic Analysis of General Cognitive Ability from 1 to 12 Years in a Sample of Adoptees, Biological Siblings, and Twins.

ERIC Educational Resources Information Center

Bishop, E. G.; Cherny, Stacey S.; Corley, Robin; Plomin, Robert; DeFries, John C.; Hewitt, John K.

2003-01-01

Studied continuity and change in general cognitive ability from infancy to adolescence in adoptees (107 children), biological siblings (87 pairs), and twins (224 monozygotic and 189 dyzygotic pairs). Findings generally support previous findings about genetic and environmental factors, with the exception that in the transition to adolescence,…

Optimal self-cleavage activity of the hepatitis delta virus RNA is dependent on a homopurine base pair in the ribozyme core.

PubMed Central

Been, M D; Perrotta, A T

1995-01-01

A non-Watson-Crick G.G interaction within the core region of the hepatitis delta virus (HDV) antigenomic ribozyme is required for optimal rates of self-cleavage activity. Base substitutions for either one or both G's revealed that full activity was obtained only when both G's were replaced with A's. At those positions, substitutions that generate potential Watson-Crick, G.U, heteropurine, or homopyrimidine combinations resulted in dramatically lower cleavage activity. A homopurine symmetric base pair, of the same type identified in the high-affinity binding site of the HIV RRE, is most consistent with this data. Additional features shared between the antigenomic ribozyme and the Rev binding site in the vicinity of the homopurine pairs suggest some structural similarity for this region of the two RNAs and a possible motif associated with this homopurine interaction. Evidence for a homopurine pair at the equivalent position in a modified form of the HDV genomic ribozyme was also found. With the postulated symmetric pairing scheme, large distortions in the nucleotide conformation, the sugar-phosphate backbone, or both would be necessary to accommodate this interaction at the end of a helix; we hypothesize that this distortion is critical to the structure of the active site of the ribozyme and it is stabilized by the homopurine base pair. PMID:8595561

Central region component1, a novel synaptonemal complex component, is essential for meiotic recombination initiation in rice.

PubMed

Miao, Chunbo; Tang, Ding; Zhang, Honggen; Wang, Mo; Li, Yafei; Tang, Shuzhu; Yu, Hengxiu; Gu, Minghong; Cheng, Zhukuan

2013-08-01

In meiosis, homologous recombination entails programmed DNA double-strand break (DSB) formation and synaptonemal complex (SC) assembly coupled with the DSB repair. Although SCs display extensive structural conservation among species, their components identified are poorly conserved at the sequence level. Here, we identified a novel SC component, designated central region component1 (CRC1), in rice (Oryza sativa). CRC1 colocalizes with ZEP1, the rice SC transverse filament protein, to the central region of SCs in a mutually dependent fashion. Consistent with this colocalization, CRC1 interacts with ZEP1 in yeast two-hybrid assays. CRC1 is orthologous to Saccharomyces cerevisiae pachytene checkpoint2 (Pch2) and Mus musculus THYROID receptor-interacting protein13 (TRIP13) and may be a conserved SC component. Additionally, we provide evidence that CRC1 is essential for meiotic DSB formation. CRC1 interacts with homologous pairing aberration in rice meiosis1 (PAIR1) in vitro, suggesting that these proteins act as a complex to promote DSB formation. PAIR2, the rice ortholog of budding yeast homolog pairing1, is required for homologous chromosome pairing. We found that CRC1 is also essential for the recruitment of PAIR2 onto meiotic chromosomes. The roles of CRC1 identified here have not been reported for Pch2 or TRIP13.

CENTRAL REGION COMPONENT1, a Novel Synaptonemal Complex Component, Is Essential for Meiotic Recombination Initiation in Rice[C][W

PubMed Central

Miao, Chunbo; Tang, Ding; Zhang, Honggen; Wang, Mo; Li, Yafei; Tang, Shuzhu; Yu, Hengxiu; Gu, Minghong; Cheng, Zhukuan

2013-01-01

In meiosis, homologous recombination entails programmed DNA double-strand break (DSB) formation and synaptonemal complex (SC) assembly coupled with the DSB repair. Although SCs display extensive structural conservation among species, their components identified are poorly conserved at the sequence level. Here, we identified a novel SC component, designated CENTRAL REGION COMPONENT1 (CRC1), in rice (Oryza sativa). CRC1 colocalizes with ZEP1, the rice SC transverse filament protein, to the central region of SCs in a mutually dependent fashion. Consistent with this colocalization, CRC1 interacts with ZEP1 in yeast two-hybrid assays. CRC1 is orthologous to Saccharomyces cerevisiae pachytene checkpoint2 (Pch2) and Mus musculus THYROID RECEPTOR-INTERACTING PROTEIN13 (TRIP13) and may be a conserved SC component. Additionally, we provide evidence that CRC1 is essential for meiotic DSB formation. CRC1 interacts with HOMOLOGOUS PAIRING ABERRATION IN RICE MEIOSIS1 (PAIR1) in vitro, suggesting that these proteins act as a complex to promote DSB formation. PAIR2, the rice ortholog of budding yeast homolog pairing1, is required for homologous chromosome pairing. We found that CRC1 is also essential for the recruitment of PAIR2 onto meiotic chromosomes. The roles of CRC1 identified here have not been reported for Pch2 or TRIP13. PMID:23943860

Predominant Non-additive Effects of Multiple Stressors on Autotroph C:N:P Ratios Propagate in Freshwater and Marine Food Webs

PubMed Central

Villar-Argaiz, Manuel; Medina-Sánchez, Juan M.; Biddanda, Bopaiah A.; Carrillo, Presentación

2018-01-01

A continuing challenge for scientists is to understand how multiple interactive stressor factors affect biological interactions, and subsequently, ecosystems–in ways not easily predicted by single factor studies. In this review, we have compiled and analyzed available research on how multiple stressor pairs composed of temperature (T), light (L), ultraviolet radiation (UVR), nutrients (Nut), carbon dioxide (CO2), dissolved organic carbon (DOC), and salinity (S) impact the stoichiometry of autotrophs which in turn shapes the nature of their ecological interactions within lower trophic levels in streams, lakes and oceans. Our analysis from 66 studies with 320 observations of 11 stressor pairs, demonstrated that non-additive responses predominate across aquatic ecosystems and their net interactive effect depends on the stressor pair at play. Across systems, there was a prevalence of antagonism in freshwater (60–67% vs. 47% in marine systems) compared to marine systems where synergism was more common (49% vs. 33–40% in freshwaters). While the lack of data impeded comparisons among all of the paired stressors, we found pronounced system differences for the L × Nut interactions. For this interaction, our data for C:P and N:P is consistent with the initial hypothesis that the interaction was primarily synergistic in the oceans, but not for C:N. Our study found a wide range of variability in the net effects of the interactions in freshwater systems, with some observations supporting antagonism, and others synergism. Our results suggest that the nature of the stressor pairs interactions on C:N:P ratios regulates the “continuum” commensalistic-competitive-predatory relationship between algae and bacteria and the food chain efficiency at the algae-herbivore interface. Overall, the scarce number of studies with even more fewer replications in each study that are available for freshwater systems have prevented a more detailed, insightful analysis. Our findings highlighting the preponderance of antagonistic and synergistic effects of stressor interactions in aquatic ecosystems—effects that play key roles in the functioning of feedback loops in the biosphere—also stress the need for further studies evaluating the interactive effects of multiple stressors in a rapidly changing world facing a confluence of tipping points. PMID:29441051

Electrostatic screening in classical Coulomb fluids: exponential or power-law decay or both? An investigation into the effect of dispersion interactions

NASA Astrophysics Data System (ADS)

Kjellander, Roland

2006-04-01

It is shown that the nature of the non-electrostatic part of the pair interaction potential in classical Coulomb fluids can have a profound influence on the screening behaviour. Two cases are compared: (i) when the non-electrostatic part equals an arbitrary finite-ranged interaction and (ii) when a dispersion r-6 interaction potential is included. A formal analysis is done in exact statistical mechanics, including an investigation of the bridge function. It is found that the Coulombic r-1 and the dispersion r-6 potentials are coupled in a very intricate manner as regards the screening behaviour. The classical one-component plasma (OCP) is a particularly clear example due to its simplicity and is investigated in detail. When the dispersion r-6 potential is turned on, the screened electrostatic potential from a particle goes from a monotonic exponential decay, exp(-κr)/r, to a power-law decay, r-8, for large r. The pair distribution function acquire, at the same time, an r-10 decay for large r instead of the exponential one. There still remains exponentially decaying contributions to both functions, but these contributions turn oscillatory when the r-6 interaction is switched on. When the Coulomb interaction is turned off but the dispersion r-6 pair potential is kept, the decay of the pair distribution function for large r goes over from the r-10 to an r-6 behaviour, which is the normal one for fluids of electroneutral particles with dispersion interactions. Differences and similarities compared to binary electrolytes are pointed out.

Quantitative analysis of task selection for brain-computer interfaces

NASA Astrophysics Data System (ADS)

Llera, Alberto; Gómez, Vicenç; Kappen, Hilbert J.

2014-10-01

Objective. To assess quantitatively the impact of task selection in the performance of brain-computer interfaces (BCI). Approach. We consider the task-pairs derived from multi-class BCI imagery movement tasks in three different datasets. We analyze for the first time the benefits of task selection on a large-scale basis (109 users) and evaluate the possibility of transferring task-pair information across days for a given subject. Main results. Selecting the subject-dependent optimal task-pair among three different imagery movement tasks results in approximately 20% potential increase in the number of users that can be expected to control a binary BCI. The improvement is observed with respect to the best task-pair fixed across subjects. The best task-pair selected for each subject individually during a first day of recordings is generally a good task-pair in subsequent days. In general, task learning from the user side has a positive influence in the generalization of the optimal task-pair, but special attention should be given to inexperienced subjects. Significance. These results add significant evidence to existing literature that advocates task selection as a necessary step towards usable BCIs. This contribution motivates further research focused on deriving adaptive methods for task selection on larger sets of mental tasks in practical online scenarios.

Infrared Colors of Dwarf-Dwarf Galaxy Interactions

NASA Astrophysics Data System (ADS)

Liss, Sandra; Stierwalt, Sabrina; Johnson, Kelsey; Patton, Dave; Kallivayalil, Nitya

2015-10-01

We request Spitzer Warm Mission IRAC Channel 1 & 2 imaging for a sample of 60 isolated dwarf galaxy pairs as a key component of a larger, multi-wavelength effort to understand the role low-mass mergers play in galaxy evolution. A systematic study of dwarf-dwarf mergers has never been done, and we wish to characterize the impact such interactions have on fueling star formation in the nearby universe. The Spitzer imaging proposed here will allow us to determine the extent to which the 3.6 and 4.5 mum bands are dominated by stellar light and investigate a) the extent to which interacting pairs show IR excess and b) whether the excess is related to the pair separation. Second, we will use this IR photometry to constrain the processes contributing to the observed color excess and scatter in each system. We will take advantage of the wealth of observations available in the Spitzer Heritage Archive for 'normal' non-interacting dwarfs by comparing the stellar populations of those dwarfs with the likely interacting dwarfs in our sample. Ultimately, we can combine the Spitzer imaging proposed here with our current, ongoing efforts to obtain groundbased optical photometry to model the star formation histories of these dwarfs and to help constrain the timescales and impact dwarf-dwarf mergers have on fueling star formation. The sensitivity and resolution offered by Spitzer are necessary to determine the dust properties of these interacting systems, and how these properties vary as a function of pair separation, mass ratio, and gas fraction.

Analysing change in music therapy interactions of children with communication difficulties

PubMed Central

2016-01-01

Music therapy has been found to improve communicative behaviours and joint attention in children with autism, but it is unclear what in the music therapy sessions drives those changes. We developed an annotation protocol and tools to accumulate large datasets of music therapy, for analysis of interaction dynamics. Analysis of video recordings of improvisational music therapy sessions focused on simple, unambiguous individual and shared behaviours: movement and facing behaviours, rhythmic activity and musical structures and the relationships between them. To test the feasibility of the protocol, early and late sessions of five client–therapist pairs were annotated and analysed to track changes in behaviours. To assess the reliability and validity of the protocol, inter-rater reliability of the annotation tiers was calculated, and the therapists provided feedback about the relevance of the analyses and results. This small-scale study suggests that there are both similarities and differences in the profiles of client–therapist sessions. For example, all therapists faced the clients most of the time, while the clients did not face back so often. Conversely, only two pairs had an increase in regular pulse from early to late sessions. More broadly, similarity across pairs at a general level is complemented by variation in the details. This perhaps goes some way to reconciling client- and context-specificity on one hand and generalizability on the other. Behavioural characteristics seem to influence each other. For instance, shared rhythmic pulse alternated with mutual facing and the occurrence of shared pulse was found to relate to the musical structure. These observations point towards a framework for looking at change in music therapy that focuses on networks of variables or broader categories. The results suggest that even when starting with simple behaviours, we can trace aspects of interaction and change in music therapy, which are seen as relevant by therapists. PMID:27069051

Analysing change in music therapy interactions of children with communication difficulties.

PubMed

Spiro, Neta; Himberg, Tommi

2016-05-05

Music therapy has been found to improve communicative behaviours and joint attention in children with autism, but it is unclear what in the music therapy sessions drives those changes. We developed an annotation protocol and tools to accumulate large datasets of music therapy, for analysis of interaction dynamics. Analysis of video recordings of improvisational music therapy sessions focused on simple, unambiguous individual and shared behaviours: movement and facing behaviours, rhythmic activity and musical structures and the relationships between them. To test the feasibility of the protocol, early and late sessions of five client-therapist pairs were annotated and analysed to track changes in behaviours. To assess the reliability and validity of the protocol, inter-rater reliability of the annotation tiers was calculated, and the therapists provided feedback about the relevance of the analyses and results. This small-scale study suggests that there are both similarities and differences in the profiles of client-therapist sessions. For example, all therapists faced the clients most of the time, while the clients did not face back so often. Conversely, only two pairs had an increase in regular pulse from early to late sessions. More broadly, similarity across pairs at a general level is complemented by variation in the details. This perhaps goes some way to reconciling client- and context-specificity on one hand and generalizability on the other. Behavioural characteristics seem to influence each other. For instance, shared rhythmic pulse alternated with mutual facing and the occurrence of shared pulse was found to relate to the musical structure. These observations point towards a framework for looking at change in music therapy that focuses on networks of variables or broader categories. The results suggest that even when starting with simple behaviours, we can trace aspects of interaction and change in music therapy, which are seen as relevant by therapists. © 2016 The Authors.

A Genome-Wide Association Analysis Reveals Epistatic Cancellation of Additive Genetic Variance for Root Length in Arabidopsis thaliana.

PubMed

Lachowiec, Jennifer; Shen, Xia; Queitsch, Christine; Carlborg, Örjan

2015-01-01

Efforts to identify loci underlying complex traits generally assume that most genetic variance is additive. Here, we examined the genetics of Arabidopsis thaliana root length and found that the genomic narrow-sense heritability for this trait in the examined population was statistically zero. The low amount of additive genetic variance that could be captured by the genome-wide genotypes likely explains why no associations to root length could be found using standard additive-model-based genome-wide association (GWA) approaches. However, as the broad-sense heritability for root length was significantly larger, and primarily due to epistasis, we also performed an epistatic GWA analysis to map loci contributing to the epistatic genetic variance. Four interacting pairs of loci were revealed, involving seven chromosomal loci that passed a standard multiple-testing corrected significance threshold. The genotype-phenotype maps for these pairs revealed epistasis that cancelled out the additive genetic variance, explaining why these loci were not detected in the additive GWA analysis. Small population sizes, such as in our experiment, increase the risk of identifying false epistatic interactions due to testing for associations with very large numbers of multi-marker genotypes in few phenotyped individuals. Therefore, we estimated the false-positive risk using a new statistical approach that suggested half of the associated pairs to be true positive associations. Our experimental evaluation of candidate genes within the seven associated loci suggests that this estimate is conservative; we identified functional candidate genes that affected root development in four loci that were part of three of the pairs. The statistical epistatic analyses were thus indispensable for confirming known, and identifying new, candidate genes for root length in this population of wild-collected A. thaliana accessions. We also illustrate how epistatic cancellation of the additive genetic variance explains the insignificant narrow-sense and significant broad-sense heritability by using a combination of careful statistical epistatic analyses and functional genetic experiments.

Double-Wronskian solitons and rogue waves for the inhomogeneous nonlinear Schrödinger equation in an inhomogeneous plasma

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

Sun, Wen-Rong; Tian, Bo, E-mail: tian_bupt@163.com; Jiang, Yan

2014-04-15

Plasmas are the main constituent of the Universe and the cause of a vast variety of astrophysical, space and terrestrial phenomena. The inhomogeneous nonlinear Schrödinger equation is hereby investigated, which describes the propagation of an electron plasma wave packet with a large wavelength and small amplitude in a medium with a parabolic density and constant interactional damping. By virtue of the double Wronskian identities, the equation is proved to possess the double-Wronskian soliton solutions. Analytic one- and two-soliton solutions are discussed. Amplitude and velocity of the soliton are related to the damping coefficient. Asymptotic analysis is applied for us tomore » investigate the interaction between the two solitons. Overtaking interaction, head-on interaction and bound state of the two solitons are given. From the non-zero potential Lax pair, the first- and second-order rogue-wave solutions are constructed via a generalized Darboux transformation, and influence of the linear and parabolic density profiles on the background density and amplitude of the rogue wave is discussed. -- Highlights: •Double-Wronskian soliton solutions are obtained and proof is finished by virtue of some double Wronskian identities. •Asymptotic analysis is applied for us to investigate the interaction between the two solitons. •First- and second-order rogue-wave solutions are constructed via a generalized Darboux transformation. •Influence of the linear and parabolic density profiles on the background density and amplitude of the rogue wave is discussed.« less

nth-Nearest-neighbor distribution functions of an interacting fluid from the pair correlation function: a hierarchical approach.

PubMed

Bhattacharjee, Biplab

2003-04-01

The paper presents a general formalism for the nth-nearest-neighbor distribution (NND) of identical interacting particles in a fluid confined in a nu-dimensional space. The nth-NND functions, W(n,r) (for n=1,2,3, em leader) in a fluid are obtained hierarchically in terms of the pair correlation function and W(n-1,r) alone. The radial distribution function (RDF) profiles obtained from the molecular dynamics (MD) simulation of Lennard-Jones (LJ) fluid is used to illustrate the results. It is demonstrated that the collective structural information contained in the maxima and minima of the RDF profiles being resolved in terms of individual NND functions may provide more insights about the microscopic neighborhood structure around a reference particle in a fluid. Representative comparison between the results obtained from the formalism and the MD simulation data shows good agreement. Apart from the quantities such as nth-NND functions and nth-nearest-neighbor distances, the average neighbor population number is defined. These quantities are evaluated for the LJ model system and interesting density dependence of the microscopic neighborhood shell structures are discussed in terms of them. The relevance of the NND functions in various phenomena is also pointed out.

nth-nearest-neighbor distribution functions of an interacting fluid from the pair correlation function: A hierarchical approach

NASA Astrophysics Data System (ADS)

Bhattacharjee, Biplab

2003-04-01

The paper presents a general formalism for the nth-nearest-neighbor distribution (NND) of identical interacting particles in a fluid confined in a ν-dimensional space. The nth-NND functions, W(n,r¯) (for n=1,2,3,…) in a fluid are obtained hierarchically in terms of the pair correlation function and W(n-1,r¯) alone. The radial distribution function (RDF) profiles obtained from the molecular dynamics (MD) simulation of Lennard-Jones (LJ) fluid is used to illustrate the results. It is demonstrated that the collective structural information contained in the maxima and minima of the RDF profiles being resolved in terms of individual NND functions may provide more insights about the microscopic neighborhood structure around a reference particle in a fluid. Representative comparison between the results obtained from the formalism and the MD simulation data shows good agreement. Apart from the quantities such as nth-NND functions and nth-nearest-neighbor distances, the average neighbor population number is defined. These quantities are evaluated for the LJ model system and interesting density dependence of the microscopic neighborhood shell structures are discussed in terms of them. The relevance of the NND functions in various phenomena is also pointed out.

Spatial variation in pollinator-mediated selection on phenology, floral display and spur length in the orchid Gymnadenia conopsea.

PubMed

Chapurlat, Elodie; Ågren, Jon; Sletvold, Nina

2015-12-01

Spatial variation in plant-pollinator interactions may cause variation in pollinator-mediated selection on floral traits, but to establish this link conclusively experimental studies are needed. We quantified pollinator-mediated selection on flowering phenology and morphology in four populations of the fragrant orchid Gymnadenia conopsea, and compared selection mediated by diurnal and nocturnal pollinators in two of the populations. Variation in pollinator-mediated selection explained most of the among-population variation in the strength of directional and correlational selection. Pollinators mediated correlational selection on pairs of display traits, and on one display trait and spur length, a trait affecting pollination efficiency. Only nocturnal pollinators selected for longer spurs, and mediated stronger selection on the number of flowers compared with diurnal pollinators in one population. The two types of pollinators caused correlational selection on different pairs of traits and selected for different combinations of spur length and number of flowers. The results demonstrate that spatial variation in interactions with pollinators may result in differences in directional and correlational selection on floral traits in a plant with a semi-generalized pollination system, and suggest that differences in the relative importance of diurnal and nocturnal pollinators can cause variation in selection. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Hartree-Fock treatment of Fermi polarons using the Lee-Low-Pine transformation

NASA Astrophysics Data System (ADS)

Kain, Ben; Ling, Hong Y.

2017-09-01

We consider the Fermi polaron problem at zero temperature, where a single impurity interacts with noninteracting host fermions. We approach the problem starting with a Fröhlich-like Hamiltonian where the impurity is described with canonical position and momentum operators. We apply the Lee-Low-Pine (LLP) transformation to change the fermionic Fröhlich Hamiltonian into the fermionic LLP Hamiltonian, which describes a many-body system containing host fermions only. We adapt the self-consistent Hartree-Fock (HF) approach, first proposed by Edwards, to the fermionic LLP Hamiltonian in which a pair of host fermions with momenta k and k' interact with a potential proportional to k .k' . We apply the HF theory, which has the advantage of not restricting the number of particle-hole pairs, to repulsive Fermi polarons in one dimension. When the impurity and host fermion masses are equal our variational ansatz, where HF orbitals are expanded in terms of free-particle states, produces results in excellent agreement with McGuire's exact analytical results based on the Bethe ansatz. This work raises the prospect of using the HF ansatz and its time-dependent generalization as building blocks for developing all-coupling theories for both equilibrium and nonequilibrium Fermi polarons in higher dimensions.

Electronic structure and normal vibrations of the 1-ethyl-3-methylimidazolium ethyl sulfate ion pair.

PubMed

Dhumal, Nilesh R; Kim, Hyung J; Kiefer, Johannes

2011-04-21

Electronic and structural properties of the ion pair 1-ethyl-3-methylimidazolium ethyl sulfate are studied using density functional methods. Three locally stable conformers of the ion pair complex are considered to analyze molecular interactions between its cation and anion. Manifestations of these interactions in the vibrational spectra are discussed and compared with experimental IR and Raman spectroscopy data. NBO analysis and difference electron density coupled with molecular electron density topography are used to interpret the frequency shifts of the normal vibrations of the ion pair, compared to the free anion and cation. Excitation energies of low-lying singlet excited states of the conformers are also studied. The density functional theory results are found to be in a reasonable agreement with experimental UV/vis absorption spectra.

Monitoring molecular interactions using photon arrival-time interval distribution analysis

DOEpatents

Laurence, Ted A [Livermore, CA; Weiss, Shimon [Los Angels, CA

2009-10-06

A method for analyzing/monitoring the properties of species that are labeled with fluorophores. A detector is used to detect photons emitted from species that are labeled with one or more fluorophores and located in a confocal detection volume. The arrival time of each of the photons is determined. The interval of time between various photon pairs is then determined to provide photon pair intervals. The number of photons that have arrival times within the photon pair intervals is also determined. The photon pair intervals are then used in combination with the corresponding counts of intervening photons to analyze properties and interactions of the molecules including brightness, concentration, coincidence and transit time. The method can be used for analyzing single photon streams and multiple photon streams.

Thermophysical properties of simple liquid metals: A brief review of theory

NASA Technical Reports Server (NTRS)

Stroud, David

1993-01-01

In this paper, we review the current theory of the thermophysical properties of simple liquid metals. The emphasis is on thermodynamic properties, but we also briefly discuss the nonequilibrium properties of liquid metals. We begin by defining a 'simple liquid metal' as one in which the valence electrons interact only weakly with the ionic cores, so that the interaction can be treated by perturbation theory. We then write down the equilibrium Hamiltonian of a liquid metal as a sum of five terms: the bare ion-ion interaction, the electron-electron interaction, the bare electron-ion interaction, and the kinetic energies of electrons and ions. Since the electron-ion interaction can be treated by perturbation, the electronic part contributes in two ways to the Helmholtz free energy: it gives a density-dependent term which is independent of the arrangement of ions, and it acts to screen the ion-ion interaction, giving rise to effective ion-ion pair potentials which are density-dependent, in general. After sketching the form of a typical pair potential, we briefly enumerate some methods for calculating the ionic distribution function and hence the Helmholtz free energy of the liquid: monte Carlo simulations, molecular dynamics simulations, and thermodynamic perturbation theory. The final result is a general expression for the Helmholtz free energy of the liquid metal. It can be used to calculate a wide range of thermodynamic properties of simple metal liquids, which we enumerate. They include not only a range of thermodynamic coefficients of both metals and alloys, but also many aspects of the phase diagram, including freezing curves of pure elements and phase diagrams of liquid alloys (including liquidus and solidus curves). We briefly mention some key discoveries resulting from previous applications of this method, and point out that the same methods work for other materials not normally considered to be liquid metals (such as colloidal suspensions, in which the suspended microspheres behave like ions screened by the salt solution in which they are suspended). We conclude with a brief discussion of some non-equilibrium (i.e., transport) properties which can be treated by an extension of these methods. These include electrical resistivity, thermal conductivity, viscosity, atomic self-diffusion coefficients, concentration diffusion coefficients in alloys, surface tension and thermal emissivity. Finally, we briefly mention two methods by which the theory might be extended to non-simple liquid metals: these are empirical techniques (i.e., empirical two- and three-body potentials), and numerical many-body approaches. Both may be potentially applicable to extremely complex systems, such as nonstoichiometric liquid semiconductor alloys.

Genome-wide gene–gene interaction analysis for next-generation sequencing

PubMed Central

Zhao, Jinying; Zhu, Yun; Xiong, Momiao

2016-01-01

The critical barrier in interaction analysis for next-generation sequencing (NGS) data is that the traditional pairwise interaction analysis that is suitable for common variants is difficult to apply to rare variants because of their prohibitive computational time, large number of tests and low power. The great challenges for successful detection of interactions with NGS data are (1) the demands in the paradigm of changes in interaction analysis; (2) severe multiple testing; and (3) heavy computations. To meet these challenges, we shift the paradigm of interaction analysis between two SNPs to interaction analysis between two genomic regions. In other words, we take a gene as a unit of analysis and use functional data analysis techniques as dimensional reduction tools to develop a novel statistic to collectively test interaction between all possible pairs of SNPs within two genome regions. By intensive simulations, we demonstrate that the functional logistic regression for interaction analysis has the correct type 1 error rates and higher power to detect interaction than the currently used methods. The proposed method was applied to a coronary artery disease dataset from the Wellcome Trust Case Control Consortium (WTCCC) study and the Framingham Heart Study (FHS) dataset, and the early-onset myocardial infarction (EOMI) exome sequence datasets with European origin from the NHLBI's Exome Sequencing Project. We discovered that 6 of 27 pairs of significantly interacted genes in the FHS were replicated in the independent WTCCC study and 24 pairs of significantly interacted genes after applying Bonferroni correction in the EOMI study. PMID:26173972

Reciprocal Altruism: The Effect of Self-Esteem and Anticipation of Face-to-Face Interaction on Reciprocation.

ERIC Educational Resources Information Center

Gregor, Gary L.; Conner, Hubert

The study attempts to measure the effects of self-esteem and face-to-face interaction on a person's giving behavior (altruism). Seventy-two introductory psychology students were paired on a task which required that one of each pair become "indebted" to the other. Their roles were then reversed, and data was collected to see if the…

Hot carrier-enhanced interlayer electron-hole pair multiplication in 2D semiconductor heterostructure photocells

NASA Astrophysics Data System (ADS)

Barati, Fatemeh; Grossnickle, Max; Su, Shanshan; Lake, Roger K.; Aji, Vivek; Gabor, Nathaniel M.

2017-12-01

Strong electronic interactions can result in novel particle-antiparticle (electron-hole, e-h) pair generation effects, which may be exploited to enhance the photoresponse of nanoscale optoelectronic devices. Highly efficient e-h pair multiplication has been demonstrated in several important nanoscale systems, including nanocrystal quantum dots, carbon nanotubes and graphene. The small Fermi velocity and nonlocal nature of the effective dielectric screening in ultrathin layers of transition-metal dichalcogenides (TMDs) indicates that e-h interactions are very strong, so high-efficiency generation of e-h pairs from hot electrons is expected. However, such e-h pair multiplication has not been observed in 2D TMD devices. Here, we report the highly efficient multiplication of interlayer e-h pairs in 2D semiconductor heterostructure photocells. Electronic transport measurements of the interlayer I-VSD characteristics indicate that layer-indirect e-h pairs are generated by hot-electron impact excitation at temperatures near T = 300 K. By exploiting this highly efficient interlayer e-h pair multiplication process, we demonstrate near-infrared optoelectronic devices that exhibit 350% enhancement of the optoelectronic responsivity at microwatt power levels. Our findings, which demonstrate efficient carrier multiplication in TMD-based optoelectronic devices, make 2D semiconductor heterostructures viable for a new class of ultra-efficient photodetectors based on layer-indirect e-h excitations.

Relationship between ion pair geometries and electrostatic strengths in proteins.

PubMed Central

Kumar, Sandeep; Nussinov, Ruth

2002-01-01

The electrostatic free energy contribution of an ion pair in a protein depends on two factors, geometrical orientation of the side-chain charged groups with respect to each other and the structural context of the ion pair in the protein. Conformers in NMR ensembles enable studies of the relationship between geometry and electrostatic strengths of ion pairs, because the protein structural contexts are highly similar across different conformers. We have studied this relationship using a dataset of 22 unique ion pairs in 14 NMR conformer ensembles for 11 nonhomologous proteins. In different NMR conformers, the ion pairs are classified as salt bridges, nitrogen-oxygen (N-O) bridges and longer-range ion pairs on the basis of geometrical criteria. In salt bridges, centroids of the side-chain charged groups and at least a pair of side-chain nitrogen and oxygen atoms of the ion-pairing residues are within a 4 A distance. In N-O bridges, at least a pair of the side-chain nitrogen and oxygen atoms of the ion-pairing residues are within 4 A distance, but the distance between the side-chain charged group centroids is greater than 4 A. In the longer-range ion pairs, the side-chain charged group centroids as well as the side-chain nitrogen and oxygen atoms are more than 4 A apart. Continuum electrostatic calculations indicate that most of the ion pairs have stabilizing electrostatic contributions when their side-chain charged group centroids are within 5 A distance. Hence, most (approximately 92%) of the salt bridges and a majority (68%) of the N-O bridges are stabilizing. Most (approximately 89%) of the destabilizing ion pairs are the longer-range ion pairs. In the NMR conformer ensembles, the electrostatic interaction between side-chain charged groups of the ion-pairing residues is the strongest for salt bridges, considerably weaker for N-O bridges, and the weakest for longer-range ion pairs. These results suggest empirical rules for stabilizing electrostatic interactions in proteins. PMID:12202384

High-T C superconductivity in Cs3C60 compounds governed by local Cs-C60 Coulomb interactions

NASA Astrophysics Data System (ADS)

Harshman, Dale R.; Fiory, Anthony T.

2017-04-01

Unique among alkali-doped A 3C60 fullerene compounds, the A15 and fcc forms of Cs3C60 exhibit superconducting states varying under hydrostatic pressure with highest transition temperatures at T\\text{C}\\text{meas}   =  38.3 and 35.2 K, respectively. Herein it is argued that these two compounds under pressure represent the optimal materials of the A 3C60 family, and that the C60-associated superconductivity is mediated through Coulombic interactions with charges on the alkalis. A derivation of the interlayer Coulombic pairing model of high-T C superconductivity employing non-planar geometry is introduced, generalizing the picture of two interacting layers to an interaction between charge reservoirs located on the C60 and alkali ions. The optimal transition temperature follows the algebraic expression, T C0  =  (12.474 nm2 K)/ℓζ, where ℓ relates to the mean spacing between interacting surface charges on the C60 and ζ is the average radial distance between the C60 surface and the neighboring Cs ions. Values of T C0 for the measured cation stoichiometries of Cs3-x C60 with x  ≈  0 are found to be 38.19 and 36.88 K for the A15 and fcc forms, respectively, with the dichotomy in transition temperature reflecting the larger ζ and structural disorder in the fcc form. In the A15 form, modeled interacting charges and Coulomb potential e2/ζ are shown to agree quantitatively with findings from nuclear-spin relaxation and mid-infrared optical conductivity. In the fcc form, suppression of T\\text{C}\\text{meas} below T C0 is ascribed to native structural disorder. Phononic effects in conjunction with Coulombic pairing are discussed.

Pairing of heterochromatin in response to cellular stress.

PubMed

Abdel-Halim, H I; Mullenders, L H F; Boei, J J W A

2006-07-01

We previously reported that exposure of human cells to DNA-damaging agents (X-rays and mitomycin C (MMC)) induces pairing of the homologous paracentromeric heterochromatin of chromosome 9 (9q12-13). Here, we show that UV irradiation and also heat shock treatment of human cells lead to similar effects. Since the various agents induce very different types and frequencies of damage to cellular constituents, the data suggest a general stress response as the underlying mechanism. Moreover, local UV irradiation experiments revealed that pairing of heterochromatin is an event that can be triggered without induction of DNA damage in the heterochromatic sequences. The repair deficient xeroderma pigmentosum cells (group F) previously shown to fail pairing after MMC displayed elevated pairing after heat shock treatment but not after UV exposure. Taken together, the present results indicate that pairing of heterochromatin following exposure to DNA-damaging agents is initiated by a general stress response and that the sensing of stress or the maintenance of the paired status of the heterochromatin might be dependent on DNA repair.

Colour assortative pairing in a colour polymorphic lizard is independent of population morph diversity

NASA Astrophysics Data System (ADS)

Pérez i de Lanuza, Guillem; Font, Enrique; Carretero, Miguel Ángel

2016-10-01

Previous work with a colour polymorphic population of Podarcis muralis (Lacertidae) revealed that lizards pair by ventral colour, favouring the same colour (i.e. homomorphic) pairs. Such assortative pairing, which probably results in colour assortative mating, can have consequences for the genetic structure of the population and potentially promote speciation. The population previously studied, located in the Pyrenees, encompasses white, yellow and orange animals, as well as intermediate white-orange and yellow-orange morphs. However, other Pyrenean populations of P. muralis have less ventral colour morphs. Our aim in this study is to test the generality of the assortative colour pairing system, extending our previous analyses to populations with different morph compositions and frequencies. The results show that the assortative pattern of pairing is similar in all the populations analysed and, hence, independent of morph composition and not restricted to pentamorphic populations. This suggests that assortative pairing by colour is a general phenomenon for colour polymorphic populations of P. muralis.

Pairing matrix elements and pairing gaps with bare, effective, and induced interactions

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

Barranco, F.; Bortignon, P.F.; Colo, G.

2005-11-01

The dependence on the single-particle states of the pairing matrix elements of the Gogny force and of the bare low-momentum nucleon-nucleon potential v{sub low-k}--designed so as to reproduce the low-energy observables avoiding the use of a repulsive core--is studied for a typical finite, superfluid nucleus ({sup 120}Sn). It is found that the matrix elements of v{sub low-k} follow closely those of v{sub Gogny} on a wide range of energy values around the Fermi energy e{sub F}, those associated with v{sub low-k} being less attractive. This result explains the fact that around e{sub F} the pairing gap {delta}{sub Gogny} associated withmore » the Gogny interaction (and with a density of single-particle levels corresponding to an effective k mass m{sub k}{approx_equal}0.7 m) is a factor of about 2 larger than {delta}{sub low-k}, being in agreement with {delta}{sub exp}=1.4 MeV. The exchange of low-lying collective surface vibrations among pairs of nucleons moving in time-reversal states gives rise to an induced pairing interaction v{sub ind} peaked at e{sub F}. The interaction (v{sub low-k}+v{sub ind}) Z{sub {omega}} arising from the renormalization of the bare nucleon-nucleon potential and of the single-particle motion ({omega}-mass and quasiparticle strength Z{sub {omega}}) associated with the particle-vibration coupling mechanism, leads to a value of the pairing gap at the Fermi energy {delta}{sub ren} that accounts for the experimental value. An important question that remains to be studied quantitatively is to what extent {delta}{sub Gogny}, which depends on average parameters, and {delta}{sub ren}, which explicitly depends on the parameters describing the (low-energy) nuclear structure, display or not a similar isotopic dependence and whether this dependence is borne out by the data.« less

Identification of expression quantitative trait loci by the interaction analysis using genetic algorithm.

PubMed

Namkung, Junghyun; Nam, Jin-Wu; Park, Taesung

2007-01-01

Many genes with major effects on quantitative traits have been reported to interact with other genes. However, finding a group of interacting genes from thousands of SNPs is challenging. Hence, an efficient and robust algorithm is needed. The genetic algorithm (GA) is useful in searching for the optimal solution from a very large searchable space. In this study, we show that genome-wide interaction analysis using GA and a statistical interaction model can provide a practical method to detect biologically interacting loci. We focus our search on transcriptional regulators by analyzing gene x gene interactions for cancer-related genes. The expression values of three cancer-related genes were selected from the expression data of the Genetic Analysis Workshop 15 Problem 1 data set. We implemented a GA to identify the expression quantitative trait loci that are significantly associated with expression levels of the cancer-related genes. The time complexity of the GA was compared with that of an exhaustive search algorithm. As a result, our GA, which included heuristic methods, such as archive, elitism, and local search, has greatly reduced computational time in a genome-wide search for gene x gene interactions. In general, the GA took one-fifth the computation time of an exhaustive search for the most significant pair of single-nucleotide polymorphisms.

Identification of expression quantitative trait loci by the interaction analysis using genetic algorithm

PubMed Central

Namkung, Junghyun; Nam, Jin-Wu; Park, Taesung

2007-01-01

Many genes with major effects on quantitative traits have been reported to interact with other genes. However, finding a group of interacting genes from thousands of SNPs is challenging. Hence, an efficient and robust algorithm is needed. The genetic algorithm (GA) is useful in searching for the optimal solution from a very large searchable space. In this study, we show that genome-wide interaction analysis using GA and a statistical interaction model can provide a practical method to detect biologically interacting loci. We focus our search on transcriptional regulators by analyzing gene × gene interactions for cancer-related genes. The expression values of three cancer-related genes were selected from the expression data of the Genetic Analysis Workshop 15 Problem 1 data set. We implemented a GA to identify the expression quantitative trait loci that are significantly associated with expression levels of the cancer-related genes. The time complexity of the GA was compared with that of an exhaustive search algorithm. As a result, our GA, which included heuristic methods, such as archive, elitism, and local search, has greatly reduced computational time in a genome-wide search for gene × gene interactions. In general, the GA took one-fifth the computation time of an exhaustive search for the most significant pair of single-nucleotide polymorphisms. PMID:18466570

Generalization of Turbulent Pair Dispersion to Large Initial Separations

NASA Astrophysics Data System (ADS)

Shnapp, Ron; Liberzon, Alex; International Collaboration for Turbulence Research

2018-06-01

We present a generalization of turbulent pair dispersion to large initial separations (η

Counteranion-Mediated Intrinsic Healing of Poly(ionic liquid) Copolymers.

PubMed

Guo, Panlong; Zhang, Houyu; Liu, Xiaokong; Sun, Junqi

2018-01-17

Fabrication of self-healing/healable materials using reversible interactions that are governed by their inherent chemical features is highly desirable because it avoids the introduction of extra groups that may present negative effects on their functions. The present study exploits the inherently featured electrostatic interactions of the ion pairs in polymeric ionic liquids (PILs) as the driving force to fabricate healable PIL copolymers. The healable PIL copolymers are fabricated through the copolymerization of the IL monomers with ethyl acrylate followed by the replacement of Br - counteranions with bulkier ones such as bis(trifluoromethanesulfonyl)imide (TFSI - ). Without modifying the chemical structures of the PIL moieties, the healing performance of the as-prepared PIL copolymers can be effectively mediated by their counteranions. The PIL copolymers that do not possess healability when paired with Br - counteranions become healable after exchanging the Br - counteranions with larger-sized ones (e.g., TFSI - ). The PIL copolymers paired with bulky counteranions exhibit enhanced chain mobility and highly reversible ion-pair interactions, which facilitate the healing process. The PIL copolymers paired with TFSI - anions can completely heal the damage/cut upon heating at 55 °C for 7.5 h. Meanwhile, the counteranions with larger sizes not only benefit the healing performance of the PIL copolymers but also enhance their ion conductivity. The ion conductivity of the PIL copolymers paired with TFSI - is an order of magnitude higher than that of the PIL copolymers paired with Br - . Therefore, the as-prepared healable PIL copolymers are potentially useful as solid electrolytes in PIL-based energy devices to improve their safety and reliability.

Hfq restructures RNA-IN and RNA-OUT and facilitates antisense pairing in the Tn10/IS10 system

PubMed Central

Ross, Joseph A.; Ellis, Michael J.; Hossain, Shahan; Haniford, David B.

2013-01-01

Hfq functions in post-transcriptional gene regulation in a wide range of bacteria, usually by promoting base-pairing of mRNAs and trans-encoded sRNAs that share partial sequence complementarity. It is less clear if Hfq is required for pairing of cis-encoded RNAs (i.e., antisense RNAs) with their target mRNAs. In the current work, we have characterized the interactions between Escherichia coli Hfq and the components of the Tn10/IS10 antisense system, RNA-IN and RNA-OUT. We show that Hfq interacts with RNA-OUT through its proximal RNA-binding surface, as is typical for Hfq and trans-encoded sRNAs. In contrast, RNA-IN binds both proximal and distal RNA-binding surfaces in Hfq with a higher affinity for the latter, as is typical for mRNA interactions in canonical sRNA-mRNA pairs. Importantly, an amino acid substitution in Hfq that interferes with RNA binding to the proximal site negatively impacts RNA-IN:OUT pairing in vitro and suppresses the ability of Hfq to negatively regulate IS10 transposition in vivo. We also show that Hfq binding to RNA-IN and RNA-OUT alters secondary structure elements in both of these RNAs and speculate that this could be important in how Hfq facilitates RNA-IN:OUT pairing. Based on the results presented here, we suggest that Hfq could be involved in regulating RNA pairing in other antisense systems, including systems encoded by other transposable elements. PMID:23510801

Electron spin resonance for the detection of long-range spin nematic order

NASA Astrophysics Data System (ADS)

Furuya, Shunsuke C.; Momoi, Tsutomu

2018-03-01

Spin nematic phase is a quantum magnetic phase characterized by a quadrupolar order parameter. Since the quadrupole operators are directly coupled to neither the magnetic field nor the neutron, currently, it is an important issue to develop a method for detecting the long-range spin nematic order. In this paper, we propose that electron spin resonance (ESR) measurements enable us to detect the long-range spin nematic order. We show that the frequency of the paramagnetic resonance peak in the ESR spectrum is shifted by the ferroquadrupolar order parameter together with other quantities. The ferroquadrupolar order parameter is extractable from the angular dependence of the frequency shift. In contrast, the antiferroquadrupolar order parameter is usually invisible in the frequency shift. Instead, the long-range antiferroquadrupolar order yields a characteristic resonance peak in the ESR spectrum, which we call a magnon-pair resonance peak. This resonance corresponds to the excitation of the bound magnon pair at the wave vector k =0 . Reflecting the condensation of bound magnon pairs, the field dependence of the magnon-pair resonance frequency shows a singular upturn at the saturation field. Moreover, the intensity of the magnon-pair resonance peak shows a characteristic angular dependence and it vanishes when the magnetic field is parallel to one of the axes that diagonalize the weak anisotropic interactions. We confirm these general properties of the magnon-pair resonance peak in the spin nematic phase by studying an S =1 bilinear-biquadratic model on the square lattice in the linear flavor-wave approximation. In addition, we argue applications to the S =1/2 frustrated ferromagnets and also the S =1/2 orthogonal dimer spin system SrCu2(BO3)2, both of which are candidate materials of spin nematics. Our theory for the antiferroquadrupolar ordered phase is consistent with many features of the magnon-pair resonance peak experimentally observed in the low-magnetization regime of SrCu2(BO3)2.

Pair correlations in low-lying T =0 states of odd-odd nuclei with six nucleons

NASA Astrophysics Data System (ADS)

Fu, G. J.; Zhao, Y. M.; Arima, A.

2018-02-01

In this paper, we study pair correlations in low-lying T =0 states for two typical cases of odd-odd N =Z nuclei. The first case is six nucleons in a single j =9 /2 shell, for which we study the S -broken-pair approximation, the isoscalar spin-1 pair condensation, and the isoscalar spin-aligned pair condensation, with schematic interactions. In the second case, we study pair approximations and correlation energies for 22Na, 34Cl, 46V, 62Ga, and 94Ag in multi-j shells with effective interactions. A few T =0 states are found to be well represented by isoscalar nucleon pairs. The isoscalar spin-aligned pairs play an important role for the yrast T =0 states with I ˜2 j and I ˜Imax in 22Na, 46V, and 94Ag. The overlap between the isoscalar J =1 pair wave function and the shell-model wave function is around 0.5 for the I =1 ,3 states of 34Cl and the I =1 state of 94Ag. The I =9 state of 62Ga is very well described by the isoscalar J =3 pair condensation. The broken-pair approximation (which is similar to the 2-quasiparticle excitation of the isovector pair condensation) is appropriate for quite few states, such as the I =1 -3 states of 34Cl and the I =5 state of 62Ga. The correlation energies are presented in this paper. It is noted that the picture based on nucleon-pair wave functions is not always in agreement with the picture based on correlation energies.

Isoscalar neutron-proton pairing and SU(4)-symmetry breaking in Gamow-Teller transitions

NASA Astrophysics Data System (ADS)

Kaneko, K.; Sun, Y.; Mizusaki, T.

2018-05-01

The isoscalar neutron-proton pairing is thought to be important for nuclei with equal number of protons and neutrons but its manifestation in structure properties remains to be understood. We investigate the Gamow-Teller (GT) transitions for the f7 /2-shell nuclei in large-scale shell-model calculations with the realistic Hamiltonian. We show that the isoscalar T =0 ,Jπ=1+ neutron-proton pairing interaction plays a decisive role for the concentration of GT strengths at the first-excited 11+ state in 42Sc, and that the suppression of these strengths in 46V, 50Mn, and 54Co is mainly caused by the spin-orbit force supplemented by the quadrupole-quadrupole interaction. Based on the good reproduction of the charge-exchange reaction data, we further analyze the interplay between the isoscalar and isovector pairing correlations. We conclude that even for the most promising A =42 nuclei where the SU(4) isoscalar-isovector-pairing symmetry is less broken, the probability of forming an isoscalar neutron-proton pairing condensation is less than 60% as compared to the expectation at the SU(4)-symmetry limit.

Direct evidence for a magnetic f-electron–mediated pairing mechanism of heavy-fermion superconductivity in CeCoIn5

PubMed Central

Van Dyke, John S.; Massee, Freek; Allan, Milan P.; Davis, J. C. Séamus; Petrovic, Cedomir; Morr, Dirk K.

2014-01-01

To identify the microscopic mechanism of heavy-fermion Cooper pairing is an unresolved challenge in quantum matter studies; it may also relate closely to finding the pairing mechanism of high-temperature superconductivity. Magnetically mediated Cooper pairing has long been the conjectured basis of heavy-fermion superconductivity but no direct verification of this hypothesis was achievable. Here, we use a novel approach based on precision measurements of the heavy-fermion band structure using quasiparticle interference imaging to reveal quantitatively the momentum space (k-space) structure of the f-electron magnetic interactions of CeCoIn5. Then, by solving the superconducting gap equations on the two heavy-fermion bands Ekα,β with these magnetic interactions as mediators of the Cooper pairing, we derive a series of quantitative predictions about the superconductive state. The agreement found between these diverse predictions and the measured characteristics of superconducting CeCoIn5 then provides direct evidence that the heavy-fermion Cooper pairing is indeed mediated by f-electron magnetism. PMID:25062692

Can honey bees discriminate between floral-fragrance isomers?

PubMed

Aguiar, João Marcelo Robazzi Bignelli Valente; Roselino, Ana Carolina; Sazima, Marlies; Giurfa, Martin

2018-05-24

Many flowering plants present variable complex fragrances, which usually include different isomers of the same molecule. As fragrance is an essential cue for flower recognition by pollinators, we ask if honey bees discriminate between floral-fragrance isomers in an appetitive context. We used the olfactory conditioning of the proboscis extension response (PER), which allows training a restrained bee to an odor paired with sucrose solution. Bees were trained under an absolute (a single odorant rewarded) or a differential conditioning regime (a rewarded vs. a non-rewarded odorant) using four different pairs of isomers. One hour after training, discrimination and generalization between pairs of isomers were tested. Bees trained under absolute conditioning exhibited high generalization between isomers and discriminated only one out of four isomer pairs; after differential conditioning, they learned to differentiate between two out of four pairs of isomers but in all cases generalization responses to the non-rewarding isomer remained high. Adding an aversive taste to the non-rewarded isomer facilitated discrimination of isomers that otherwise seemed non-discriminable, but generalization remained high. Although honey bees discriminated isomers under certain conditions, they achieved the task with difficulty and tended to generalize between them, thus showing that these molecules were perceptually similar to them. We conclude that the presence of isomers within floral fragrances might not necessarily contribute to a dramatic extent to floral odor diversity. © 2018. Published by The Company of Biologists Ltd.

A first-principles model of copper-boron interactions in Si: implications for the light-induced degradation of solar Si

NASA Astrophysics Data System (ADS)

Wright, E.; Coutinho, J.; Öberg, S.; Torres, V. J. B.

2017-02-01

The recent discovery that Cu contamination of Si combined with light exposure has a significant detrimental impact on carrier life-time has drawn much concern within the solar-Si community. The effect, known as the copper-related light-induced degradation (Cu-LID) of Si solar cells, has been connected to the release of Cu interstitials within the bulk (2016 Sol. Energy Mater. Sol. Cells 147 115-26). In this paper, we describe a comprehensive analysis of the formation/dissociation process of the CuB pair in Si by means of first-principles modelling, as well as the interaction of CuB defects with photo-excited minority carriers. We confirm that the long-range interaction between the \\text{Cu}\\text{i}+ cation and the \\text{B}\\text{s}- anion has a Coulomb-like behaviour, in line with the trapping-limited diffusivity of Cu observed by transient ion drift measurements. On the other hand, the short-range interaction between the d-electrons of Cu and the excess of negative charge on \\text{B}\\text{s}- produces a repulsive effect, thereby decreasing the binding energy of the pair when compared to the ideal point-charge Coulomb model. We also find that metastable CuB pairs produce acceptor states just below the conduction band minimum, which arise from the Cu level emptied by the B acceptor. Based on these results, we argue that photo-generated minority carriers trapped by the metastable pairs can switch off the Coulomb interaction that holds the pairs together, enhancing the release of Cu interstitials, and acting as a catalyst for Cu-LID.

Social Experience Is Sufficient to Modulate Sleep Need of Drosophila without Increasing Wakefulness.

PubMed

Lone, Shahnaz Rahman; Potdar, Sheetal; Srivastava, Manishi; Sharma, Vijay Kumar

2016-01-01

Organisms quickly learn about their surroundings and display synaptic plasticity which is thought to be critical for their survival. For example, fruit flies Drosophila melanogaster exposed to highly enriched social environment are found to show increased synaptic connections and a corresponding increase in sleep. Here we asked if social environment comprising a pair of same-sex individuals could enhance sleep in the participating individuals. To study this, we maintained individuals of D. melanogaster in same-sex pairs for a period of 1 to 4 days, and after separation, monitored sleep of the previously socialized and solitary individuals under similar conditions. Males maintained in pairs for 3 or more days were found to sleep significantly more during daytime and showed a tendency to fall asleep sooner as compared to solitary controls (both measures together are henceforth referred to as "sleep-enhancement"). This sleep phenotype is not strain-specific as it is observed in males from three different "wild type" strains of D. melanogaster. Previous studies on social interaction mediated sleep-enhancement presumed 'waking experience' during the interaction to be the primary underlying cause; however, we found sleep-enhancement to occur without any significant increase in wakefulness. Furthermore, while sleep-enhancement due to group-wise social interaction requires Pigment Dispersing Factor (PDF) positive neurons; PDF positive and CRYPTOCHROME (CRY) positive circadian clock neurons and the core circadian clock genes are not required for sleep-enhancement to occur when males interact in pairs. Pair-wise social interaction mediated sleep-enhancement requires dopamine and olfactory signaling, while visual and gustatory signaling systems seem to be dispensable. These results suggest that socialization alone (without any change in wakefulness) is sufficient to cause sleep-enhancement in fruit fly D. melanogaster males, and that its neuronal control is context-specific.

Resonance energy transfer (RET)-Induced intermolecular pairing force: a tunable weak interaction and its application in SWNT separation.

PubMed

Pan, Xiaoyong; Chen, Hui; Wang, Wei Zhi; Ng, Siu Choon; Chan-Park, Mary B

2011-07-21

This paper explores evidence of an optically mediated interaction that is active in the separation mechanism of certain selective agents through consideration of the contrasting selective behaviors of two conjugated polymers with distinct optical properties. The involvement of a RET-induced intermolecular pairing force is implied by the different illumination response behaviors. The magnitude of this interaction scales with the external stimulus parameter, the illumination irradiance (I), and thus is tunable. This suggests a facile technique to modify the selectivity of polymers toward specific SWNT species by altering the polymer structure to adjust the corresponding intermolecular interaction. This is the first experimental verification and application of a RET-induced intermolecular pairing force to SWNT separation. With this kind of interaction taken into account, reasonable interpretation of some conflicting data, especially PLE maps, can be easily made. The above conclusion can be applied to other substances as long as they are electrically neutral and there is photon-induced RET between them. The significant magnitude of this interaction makes direct manipulation of molecules/particles possible and is expected to have applications in molecular engineering. © 2011 American Chemical Society

DNA–protein π-interactions in nature: abundance, structure, composition and strength of contacts between aromatic amino acids and DNA nucleobases or deoxyribose sugar

PubMed Central

Wilson, Katie A.; Kellie, Jennifer L.; Wetmore, Stacey D.

2014-01-01

Four hundred twenty-eight high-resolution DNA–protein complexes were chosen for a bioinformatics study. Although 164 crystal structures (38% of those searched) contained no interactions, 574 discrete π–contacts between the aromatic amino acids and the DNA nucleobases or deoxyribose were identified using strict criteria, including visual inspection. The abundance and structure of the interactions were determined by unequivocally classifying the contacts as either π–π stacking, π–π T-shaped or sugar–π contacts. Three hundred forty-four nucleobase–amino acid π–π contacts (60% of all interactions identified) were identified in 175 of the crystal structures searched. Unprecedented in the literature, 230 DNA–protein sugar–π contacts (40% of all interactions identified) were identified in 137 crystal structures, which involve C–H···π and/or lone–pair···π interactions, contain any amino acid and can be classified according to sugar atoms involved. Both π–π and sugar–π interactions display a range of relative monomer orientations and therefore interaction energies (up to –50 (–70) kJ mol−1 for neutral (charged) interactions as determined using quantum chemical calculations). In general, DNA–protein π-interactions are more prevalent than perhaps currently accepted and the role of such interactions in many biological processes may yet to be uncovered. PMID:24744240

Schizophrenic Patients' Perceptions of Stress, Expressed Emotion, and Sensitivity To Criticism

PubMed Central

Cutting, Linda P.; Aakre, Jennifer M.; Docherty, Nancy M.

2006-01-01

This study was designed to get an “insider's view” of expressed emotion (EE) from the perspective of schizophrenic patients. Thirty-two patient and “influential other” pairs participated in the study. Patients' perceptions of EE attitudes in influential others were examined to determine whether they corresponded with actual EE ratings. Patients also rated how “stressed” they felt when interacting with their influential others, and patients' general sensitivity to criticism (STC) was assessed. As predicted, patients' perceptions of critical attitudes were related to actual EE ratings of criticism, although patients' perceptions of emotional overinvolvement (EOI) were not related to EOI ratings. Patients reported feeling more stressed when interacting with high-EE influential others, supporting an “EE as stressor” hypothesis. Finally, patients' STC influenced the level of stress they reported. PMID:16731686

Molecular Interaction Control in Diblock Copolymer Blends and Multiblock Copolymers with Opposite Phase Behaviors

NASA Astrophysics Data System (ADS)

Cho, Junhan

2014-03-01

Here we show how to control molecular interactions via mixing AB and AC diblock copolymers, where one copolymer exhibits upper order-disorder transition and the other does lower disorder-order transition. Linear ABC triblock copolymers possessing both barotropic and baroplastic pairs are also taken into account. A recently developed random-phase approximation (RPA) theory and the self-consistent field theory (SCFT) for general compressible mixtures are used to analyze stability criteria and morphologies for the given systems. It is demonstrated that the copolymer systems can yield a variety of phase behaviors in their temperature and pressure dependence upon proper mixing conditions and compositions, which is caused by the delicate force fields generated in the systems. We acknowledge the financial support from National Research Foundation of Korea and Center for Photofunctional Energy Materials.

"iBIM"--internet-based interactive modules: an easy and interesting learning tool for general surgery residents.

PubMed

Azer, Nader; Shi, Xinzhe; de Gara, Chris; Karmali, Shahzeer; Birch, Daniel W

2014-04-01

The increased use of information technology supports a resident- centred educational approach that promotes autonomy, flexibility and time management and helps residents to assess their competence, promoting self-awareness. We established a web-based e-learning tool to introduce general surgery residents to bariatric surgery and evaluate them to determine the most appropriate implementation strategy for Internet-based interactive modules (iBIM) in surgical teaching. Usernames and passwords were assigned to general surgery residents at the University of Alberta. They were directed to the Obesity101 website and prompted to complete a multiple-choice precourse test. Afterwards, they were able to access the interactive modules. Residents could review the course material as often as they wanted before completing a multiple-choice postcourse test and exit survey. We used paired t tests to assess the difference between pre- and postcourse scores. Out of 34 residents who agreed to participate in the project, 12 completed the project (35.3%). For these 12 residents, the precourse mean score was 50 ± 17.3 and the postcourse mean score was 67 ± 14 (p = 0.020). Most residents who participated in this study recommended using the iBIMs as a study tool for bariatric surgery. Course evaluation scores suggest this novel approach was successful in transferring knowledge to surgical trainees. Further development of this tool and assessment of implementation strategies will determine how iBIM in bariatric surgery may be integrated into the curriculum.

Hidden Sector Dark Matter Models for the Galactic Center Gamma-Ray Excess

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

Berlin, Asher; Gratia, Pierre; Hooper, Dan

2014-07-24

The gamma-ray excess observed from the Galactic Center can be interpreted as dark matter particles annihilating into Standard Model fermions with a cross section near that expected for a thermal relic. Although many particle physics models have been shown to be able to account for this signal, the fact that this particle has not yet been observed in direct detection experiments somewhat restricts the nature of its interactions. One way to suppress the dark matter's elastic scattering cross section with nuclei is to consider models in which the dark matter is part of a hidden sector. In such models, themore » dark matter can annihilate into other hidden sector particles, which then decay into Standard Model fermions through a small degree of mixing with the photon, Z, or Higgs bosons. After discussing the gamma-ray signal from hidden sector dark matter in general terms, we consider two concrete realizations: a hidden photon model in which the dark matter annihilates into a pair of vector gauge bosons that decay through kinetic mixing with the photon, and a scenario within the generalized NMSSM in which the dark matter is a singlino-like neutralino that annihilates into a pair of singlet Higgs bosons, which decay through their mixing with the Higgs bosons of the MSSM.« less

Majorana spin liquids, topology, and superconductivity in ladders

NASA Astrophysics Data System (ADS)

Le Hur, Karyn; Soret, Ariane; Yang, Fan

2017-11-01

We theoretically address spin chain analogs of the Kitaev quantum spin model on the honeycomb lattice. The emergent quantum spin-liquid phases or Anderson resonating valence-bond (RVB) states can be understood, as an effective model, in terms of p -wave superconductivity and Majorana fermions. We derive a generalized phase diagram for the two-leg ladder system with tunable interaction strengths between chains allowing us to vary the shape of the lattice (from square to honeycomb ribbon or brickwall ladder). We evaluate the winding number associated with possible emergent (topological) gapless modes at the edges. In the Az phase, as a result of the emergent Z2 gauge fields and π -flux ground state, one may build spin-1/2 (loop) qubit operators by analogy to the toric code. In addition, we show how the intermediate gapless B phase evolves in the generalized ladder model. For the brick-wall ladder, the B phase is reduced to one line, which is analyzed through perturbation theory in a rung tensor product states representation and bosonization. Finally, we show that doping with a few holes can result in the formation of hole pairs and leads to a mapping with the Su-Schrieffer-Heeger model in polyacetylene; a superconducting-insulating quantum phase transition for these hole pairs is accessible, as well as related topological properties.

Coherent lepton pair production in hadronic heavy ion collisions

NASA Astrophysics Data System (ADS)

Zha, W.; Ruan, L.; Tang, Z.; Xu, Z.; Yang, S.

2018-06-01

Recently, significant enhancements of e+e- pair production at very low transverse momentum (pT < 0.15 GeV/c) were observed by the STAR collaboration in peripheral hadronic A+A collisions. This excesses can not be described by the QGP thermal radiation and ρ in-medium broadening calculations. This is a sign of coherent photon-photon interactions, which were conventionally studied only in ultra-peripheral collisions. In this article, we present calculations of lepton pair (e+e- and μ+μ-) production from coherent photon-photon interactions in hadronic A+A collisions at RHIC and LHC energies within the STAR and ALICE acceptance.

Coherent lepton pair production in hadronic heavy ion collisions

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

Zha, W.; Ruan, L.; Tang, Z.

Recently, significant enhancements of e +e - pair production at very low transverse momentum (p T < 0.15 GeV/c) were observed by the STAR collaboration in peripheral hadronic A+A collisions. This excesses can not be described by the QGP thermal radiation and Rho in-medium broadening calculations. This is a sign of coherent photon-photon interactions, which were conventionally studied only in ultra-peripheral collisions. Here in this article, we present calculations of lepton pair (e +e - and μ +μ -) production from coherent photon-photon interactions in hadronic A+A collisions at RHIC and LHC energies within the STAR and ALICE acceptance.

Effects of the plasma profiles on photon and pair production in ultrahigh intensity laser solid interaction

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

Tian, Y. X.; Jin, X. L., E-mail: jinxiaolin@uestc.edu.cn; Yan, W. Z.

The model of photon and pair production in strong field quantum electrodynamics is implemented into our 1D3V particle-in-cell code with Monte Carlo algorithm. Using this code, the evolution of the particles in ultrahigh intensity laser (∼10{sup 23} W/cm{sup 2}) interaction with aluminum foil target is observed. Four different initial plasma profiles are considered in the simulations. The effects of initial plasma profiles on photon and pair production, energy spectra, and energy evolution are analyzed. The results imply that one can set an optimal initial plasma profile to obtain the desired photon distributions.

Coherent lepton pair production in hadronic heavy ion collisions

DOE PAGES

Zha, W.; Ruan, L.; Tang, Z.; ...

2018-04-06

Recently, significant enhancements of e +e - pair production at very low transverse momentum (p T < 0.15 GeV/c) were observed by the STAR collaboration in peripheral hadronic A+A collisions. This excesses can not be described by the QGP thermal radiation and Rho in-medium broadening calculations. This is a sign of coherent photon-photon interactions, which were conventionally studied only in ultra-peripheral collisions. Here in this article, we present calculations of lepton pair (e +e - and μ +μ -) production from coherent photon-photon interactions in hadronic A+A collisions at RHIC and LHC energies within the STAR and ALICE acceptance.

Indirect photometric detection of boron cluster anions electrophoretically separated in methanol.

PubMed

Vítová, Lada; Fojt, Lukáš; Vespalec, Radim

2014-04-18

3,5-Dinitrobenzoate and picrate are light absorbing anions pertinent to indirect photometric detection of boron cluster anions in buffered methanolic background electrolytes (BGEs). Tris(hydroxymethyl)aminomethane and morpholine have been used as buffering bases, which eliminated baseline steps, and minimized the baseline noise. In methanolic BGEs, mobilities of boron cluster anions depend on both ionic constituents of the BGE buffer. This dependence can be explained by ion pair interaction of detected anions with BGE cations, which are not bonded into ion pairs with the BGE anions. The former ion pair interaction decreases sensitivity of the indirect photometric detection. Copyright © 2014 Elsevier B.V. All rights reserved.

Multiple eigenmodes of the Rayleigh-Taylor instability observed for a fluid interface with smoothly varying density

NASA Astrophysics Data System (ADS)

Yu, C. X.; Xue, C.; Liu, J.; Hu, X. Y.; Liu, Y. Y.; Ye, W. H.; Wang, L. F.; Wu, J. F.; Fan, Z. F.

2018-01-01

In this article, multiple eigen-systems including linear growth rates and eigen-functions have been discovered for the Rayleigh-Taylor instability (RTI) by numerically solving the Sturm-Liouville eigen-value problem in the case of two-dimensional plane geometry. The system called the first mode has the maximal linear growth rate and is just extensively studied in literature. Higher modes have smaller eigen-values, but possess multi-peak eigen-functions which bring on multiple pairs of vortices in the vorticity field. A general fitting expression for the first four eigen-modes is presented. Direct numerical simulations show that high modes lead to appearances of multi-layered spike-bubble pairs, and lots of secondary spikes and bubbles are also generated due to the interactions between internal spikes and bubbles. The present work has potential applications in many research and engineering areas, e.g., in reducing the RTI growth during capsule implosions in inertial confinement fusion.

Juvenile social experience affects pairing success at adulthood: congruence with the loser effect?

PubMed Central

Mariette, Mylene M.; Cathaud, Charlène; Chambon, Rémi; Vignal, Clémentine

2013-01-01

Social interactions with adults are often critical for the development of mating behaviours. However, the potential role of other primary social partners such as juvenile counterparts is rarely considered. Most interestingly, it is not known whether interactions with juvenile females improve males’ courtship and whether, similar to the winner and loser effects in a fighting context—outcome of these interactions shapes males’ behaviour in future encounters. We investigated the combined effects of male quality and juvenile social experience on pairing success at adulthood in zebra finches (Taeniopygia guttata). We manipulated brood size to alter male quality and then placed males in either same- or mixed-sex juvenile dyads until adulthood. We found that males from reduced broods obtained more copulations and males from mixed-sex dyads had more complete courtships. Furthermore, independent of their quality, males that failed to pair with juvenile females, but not juvenile males, had a lower pairing success at adulthood. Our study shows that negative social experience with peers during adolescence may be a potent determinant of pairing success that can override the effects of early environmental conditions on male attractiveness and thereby supports the occurrence of an analogous process to the loser effect in a mating context. PMID:23902911

Aging effects in sequential modulations of poorer-strategy effects during execution of memory strategies.

PubMed

Hinault, Thomas; Lemaire, Patrick; Touron, Dayna

2017-02-01

In this study, we asked young adults and older adults to encode pairs of words. For each item, they were told which strategy to use, interactive imagery or rote repetition. Data revealed poorer-strategy effects in both young adults and older adults: Participants obtained better performance when executing better strategies (i.e., interactive-imagery strategy to encode pairs of concrete words; rote-repetition strategy on pairs of abstract words) than with poorer strategies (i.e., interactive-imagery strategy on pairs of abstract words; rote-repetition strategy on pairs of concrete words). Crucially, we showed that sequential modulations of poorer-strategy effects (i.e., poorer-strategy effects being larger when previous items were encoded with better relative to poorer strategies), previously demonstrated in arithmetic, generalise to memory strategies. We also found reduced sequential modulations of poorer-strategy effects in older adults relative to young adults. Finally, sequential modulations of poorer-strategy effects correlated with measures of cognitive control processes, suggesting that these processes underlie efficient trial-to-trial modulations during strategy execution. Differences in correlations with cognitive control processes were also found between older adults and young adults. These findings have important implications regarding mechanisms underlying memory strategy execution and age differences in memory performance.

Isotope and multiband effects in layered superconductors.

PubMed

Bussmann-Holder, Annette; Keller, Hugo

2012-06-13

In this review we consider three classes of superconductors, namely cuprate superconductors, MgB(2) and the new Fe based superconductors. All of these three systems are layered materials and multiband compounds. Their pairing mechanisms are under discussion with the exception of MgB(2), which is widely accepted to be a 'conventional' electron-phonon interaction mediated superconductor, but extending the Bardeen-Cooper-Schrieffer (BCS) theory to account for multiband effects. Cuprates and Fe based superconductors have higher superconducting transition temperatures and more complex structures. Superconductivity is doping dependent in these material classes unlike in MgB(2) which, as a pure compound, has the highest values of T(c) and a rapid suppression of superconductivity with doping takes place. In all three material classes isotope effects have been observed, including exotic ones in the cuprates, and controversial ones in the Fe based materials. Before the area of high-temperature superconductivity, isotope effects on T(c) were the signature for phonon mediated superconductivity-even when deviations from the BCS value to smaller values were observed. Since the discovery of high T(c) materials this is no longer evident since competing mechanisms might exist and other mediating pairing interactions are discussed which are of purely electronic origin. In this work we will compare the three different material classes and especially discuss the experimentally observed isotope effects of all three systems and present a rather general analysis of them. Furthermore, we will concentrate on multiband signatures which are not generally accepted in cuprates even though they are manifest in various experiments, the evidence for those in MgB(2), and indications for them in the Fe based compounds. Mostly we will consider experimental data, but when possible also discuss theoretical models which are suited to explain the data.

The influence of salt chaotropicity, column hydrophobicity and analytes' molecular properties on the retention of pramipexole and its impurities.

PubMed

Vemić, Ana; Kalinić, Marko; Erić, Slavica; Malenović, Anđelija; Medenica, Mirjana

2015-03-20

The aim of this study was to examine the interaction of the chaotropic salts of different position in Hofmeister series (CF3COONa, NaClO4, NaPF6) added to the mobile phase with the stationary phases of different hydrophobicity (C8 and C18 XTerra(®) columns), as well as their common influence on the retention behavior of pramipexole and its structurally related impurities. The extended thermodynamic approach enabled the understanding of the underlying separation mechanism. Comparing six different column-salt systems it was observed that general system hydrophobicity presented by salt chaotropicity and column hydrophobicity favors stationary phase ion-pairing over the ion-pair formation in the eluent. Further, an attempt was made to describe the influence of analytes' nature on their retention behavior in such chromatographic systems. An analysis is performed in order to select and elucidate the molecular descriptors (electrostatical, quantum-chemical, geometrical, topological, and constitutional) that best explain the experimental evidence and findings obtained by the thermodynamic approach. The results of this analysis suggest that analytes' charge distribution and its complementarity to the structure of the electric double layer formed on the surface of the stationary phase upon the addition of chaotropic additives can be useful for understanding the differences in retention of structurally related analytes. These findings provide a novel understanding of the interactions between all the components of the chromatographic system containing chaotropic additive and a good basis for further investigations suggesting the development of generally applicable predictors in structure-retention relationship studies in related chromatographic systems. Copyright © 2015 Elsevier B.V. All rights reserved.

Computational prediction of virus-human protein-protein interactions using embedding kernelized heterogeneous data.

PubMed

Nourani, Esmaeil; Khunjush, Farshad; Durmuş, Saliha

2016-05-24

Pathogenic microorganisms exploit host cellular mechanisms and evade host defense mechanisms through molecular pathogen-host interactions (PHIs). Therefore, comprehensive analysis of these PHI networks should be an initial step for developing effective therapeutics against infectious diseases. Computational prediction of PHI data is gaining increasing demand because of scarcity of experimental data. Prediction of protein-protein interactions (PPIs) within PHI systems can be formulated as a classification problem, which requires the knowledge of non-interacting protein pairs. This is a restricting requirement since we lack datasets that report non-interacting protein pairs. In this study, we formulated the "computational prediction of PHI data" problem using kernel embedding of heterogeneous data. This eliminates the abovementioned requirement and enables us to predict new interactions without randomly labeling protein pairs as non-interacting. Domain-domain associations are used to filter the predicted results leading to 175 novel PHIs between 170 human proteins and 105 viral proteins. To compare our results with the state-of-the-art studies that use a binary classification formulation, we modified our settings to consider the same formulation. Detailed evaluations are conducted and our results provide more than 10 percent improvements for accuracy and AUC (area under the receiving operating curve) results in comparison with state-of-the-art methods.

Effects of sugar functional groups, hydrophobicity, and fluorination on carbohydrate-DNA stacking interactions in water.

PubMed

Lucas, Ricardo; Peñalver, Pablo; Gómez-Pinto, Irene; Vengut-Climent, Empar; Mtashobya, Lewis; Cousin, Jonathan; Maldonado, Olivia S; Perez, Violaine; Reynes, Virginie; Aviñó, Anna; Eritja, Ramón; González, Carlos; Linclau, Bruno; Morales, Juan C

2014-03-21

Carbohydrate-aromatic interactions are highly relevant for many biological processes. Nevertheless, experimental data in aqueous solution relating structure and energetics for sugar-arene stacking interactions are very scarce. Here, we evaluate how structural variations in a monosaccharide including carboxyl, N-acetyl, fluorine, and methyl groups affect stacking interactions with aromatic DNA bases. We find small differences on stacking interaction among the natural carbohydrates examined. The presence of fluorine atoms within the pyranose ring slightly increases the interaction with the C-G DNA base pair. Carbohydrate hydrophobicity is the most determinant factor. However, gradual increase in hydrophobicity of the carbohydrate does not translate directly into a steady growth in stacking interaction. The energetics correlates better with the amount of apolar surface buried upon sugar stacking on top of the aromatic DNA base pair.

Analyzing the Fierz rearrangement freedom for local chiral two-nucleon potentials

NASA Astrophysics Data System (ADS)

Huth, L.; Tews, I.; Lynn, J. E.; Schwenk, A.

2017-11-01

Chiral effective field theory is a framework to derive systematic nuclear interactions. It is based on the symmetries of quantum chromodynamics and includes long-range pion physics explicitly, while shorter-range physics is expanded in a general operator basis. The number of low-energy couplings at a particular order in the expansion can be reduced by exploiting the fact that nucleons are fermions and therefore obey the Pauli exclusion principle. The antisymmetry permits the selection of a subset of the allowed contact operators at a given order. When local regulators are used for these short-range interactions, however, this "Fierz rearrangement freedom" is violated. In this paper, we investigate the impact of this violation at leading order (LO) in the chiral expansion. We construct LO and next-to-leading order (NLO) potentials for all possible LO-operator pairs and study their reproduction of phase shifts, the 4He ground-state energy, and the neutron-matter energy at different densities. We demonstrate that the Fierz rearrangement freedom is partially restored at NLO where subleading contact interactions enter. We also discuss implications for local chiral three-nucleon interactions.

Study of human salivary proline-rich proteins interaction with food tannins.

PubMed

Soares, Susana; García-Estévez, Ignacio; Ferrer-Galego, Raúl; Brás, Natércia F; Brandão, Elsa; Silva, Mafalda; Teixeira, Natércia; Fonseca, Fátima; Sousa, Sérgio F; Ferreira-da-Silva, Frederico; Mateus, Nuno; de Freitas, Victor

2018-03-15

In this work, saturation transfer difference-NMR, isothermal microcalorimetry and molecular dynamics simulations have been used to study the individual interactions between basic, glycosylated and acidic proline-rich proteins (bPRPS, gPRPs, aPRPs) and P-B peptide with some representative food tannins [procyanidin B2, procyanidin B2 3'-O-gallate (B2g) and procyanidin trimer (catechin-4-8-catechin-4-8-catechin)]. Results showed that P-B peptide was in general the salivary protein (SP) with higher affinity whereas aPRPs showed lower affinity to the studied procyanidins. Moreover, B2g was the procyanidin with higher affinity for all SP. Hydrophobic and hydrogen bonds were present in all interactions but the major driving force depended on the procyanidin-SP pair. Furthermore, proline clusters or residues in their vicinity were identified as the probable sites of proteins for interaction with procyanidins. For bPRP and aPRP a significant change to less extended conformations was observed, while P-B peptide did not display any structural rearrangement upon procyanidins binding. Copyright © 2017. Published by Elsevier Ltd.

Controlled Interactions between Two Dimensional Layered Inorganic Nanosheets and Polymers

DTIC Science & Technology

2016-06-15

transition metal and non- pair electrons of amine allows us to develop scalable, stable and uniform composite films with numerous combinations of TMD...modification of TMDs sheets with amine-terminated polymers is introduced and the strong Lewis acid-base interaction between transition metal and non- pair ...can be readily entangled with other chains of the matrix polymer, thereby ensuring homogeneous PNC formation. The solvent medium offers an extra

Quantum turbulence in cold multicomponent matter

NASA Astrophysics Data System (ADS)

Pshenichnyuk, Ivan A.

2018-02-01

Quantum vortices are pivotal for understanding of phenomena in quantum hydrodynamics. Vortices were observed in different physical systems like trapped dilute Bose-Einstein condensates, liquid helium, exciton-polariton condensates and other types of systems. Foreign particles attached to the vortices often serve for a visualization of the vortex shape and kinematics in superfluid experiments. Fascinating discoveries were made in the field of cold quantum mixtures, where vortices created in one component may interact with the other component. This works raise the fundamental question of the interaction between quantum vortices and matter. The generalized nonlinear Schrodinger equation based formalism is applied here to model three different processes involving the interaction of quantum vortices with foreign particles: propagation of a fast classical particle in a superfluid under the influence of sound waves, scattering of a single fermion by a quantized vortex line and dynamics of vortex pairs doped with heavy bosonic matter. The obtained results allow to to clarify the details of recent experiments and acquire a better understanding of the multicomponent quantum turbulence.

Four classes of interactions for evolutionary games.

PubMed

Szabó, György; Bodó, Kinga S; Allen, Benjamin; Nowak, Martin A

2015-08-01

The symmetric four-strategy games are decomposed into a linear combination of 16 basis games represented by orthogonal matrices. Among these basis games four classes can be distinguished as it is already found for the three-strategy games. The games with self-dependent (cross-dependent) payoffs are characterized by matrices consisting of uniform rows (columns). Six of 16 basis games describe coordination-type interactions among the strategy pairs and three basis games span the parameter space of the cyclic components that are analogous to the rock-paper-scissors games. In the absence of cyclic components the game is a potential game and the potential matrix is evaluated. The main features of the four classes of games are discussed separately and we illustrate some characteristic strategy distributions on a square lattice in the low noise limit if logit rule controls the strategy evolution. Analysis of the general properties indicates similar types of interactions at larger number of strategies for the symmetric matrix games.