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

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.

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).

Determinants of Chromosome Architecture: Insulator Pairing in cis and in trans

PubMed Central

Fujioka, Miki; Mistry, Hemlata; Schedl, Paul; Jaynes, James B.

2016-01-01

The chromosomes of multicellular animals are organized into a series of topologically independent looped domains. This domain organization is critical for the proper utilization and propagation of the genetic information encoded by the chromosome. A special set of architectural elements, called boundaries or insulators, are responsible both for subdividing the chromatin into discrete domains and for determining the topological organization of these domains. Central to the architectural functions of insulators are homologous and heterologous insulator:insulator pairing interactions. The former (pairing between copies of the same insulator) dictates the process of homolog alignment and pairing in trans, while the latter (pairing between different insulators) defines the topology of looped domains in cis. To elucidate the principles governing these architectural functions, we use two insulators, Homie and Nhomie, that flank the Drosophila even skipped locus. We show that homologous insulator interactions in trans, between Homie on one homolog and Homie on the other, or between Nhomie on one homolog and Nhomie on the other, mediate transvection. Critically, these homologous insulator:insulator interactions are orientation-dependent. Consistent with a role in the alignment and pairing of homologs, self-pairing in trans is head-to-head. Head-to-head self-interactions in cis have been reported for other fly insulators, suggesting that this is a general principle of self-pairing. Homie and Nhomie not only pair with themselves, but with each other. Heterologous Homie-Nhomie interactions occur in cis, and we show that they serve to delimit a looped chromosomal domain that contains the even skipped transcription unit and its associated enhancers. The topology of this loop is defined by the heterologous pairing properties of Homie and Nhomie. Instead of being head-to-head, which would generate a circular loop, Homie-Nhomie pairing is head-to-tail. Head-to-tail pairing in cis generates a stem-loop, a configuration much like that observed in classical lampbrush chromosomes. These pairing principles provide a mechanistic underpinning for the observed topologies within and between chromosomes. PMID:26910731

Like-Charge Guanidinium Pairing between Ligand and Receptor: An Unusual Interaction for Drug Discovery and Design?

PubMed

Yang, Yang; Xu, Zhijian; Zhang, Zhengyan; Yang, Zhuo; Liu, Yingtao; Wang, Jinan; Cai, Tingting; Li, Shujin; Chen, Kaixian; Shi, Jiye; Zhu, Weiliang

2015-09-10

A database survey in this study revealed for the first time that there are 227 counterintuitive like-charge guanidinium pairings (Gdm(+)-Arg pairings) between ligands and receptors in the Protein Data Bank, implying the potential guanidinium-arginine binding between guanidine-containing drugs and their target proteins. Furthermore, there are 145 guanidine-containing molecules in the DrugBank, showing the prevalence of guanidinium groups in drugs. It has also been reported that the introduction of a guanidinium group forming Gdm(+)-Arg pairing improved the potency of the drug by more than 8-fold in a typical case. On the basis of the survey, six ligand-protein complexes with typical Gdm(+)-Arg pairings were chosen for QM/MM calculations. The calculations at the B97-D/6-311++g(d,p) level revealed that the interaction could be as strong as -1.0 to -2.5 kcal/mol in DMSO and water, comparable to common intermolecular interactions. The calculations also unveiled that the Gdm(+)-Arg pairing interactions change from repulsive to attractive with the increase of dielectric constant, suggesting that the dielectric constant has a general stabilization effect on the Gdm(+)-Arg pairing. This study suggested that the like-charge guanidinium pairing interaction could be used not only for tuning the physical and chemical properties of drug leads but also for improving ligand binding affinity.

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

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

Co-evolutionary Analysis of Domains in Interacting Proteins Reveals Insights into Domain–Domain Interactions Mediating Protein–Protein Interactions

PubMed Central

Jothi, Raja; Cherukuri, Praveen F.; Tasneem, Asba; Przytycka, Teresa M.

2006-01-01

Recent advances in functional genomics have helped generate large-scale high-throughput protein interaction data. Such networks, though extremely valuable towards molecular level understanding of cells, do not provide any direct information about the regions (domains) in the proteins that mediate the interaction. Here, we performed co-evolutionary analysis of domains in interacting proteins in order to understand the degree of co-evolution of interacting and non-interacting domains. Using a combination of sequence and structural analysis, we analyzed protein–protein interactions in F1-ATPase, Sec23p/Sec24p, DNA-directed RNA polymerase and nuclear pore complexes, and found that interacting domain pair(s) for a given interaction exhibits higher level of co-evolution than the noninteracting domain pairs. Motivated by this finding, we developed a computational method to test the generality of the observed trend, and to predict large-scale domain–domain interactions. Given a protein–protein interaction, the proposed method predicts the domain pair(s) that is most likely to mediate the protein interaction. We applied this method on the yeast interactome to predict domain–domain interactions, and used known domain–domain interactions found in PDB crystal structures to validate our predictions. Our results show that the prediction accuracy of the proposed method is statistically significant. Comparison of our prediction results with those from two other methods reveals that only a fraction of predictions are shared by all the three methods, indicating that the proposed method can detect known interactions missed by other methods. We believe that the proposed method can be used with other methods to help identify previously unrecognized domain–domain interactions on a genome scale, and could potentially help reduce the search space for identifying interaction sites. PMID:16949097

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

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…

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…

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

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

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.

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…

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.

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…

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.

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...

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.

Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. V. Like-charged side chains.

PubMed

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

2011-05-19

A new model of side-chain-side-chain interactions for charged side-chains of amino acids, to be used in the UNRES force-field, has been developed, in which a side chain consists of a nonpolar and a charged site. The interaction energy between the nonpolar sites is composed of a Gay-Berne and a cavity term; the interaction energy between the charged sites consists of a Lennard-Jones term, a Coulombic term, a generalized-Born term, and a cavity term, while the interaction energy between the nonpolar and charged sites is composed of a Gay-Berne and a polarization term. We parametrized the energy function for the models of all six pairs of natural like-charged amino-acid side chains, namely propionate-propionate (for the aspartic acid-aspartic acid pair), butyrate-butyrate (for the glutamic acid-glutamic acid pair), propionate-butyrate (for the aspartic acid-glutamic acid pair), pentylamine cation-pentylamine cation (for the lysine-lysine pair), 1-butylguanidine cation-1-butylguanidine cation (for the arginine-arginine pair), and pentylamine cation-1-butylguanidine cation (for the lysine-arginine pair). By using umbrella-sampling molecular dynamics simulations in explicit TIP3P water, we determined the potentials of mean force of the above-mentioned pairs as functions of distance and orientation and fitted analytical expressions to them. The positions and depths of the contact minima and the positions and heights of the desolvation maxima, including their dependence on the orientation of the molecules were well represented by analytical expressions for all systems. The values of the parameters of all the energy components are physically reasonable, which justifies use of such potentials in coarse-grain protein-folding simulations. © 2011 American Chemical Society

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.

Dual origin of pairing in nuclei

NASA Astrophysics Data System (ADS)

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

2016-11-01

The pairing correlations of the nucleus 120Sn are calculated by solving the Nambu-Gor'kov equations, including medium polarization effects resulting from the interweaving of quasiparticles, spin and density vibrations, taking into account, within the framework of nuclear field theory (NFT), processes leading to self-energy and vertex corrections and to the induced pairing interaction. From these results one can not only demonstrate the inevitability of the dual origin of pairing in nuclei, but also extract information which can be used at profit to quantitatively disentangle the contributions to the pairing gap Δ arising from the bare and from the induced pairing interaction. The first is the strong 1 S 0 short-range NN potential resulting from meson exchange between nucleons moving in time reversal states within an energy range of hundreds of MeV from the Fermi energy. The second results from the exchange of vibrational modes between nucleons moving within few MeV from the Fermi energy. Short- ( v p bare) and long-range ( v p ind) pairing interactions contribute essentially equally to nuclear Cooper pair stability. That is to the breaking of gauge invariance in open-shell superfluid nuclei and thus to the order parameter, namely to the ground state expectation value of the pair creation operator. In other words, to the emergent property of generalized rigidity in gauge space, and associated rotational bands and Cooper pair tunneling between members of these bands.

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.

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.

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.

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.

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

Cooper-pair size and binding energy for unconventional superconducting systems

NASA Astrophysics Data System (ADS)

Dinóla Neto, F.; Neto, Minos A.; Salmon, Octavio D. Rodriguez

2018-06-01

The main proposal of this paper is to analyze the size of the Cooper pairs composed by unbalanced mass fermions from different electronic bands along the BCS-BEC crossover and study the binding energy of the pairs. We are considering an interaction between fermions with different masses leading to an inter-band pairing. In addiction to the attractive interaction we have an hybridization term to couple both bands, which in general acts unfavorable for the pairing between the electrons. We get first order phase transitions as the hybridization breaks the Cooper pairs for the s-wave symmetry of the gap amplitude. The results show the dependence of the Cooper-pair size as a function of the hybridization for T = 0 . We also propose the structure of the binding energy of the inter-band system as a function of the two-bands quasi-particle energies.

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.

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,…

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.

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.

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.

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.

Dual origin of pairing in nuclei

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

Idini, A.; Potel, G.; Barranco, F.

The pairing correlations of the nucleus {sup 120}Sn are calculated by solving the Nambu–Gor’kov equations, including medium polarization effects resulting from the interweaving of quasiparticles, spin and density vibrations, taking into account, within the framework of nuclear field theory (NFT), processes leading to self-energy and vertex corrections and to the induced pairing interaction. From these results one can not only demonstrate the inevitability of the dual origin of pairing in nuclei, but also extract information which can be used at profit to quantitatively disentangle the contributions to the pairing gap Δ arising from the bare and from the induced pairingmore » interaction. The first is the strong {sup 1}S{sub 0} short-range NN potential resulting from meson exchange between nucleons moving in time reversal states within an energy range of hundreds of MeV from the Fermi energy. The second results from the exchange of vibrational modes between nucleons moving within few MeV from the Fermi energy. Short- (v{sub p}{sup bare}) and long-range (v{sub p}{sup ind}) pairing interactions contribute essentially equally to nuclear Cooper pair stability. That is to the breaking of gauge invariance in open-shell superfluid nuclei and thus to the order parameter, namely to the ground state expectation value of the pair creation operator. In other words, to the emergent property of generalized rigidity in gauge space, and associated rotational bands and Cooper pair tunneling between members of these bands.« less

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.

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.

Mesoscopic pairing without superconductivity

NASA Astrophysics Data System (ADS)

Hofmann, Johannes

2017-12-01

We discuss pairing signatures in mesoscopic nanowires with a variable attractive pairing interaction. Depending on the wire length, density, and interaction strength, these systems realize a simultaneous bulk-to-mesoscopic and BCS-BEC crossover, which we describe in terms of the parity parameter that quantifies the odd-even energy difference and generalizes the bulk Cooper pair binding energy to mesoscopic systems. We show that the parity parameter can be extracted from recent measurements of conductance oscillations in SrTiO3 nanowires by Cheng et al. [Nature (London) 521, 196 (2015), 10.1038/nature14398], where it marks the critical magnetic field that separates pair and single-particle currents. Our results place the experiment in the fluctuation-dominated mesoscopic regime on the BCS side of the crossover.

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.

ClaRNA: a classifier of contacts in RNA 3D structures based on a comparative analysis of various classification schemes

PubMed Central

Waleń, Tomasz; Chojnowski, Grzegorz; Gierski, Przemysław; Bujnicki, Janusz M.

2014-01-01

The understanding of folding and function of RNA molecules depends on the identification and classification of interactions between ribonucleotide residues. We developed a new method named ClaRNA for computational classification of contacts in RNA 3D structures. Unique features of the program are the ability to identify imperfect contacts and to process coarse-grained models. Each doublet of spatially close ribonucleotide residues in a query structure is compared to clusters of reference doublets obtained by analysis of a large number of experimentally determined RNA structures, and assigned a score that describes its similarity to one or more known types of contacts, including pairing, stacking, base–phosphate and base–ribose interactions. The accuracy of ClaRNA is 0.997 for canonical base pairs, 0.983 for non-canonical pairs and 0.961 for stacking interactions. The generalized squared correlation coefficient (GC2) for ClaRNA is 0.969 for canonical base pairs, 0.638 for non-canonical pairs and 0.824 for stacking interactions. The classifier can be easily extended to include new types of spatial relationships between pairs or larger assemblies of nucleotide residues. ClaRNA is freely available via a web server that includes an extensive set of tools for processing and visualizing structural information about RNA molecules. PMID:25159614

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.

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.

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...

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.

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).

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.

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

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

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.

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

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

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.

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.

A global interaction network maps a wiring diagram of cellular function

PubMed Central

Costanzo, Michael; VanderSluis, Benjamin; Koch, Elizabeth N.; Baryshnikova, Anastasia; Pons, Carles; Tan, Guihong; Wang, Wen; Usaj, Matej; Hanchard, Julia; Lee, Susan D.; Pelechano, Vicent; Styles, Erin B.; Billmann, Maximilian; van Leeuwen, Jolanda; van Dyk, Nydia; Lin, Zhen-Yuan; Kuzmin, Elena; Nelson, Justin; Piotrowski, Jeff S.; Srikumar, Tharan; Bahr, Sondra; Chen, Yiqun; Deshpande, Raamesh; Kurat, Christoph F.; Li, Sheena C.; Li, Zhijian; Usaj, Mojca Mattiazzi; Okada, Hiroki; Pascoe, Natasha; Luis, Bryan-Joseph San; Sharifpoor, Sara; Shuteriqi, Emira; Simpkins, Scott W.; Snider, Jamie; Suresh, Harsha Garadi; Tan, Yizhao; Zhu, Hongwei; Malod-Dognin, Noel; Janjic, Vuk; Przulj, Natasa; Troyanskaya, Olga G.; Stagljar, Igor; Xia, Tian; Ohya, Yoshikazu; Gingras, Anne-Claude; Raught, Brian; Boutros, Michael; Steinmetz, Lars M.; Moore, Claire L.; Rosebrock, Adam P.; Caudy, Amy A.; Myers, Chad L.; Andrews, Brenda; Boone, Charles

2017-01-01

We generated a global genetic interaction network for Saccharomyces cerevisiae, constructing over 23 million double mutants, identifying ~550,000 negative and ~350,000 positive genetic interactions. This comprehensive network maps genetic interactions for essential gene pairs, highlighting essential genes as densely connected hubs. Genetic interaction profiles enabled assembly of a hierarchical model of cell function, including modules corresponding to protein complexes and pathways, biological processes, and cellular compartments. Negative interactions connected functionally related genes, mapped core bioprocesses, and identified pleiotropic genes, whereas positive interactions often mapped general regulatory connections among gene pairs, rather than shared functionality. The global network illustrates how coherent sets of genetic interactions connect protein complex and pathway modules to map a functional wiring diagram of the cell. PMID:27708008

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.

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.

A general way of analyzing EPR spectroscopy for a pair of magnetically equivalent lanthanide ions in crystal: A case study of BaY2F8:Yb3+ crystal

NASA Astrophysics Data System (ADS)

Liu, Honggang; Zheng, Wenchen

2018-01-01

Electron paramagnetic resonance (EPR) is an important tool to study the complex interactions (e.g., exchange and magnetic dipole-dipole interactions) for a pair of lanthanide (Ln) ions in crystals. How to analyze these EPR spectra and obtain the strength of each interaction is a challenge for experimentalists. In this work, a general way of calculating the EPR lines for two magnetically equivalent Ln ions is given by us to solve this problem. In order to explain their EPR spectra and obtain exchange interaction parameters Ji (i = x, y, z) between them, we deduce the analytic formulas for computing the angular dependent EPR lines for such Ln pairs under the condition of weak coupling (|Ji| ≪ hv, where v is the microwave frequency in the EPR experiment) and set up the spin-Hamiltonian energy matrix that should be diagonalized to obtain these lines if intermediate (|Ji| ˜ hv) and strong (|Ji| > hv) couplings are encountered. To verify our method, the experimental EPR spectra for the Yb3+ doped BaY2F8 crystal are considered by us and the EPR lines from the isolated Yb3+ ion and Yb3+-Yb3+ pair with distance R equal to 0.371 nm are identified clearly. Moreover, exchange interaction parameters (Jx ≈ -0.04 cm-1, Jy ≈ -0.24 cm-1, and Jz ≈ -0.1 cm-1) for such a pair are also determined by our calculations. This case study demonstrates that the theoretical method given in this work would be useful and could be applied to understand interactions between Ln ions in crystals.

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.

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.

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.

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.

Soliton interactions, Bäcklund transformations, Lax pair for a variable-coefficient generalized dispersive water-wave system

NASA Astrophysics Data System (ADS)

Liu, Lei; Tian, Bo; Zhen, Hui-Ling; Liu, De-Yin; Xie, Xi-Yang

2018-04-01

Under investigation in this paper is a variable-coefficient generalized dispersive water-wave system, which can simulate the propagation of the long weakly non-linear and weakly dispersive surface waves of variable depth in the shallow water. Under certain variable-coefficient constraints, by virtue of the Bell polynomials, Hirota method and symbolic computation, the bilinear forms, one- and two-soliton solutions are obtained. Bäcklund transformations and new Lax pair are also obtained. Our Lax pair is different from that previously reported. Based on the asymptotic and graphic analysis, with different forms of the variable coefficients, we find that there exist the elastic interactions for u, while either the elastic or inelastic interactions for v, with u and v as the horizontal velocity field and deviation height from the equilibrium position of the water, respectively. When the interactions are inelastic, we see the fission and fusion phenomena.

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

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

``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

Young Learners' Interactional Development in Task-Based Paired-Assessment in Their First and Foreign Languages: A Case of English Learners in China

ERIC Educational Resources Information Center

Butler, Yuko Goto; Zeng, Wei

2015-01-01

In response to the growing interest in evaluating young learners' foreign language (FL) performance, this study aims to deepen our understanding of young learners' developmental differences in interaction during task-based paired-language assessments. To examine age effects separately from the effect of general language proficiency, we analysed…

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).

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.

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

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.

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.

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.

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.

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…

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.

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

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

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

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

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.

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 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

Quasi-planar elemental clusters in pair interactions approximation

NASA Astrophysics Data System (ADS)

Chkhartishvili, Levan

2016-01-01

The pair-interactions approximation, when applied to describe elemental clusters, only takes into account bonding between neighboring atoms. According to this approach, isomers of wrapped forms of 2D clusters - nanotubular and fullerene-like structures - and truly 3D clusters, are generally expected to be more stable than their quasi-planar counterparts. This is because quasi-planar clusters contain more peripheral atoms with dangling bonds and, correspondingly, fewer atoms with saturated bonds. However, the differences in coordination numbers between central and peripheral atoms lead to the polarization of bonds. The related corrections to the molar binding energy can make small, quasi-planar clusters more stable than their 2D wrapped allotropes and 3D isomers. The present work provides a general theoretical frame for studying the relative stability of small elemental clusters within the pair interactions approximation.

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.

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.

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.

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

Ovarian development in a primitively eusocial wasp: social interactions affect behaviorally dominant and subordinate wasps in opposite directions relative to solitary females.

PubMed

Shukla, Shantanu; Pareek, Vidhi; Gadagkar, Raghavendra

2014-07-01

In many primitively eusocial wasp species new nests are founded either by a single female or by a small group of females. In the single foundress nests, the lone female develops her ovaries, lays eggs as well as tends her brood. In multiple foundress nests social interactions, especially dominance-subordinate interactions, result in only one 'dominant' female developing her ovaries and laying eggs. Ovaries of the remaining 'subordinate' cofoundresses remain suppressed and these individuals function as workers and tend the dominant's brood. Using the tropical, primitively eusocial polistine wasp Ropalidia marginata and by comparing wasps held in isolation and those kept as pairs in the laboratory, we demonstrate that social interactions affect ovarian development of dominant and subordinate wasps among the pairs in opposite directions, suppressing the ovaries of the subordinate member of the pair below that of solitary wasps and boosting the ovaries of dominant member of the pair above that of solitary females. In addition to being of physiological interest, such mirror image effects of aggression on the ovaries of the aggressors and their victims, suggest yet another mechanism by which subordinates can enhance their indirect fitness and facilitate the evolution of worker behavior by kin selection. Copyright © 2014 Elsevier B.V. All rights reserved.

Hydrophobic environment is a key factor for the stability of thermophilic proteins.

PubMed

Gromiha, M Michael; Pathak, Manish C; Saraboji, Kadhirvel; Ortlund, Eric A; Gaucher, Eric A

2013-04-01

The stability of thermophilic proteins has been viewed from different perspectives and there is yet no unified principle to understand this stability. It would be valuable to reveal the most important interactions for designing thermostable proteins for such applications as industrial protein engineering. In this work, we have systematically analyzed the importance of various interactions by computing different parameters such as surrounding hydrophobicity, inter-residue interactions, ion-pairs and hydrogen bonds. The importance of each interaction has been determined by its predicted relative contribution in thermophiles versus the same contribution in mesophilic homologues based on a dataset of 373 protein families. We predict that hydrophobic environment is the major factor for the stability of thermophilic proteins and found that 80% of thermophilic proteins analyzed showed higher hydrophobicity than their mesophilic counterparts. Ion pairs, hydrogen bonds, and interaction energy are also important and favored in 68%, 50%, and 62% of thermophilic proteins, respectively. Interestingly, thermophilic proteins with decreased hydrophobic environments display a greater number of hydrogen bonds and/or ion pairs. The systematic elimination of mesophilic proteins based on surrounding hydrophobicity, interaction energy, and ion pairs/hydrogen bonds, led to correctly identifying 95% of the thermophilic proteins in our analyses. Our analysis was also applied to another, more refined set of 102 thermophilic-mesophilic pairs, which again identified hydrophobicity as a dominant property in 71% of the thermophilic proteins. Further, the notion of surrounding hydrophobicity, which characterizes the hydrophobic behavior of residues in a protein environment, has been applied to the three-dimensional structures of elongation factor-Tu proteins and we found that the thermophilic proteins are enriched with a hydrophobic environment. The results obtained in this work highlight the importance of hydrophobicity as the dominating characteristic in the stability of thermophilic proteins, and we anticipate this will be useful in our attempts to engineering thermostable proteins. Copyright © 2013 Wiley Periodicals, Inc.

Genes involved in host-parasite interactions can be revealed by their correlated expression.

PubMed

Reid, Adam James; Berriman, Matthew

2013-02-01

Molecular interactions between a parasite and its host are key to the ability of the parasite to enter the host and persist. Our understanding of the genes and proteins involved in these interactions is limited. To better understand these processes it would be advantageous to have a range of methods to predict pairs of genes involved in such interactions. Correlated gene expression profiles can be used to identify molecular interactions within a species. Here we have extended the concept to different species, showing that genes with correlated expression are more likely to encode proteins, which directly or indirectly participate in host-parasite interaction. We go on to examine our predictions of molecular interactions between the malaria parasite and both its mammalian host and insect vector. Our approach could be applied to study any interaction between species, for example, between a host and its parasites or pathogens, but also symbiotic and commensal pairings.

Effect of charged amino acid side chain length on lateral cross-strand interactions between carboxylate- and guanidinium-containing residues in a β-hairpin.

PubMed

Kuo, Hsiou-Ting; Liu, Shing-Lung; Chiu, Wen-Chieh; Fang, Chun-Jen; Chang, Hsien-Chen; Wang, Wei-Ren; Yang, Po-An; Li, Jhe-Hao; Huang, Shing-Jong; Huang, Shou-Ling; Cheng, Richard P

2015-05-01

β-Sheet is one of the major protein secondary structures. Oppositely charged residues are frequently observed across neighboring strands in antiparallel sheets, suggesting the importance of cross-strand ion pairing interactions. The charged amino acids Asp, Glu, Arg, and Lys have different numbers of hydrophobic methylenes linking the charged functionality to the backbone. To investigate the effect of side chain length of guanidinium- and carboxylate-containing residues on lateral cross-strand ion pairing interactions at non-hydrogen-bonded positions, β-hairpin peptides containing Zbb-Agx (Zbb = Asp, Glu, Aad in increasing length; Agx = Agh, Arg, Agb, Agp in decreasing length) sequence patterns were studied by NMR methods. The fraction folded population and folding energy were derived from the chemical shift deviation data. Peptides with high fraction folded populations involved charged residue side chain lengths that supported high strand propensity. Double mutant cycle analysis was used to determine the interaction energy for the potential lateral ion pairs. Minimal interaction was observed between residues with short side chains, most likely due to the diffused positive charge on the guanidinium group, which weakened cross-strand electrostatic interactions with the carboxylate side chain. Only the Aad-Arg/Agh interactions with long side chains clearly exhibited stabilizing energetics, possibly relying on hydrophobics. A survey of a non-redundant protein structure database revealed that the statistical sheet pair propensity followed the trend Asp-Arg < Glu-Arg, implying the need for matching long side chains. This suggested the need for long side chains on both guanidinium-bearing and carboxylate-bearing residues to stabilize the β-hairpin motif.

Cooper-pair-condensate fluctuations and plasmons in layered superconductors

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

Cote, R.; Griffin, A.

1993-10-01

Starting from a given attractive potential, we give a systematic analysis of the spin-singlet [ital s]-wave Cooper-pair-condensate fluctuations in a two-dimensional (2D) superconductor. These results are applied to a superlattice of superconducting sheets in which the 2D charge fluctuations are coupled via the Coulomb interaction. Our main interest is how the low-energy Anderson-Bogoliubov (AB) phonon mode in the pair-breaking gap [omega][lt]2[Delta] is modified by the Coulomb interaction. Our formal analysis is valid at arbitrary temperatures. It describes the weakly bound, large-Cooper-pair limit as well as the strongly bound, small-Cooper-pair limit and thus includes both the BCS and Bose-Einstein scenarios (asmore » discussed by Nozieres and Schmitt-Rink as well as Randeira [ital et] [ital al].). A comlete normal-mode analysis is given for a charged BCS superconductor, showing how the repulsive (Coulomb) interaction modifies the collective modes of a neutral superconductor. This complements the recent numerical study carried out by Fertig and Das Sarma. We show that the pair-response function shares the same spectrum as the charge-response function, given by the zero of the longitudinal dielectric function [epsilon]([bold q],[omega]). In 2D and layered superconductors, there is a low-frequency and high-frequency plasmon branch, separated by a relatively narrow particle-hole continuum at around 2[Delta]. The low-frequency ([omega][lt]2[Delta]) plasmon branch is a renormalized version of the AB phonon mode.« less

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.

Observing Pair-Work Task in an English Speaking Class

ERIC Educational Resources Information Center

Achmad, Diana; Yusuf, Yunisrina Qismullah

2014-01-01

This paper reports on students' pair-work interactions to develop their speaking skills in an ELT classroom which consisted of international learners. A number of 16 learners of intermediate proficiency with IELTS score band 5.5 were observed. The teacher had paired those he considered among them to be the more competent ones (hereafter, stronger)…

Search and Characterization of Optical Ceramics and Crystals for Diode-pumped Laser Oscillations

DTIC Science & Technology

2013-04-01

results in a lower oscillation efficiency due to a strong loss of excitation energy during fast nonradiative interactions in Nd-Nd pairs than...associated nonradiative losses due to the formation of unquenched Nd-La pairs. To ensure that Nd-La pairs predominate in a SrF2-LaF3 solid solution, a

Vocabulary Learning in Collaborative Tasks: A Comparison of Pair and Small Group Work

ERIC Educational Resources Information Center

Dobao, Ana Fernández

2014-01-01

This study examined the opportunities that pair and small group interaction offer for collaborative dialogue and second language (L2) vocabulary learning. It compared the performance of the same collaborative writing task by learners working in groups of four (n = 60) and in pairs (n = 50), focusing on the occurrence of lexical language-related…

Cluster approach to the prediction of thermodynamic and transport properties of ionic liquids

NASA Astrophysics Data System (ADS)

Seeger, Zoe L.; Kobayashi, Rika; Izgorodina, Ekaterina I.

2018-05-01

The prediction of physicochemical properties of ionic liquids such as conductivity and melting point would substantially aid the targeted design of ionic liquids for specific applications ranging from solvents for extraction of valuable chemicals to biowaste to electrolytes in alternative energy devices. The previously published study connecting the interaction energies of single ion pairs (1 IP) of ionic liquids to their thermodynamic and transport properties has been extended to larger systems consisting of two ion pairs (2 IPs), in which many-body and same-ion interactions are included. Routinely used cations, of the imidazolium and pyrrolidinium families, were selected in the study coupled with chloride, tetrafluoroborate, and dicyanamide. Their two ion pair clusters were subjected to extensive configuration screening to establish most stable structures. Interaction energies of these clusters were calculated at the spin-ratio scaled MP2 (SRS-MP2) level for the correlation interaction energy, and a newly developed scaled Hartree-Fock method for the rest of energetic contributions to interaction energy. A full geometry screening for each cation-anion combination resulted in 192 unique structures, whose stability was assessed using two criteria—widely used interaction energy and total electronic energy. Furthermore, the ratio of interaction energy to its dispersion component was correlated with experimentally observed melting points in 64 energetically favourable structures. These systems were also used to test the correlation of the dispersion contribution to interaction energy with measured conductivity.

Assessment of the significance of patent-derived information for the early identification of compound-target interaction hypotheses.

PubMed

Senger, Stefan

2017-04-21

Patents are an important source of information for effective decision making in drug discovery. Encouragingly, freely accessible patent-chemistry databases are now in the public domain. However, at present there is still a wide gap between relatively low coverage-high quality manually-curated data sources and high coverage data sources that use text mining and automated extraction of chemical structures. To secure much needed funding for further research and an improved infrastructure, hard evidence is required to demonstrate the significance of patent-derived information in drug discovery. Surprisingly little such evidence has been reported so far. To address this, the present study attempts to quantify the relevance of patents for formulating and substantiating hypotheses for compound-target interactions. A manually-curated set of 130 compound-target interaction pairs annotated with what are considered to be the earliest patent and publication has been produced. The analysis of this set revealed that in stark contrast to what has been reported for novel chemical structures, only about 10% of the compound-target interaction pairs could be found in publications in the scientific literature within one year of being reported in patents. The average delay across all interaction pairs is close to 4 years. In an attempt to benchmark current capabilities, it was also examined how much of the benefit of using patent-derived information can be retained when a bioannotated version of SureChEMBL is used as secondary source for the patent literature. Encouragingly, this approach found the patents in the annotated set for 72% of the compound-target interaction pairs. Similarly, the effect of using the bioactivity database ChEMBL as secondary source for the scientific literature was studied. Here, the publications from the annotated set were only found for 46% of the compound-target interaction pairs. Patent-derived information is a significant enabler for formulating compound-target interaction hypotheses even in cases where the respective interaction is later reported in the scientific literature. The findings of this study clearly highlight the significance of future investments in the development and provision of databases and tools that will allow scientists to search patent information in a comprehensive, reliable, and efficient manner.

A Mapping of the Electron Localization Function for Earth Materials

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

Gibbs, Gerald V.; Cox, David F.; Ross, Nancy

2005-06-01

The electron localization function, ELF, generated for a number of geometry-optimized earth materials, provides a graphical representation of the spatial localization of the probability electron density distribution as embodied in domains ascribed to localized bond and lone pair electrons. The lone pair domains, displayed by the silica polymorphs quartz, coesite and cristobalite, are typically banana-shaped and oriented perpendicular to the plane of the SiOSi angle at ~0.60 Å from the O atom on the reflex side of the angle. With decreasing angle, the domains increase in magnitude, indicating an increase in the nucleophilic character of the O atom, rendering itmore » more susceptible to potential electrophilic attack. The Laplacian isosurface maps of the experimental and theoretical electron density distribution for coesite substantiates the increase in the size of the domain with decreasing angle. Bond pair domains are displayed along each of the SiO bond vectors as discrete concave hemispherically-shaped domains at ~0.70 Å from the O atom. For more closed-shell ionic bonded interactions, the bond and lone pair domains are often coalesced, resulting in concave hemispherical toroidal-shaped domains with local maxima centered along the bond vectors. As the shared covalent character of the bonded interactions increases, the bond and lone pair domains are better developed as discrete domains. ELF isosurface maps generated for the earth materials tremolite, diopside, talc and dickite display banana-shaped lone pair domains associated with the bridging O atoms of SiOSi angles and concave hemispherical toroidal bond pair domains associated with the nonbridging ones. The lone pair domains in dickite and talc provide a basis for understanding the bonded interactions between the adjacent neutral layers. Maps were also generated for beryl, cordierite, quartz, low albite, forsterite, wadeite, åkermanite, pectolite, periclase, hurlbutite, thortveitite and vanthoffite. Strategies are reviewed for finding potential H docking sites in the silica polymorphs and related materials. As observed in an earlier study, the ELF is capable of generating bond and lone pair domains that are similar in number and arrangement to those provided by Laplacian and deformation electron density distributions. The formation of the bond and lone pair domains in the silica polymorphs and the progressive decrease in the SiO length as the value of the electron density at the bond critical point increases indicates that the SiO bonded interaction has a substantial component of covalent character.« less

Evolution from BCS superconductivity to Bose condensation: Calculation of the zero-temperature phase coherence length

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

Pistolesi, F.; Strinati, G.C.

1996-06-01

We consider a fermionic system at zero temperature interacting through an effective nonretarded potential of the type introduced by Nozi{grave e}res and Schmitt-Rink, and calculate the {ital phase} coherence length {xi}{sub phase} (associated with the spatial fluctuations of the superconducting order parameter) by exploiting a functional-integral formulation for the correlation functions and the associated loop expansion. This formulation is especially suited to follow the evolution of the fermionic system from a BCS-type superconductor for weak coupling to a Bose-condensed system for strong coupling, since in the latter limit a {ital direct} mapping of the original fermionic system onto an effectivemore » system of bosons with a residual boson-boson interaction can be established. Explicit calculations are performed at the one-loop order. The phase coherence length {xi}{sub phase} is compared with the coherence length {xi}{sub pair} for two-electron correlation, which is relevant to distinguish the weak- ({ital k}{sub {ital F}}{xi}{sub pair}{gt}1) from the strong- ({ital k}{sub {ital F}}{xi}{sub pair}{lt}1) coupling limits ({ital k}{sub {ital F}} being the Fermi wave vector) {ital as} {ital well} {ital as} to follow the crossover in between. It is shown that {xi}{sub phase} coincides with {xi}{sub pair} down to {ital k}{sub {ital F}}{xi}{sub pair}{approx_equal}10, {xi}{sub pair} in turn coinciding with the Pippard coherence length. In the strong-coupling limit we find instead that {xi}{sub phase}{gt}{xi}{sub pair}, with {xi}{sub pair} coinciding with the radius of the bound-electron pair. From the mapping onto an effective system of bosons in the strong-coupling limit we further relate {xi}{sub pair} with the {open_quote}{open_quote}range{close_quote}{close_quote} of the residual boson-boson interaction, which is physically the only significant length associated with the dynamics of the bosonic system. {copyright} {ital 1996 The American Physical Society.}« less

Non-additive interactions involving two distinct elements mediate sloppy-paired regulation by pair-rule transcription factors

PubMed Central

Prazak, Lisa; Fujioka, Miki; Gergen, J. Peter

2010-01-01

The relatively simple combinatorial rules responsible for establishing the initial metameric expression of sloppy-paired-1 (slp1) in the Drosophila blastoderm embryo make this system an attractive model for investigating the mechanism of regulation by pair rule transcription factors. This investigation of slp1 cis-regulatory architecture identifies two distinct elements, a proximal early stripe element (PESE) and a distal early stripe element (DESE) located from −3.1 kb to −2.5 kb and from −8.1 kb to −7.1 kb upstream of the slp1 promoter, respectively, that mediate this early regulation. The proximal element expresses only even-numbered stripes and mediates repression by Even-skipped (Eve) as well as by the combination of Runt and Fushi-tarazu (Ftz). A 272 basepair sub-element of PESE retains Eve-dependent repression, but is expressed throughout the even-numbered parasegments due to the loss of repression by Runt and Ftz. In contrast, the distal element expresses both odd and even-numbered stripes and also drives inappropriate expression in the anterior half of the odd-numbered parasegments due to an inability to respond to repression by Eve. Importantly, a composite reporter gene containing both early stripe elements recapitulates pair-rule gene-dependent regulation in a manner beyond what is expected from combining their individual patterns. These results indicate interactions involving distinct cis-elements contribute to the proper integration of pair-rule regulatory information. A model fully accounting for these results proposes that metameric slp1 expression is achieved through the Runt-dependent regulation of interactions between these two pair-rule response elements and the slp1 promoter. PMID:20435028

Investigating the role of ion-pair strategy in regulating nicotine release from patch: Mechanistic insights based on intermolecular interaction and mobility of pressure sensitive adhesive.

PubMed

Li, Qiaoyun; Wan, Xiaocao; Liu, Chao; Fang, Liang

2018-07-01

The aim of this study was to prepare a drug-in-adhesive patch of nicotine (NIC) and use ion-pair strategy to regulate drug delivery rate. Moreover, the mechanism of how ion-pair strategy regulated drug release was elucidated at molecular level. Formulation factors including pressure sensitive adhesives (PSAs), drug loading and counter ions (C 4 , C 6 , C 8 , C 10 , and C 12 ) were screened. In vitro release experiment and in vitro transdermal experiment were conducted to determine the rate-limiting step in drug delivery process. FT-IR and molecular modeling were used to characterize the interaction between drug and PSA. Thermal analysis and rheology study were conducted to investigate the mobility variation of PSA. The optimized patch prepared with NIC-C 8 had the transdermal profile fairly close to that of the commercial product (p > 0.05). The release rate constants (k) of NIC, NIC-C 4 and NIC-C 10 were 21.1, 14.4 and 32.4, respectively. Different release rates of NIC ion-pair complexes were attributed to the dual effect of ion-pair strategy on drug release. On one hand, ion-pair strategy enhanced the interaction between drug and PSA, which inhibited drug release. On the other hand, using ion-pair strategy improved the mobility of PSA, which facilitated drug release. Drug release behavior was determined by combined effect of two aspects above. These conclusions provided a new idea for us to regulate drug release behavior from patch. Copyright © 2018 Elsevier B.V. All rights reserved.

Interpreting anomalous electron pairs as new particle decays

NASA Astrophysics Data System (ADS)

Wilczynski, Henryk

1999-08-01

In heavy particle decays found in cosmic ray interactions recorded in the JACEE emulsion chambers, multiple electron pairs were previously reported. These pairs apparently originated from conversions of photons emitted in the decays. It is difficult to explain the overall properties of these decays in terms of known heavy particle decay modes. A recently published compilation of low-energy nuclear data suggests existence of excess electron pairs with invariant mass about 9 MeV/c2 , which may be explained by postulating a new neutral boson decaying into the electron pair. The feasibility of explaining the JACEE electron pairs with this hypothesis is presented.

Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development

PubMed Central

Kazemian, Majid; Pham, Hannah; Wolfe, Scot A.; Brodsky, Michael H.; Sinha, Saurabh

2013-01-01

Regulation of eukaryotic gene transcription is often combinatorial in nature, with multiple transcription factors (TFs) regulating common target genes, often through direct or indirect mutual interactions. Many individual examples of cooperative binding by directly interacting TFs have been identified, but it remains unclear how pervasive this mechanism is during animal development. Cooperative TF binding should be manifest in genomic sequences as biased arrangements of TF-binding sites. Here, we explore the extent and diversity of such arrangements related to gene regulation during Drosophila embryogenesis. We used the DNA-binding specificities of 322 TFs along with chromatin accessibility information to identify enriched spacing and orientation patterns of TF-binding site pairs. We developed a new statistical approach for this task, specifically designed to accurately assess inter-site spacing biases while accounting for the phenomenon of homotypic site clustering commonly observed in developmental regulatory regions. We observed a large number of short-range distance preferences between TF-binding site pairs, including examples where the preference depends on the relative orientation of the binding sites. To test whether these binding site patterns reflect physical interactions between the corresponding TFs, we analyzed 27 TF pairs whose binding sites exhibited short distance preferences. In vitro protein–protein binding experiments revealed that >65% of these TF pairs can directly interact with each other. For five pairs, we further demonstrate that they bind cooperatively to DNA if both sites are present with the preferred spacing. This study demonstrates how DNA-binding motifs can be used to produce a comprehensive map of sequence signatures for different mechanisms of combinatorial TF action. PMID:23847101

Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development.

PubMed

Kazemian, Majid; Pham, Hannah; Wolfe, Scot A; Brodsky, Michael H; Sinha, Saurabh

2013-09-01

Regulation of eukaryotic gene transcription is often combinatorial in nature, with multiple transcription factors (TFs) regulating common target genes, often through direct or indirect mutual interactions. Many individual examples of cooperative binding by directly interacting TFs have been identified, but it remains unclear how pervasive this mechanism is during animal development. Cooperative TF binding should be manifest in genomic sequences as biased arrangements of TF-binding sites. Here, we explore the extent and diversity of such arrangements related to gene regulation during Drosophila embryogenesis. We used the DNA-binding specificities of 322 TFs along with chromatin accessibility information to identify enriched spacing and orientation patterns of TF-binding site pairs. We developed a new statistical approach for this task, specifically designed to accurately assess inter-site spacing biases while accounting for the phenomenon of homotypic site clustering commonly observed in developmental regulatory regions. We observed a large number of short-range distance preferences between TF-binding site pairs, including examples where the preference depends on the relative orientation of the binding sites. To test whether these binding site patterns reflect physical interactions between the corresponding TFs, we analyzed 27 TF pairs whose binding sites exhibited short distance preferences. In vitro protein-protein binding experiments revealed that >65% of these TF pairs can directly interact with each other. For five pairs, we further demonstrate that they bind cooperatively to DNA if both sites are present with the preferred spacing. This study demonstrates how DNA-binding motifs can be used to produce a comprehensive map of sequence signatures for different mechanisms of combinatorial TF action.

Mapping PrBn and Other Quantitative Trait Loci Responsible for the Control of Homeologous Chromosome Pairing in Oilseed Rape (Brassica napus L.) Haploids

PubMed Central

Liu, Zhiqian; Adamczyk, Katarzyna; Manzanares-Dauleux, Maria; Eber, Frédérique; Lucas, Marie-Odile; Delourme, Régine; Chèvre, Anne Marie; Jenczewski, Eric

2006-01-01

In allopolyploid species, fair meiosis could be challenged by homeologous chromosome pairing and is usually achieved by the action of homeologous pairing suppressor genes. Oilseed rape (Brassica napus) haploids (AC, n = 19) represent an attractive model for studying the mechanisms used by allopolyploids to ensure the diploid-like meiotic pairing pattern. In oilseed rape haploids, homeologous chromosome pairing at metaphase I was found to be genetically based and controlled by a major gene, PrBn, segregating in a background of polygenic variation. In this study, we have mapped PrBn within a 10-cM interval on the C genome linkage group DY15 and shown that PrBn displays incomplete penetrance or variable expressivity. We have identified three to six minor QTL/BTL that have slight additive effects on the amount of pairing at metaphase I but do not interact with PrBn. We have also detected a number of other loci that interact epistatically, notably with PrBn. Our results support the idea that, as in other polyploid species, metaphase I homeologous pairing in oilseed rape haploids is controlled by an integrated system of several genes, which function in a complex manner. PMID:16951054

Ab initio O(N) elongation-counterpoise method for BSSE-corrected interaction energy analyses in biosystems

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

Orimoto, Yuuichi; Xie, Peng; Liu, Kai

2015-03-14

An Elongation-counterpoise (ELG-CP) method was developed for performing accurate and efficient interaction energy analysis and correcting the basis set superposition error (BSSE) in biosystems. The method was achieved by combining our developed ab initio O(N) elongation method with the conventional counterpoise method proposed for solving the BSSE problem. As a test, the ELG-CP method was applied to the analysis of the DNAs’ inter-strands interaction energies with respect to the alkylation-induced base pair mismatch phenomenon that causes a transition from G⋯C to A⋯T. It was found that the ELG-CP method showed high efficiency (nearly linear-scaling) and high accuracy with a negligiblymore » small energy error in the total energy calculations (in the order of 10{sup −7}–10{sup −8} hartree/atom) as compared with the conventional method during the counterpoise treatment. Furthermore, the magnitude of the BSSE was found to be ca. −290 kcal/mol for the calculation of a DNA model with 21 base pairs. This emphasizes the importance of BSSE correction when a limited size basis set is used to study the DNA models and compare small energy differences between them. In this work, we quantitatively estimated the inter-strands interaction energy for each possible step in the transition process from G⋯C to A⋯T by the ELG-CP method. It was found that the base pair replacement in the process only affects the interaction energy for a limited area around the mismatch position with a few adjacent base pairs. From the interaction energy point of view, our results showed that a base pair sliding mechanism possibly occurs after the alkylation of guanine to gain the maximum possible number of hydrogen bonds between the bases. In addition, the steps leading to the A⋯T replacement accompanied with replications were found to be unfavorable processes corresponding to ca. 10 kcal/mol loss in stabilization energy. The present study indicated that the ELG-CP method is promising for performing effective interaction energy analyses in biosystems.« less

Using an innovative multiple regression procedure in a cancer population (Part 1): detecting and probing relationships of common interacting symptoms (pain, fatigue/weakness, sleep problems) as a strategy to discover influential symptom pairs and clusters

PubMed Central

Francoeur, Richard B

2015-01-01

Background The majority of patients with advanced cancer experience symptom pairs or clusters among pain, fatigue, and insomnia. Improved methods are needed to detect and interpret interactions among symptoms or diesease markers to reveal influential pairs or clusters. In prior work, I developed and validated sequential residual centering (SRC), a method that improves the sensitivity of multiple regression to detect interactions among predictors, by conditioning for multicollinearity (shared variation) among interactions and component predictors. Materials and methods Using a hypothetical three-way interaction among pain, fatigue, and sleep to predict depressive affect, I derive and explain SRC multiple regression. Subsequently, I estimate raw and SRC multiple regressions using real data for these symptoms from 268 palliative radiation outpatients. Results Unlike raw regression, SRC reveals that the three-way interaction (pain × fatigue/weakness × sleep problems) is statistically significant. In follow-up analyses, the relationship between pain and depressive affect is aggravated (magnified) within two partial ranges: 1) complete-to-some control over fatigue/weakness when there is complete control over sleep problems (ie, a subset of the pain–fatigue/weakness symptom pair), and 2) no control over fatigue/weakness when there is some-to-no control over sleep problems (ie, a subset of the pain–fatigue/weakness–sleep problems symptom cluster). Otherwise, the relationship weakens (buffering) as control over fatigue/weakness or sleep problems diminishes. Conclusion By reducing the standard error, SRC unmasks a three-way interaction comprising a symptom pair and cluster. Low-to-moderate levels of the moderator variable for fatigue/weakness magnify the relationship between pain and depressive affect. However, when the comoderator variable for sleep problems accompanies fatigue/weakness, only frequent or unrelenting levels of both symptoms magnify the relationship. These findings suggest that a countervailing mechanism involving depressive affect could account for the effectiveness of a cognitive behavioral intervention to reduce the severity of a pain, fatigue, and sleep disturbance cluster in a previous randomized trial. PMID:25565865

Using an innovative multiple regression procedure in a cancer population (Part 1): detecting and probing relationships of common interacting symptoms (pain, fatigue/weakness, sleep problems) as a strategy to discover influential symptom pairs and clusters.

PubMed

Francoeur, Richard B

2015-01-01

The majority of patients with advanced cancer experience symptom pairs or clusters among pain, fatigue, and insomnia. Improved methods are needed to detect and interpret interactions among symptoms or diesease markers to reveal influential pairs or clusters. In prior work, I developed and validated sequential residual centering (SRC), a method that improves the sensitivity of multiple regression to detect interactions among predictors, by conditioning for multicollinearity (shared variation) among interactions and component predictors. Using a hypothetical three-way interaction among pain, fatigue, and sleep to predict depressive affect, I derive and explain SRC multiple regression. Subsequently, I estimate raw and SRC multiple regressions using real data for these symptoms from 268 palliative radiation outpatients. Unlike raw regression, SRC reveals that the three-way interaction (pain × fatigue/weakness × sleep problems) is statistically significant. In follow-up analyses, the relationship between pain and depressive affect is aggravated (magnified) within two partial ranges: 1) complete-to-some control over fatigue/weakness when there is complete control over sleep problems (ie, a subset of the pain-fatigue/weakness symptom pair), and 2) no control over fatigue/weakness when there is some-to-no control over sleep problems (ie, a subset of the pain-fatigue/weakness-sleep problems symptom cluster). Otherwise, the relationship weakens (buffering) as control over fatigue/weakness or sleep problems diminishes. By reducing the standard error, SRC unmasks a three-way interaction comprising a symptom pair and cluster. Low-to-moderate levels of the moderator variable for fatigue/weakness magnify the relationship between pain and depressive affect. However, when the comoderator variable for sleep problems accompanies fatigue/weakness, only frequent or unrelenting levels of both symptoms magnify the relationship. These findings suggest that a countervailing mechanism involving depressive affect could account for the effectiveness of a cognitive behavioral intervention to reduce the severity of a pain, fatigue, and sleep disturbance cluster in a previous randomized trial.

Epistasis analysis for quantitative traits by functional regression model.

PubMed

Zhang, Futao; Boerwinkle, Eric; Xiong, Momiao

2014-06-01

The critical barrier in interaction analysis for rare variants is that most traditional statistical methods for testing interactions were originally designed for testing the interaction between common variants and are difficult to apply to rare variants because of their prohibitive computational time and poor ability. The great challenges for successful detection of interactions with next-generation sequencing (NGS) data are (1) lack of methods for interaction analysis with rare variants, (2) severe multiple testing, and (3) time-consuming computations. To meet these challenges, we shift the paradigm of interaction analysis between two loci to interaction analysis between two sets of loci or genomic regions and collectively test interactions between all possible pairs of SNPs within two genomic regions. In other words, we take a genome region as a basic unit of interaction analysis and use high-dimensional data reduction and functional data analysis techniques to develop a novel functional regression model to collectively test interactions between all possible pairs of single nucleotide polymorphisms (SNPs) within two genome regions. By intensive simulations, we demonstrate that the functional regression models for interaction analysis of the quantitative trait have the correct type 1 error rates and a much better ability to detect interactions than the current pairwise interaction analysis. The proposed method was applied to exome sequence data from the NHLBI's Exome Sequencing Project (ESP) and CHARGE-S study. We discovered 27 pairs of genes showing significant interactions after applying the Bonferroni correction (P-values < 4.58 × 10(-10)) in the ESP, and 11 were replicated in the CHARGE-S study. © 2014 Zhang et al.; Published by Cold Spring Harbor Laboratory Press.

Kraus Operators for a Pair of Interacting Qubits: a Case Study

NASA Astrophysics Data System (ADS)

Arsenijević, M.; Jeknić-Dugić, J.; Dugić, M.

2018-04-01

The Kraus form of the completely positive dynamical maps is appealing from the mathematical and the point of the diverse applications of the open quantum systems theory. Unfortunately, the Kraus operators are poorly known for the two-qubit processes. In this paper, we derive the Kraus operators for a pair of interacting qubits, while the strength of the interaction is arbitrary. One of the qubits is subjected to the x-projection spin measurement. The obtained results are applied to calculate the dynamics of the entanglement in the qubits system. We obtain the loss of the correlations in the finite time interval; the stronger the inter-qubit interaction, the longer lasting entanglement in the system.

Kraus Operators for a Pair of Interacting Qubits: a Case Study

NASA Astrophysics Data System (ADS)

Arsenijević, M.; Jeknić-Dugić, J.; Dugić, M.

2018-06-01

The Kraus form of the completely positive dynamical maps is appealing from the mathematical and the point of the diverse applications of the open quantum systems theory. Unfortunately, the Kraus operators are poorly known for the two-qubit processes. In this paper, we derive the Kraus operators for a pair of interacting qubits, while the strength of the interaction is arbitrary. One of the qubits is subjected to the x-projection spin measurement. The obtained results are applied to calculate the dynamics of the entanglement in the qubits system. We obtain the loss of the correlations in the finite time interval; the stronger the inter-qubit interaction, the longer lasting entanglement in the system.

Recognition tunneling measurement of the conductance of DNA bases embedded in self-assembled monolayers.

PubMed

Huang, Shuo; Chang, Shuai; He, Jin; Zhang, Peiming; Liang, Feng; Tuchband, Michael; Li, Shengqing; Lindsay, Stuart

2010-12-09

The DNA bases interact strongly with gold electrodes, complicating efforts to measure the tunneling conductance through hydrogen-bonded Watson Crick base pairs. When bases are embedded in a self-assembled alkane-thiol monolayer to minimize these interactions, new features appear in the tunneling data. These new features track the predictions of density-functional calculations quite well, suggesting that they reflect tunnel conductance through hydrogen-bonded base pairs.

Recognition tunneling measurement of the conductance of DNA bases embedded in self-assembled monolayers

PubMed Central

Huang, Shuo; Chang, Shuai; He, Jin; Zhang, Peiming; Liang, Feng; Tuchband, Michael; Li, Shengqing; Lindsay, Stuart

2010-01-01

The DNA bases interact strongly with gold electrodes, complicating efforts to measure the tunneling conductance through hydrogen-bonded Watson Crick base pairs. When bases are embedded in a self-assembled alkane-thiol monolayer to minimize these interactions, new features appear in the tunneling data. These new features track the predictions of density-functional calculations quite well, suggesting that they reflect tunnel conductance through hydrogen-bonded base pairs. PMID:21197382

Patterns of call communication between group-housed zebra finches change during the breeding cycle.

PubMed

Gill, Lisa F; Goymann, Wolfgang; Ter Maat, Andries; Gahr, Manfred

2015-10-06

Vocal signals such as calls play a crucial role for survival and successful reproduction, especially in group-living animals. However, call interactions and call dynamics within groups remain largely unexplored because their relation to relevant contexts or life-history stages could not be studied with individual-level resolution. Using on-bird microphone transmitters, we recorded the vocalisations of individual zebra finches (Taeniopygia guttata) behaving freely in social groups, while females and males previously unknown to each other passed through different stages of the breeding cycle. As birds formed pairs and shifted their reproductive status, their call repertoire composition changed. The recordings revealed that calls occurred non-randomly in fine-tuned vocal interactions and decreased within groups while pair-specific patterns emerged. Call-type combinations of vocal interactions changed within pairs and were associated with successful egg-laying, highlighting a potential fitness relevance of calling dynamics in communication systems.

Importance of the ion-pair interactions in the OPEP coarse-grained force field: parametrization and validation.

PubMed

Sterpone, Fabio; Nguyen, Phuong H; Kalimeri, Maria; Derreumaux, Philippe

2013-10-08

We have derived new effective interactions that improve the description of ion-pairs in the OPEP coarse-grained force field without introducing explicit electrostatic terms. The iterative Boltzmann inversion method was used to extract these potentials from all atom simulations by targeting the radial distribution function of the distance between the center of mass of the side-chains. The new potentials have been tested on several systems that differ in structural properties, thermodynamic stabilities and number of ion-pairs. Our modeling, by refining the packing of the charged amino-acids, impacts the stability of secondary structure motifs and the population of intermediate states during temperature folding/unfolding; it also improves the aggregation propensity of peptides. The new version of the OPEP force field has the potentiality to describe more realistically a large spectrum of situations where salt-bridges are key interactions.

Configurations of base-pair complexes in solutions. [nucleotide chemistry

NASA Technical Reports Server (NTRS)

Egan, J. T.; Nir, S.; Rein, R.; Macelroy, R.

1978-01-01

A theoretical search for the most stable conformations (i.e., stacked or hydrogen bonded) of the base pairs A-U and G-C in water, CCl4, and CHCl3 solutions is presented. The calculations of free energies indicate a significant role of the solvent in determining the conformations of the base-pair complexes. The application of the continuum method yields preferred conformations in good agreement with experiment. Results of the calculations with this method emphasize the importance of both the electrostatic interactions between the two bases in a complex, and the dipolar interaction of the complex with the entire medium. In calculations with the solvation shell method, the last term, i.e., dipolar interaction of the complex with the entire medium, was added. With this modification the prediction of the solvation shell model agrees both with the continuum model and with experiment, i.e., in water the stacked conformation of the bases is preferred.

Quantum phases of dipolar soft-core bosons

NASA Astrophysics Data System (ADS)

Grimmer, D.; Safavi-Naini, A.; Capogrosso-Sansone, B.; Söyler, Ş. G.

2014-10-01

We study the phase diagram of a system of soft-core dipolar bosons confined to a two-dimensional optical lattice layer. We assume that dipoles are aligned perpendicular to the layer such that the dipolar interactions are purely repulsive and isotropic. We consider the full dipolar interaction and perform path-integral quantum Monte Carlo simulations using the worm algorithm. Besides a superfluid phase, we find various solid and supersolid phases. We show that, unlike what was found previously for the case of nearest-neighbor interaction, supersolid phases are stabilized by doping the solids not only with particles but with holes as well. We further study the stability of these quantum phases against thermal fluctuations. Finally, we discuss pair formation and the stability of the pair checkerboard phase formed in a bilayer geometry, and we suggest experimental conditions under which the pair checkerboard phase can be observed.

Predicting drug-disease interactions by semi-supervised graph cut algorithm and three-layer data integration.

PubMed

Wu, Guangsheng; Liu, Juan; Wang, Caihua

2017-12-28

Prediction of drug-disease interactions is promising for either drug repositioning or disease treatment fields. The discovery of novel drug-disease interactions, on one hand can help to find novel indictions for the approved drugs; on the other hand can provide new therapeutic approaches for the diseases. Recently, computational methods for finding drug-disease interactions have attracted lots of attention because of their far more higher efficiency and lower cost than the traditional wet experiment methods. However, they still face several challenges, such as the organization of the heterogeneous data, the performance of the model, and so on. In this work, we present to hierarchically integrate the heterogeneous data into three layers. The drug-drug and disease-disease similarities are first calculated separately in each layer, and then the similarities from three layers are linearly fused into comprehensive drug similarities and disease similarities, which can then be used to measure the similarities between two drug-disease pairs. We construct a novel weighted drug-disease pair network, where a node is a drug-disease pair with known or unknown treatment relation, an edge represents the node-node relation which is weighted with the similarity score between two pairs. Now that similar drug-disease pairs are supposed to show similar treatment patterns, we can find the optimal graph cut of the network. The drug-disease pair with unknown relation can then be considered to have similar treatment relation with that within the same cut. Therefore, we develop a semi-supervised graph cut algorithm, SSGC, to find the optimal graph cut, based on which we can identify the potential drug-disease treatment interactions. By comparing with three representative network-based methods, SSGC achieves the highest performances, in terms of both AUC score and the identification rates of true drug-disease pairs. The experiments with different integration strategies also demonstrate that considering several sources of data can improve the performances of the predictors. Further case studies on four diseases, the top-ranked drug-disease associations have been confirmed by KEGG, CTD database and the literature, illustrating the usefulness of SSGC. The proposed comprehensive similarity scores from multi-views and multiple layers and the graph-cut based algorithm can greatly improve the prediction performances of drug-disease associations.

Effects of visual and verbal interaction on unintentional interpersonal coordination.

PubMed

Richardson, Michael J; Marsh, Kerry L; Schmidt, R C

2005-02-01

Previous research has demonstrated that people's movements can become unintentionally coordinated during interpersonal interaction. The current study sought to uncover the degree to which visual and verbal (conversation) interaction constrains and organizes the rhythmic limb movements of coactors. Two experiments were conducted in which pairs of participants completed an interpersonal puzzle task while swinging handheld pendulums with instructions that minimized intentional coordination but facilitated either visual or verbal interaction. Cross-spectral analysis revealed a higher degree of coordination for conditions in which the pairs were visually coupled. In contrast, verbal interaction alone was not found to provide a sufficient medium for unintentional coordination to occur, nor did it enhance the unintentional coordination that emerged during visual interaction. The results raise questions concerning differences between visual and verbal informational linkages during interaction and how these differences may affect interpersonal movement production and its coordination.

Contribution of cation-π interactions to the stability of Sm/LSm oligomeric assemblies.

PubMed

Mucić, Ivana D; Nikolić, Milan R; Stojanović, Srđan Đ

2015-07-01

In this work, we have analyzed the influence of cation-π interactions to the stability of Sm/LSm assemblies and their environmental preferences. The number of interactions formed by arginine is higher than lysine in the cationic group, while histidine is comparatively higher than phenylalanine and tyrosine in the π group. Arg-Tyr interactions are predominant among the various pairs analyzed. The furcation level of multiple cation-π interactions is much higher than that of single cation-π interactions in Sm/LSm interfaces. We have found hot spot residues forming cation-π interactions, and hot spot composition is similar for all aromatic residues. The Arg-Phe pair has the strongest interaction energy of -8.81 kcal mol(-1) among all the possible pairs of amino acids. The extent of burial of the residue side-chain correlates with the ΔΔG of binding for residues in the core and also for hot spot residues cation-π bonded across the interface. Secondary structure of the cation-π residues shows that Arg and Lys preferred to be in strand. Among the π residues, His prefers to be in helix, Phe prefers to be in turn, and Tyr prefers to be in strand. Stabilization centers for these proteins showed that all the five residues found in cation-π interactions are important in locating one or more of such centers. More than 50 % of the cation-π interacting residues are highly conserved. It is likely that the cation-π interactions contribute significantly to the overall stability of Sm/LSm proteins.

Shifts in a fish's resource holding power during a contact paired interaction: the influence of a copper-contaminated diet in rainbow trout.

PubMed

Campbell, H A; Handy, R D; Sims, D W

2005-01-01

The influence of sublethal chronic dietary copper (Cu) exposure on the dominant-subordinate relationship between pairs of juvenile rainbow trout (Oncorhynchus mykiss) was examined. Fish were fed either a normal (11 mg Cu kg(-1) food) or Cu-contaminated (721 mg Cu kg(-1) food) diet for 8 wk. Paired interactions were observed--control versus control, Cu-exposed versus Cu-exposed, and control versus Cu-exposed fish--using a computer-aided video tracking system to measure duration of interactions, total distance moved, and the number of encounters during each contest. In concurrence with game theory, each interaction became escalated with a lesser size disparity between contestants. However, in Cu-exposed versus Cu-exposed fish interactions, the dominant-subordinate relationship was decided sooner and with less aggression than a control versus control fish interaction with fish of a similar relative body mass disparity. During control versus Cu-exposed fish interactions, control fish would normally dominate interactions (12 out of 16 bouts) unless the Cu-exposed fish had a 15% body mass advantage. Muscle glycogen and lactate levels after each contest reflected the duration of bouts and winners of the contests, irrespective of Cu exposure. We conclude that Cu-contaminated fish are less able to compete and have lower resource holding power than controls and will withdraw from a contest at a lower level of interaction, unless a size advantage in the Cu-exposed fish increases the probability of winning.

HERSCHEL OBSERVATIONS OF MAJOR MERGER PAIRS AT z = 0: DUST MASS AND STAR FORMATION

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

Cao, Chen; Xu, Cong Kevin; Lu, Nanyao

We present Herschel PACS and SPIRE far-infrared (FIR) and submillimeter imaging observations for a large K-band selected sample of 88 close major-merger pairs of galaxies (H-KPAIRs) in 6 photometric bands (70, 100, 160, 250, 350, and 500 μm). Among 132 spiral galaxies in the 44 spiral–spiral (S+S) pairs and 44 spiral–elliptical (S+E) pairs, 113 are detected in at least 1 Herschel band. The star formation rate (SFR) and dust mass (M{sub dust}) are derived from the IR SED fitting. The mass of total gas (M{sub gas}) is estimated by assuming a constant dust-to-gas mass ratio of 0.01. Star-forming spiral galaxiesmore » (SFGs) in S+S pairs show significant enhancements in both specific star formation rate (sSFR) and star formation efficiency (SFE), while having nearly the same gas mass compared to control galaxies. On the other hand, for SFGs in S+E pairs, there is no significant sSFR enhancement and the mean SFE enhancement is significantly lower than that of SFGs in S+S pairs. This suggests an important role for the disk–disk collision in the interaction-induced star formation. The M{sub gas} of SFGs in S+E pairs is marginally lower than that of their counterparts in both S+S pairs and the control sample. Paired galaxies with and without interaction signs do not differ significantly in their mean sSFR and SFE. As found in previous works, this much larger sample confirms that the primary and secondary spirals in S+S pairs follow a Holmberg effect correlation on sSFR.« less

Comparing Pair and Small Group Interactions on Oral Tasks

ERIC Educational Resources Information Center

Lasito,; Storch, Neomy

2013-01-01

Although pair and small group activities are commonly used in second language (L2) classrooms, there are very few studies which can inform teachers about whether it is best to have students work in pairs or in small groups. In this study, conducted in a junior high school in Indonesia with learners of English as a Foreign Language (EFL), we…

Detecting reciprocity at a global scale

PubMed Central

Frank, Morgan R.; Obradovich, Nick; Sun, Lijun; Woon, Wei Lee; LeVeck, Brad L.; Rahwan, Iyad

2018-01-01

Reciprocity stabilizes cooperation from the level of microbes all the way up to humans interacting in small groups, but does reciprocity also underlie stable cooperation between larger human agglomerations, such as nation states? Famously, evolutionary models show that reciprocity could emerge as a widespread strategy for achieving international cooperation. However, existing studies have only detected reciprocity-driven cooperation in a small number of country pairs. We apply a new method for detecting mutual influence in dynamical systems to a new large-scale data set that records state interactions with high temporal resolution. Doing so, we detect reciprocity between many country pairs in the international system and find that these reciprocating country pairs exhibit qualitatively different cooperative dynamics when compared to nonreciprocating pairs. Consistent with evolutionary theories of cooperation, reciprocating country pairs exhibit higher levels of stable cooperation and are more likely to punish instances of noncooperation. However, countries in reciprocity-based relationships are also quicker to forgive single acts of noncooperation by eventually returning to previous levels of mutual cooperation. By contrast, nonreciprocating pairs are more likely to exploit each other’s cooperation via higher rates of defection. Together, these findings provide the strongest evidence to date that reciprocity is a widespread mechanism for achieving international cooperation. PMID:29326983

Detecting reciprocity at a global scale.

PubMed

Frank, Morgan R; Obradovich, Nick; Sun, Lijun; Woon, Wei Lee; LeVeck, Brad L; Rahwan, Iyad

2018-01-01

Reciprocity stabilizes cooperation from the level of microbes all the way up to humans interacting in small groups, but does reciprocity also underlie stable cooperation between larger human agglomerations, such as nation states? Famously, evolutionary models show that reciprocity could emerge as a widespread strategy for achieving international cooperation. However, existing studies have only detected reciprocity-driven cooperation in a small number of country pairs. We apply a new method for detecting mutual influence in dynamical systems to a new large-scale data set that records state interactions with high temporal resolution. Doing so, we detect reciprocity between many country pairs in the international system and find that these reciprocating country pairs exhibit qualitatively different cooperative dynamics when compared to nonreciprocating pairs. Consistent with evolutionary theories of cooperation, reciprocating country pairs exhibit higher levels of stable cooperation and are more likely to punish instances of noncooperation. However, countries in reciprocity-based relationships are also quicker to forgive single acts of noncooperation by eventually returning to previous levels of mutual cooperation. By contrast, nonreciprocating pairs are more likely to exploit each other's cooperation via higher rates of defection. Together, these findings provide the strongest evidence to date that reciprocity is a widespread mechanism for achieving international cooperation.

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

Leszczynski, Jerzy; Sponer, Judit; Sponer, Jiri

Recent experimental studies on the Watson Crick type base pairing of triazine and aminopyrimidine derivatives suggest that acid/base properties of the constituent bases might be related to the duplex stabilities measured in solution. Herein we use high-level quantum chemical calculations and molecular dynamics simulations to evaluate the base pairing and stacking interactions of seven selected base pairs, which are common in that they are stabilized by two NH O hydrogen bonds separated by one NH N hydrogen bond. We show that neither the base pairing nor the base stacking interaction energies correlate with the reported pKa data of the basesmore » and the melting points of the duplexes. This suggests that the experimentally observed correlation between the melting point data of the duplexes and the pKa values of the constituent bases is not rooted in the intrinsic base pairing and stacking properties. The physical chemistry origin of the observed experimental correlation thus remains unexplained and requires further investigations. In addition, since our calculations are carried out with extrapolation to the complete basis set of atomic orbitals and with inclusion of higher electron correlation effects, they provide reference data for stacking and base pairing energies of non-natural bases.« less

Recounting a Common Experience: On the Effectiveness of Instructing Eyewitness Pairs

PubMed Central

Vredeveldt, Annelies; van Koppen, Peter J.

2018-01-01

Pairs of eyewitnesses with a content-focused interaction style remember significantly more about witnessed incidents. We examined whether content-focused retrieval strategies can be taught. Seventy-five pairs of witnesses were interviewed thrice about an event. The first and third interview were conducted individually for all witnesses. The second interview was individual, collaborative without instruction, or collaborative with instruction. Pairs in the latter condition were instructed to actively listen to and elaborate upon each other's contributions. The strategy instruction had no effect on retrieval strategies used, nor on the amount or accuracy of reported information. However, pairs who spontaneously adopted a content-focused interaction style during the collaborative interview remembered significantly more. Thus, our findings show that effective retrieval strategies cannot be taught, at least not with the current instructions. During the second interview, we observed collaborative inhibition and error pruning. When considering the total amount of information reported across the first two interviews, however, collaboration had no inhibitory effect on correct recall, yet the error pruning benefits remained. These findings suggest that investigative interviewers should interview witnesses separately first, and then interview pairs of witnesses collaboratively. PMID:29593599

Exotic superfluidity and pairing phenomena in atomic Fermi gases in mixed dimensions.

PubMed

Zhang, Leifeng; Che, Yanming; Wang, Jibiao; Chen, Qijin

2017-10-11

Atomic Fermi gases have been an ideal platform for simulating conventional and engineering exotic physical systems owing to their multiple tunable control parameters. Here we investigate the effects of mixed dimensionality on the superfluid and pairing phenomena of a two-component ultracold atomic Fermi gas with a short-range pairing interaction, while one component is confined on a one-dimensional (1D) optical lattice whereas the other is in a homogeneous 3D continuum. We study the phase diagram and the pseudogap phenomena throughout the entire BCS-BEC crossover, using a pairing fluctuation theory. We find that the effective dimensionality of the non-interacting lattice component can evolve from quasi-3D to quasi-1D, leading to strong Fermi surface mismatch. Upon pairing, the system becomes effectively quasi-two dimensional in the BEC regime. The behavior of T c bears similarity to that of a regular 3D population imbalanced Fermi gas, but with a more drastic departure from the regular 3D balanced case, featuring both intermediate temperature superfluidity and possible pair density wave ground state. Unlike a simple 1D optical lattice case, T c in the mixed dimensions has a constant BEC asymptote.

Fermion superfluid with hybridized s- and p-wave pairings

NASA Astrophysics Data System (ADS)

Zhou, LiHong; Yi, Wei; Cui, XiaoLing

2017-12-01

Ever since the pioneering work of Bardeen, Cooper and Schrieffer in the 1950s, exploring novel pairing mechanisms for fermion superfluids has become one of the central tasks in modern physics. Here, we investigate a new type of fermion superfluid with hybridized s- and p-wave pairings in an ultracold spin-1/2 Fermi gas. Its occurrence is facilitated by the co-existence of comparable s- and p-wave interactions, which is realizable in a two-component 40K Fermi gas with close-by s- and p-wave Feshbach resonances. The hybridized superfluid state is stable over a considerable parameter region on the phase diagram, and can lead to intriguing patterns of spin densities and pairing fields in momentum space. In particular, it can induce a phase-locked p-wave pairing in the fermion species that has no p-wave interactions. The hybridized nature of this novel superfluid can also be confirmed by measuring the s- and p-wave contacts, which can be extracted from the high-momentum tail of the momentum distribution of each spin component. These results enrich our knowledge of pairing superfluidity in Fermi systems, and open the avenue for achieving novel fermion superfluids with multiple partial-wave scatterings in cold atomic gases.

MRMer, an interactive open source and cross-platform system for data extraction and visualization of multiple reaction monitoring experiments.

PubMed

Martin, Daniel B; Holzman, Ted; May, Damon; Peterson, Amelia; Eastham, Ashley; Eng, Jimmy; McIntosh, Martin

2008-11-01

Multiple reaction monitoring (MRM) mass spectrometry identifies and quantifies specific peptides in a complex mixture with very high sensitivity and speed and thus has promise for the high throughput screening of clinical samples for candidate biomarkers. We have developed an interactive software platform, called MRMer, for managing highly complex MRM-MS experiments, including quantitative analyses using heavy/light isotopic peptide pairs. MRMer parses and extracts information from MS files encoded in the platform-independent mzXML data format. It extracts and infers precursor-product ion transition pairings, computes integrated ion intensities, and permits rapid visual curation for analyses exceeding 1000 precursor-product pairs. Results can be easily output for quantitative comparison of consecutive runs. Additionally MRMer incorporates features that permit the quantitative analysis experiments including heavy and light isotopic peptide pairs. MRMer is open source and provided under the Apache 2.0 license.

Life Events, Genetic Susceptibility, and Smoking among Adolescents

PubMed Central

Pampel, Fred C.; Boardman, Jason D.; Daw, Jonathan; Stallings, Michael C.; Smolen, Andrew; Haberstick, Brett; Widaman, Keith F.; Neppl, Tricia K.; Conger, Rand D.

2015-01-01

Although stressful life events during adolescence are associated with the adoption of unhealthy behaviors such as smoking, both social circumstances and physical traits can moderate the relationship. This study builds on the stress paradigm and gene-environment approach to social behavior by examining how a polymorphism in the serotonin transporter gene 5-HTTLPR moderates the effect of life events on adolescent smoking. Tests of interaction hypotheses use data from the Family Transitions Project, a longitudinal study of 7th graders followed for 5 years. A sibling-pair design with separate models for the gender composition of pairs (brothers, sisters, or brother/sister) controls for unmeasured family background. The results show that negative life events are significantly and positively associated with smoking. Among brother pairs but not other pairs, the results provide evidence of gene-environment interaction by showing that life events more strongly influence smoking behavior for those with more copies of the 5-HTTLPR S allele. PMID:26463545

Kosterlitz-Thouless transition and vortex-antivortex lattice melting in two-dimensional Fermi gases with p - or d -wave pairing

NASA Astrophysics Data System (ADS)

Cao, Gaoqing; He, Lianyi; Huang, Xu-Guang

2017-12-01

We present a theoretical study of the finite-temperature Kosterlitz-Thouless (KT) and vortex-antivortex lattice (VAL) melting transitions in two-dimensional Fermi gases with p - or d -wave pairing. For both pairings, when the interaction is tuned from weak to strong attractions, we observe a quantum phase transition from the Bardeen-Cooper-Schrieffer (BCS) superfluidity to the Bose-Einstein condensation (BEC) of difermions. The KT and VAL transition temperatures increase during this BCS-BEC transition and approach constant values in the deep BEC region. The BCS-BEC transition is characterized by the nonanalyticities of the chemical potential, the superfluid order parameter, and the sound velocities as functions of the interaction strength at both zero and finite temperatures; however, the temperature effect tends to weaken the nonanalyticities compared to the zero-temperature case. The effect of mismatched Fermi surfaces on the d -wave pairing is also studied.

Pairing from strong repulsion in triangular lattice Hubbard model

NASA Astrophysics Data System (ADS)

Zhang, Shang-Shun; Zhu, Wei; Batista, Cristian D.

2018-04-01

We propose a pairing mechanism between holes in the dilute limit of doped frustrated Mott insulators. Hole pairing arises from a hole-hole-magnon three-body bound state. This pairing mechanism has its roots on single-hole kinetic energy frustration, which favors antiferromagnetic (AFM) correlations around the hole. We demonstrate that the AFM polaron (hole-magnon bound state) produced by a single hole propagating on a field-induced polarized background is strong enough to bind a second hole. The effective interaction between these three-body bound states is repulsive, implying that this pairing mechanism is relevant for superconductivity.

diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data.

PubMed

Lun, Aaron T L; Smyth, Gordon K

2015-08-19

Chromatin conformation capture with high-throughput sequencing (Hi-C) is a technique that measures the in vivo intensity of interactions between all pairs of loci in the genome. Most conventional analyses of Hi-C data focus on the detection of statistically significant interactions. However, an alternative strategy involves identifying significant changes in the interaction intensity (i.e., differential interactions) between two or more biological conditions. This is more statistically rigorous and may provide more biologically relevant results. Here, we present the diffHic software package for the detection of differential interactions from Hi-C data. diffHic provides methods for read pair alignment and processing, counting into bin pairs, filtering out low-abundance events and normalization of trended or CNV-driven biases. It uses the statistical framework of the edgeR package to model biological variability and to test for significant differences between conditions. Several options for the visualization of results are also included. The use of diffHic is demonstrated with real Hi-C data sets. Performance against existing methods is also evaluated with simulated data. On real data, diffHic is able to successfully detect interactions with significant differences in intensity between biological conditions. It also compares favourably to existing software tools on simulated data sets. These results suggest that diffHic is a viable approach for differential analyses of Hi-C data.

Control of the Ability of Profilin to Bind and Facilitate Nucleotide Exchange from G-actin*

PubMed Central

Wen, Kuo-Kuang; McKane, Melissa; Houtman, Jon C. D.; Rubenstein, Peter A.

2008-01-01

A major factor in profilin regulation of actin cytoskeletal dynamics is its facilitation of G-actin nucleotide exchange. However, the mechanism of this facilitation is unknown. We studied the interaction of yeast (YPF) and human profilin 1 (HPF1) with yeast and mammalian skeletal muscle actins. Homologous pairs (YPF and yeast actin, HPF1 and muscle actin) bound more tightly to one another than heterologous pairs. However, with saturating profilin, HPF1 caused a faster etheno-ATP exchange with both yeast and muscle actins than did YPF. Based on the -fold change in ATP exchange rate/Kd, however, the homologous pairs are more efficient than the heterologous pairs. Thus, strength of binding of profilin to actin and nucleotide exchange rate are not tightly coupled. Actin/HPF interactions were entropically driven, whereas YPF interactions were enthalpically driven. Hybrid yeast actins containing subdomain 1 (sub1) or subdomain 1 and 2 (sub12) muscle actin residues bound more weakly to YPF than did yeast actin (Kd = 2 μm versus 0.6 μm). These hybrids bound even more weakly to HPF than did yeast actin (Kd = 5 μm versus 3.2 μm). sub1/YPF interactions were entropically driven, whereas the sub12/YPF binding was enthalpically driven. Compared with WT yeast actin, YPF binding to sub1 occurred with a 5 times faster koff and a 2 times faster kon. sub12 bound with a 3 times faster koff and a 1.5 times slower kon. Profilin controls the energetics of its interaction with nonhybrid actin, but interactions between actin subdomains 1 and 2 affect the topography of the profilin binding site. PMID:18223293

Global Well-Posedness of the NLS System for Infinitely Many Fermions

NASA Astrophysics Data System (ADS)

Chen, Thomas; Hong, Younghun; Pavlović, Nataša

2017-04-01

In this paper, we study the mean field quantum fluctuation dynamics for a system of infinitely many fermions with delta pair interactions in the vicinity of an equilibrium solution (the Fermi sea) at zero temperature, in dimensions d = 2, 3, and prove global well-posedness of the corresponding Cauchy problem. Our work extends some of the recent important results obtained by Lewin and Sabin in [33,34], who addressed this problem for more regular pair interactions.

Potential Drug-Drug Interactions among Patients prescriptions collected from Medicine Out-patient Setting.

PubMed

Farooqui, Riffat; Hoor, Talea; Karim, Nasim; Muneer, Mehtab

2018-01-01

To identify and evaluate the frequency, severity, mechanism and common pairs of drug-drug interactions (DDIs) in prescriptions by consultants in medicine outpatient department. This cross sectional descriptive study was done by Pharmacology department of Bahria University Medical & Dental College (BUMDC) in medicine outpatient department (OPD) of a private hospital in Karachi from December 2015 to January 2016. A total of 220 prescriptions written by consultants were collected. Medications given with patient's diagnosis were recorded. Drugs were analyzed for interactions by utilizing Medscape drug interaction checker, drugs.com checker and stockley`s drug interactions index. Two hundred eleven prescriptions were selected while remaining were excluded from the study because of unavailability of the prescribed drugs in the drug interaction checkers. In 211 prescriptions, two common diagnoses were diabetes mellitus (28.43%) and hypertension (27.96%). A total of 978 medications were given. Mean number of medications per prescription was 4.6. A total of 369 drug-drug interactions were identified in 211 prescriptions (175%). They were serious 4.33%, significant 66.12% and minor 29.53%. Pharmacokinetic and pharmacodynamic interactions were 37.94% and 51.21% respectively while 10.84% had unknown mechanism. Number wise common pairs of DDIs were Omeprazole-Losartan (S), Gabapentine- Acetaminophen (M), Losartan-Diclofenac (S). The frequency of DDIs is found to be too high in prescriptions of consultants from medicine OPD of a private hospital in Karachi. Significant drug-drug interactions were more and mostly caused by Pharmacodynamic mechanism. Number wise evaluation showed three common pairs of drugs involved in interactions.

Potential Drug-Drug Interactions among Patients prescriptions collected from Medicine Out-patient Setting

PubMed Central

Farooqui, Riffat; Hoor, Talea; Karim, Nasim; Muneer, Mehtab

2018-01-01

Objective: To identify and evaluate the frequency, severity, mechanism and common pairs of drug-drug interactions (DDIs) in prescriptions by consultants in medicine outpatient department. Methods: This cross sectional descriptive study was done by Pharmacology department of Bahria University Medical & Dental College (BUMDC) in medicine outpatient department (OPD) of a private hospital in Karachi from December 2015 to January 2016. A total of 220 prescriptions written by consultants were collected. Medications given with patient's diagnosis were recorded. Drugs were analyzed for interactions by utilizing Medscape drug interaction checker, drugs.com checker and stockley`s drug interactions index. Two hundred eleven prescriptions were selected while remaining were excluded from the study because of unavailability of the prescribed drugs in the drug interaction checkers. Results: In 211 prescriptions, two common diagnoses were diabetes mellitus (28.43%) and hypertension (27.96%). A total of 978 medications were given. Mean number of medications per prescription was 4.6. A total of 369 drug-drug interactions were identified in 211 prescriptions (175%). They were serious 4.33%, significant 66.12% and minor 29.53%. Pharmacokinetic and pharmacodynamic interactions were 37.94% and 51.21% respectively while 10.84% had unknown mechanism. Number wise common pairs of DDIs were Omeprazole-Losartan (S), Gabapentine- Acetaminophen (M), Losartan-Diclofenac (S). Conclusion: The frequency of DDIs is found to be too high in prescriptions of consultants from medicine OPD of a private hospital in Karachi. Significant drug-drug interactions were more and mostly caused by Pharmacodynamic mechanism. Number wise evaluation showed three common pairs of drugs involved in interactions. PMID:29643896

Insight of endo-1,4-xylanase II from Trichoderma reesei: conserved water-mediated H-bond and ion pairs interactions.

PubMed

Vijayakumar, Balakrishnan; Velmurugan, Devadasan

2013-12-01

Endo-1,4-Xylanase II is an enzyme which degrades the linear polysaccharide beta-1,4-xylan into xylose. This enzyme shows highest enzyme activity around 55 °C, even without being stabilized by the disulphide bridges. A set of nine high resolution crystal structures of Xylanase II (1.11-1.80 Å) from Trichoderma reesei were selected and analyzed in order to identify the invariant water molecules, ion pairs and water-mediated ionic interactions. The crystal structure (PDB-id: 2DFB) solved at highest resolution (1.11 Å) was chosen as the reference and the remaining structures were treated as mobile molecules. These structures were then superimposed with the reference molecule to observe the invariant water molecules using 3-dimensional structural superposition server. A total of 37 water molecules were identified to be invariant molecules in all the crystal structures, of which 26 invariant molecules have hydrogen bond interactions with the back bone of residues and 21 invariant water molecules have interactions with side chain residues. The structural and functional roles of these water molecules and ion pairs have been discussed. The results show that the invariant water molecules and ion pairs may be involved in maintaining the structural architecture, dynamics and function of the Endo-1,4-Xylanase II.

Integral representation of channel flow with interacting particles

NASA Astrophysics Data System (ADS)

Fouxon, Itzhak; Ge, Zhouyang; Brandt, Luca; Leshansky, Alexander

2017-12-01

We construct a boundary integral representation for the low-Reynolds-number flow in a channel in the presence of freely suspended particles (or droplets) of arbitrary size and shape. We demonstrate that lubrication theory holds away from the particles at horizontal distances exceeding the channel height and derive a multipole expansion of the flow which is dipolar to the leading approximation. We show that the dipole moment of an arbitrary particle is a weighted integral of the stress and the flow at the particle surface, which can be determined numerically. We introduce the equation of motion that describes hydrodynamic interactions between arbitrary, possibly different, distant particles, with interactions determined by the product of the mobility matrix and the dipole moment. Further, the problem of three identical interacting spheres initially aligned in the streamwise direction is considered and the experimentally observed "pair exchange" phenomenon is derived analytically and confirmed numerically. For nonaligned particles, we demonstrate the formation of a configuration with one particle separating from a stable pair. Our results suggest that in a dilute initially homogenous particulate suspension flowing in a channel the particles will eventually separate into singlets and pairs.

Pooled-matrix protein interaction screens using Barcode Fusion Genetics.

PubMed

Yachie, Nozomu; Petsalaki, Evangelia; Mellor, Joseph C; Weile, Jochen; Jacob, Yves; Verby, Marta; Ozturk, Sedide B; Li, Siyang; Cote, Atina G; Mosca, Roberto; Knapp, Jennifer J; Ko, Minjeong; Yu, Analyn; Gebbia, Marinella; Sahni, Nidhi; Yi, Song; Tyagi, Tanya; Sheykhkarimli, Dayag; Roth, Jonathan F; Wong, Cassandra; Musa, Louai; Snider, Jamie; Liu, Yi-Chun; Yu, Haiyuan; Braun, Pascal; Stagljar, Igor; Hao, Tong; Calderwood, Michael A; Pelletier, Laurence; Aloy, Patrick; Hill, David E; Vidal, Marc; Roth, Frederick P

2016-04-22

High-throughput binary protein interaction mapping is continuing to extend our understanding of cellular function and disease mechanisms. However, we remain one or two orders of magnitude away from a complete interaction map for humans and other major model organisms. Completion will require screening at substantially larger scales with many complementary assays, requiring further efficiency gains in proteome-scale interaction mapping. Here, we report Barcode Fusion Genetics-Yeast Two-Hybrid (BFG-Y2H), by which a full matrix of protein pairs can be screened in a single multiplexed strain pool. BFG-Y2H uses Cre recombination to fuse DNA barcodes from distinct plasmids, generating chimeric protein-pair barcodes that can be quantified via next-generation sequencing. We applied BFG-Y2H to four different matrices ranging in scale from ~25 K to 2.5 M protein pairs. The results show that BFG-Y2H increases the efficiency of protein matrix screening, with quality that is on par with state-of-the-art Y2H methods. © 2016 The Authors. Published under the terms of the CC BY 4.0 license.

Hydrodynamic and kinetic models for spin-1/2 electron-positron quantum plasmas: Annihilation interaction, helicity conservation, and wave dispersion in magnetized plasmas

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

Andreev, Pavel A., E-mail: andreevpa@physics.msu.ru

2015-06-15

We discuss the complete theory of spin-1/2 electron-positron quantum plasmas, when electrons and positrons move with velocities mach smaller than the speed of light. We derive a set of two fluid quantum hydrodynamic equations consisting of the continuity, Euler, spin (magnetic moment) evolution equations for each species. We explicitly include the Coulomb, spin-spin, Darwin and annihilation interactions. The annihilation interaction is the main topic of the paper. We consider the contribution of the annihilation interaction in the quantum hydrodynamic equations and in the spectrum of waves in magnetized electron-positron plasmas. We consider the propagation of waves parallel and perpendicular tomore » an external magnetic field. We also consider the oblique propagation of longitudinal waves. We derive the set of quantum kinetic equations for electron-positron plasmas with the Darwin and annihilation interactions. We apply the kinetic theory to the linear wave behavior in absence of external fields. We calculate the contribution of the Darwin and annihilation interactions in the Landau damping of the Langmuir waves. We should mention that the annihilation interaction does not change number of particles in the system. It does not related to annihilation itself, but it exists as a result of interaction of an electron-positron pair via conversion of the pair into virtual photon. A pair of the non-linear Schrodinger equations for the electron-positron plasmas including the Darwin and annihilation interactions is derived. Existence of the conserving helicity in electron-positron quantum plasmas of spinning particles with the Darwin and annihilation interactions is demonstrated. We show that the annihilation interaction plays an important role in the quantum electron-positron plasmas giving the contribution of the same magnitude as the spin-spin interaction.« less

Gas flows in S-E binary systems of galaxies

NASA Technical Reports Server (NTRS)

Sotnikova, N. YA.

1990-01-01

Tidal interaction between the galaxies in binary systems leads to important consequences. Some peculiarities in galactic morphology as well as the transfer of matter from one galaxy to another may be due to this factor. In particular, gas flows in intergalactic space may be formed. Such flows enriching one component with gas from the other may play a substantial role in the evolution of mixed (S-E) pairs. One can mention several facts corroborating the possibility of the gas transfer from the spiral to the elliptical galaxy. High HI content (10(exp 7) to 10(exp 9) solar mass) is detected in nearly 40 E galaxies (Bottinelli and Gougenheim, 1979; Knapp et al., 1985). Such galaxies are often members of pairs or of multiple systems including an S galaxy, which may be the source of gas (Smirnov and Komberg, 1980). Moreover, the gas kinematics and its distribution also indicate an external origin for this gas (Knapp et al., 1985). In many cases there is an outer gaseous disk. The directions of the disk and of stellar rotation don't always coincide (van Gorkom et al., 1985; Varnas et al., 1987). The galaxy colors in S-E pairs are correlated (the Holmberg effect): bluer ellipticals have spiral components that are usually bluer (Demin et al., 1984). The fraction of E galaxies with emission lines (N sub em) in S-E pairs showing traces of tidal interaction is twice as large (N sub em approx. equals 0.24) as in pairs without interaction (N sub em approx. equals 0.12) (Sotnikova, 1988b). Since the presence of emission lines in a galaxy spectrum strongly depends on gas content, this fact also leads to the conclusion that ellipticals in interacting S-E pairs are enriched with gas. These facts may be considered as a serious indication of the existence of gas transfer. Hence, investigation of this process is of interest.

An Insightful Problem Involving the Electromagnetic Radiation from a Pair of Dipoles

ERIC Educational Resources Information Center

Smith, Glenn S.

2010-01-01

The time-average power radiated by a pair of infinitesimal dipoles is examined as their spacing is varied. The results elucidate the effect of the interaction of the dipoles on their radiation. (Contains 4 figures.)

Helix-packing motifs in membrane proteins.

PubMed

Walters, R F S; DeGrado, W F

2006-09-12

The fold of a helical membrane protein is largely determined by interactions between membrane-imbedded helices. To elucidate recurring helix-helix interaction motifs, we dissected the crystallographic structures of membrane proteins into a library of interacting helical pairs. The pairs were clustered according to their three-dimensional similarity (rmsd

Fully gapped superconductivity with no sign change in the prototypical heavy-fermion CeCu2Si2.

PubMed

Yamashita, Takuya; Takenaka, Takaaki; Tokiwa, Yoshifumi; Wilcox, Joseph A; Mizukami, Yuta; Terazawa, Daiki; Kasahara, Yuichi; Kittaka, Shunichiro; Sakakibara, Toshiro; Konczykowski, Marcin; Seiro, Silvia; Jeevan, Hirale S; Geibel, Christoph; Putzke, Carsten; Onishi, Takafumi; Ikeda, Hiroaki; Carrington, Antony; Shibauchi, Takasada; Matsuda, Yuji

2017-06-01

In exotic superconductors, including high- T c copper oxides, the interactions mediating electron Cooper pairing are widely considered to have a magnetic rather than a conventional electron-phonon origin. Interest in this exotic pairing was initiated by the 1979 discovery of heavy-fermion superconductivity in CeCu 2 Si 2 , which exhibits strong antiferromagnetic fluctuations. A hallmark of unconventional pairing by anisotropic repulsive interactions is that the superconducting energy gap changes sign as a function of the electron momentum, often leading to nodes where the gap goes to zero. We report low-temperature specific heat, thermal conductivity, and magnetic penetration depth measurements in CeCu 2 Si 2 , demonstrating the absence of gap nodes at any point on the Fermi surface. Moreover, electron irradiation experiments reveal that the superconductivity survives even when the electron mean free path becomes substantially shorter than the superconducting coherence length. This indicates that superconductivity is robust against impurities, implying that there is no sign change in the gap function. These results show that, contrary to long-standing belief, heavy electrons with extremely strong Coulomb repulsions can condense into a fully gapped s-wave superconducting state, which has an on-site attractive pairing interaction.

Functional renormalization group study of orbital fluctuation mediated superconductivity: Impact of the electron-boson coupling vertex corrections

NASA Astrophysics Data System (ADS)

Tazai, Rina; Yamakawa, Youichi; Tsuchiizu, Masahisa; Kontani, Hiroshi

2016-09-01

In various multiorbital systems, the emergence of the orbital fluctuations and their role on the pairing mechanism attract increasing attention. To achieve deep understanding on these issues, we perform a functional renormalization group (fRG) study for the two-orbital Hubbard model. The vertex corrections for the electron-boson coupling (U -VC), which are dropped in the Migdal-Eliashberg gap equation, are obtained by solving the RG equation. We reveal that the dressed electron-boson coupling for the charge channel Ûeffc becomes much larger than the bare Coulomb interaction Û 0 due to the U -VC in the presence of moderate spin fluctuations. For this reason, the attractive pairing interaction due to the charge or orbital fluctuations is enlarged by the factor (Ûeffc/Û0) 2≫1 . In contrast, the spin fluctuation pairing interaction is suppressed by the spin-channel U -VC, because of the relation Ûeffs≪Û 0 . The present study demonstrates that the orbital or charge fluctuation pairing mechanism can be realized in various multiorbital systems thanks to the U -VC, such as in Fe-based superconductors.

Using an innovative multiple regression procedure in a cancer population (Part II): fever, depressive affect, and mobility problems clarify an influential symptom pair (pain-fatigue/weakness) and cluster (pain-fatigue/weakness-sleep problems).

PubMed

Francoeur, Richard B

2015-01-01

Most patients with advanced cancer experience symptom pairs or clusters among pain, fatigue, and insomnia. However, only combinations where symptoms are mutually influential hold potential for identifying patient subgroups at greater risk, and in some contexts, interventions with "cross-over" (multisymptom) effects. Improved methods to detect and interpret interactions among symptoms, signs, or biomarkers are needed to reveal these influential pairs and clusters. I recently created sequential residual centering (SRC) to reduce multicollinearity in moderated regression, which enhances sensitivity to detect these interactions. I applied SRC to moderated regressions of single-item symptoms that interact to predict outcomes from 268 palliative radiation outpatients. I investigated: 1) the hypothesis that the interaction, pain × fatigue/weakness × sleep problems, predicts depressive affect only when fever presents, and 2) an exploratory analysis, when fever is absent, that the interaction, pain × fatigue/weakness × sleep problems × depressive affect, predicts mobility problems. In the fever context, three-way interactions (and derivative terms) of the four symptoms (pain, fatigue/weakness, fever, sleep problems) are tested individually and simultaneously; in the non-fever context, a single four-way interaction (and derivative terms) is tested. Fever interacts separately with fatigue/weakness and sleep problems; these comoderators each magnify the pain-depressive affect relationship along the upper or full range of pain values. In non-fever contexts, fatigue/weakness, sleep problems, and depressive affect comagnify the relationship between pain and mobility problems. Different mechanisms contribute to the pain × fatigue/weakness × sleep problems interaction, but all depend on the presence of fever, a sign/biomarker/symptom of proinflammatory sickness behavior. In non-fever contexts, depressive affect is no longer an outcome representing malaise from the physical symptoms of sickness, but becomes a fourth symptom of the interaction. In outpatient subgroups at heightened risk, single interventions could potentially relieve multiple symptoms when fever accompanies sickness malaise and in non-fever contexts with mobility problems. SRC strengthens insights into symptom pairs/clusters.

Content and cultural validity in the development of the Indigenous Play Partner Scale.

PubMed

Dender, Alma M; Stagnitti, Karen E

2017-08-01

Culturally relevant assessments of Australian Indigenous children's social pretend play do not exist. This study investigated the content validity and cultural validity of the Indigenous Play Partner Scale (I-PPS). Six pairs of children (i.e. 12 children) aged four-six years from a remote Australian town were videoed playing in pairs, and 14 community elders and mothers participated across three focus groups. The social interactions between the children were transcribed from the videos. Nineteen verbs, grouped into five categories of social interaction, described the social interactions between the pairs of children. The descriptions of the social interaction verbs were presented to the community elders and mothers in a focus group. The themes from the focus groups were 'background of Indigenous understanding of play' and 'proposed social interaction verbs'. The first theme reflected community collaboration, children playing in multi-aged groups and the role of older children within the play. Guided by the focus group discussion, the videos were re-analysed and 20 social interaction verbs were described that reflected the cultural context of play. The content and cultural validity of the I-PPS was established through community consultation. Twenty social interaction verbs, which form the basis of the items of the I-PPS, reflected Indigenous cultural values of being non-judgemental of Indigenous children's social interactions during pretend play. Culturally relevant assessments for Australian Indigenous children do not disadvantage this population group and are essential for practice in occupational therapy. © 2017 Occupational Therapy Australia.

Perturbation theory of structure in classical liquid mixtures: Application to metallic systems near phase separation. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Henderson, R. L.

1974-01-01

The partial structure factors of classical simple liquid mixtures near phase separation are dicussed. The theory is developed for particles interacting through pair potentials, and is thus appropriate both to insulating fluids, and also to metallic systems if these may be described by an effective ion-ion pair interaction. The motivation arose from consideration of metallic liquid mixtures, in which resistive anomalies have been observed near phase separation. A mean field theory correction appropriate to 3 pair potential for the effects of correlated motions in the reference fluid is studied. The work is cast in terms of functions which are closely related to the direct correlation functions of Ornstein and Zernike. The results are qualitatively in accord with physical expectations. Quantitative agreement with experiment seems to turn on the selection of the hard core reference potential in terms of the metallic effective pair potential. It is suggested that the present effective pair potentials are perhaps not properly used to calculate the metallic structure factors at long wavelength.

Unitary Fermi gas in a harmonic trap

NASA Astrophysics Data System (ADS)

Chang, S. Y.; Bertsch, G. F.

2007-08-01

We present an ab initio calculation of small numbers of trapped, strongly interacting fermions using the Green’s function Monte Carlo method. The ground-state energy, density profile, and pairing gap are calculated for particle numbers N=2 22 using the parameter-free “unitary” interaction. Trial wave functions are taken in the form of correlated pairs in a harmonic oscillator basis. We find that the lowest energies are obtained with a minimum explicit pair correlation beyond that needed to exploit the degeneracy of oscillator states. We find that the energies can be well fitted by the expression aTFETF+Δmod(N,2) where ETF is the Thomas-Fermi energy of a noninteracting gas in the trap and Δ is the pairing gap. There is no evidence of a shell correction energy in the systematics, but the density distributions show pronounced shell effects. We find the value Δ=0.7±0.2ω for the pairing gap. This is smaller than the value found for the uniform gas at a density corresponding to the central density of the trapped gas.

Skin self-examination education for early detection of melanoma: a randomized controlled trial of Internet, workbook, and in-person interventions.

PubMed

Robinson, June K; Gaber, Rikki; Hultgren, Brittney; Eilers, Steven; Blatt, Hanz; Stapleton, Jerod; Mallett, Kimberly; Turrisi, Rob; Duffecy, Jenna; Begale, Mark; Martini, Mary; Bilimoria, Karl; Wayne, Jeffrey

2014-01-13

Early detection of melanoma improves survival. Since many melanoma patients and their spouses seek the care of a physician after discovering their melanoma, an ongoing study will determine the efficacy of teaching at-risk melanoma patients and their skin check partner how to conduct skin self-examinations (SSEs). Internet-based health behavior interventions have proven efficacious in creating behavior change in patients to better prevent, detect, or cope with their health issues. The efficacy of electronic interactive SSE educational intervention provided on a tablet device has not previously been determined. The electronic interactive educational intervention was created to develop a scalable, effective intervention to enhance performance and accuracy of SSE among those at-risk to develop melanoma. The intervention in the office was conducted using one of the following three methods: (1) in-person through a facilitator, (2) with a paper workbook, or (3) with a tablet device used in the clinical office. Differences related to method of delivery were elucidated by having the melanoma patient and their skin check partner provide a self-report of their confidence in performing SSE and take a knowledge-based test immediately after receiving the intervention. The three interventions used 9 of the 26 behavioral change techniques defined by Abraham and Michie to promote planning of monthly SSE, encourage performing SSE, and reinforce self-efficacy by praising correct responses to knowledge-based decision making and offering helpful suggestions to improve performance. In creating the electronic interactive SSE educational intervention, the educational content was taken directly from both the scripted in-person presentation delivered with Microsoft PowerPoint by a trained facilitator and the paper workbook training arms of the study. Enrollment totaled 500 pairs (melanoma patient and their SSE partner) with randomization of 165 pairs to the in-person, 165 pairs to the workbook, and 70 pairs to electronic interactive SSE educational intervention. The demographic survey data showed no significant mean differences between groups in age, education, or income. The tablet usability survey given to the first 30 tablet pairs found that, overall, participants found the electronic interactive intervention easy to use and that the video of the doctor-patient-partner dialogue accompanying the dermatologist's examination was particularly helpful in understanding what they were asked to do for the study. The interactive group proved to be just as good as the workbook group in self-confidence of scoring moles, and just as good as both the workbook and the in-person intervention groups in self-confidence of monitoring their moles. While the in-person intervention performed significantly better on a skill-based quiz, the electronic interactive group performed significantly better than the workbook group. The electronic interactive and in-person interventions were more efficient (30 minutes), while the workbook took longer (45 minutes). This study suggests that an electronic interactive intervention can deliver skills training comparable to other training methods, and the experience can be accommodated during the customary outpatient office visit with the physician. Further testing of the electronic interactive intervention's role in the anxiety of the pair and pair-discovered melanomas upon self-screening will elucidate the impact of these tools on outcomes in at-risk patient populations. ClinicalTrials.gov NCT01013844; http://clinicaltrials.gov/show/NCT01013844 (Archived by WebCite at http://www.webcitation.org/6LvGGSTKK).

Domain-based prediction of the human isoform interactome provides insights into the functional impact of alternative splicing.

PubMed

Ghadie, Mohamed Ali; Lambourne, Luke; Vidal, Marc; Xia, Yu

2017-08-01

Alternative splicing is known to remodel protein-protein interaction networks ("interactomes"), yet large-scale determination of isoform-specific interactions remains challenging. We present a domain-based method to predict the isoform interactome from the reference interactome. First, we construct the domain-resolved reference interactome by mapping known domain-domain interactions onto experimentally-determined interactions between reference proteins. Then, we construct the isoform interactome by predicting that an isoform loses an interaction if it loses the domain mediating the interaction. Our prediction framework is of high-quality when assessed by experimental data. The predicted human isoform interactome reveals extensive network remodeling by alternative splicing. Protein pairs interacting with different isoforms of the same gene tend to be more divergent in biological function, tissue expression, and disease phenotype than protein pairs interacting with the same isoforms. Our prediction method complements experimental efforts, and demonstrates that integrating structural domain information with interactomes provides insights into the functional impact of alternative splicing.

Domain-based prediction of the human isoform interactome provides insights into the functional impact of alternative splicing

PubMed Central

Lambourne, Luke; Vidal, Marc

2017-01-01

Alternative splicing is known to remodel protein-protein interaction networks (“interactomes”), yet large-scale determination of isoform-specific interactions remains challenging. We present a domain-based method to predict the isoform interactome from the reference interactome. First, we construct the domain-resolved reference interactome by mapping known domain-domain interactions onto experimentally-determined interactions between reference proteins. Then, we construct the isoform interactome by predicting that an isoform loses an interaction if it loses the domain mediating the interaction. Our prediction framework is of high-quality when assessed by experimental data. The predicted human isoform interactome reveals extensive network remodeling by alternative splicing. Protein pairs interacting with different isoforms of the same gene tend to be more divergent in biological function, tissue expression, and disease phenotype than protein pairs interacting with the same isoforms. Our prediction method complements experimental efforts, and demonstrates that integrating structural domain information with interactomes provides insights into the functional impact of alternative splicing. PMID:28846689

Embodied social interaction constitutes social cognition in pairs of humans: a minimalist virtual reality experiment.

PubMed

Froese, Tom; Iizuka, Hiroyuki; Ikegami, Takashi

2014-01-14

Scientists have traditionally limited the mechanisms of social cognition to one brain, but recent approaches claim that interaction also realizes cognitive work. Experiments under constrained virtual settings revealed that interaction dynamics implicitly guide social cognition. Here we show that embodied social interaction can be constitutive of agency detection and of experiencing another's presence. Pairs of participants moved their "avatars" along an invisible virtual line and could make haptic contact with three identical objects, two of which embodied the other's motions, but only one, the other's avatar, also embodied the other's contact sensor and thereby enabled responsive interaction. Co-regulated interactions were significantly correlated with identifications of the other's avatar and reports of the clearest awareness of the other's presence. These results challenge folk psychological notions about the boundaries of mind, but make sense from evolutionary and developmental perspectives: an extendible mind can offload cognitive work into its environment.

Tunable Electron-Electron Interactions in LaAlO 3 / SrTiO 3 Nanostructures

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

Cheng, Guanglei; Tomczyk, Michelle; Tacla, Alexandre B.

The interface between the two complex oxides LaAlO 3 and SrTiO 3 has remarkable properties that can be locally reconfigured between conducting and insulating states using a conductive atomic force microscope. Prior investigations of “sketched” quantum dot devices revealed a phase in which electrons form pairs, implying a strongly attractive electron-electron interaction. Here, we show that these devices with strong electron-electron interactions can exhibit a gate-tunable transition from a pair-tunneling regime to a single-electron (Andreev bound state) tunneling regime where the interactions become repulsive. The electron-electron interaction sign change is associated with a Lifshitz transition where the d xz andmore » d yz bands start to become occupied. This electronically tunable electron-electron interaction, combined with the nanoscale reconfigurability of this system, provides an interesting starting point towards solid-state quantum simulation.« less

Genetic interactions contribute less than additive effects to quantitative trait variation in yeast

PubMed Central

Bloom, Joshua S.; Kotenko, Iulia; Sadhu, Meru J.; Treusch, Sebastian; Albert, Frank W.; Kruglyak, Leonid

2015-01-01

Genetic mapping studies of quantitative traits typically focus on detecting loci that contribute additively to trait variation. Genetic interactions are often proposed as a contributing factor to trait variation, but the relative contribution of interactions to trait variation is a subject of debate. Here we use a very large cross between two yeast strains to accurately estimate the fraction of phenotypic variance due to pairwise QTL–QTL interactions for 20 quantitative traits. We find that this fraction is 9% on average, substantially less than the contribution of additive QTL (43%). Statistically significant QTL–QTL pairs typically have small individual effect sizes, but collectively explain 40% of the pairwise interaction variance. We show that pairwise interaction variance is largely explained by pairs of loci at least one of which has a significant additive effect. These results refine our understanding of the genetic architecture of quantitative traits and help guide future mapping studies. PMID:26537231

Embodied social interaction constitutes social cognition in pairs of humans: A minimalist virtual reality experiment

PubMed Central

Froese, Tom; Iizuka, Hiroyuki; Ikegami, Takashi

2014-01-01

Scientists have traditionally limited the mechanisms of social cognition to one brain, but recent approaches claim that interaction also realizes cognitive work. Experiments under constrained virtual settings revealed that interaction dynamics implicitly guide social cognition. Here we show that embodied social interaction can be constitutive of agency detection and of experiencing another's presence. Pairs of participants moved their “avatars” along an invisible virtual line and could make haptic contact with three identical objects, two of which embodied the other's motions, but only one, the other's avatar, also embodied the other's contact sensor and thereby enabled responsive interaction. Co-regulated interactions were significantly correlated with identifications of the other's avatar and reports of the clearest awareness of the other's presence. These results challenge folk psychological notions about the boundaries of mind, but make sense from evolutionary and developmental perspectives: an extendible mind can offload cognitive work into its environment. PMID:24419102

Tunable Electron-Electron Interactions in LaAlO 3 / SrTiO 3 Nanostructures

DOE PAGES

Cheng, Guanglei; Tomczyk, Michelle; Tacla, Alexandre B.; ...

2016-12-01

The interface between the two complex oxides LaAlO 3 and SrTiO 3 has remarkable properties that can be locally reconfigured between conducting and insulating states using a conductive atomic force microscope. Prior investigations of “sketched” quantum dot devices revealed a phase in which electrons form pairs, implying a strongly attractive electron-electron interaction. Here, we show that these devices with strong electron-electron interactions can exhibit a gate-tunable transition from a pair-tunneling regime to a single-electron (Andreev bound state) tunneling regime where the interactions become repulsive. The electron-electron interaction sign change is associated with a Lifshitz transition where the d xz andmore » d yz bands start to become occupied. This electronically tunable electron-electron interaction, combined with the nanoscale reconfigurability of this system, provides an interesting starting point towards solid-state quantum simulation.« less

A nucleon-pair and boson coexistent description of nuclei

NASA Astrophysics Data System (ADS)

Dai, Lianrong; Pan, Feng; Draayer, J. P.

2017-07-01

We study a mixture of s-bosons and like-nucleon pairs with the standard pairing interaction outside an inert core. Competition between the nucleon-pairs and s-bosons is investigated in this scenario. The robustness of the BCS-BEC coexistence and crossover phenomena are examined through an analysis of pf-shell nuclei with realistic single-particle energies, in which two configurations with Pauli blocking of nucleon-pair orbits due to the formation of the s-bosons is taken into account. When the nucleon-pair orbits are considered to be independent of the s-bosons, the BCS-BEC crossover becomes smooth, with the number of the s-bosons noticeably more than that of the nucleon-pairs near the half-shell point, a feature that is demonstrated in the pf-shell for several values of the standard pairing interaction strength. As a further test of the robustness of the BCS-BEC coexistence and crossover phenomena in nuclei, results are given for values of even-even 102-130Sn with 100Sn taken as a core and valence neutron pairs confined within the 1d 5/2, 0g 7/2, 1d 3/2, 2s 1/2, 1h 11/2 orbits in the nucleon-pair orbit and the s-boson independent approximation. The results indicate that the B(E2) values are reproduced well. Supported by National Natural Science Foundation of China (11375080, 11675071), the U.S. National Science Foundation (OCI-0904874 and ACI-1516338), U. S. Department of Energy (DE-SC0005248), the Southeastern Universities Research Association, the China-U. S. Theory Institute for Physics with Exotic Nuclei (CUSTIPEN) (DE-SC0009971), and the LSU-LNNU joint research program (9961) is acknowledged

Prevalence of the prescription of potentially interacting drugs.

PubMed

Tragni, Elena; Casula, Manuela; Pieri, Vasco; Favato, Giampiero; Marcobelli, Alberico; Trotta, Maria Giovanna; Catapano, Alberico Luigi

2013-01-01

The use of multiple medications is becoming more common, with a correspondingly increased risk of untoward effects and drug-related morbidity and mortality. We aimed at estimating the prevalence of prescription of relevant potentially interacting drugs and at evaluating possible predictors of potentially interacting drug exposure. We retrospectively analyzed data on prescriptions dispensed from January 2004 to August 2005 to individuals of two Italian regions with a population of almost 2.1 million individuals. We identified 27 pairs of potentially interacting drugs by examining clinical relevance, documentation, and volume of use in Italy. Subjects who received at least one prescription of both drugs were selected. Co-prescribing denotes "two prescriptions in the same day", and concomitant medication "the prescription of two drugs with overlapping coverage". A logistic regression analysis was conducted to examine the predictors of potential Drug-Drug Interaction (pDDIs). 957,553 subjects (45.3% of study population) were exposed to at least one of the drugs/classes of the 27 pairs. Overall, pDDIs occurred 2,465,819 times. The highest rates of concomitant prescription and of co-prescription were for ACE inhibitors+NSAIDs (6,253 and 4,621/100,000 plan participants). Considering concomitance, the male/female ratio was <1 in 17/27 pairs (from 0.31 for NSAIDs-ASA+SSRI to 0.74 for omeprazole+clopidogrel). The mean age was lowest for methotrexate pairs (+omeprazole, 59.9 years; +NSAIDs-ASA, 59.1 years) and highest for digoxin+verapamil (75.4 years). In 13/27 pairs, the mean ages were ≥70 years. On average, subjects involved in pDDIs received ≥10 drugs. The odds of exposure were more frequently higher for age ≥65 years, males, and those taking a large number of drugs. A substantial number of clinically important pDDIs were observed, particularly among warfarin users. Awareness of the most prevalent pDDIs could help practitioners in preventing concomitant use, resulting in a better quality of drug prescription and potentially avoiding unwanted side 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

Stellar dynamics in E+E pairs of galaxies. 2: Simulations and interpretation

NASA Astrophysics Data System (ADS)

Combes, F.; Rampazzo, R.; Bonfanti, P. P.; Prugniel, P.; Sulentic, J. W.

1995-05-01

We have presented in a companion article a kinematic study of three E+E galaxy pairs, NGC741/742, 1587/1588 (CPG 99) and 2672/2673 (CPG 175). We find some evidence for perturbed velocity dispersion profiles. These perturbation features are now reported for 14 galaxies in the literature. They occur, or require observations for detection, at large radii where the S/N in the data is low. While observations of individual galaxies are sometimes uncertain, the large number of objects where such features are suspected gives confidence that they are real. These perturbations can be attributed to projection effects contamination along the line of sight, or directly to the tidal interaction. We report the results of several self-gravitating simulations of unbound pairs in an effort to better understand these perturbations another generic features of close E+E pairs reported in the literature. The models frequently show off-center envelopes created by the asymmetry of tidal forces during interpenetrating encounters. The envelopes last for a few 108 yrs, which explains the frequency of such features in observed pairs. This phenomenon is stronger in the self-gravitating simulations than in the MTBA runs. U-shaped (and an equal number of inverse U shaped velocity profiles are seen in the simulations, a result of ablation in the outer envelopes. Simulations including inner galaxy rotation also preserve this feature, irrespective of the spin vector direction in each galaxy. U-shape velocity structure is found to be a robust indicator of the ongoing interaction. All simulations show evidence for enhanced velocity dispersion between the galaxies even in the case of simple superposition of two non interacting objects. We therefore conclude that this cannot be considered an unambiguous indicator of the interaction.

Identification of stepped changes of binding affinity during interactions between the disintegrin rhodostomin and integrin αIIbβ3 in living cells using optical tweezers

NASA Astrophysics Data System (ADS)

Hsieh, Chia-Fen; Chang, Bo-Jui; Pai, Chyi-Huey; Chen, Hsuan-Yi; Chi, Sien; Hsu, Long; Tsai, Jin-Wu; Lin, Chi-Hung

2004-10-01

Integrin receptors serve as both mechanical links and signal transduction mediators between the cell and its environment. Experimental evidence demonstrates that conformational changes and lateral clustering of the integrin proteins may affect their binding to ligands and regulate downstream cellular responses; however, experimental links between the structural and functional correlations of the ligand-receptor interactions are not yet elucidated. In the present report, we utilized optical tweezers to measure the dynamic binding between the snake venom rhodostomin, coated on a microparticle and functioned as a ligand, and the membrane receptor integrin alpha(IIb)beta(3) expressed on a Chinese Hamster Ovary (CHO) cell. A progressive increase of total binding affinity was found between the bead and CHO cell in the first 300 sec following optical tweezers-guided contact. Further analysis of the cumulative data revealed the presence of "unit binding force" presumably exerted by a single rhodostomin-integrin pair. Interestingly, two such units were found. Among the measurements of less total binding forces, presumably taken at the early stage of ligand-receptor interactions, a unit of 4.15 pN per molecule pair was derived. This unit force dropped to 2.54 pN per molecule pair toward the later stage of interactions when the total binding forces were relatively large. This stepped change of single molecule pair binding affinity was not found when mutant rhodostomin proteins were used as ligands (a single unit of 1.81 pN per pair was found). These results were interpreted along with the current knowledge about the conformational changes of integrins during the "molecule activation" process.

Crystal structure of an intermolecular 2:1 complex between adenine and thymine. Evidence for both Hoogsteen and 'quasi-Watson-Crick' interactions.

PubMed

Chandrasekhar, Sosale; Naik, Tangali R Ravikumar; Nayak, Susanta K; Row, Tayur N Guru

2010-06-15

The titled complex, obtained by co-crystallization (EtOH/25 degrees C), is apparently the only known complex of the free bases. Its crystal structure, as determined by X-ray diffraction at both 90 K and 313 K, showed that one A-T pair involves a Hoogsteen interaction, and the other a Watson-Crick interaction but only with respect to the adenine unit. The absence of a clear-cut Watson-Crick base pair raises intriguing questions about the basis of the DNA double helix. Copyright 2010 Elsevier Ltd. All rights reserved.

High-temperature atomic superfluidity in lattice Bose-Fermi mixtures.

PubMed

Illuminati, Fabrizio; Albus, Alexander

2004-08-27

We consider atomic Bose-Fermi mixtures in optical lattices and study the superfluidity of fermionic atoms due to s-wave pairing induced by boson-fermion interactions. We prove that the induced fermion-fermion coupling is always attractive if the boson-boson on-site interaction is repulsive, and predict the existence of an enhanced BEC-BCS crossover as the strength of the lattice potential is varied. We show that for direct on-site fermion-fermion repulsion, the induced attraction can give rise to superfluidity via s-wave pairing at striking variance with the case of pure systems of fermionic atoms with direct repulsive interactions.

Spatial interactions between urban areas and cause-specific mortality differentials in France.

PubMed

Ghosn, Walid; Kassie, Daouda; Jougla, Eric; Rican, Stéphane; Rey, Grégoire

2013-11-01

Spatial interactions constitute a challenging but promising approach for investigation of spatial mortality inequalities. Among spatial interactions measures, between-spatial unit migration differentials are a marker of socioeconomic imbalance, but also reflect discrepancies due to other factors. Specifically, this paper asks whether population exchange intensities measure differentials or similarities that are not captured by usual socioeconomic indicators. Urban areas were grouped pairwise by the intensity of connection estimated from a gravity model. The mortality differences for several causes of death were observed to be significantly smaller for strongly connected pairs than for weakly connected pairs even after adjustment on deprivation. © 2013 Published by Elsevier Ltd.

Ab initio study on electronically excited states of lithium isocyanide, LiNC

NASA Astrophysics Data System (ADS)

Yasumatsu, Hisato; Jeung, Gwang-Hi

2014-01-01

The electronically excited states of the lithium isocyanide molecule, LiNC, were studied by means of ab initio calculations. The bonding nature of LiNC up to ∼10 eV is discussed on the basis of the potential energy surfaces according to the interaction between the ion-pair and covalent states. The ion-pair states are described by Coulomb attractive interaction in the long distance range, while the covalent ones are almost repulsive or bound with a very shallow potential dent. These two states interact each other to form adiabatic potential energy surfaces with non-monotonic change in the potential energy with the internuclear distance.

Interaction and particle{endash}hole symmetry of Laughlin quasiparticles

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

Wojs, Arkadiusz

2001-06-15

The pseudopotentials describing interaction of Laughlin quasielectrons (QE) and quasiholes (QH) in an infinite fractional quantum Hall system are studied. The QE and QH pseudopotentials are similar, which suggests the (approximate) particle{endash}hole symmetry recovered in the thermodynamical limit. The problem of the hypothetical symmetry-breaking QE hard-core repulsion is resolved by the estimate that the {open_quotes}forbidden{close_quotes} QE pair state has too high an energy and is unstable. Strong oscillations of the QE and QH pseudopotentials persist in an infinite system, and the analogous QE and QH pair states with small relative angular momentum and nearly vanishing interaction energy are predicted.

Enzyme-Inspired Chiral Secondary-Phosphine-Oxide Ligand with Dual Noncovalent Interactions for Asymmetric Hydrogenation.

PubMed

Chen, Caiyou; Zhang, Zhefan; Jin, Shicheng; Fan, Xiangru; Geng, Mingyu; Zhou, Yan; Wen, Songwei; Wang, Xinrui; Chung, Lung Wa; Dong, Xiu-Qin; Zhang, Xumu

2017-06-06

Inspired by the unique character of enzymes, we developed novel chiral SPO (secondary-phosphine-oxide) ligand (SPO-Wudaphos) which can enter into both ion pair and H-bond noncovalent interactions. The novel chiral SPO-Wudaphos exhibited excellent results in the asymmetric hydrogenation of α-methylene-γ-keto carboxylic acids, affording the chiral γ-keto acids with up to over 99 % ee. A series of control experiments and DFT calculations were conducted to illustrate the critical roles of both the ion pair and H-bond noncovalent interactions. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Loss of G-A base pairs is insufficient for achieving a large opening of U4 snRNA K-turn motif.

PubMed

Cojocaru, Vlad; Klement, Reinhard; Jovin, Thomas M

2005-01-01

Upon binding to the 15.5K protein, two tandem-sheared G-A base pairs are formed in the internal loop of the kink-turn motif of U4 snRNA (Kt-U4). We have reported that the folding of Kt-U4 is assisted by protein binding. Unstable interactions that contribute to a large opening of the free RNA ('k-e motion') were identified using locally enhanced sampling molecular dynamics simulations, results that agree with experiments. A detailed analysis of the simulations reveals that the k-e motion in Kt-U4 is triggered both by loss of G-A base pairs in the internal loop and backbone flexibility in the stems. Essential dynamics show that the loss of G-A base pairs is correlated along the first mode but anti-correlated along the third mode with the k-e motion. Moreover, when enhanced sampling was confined to the internal loop, the RNA adopted an alternative conformation characterized by a sharper kink, opening of G-A base pairs and modified stacking interactions. Thus, loss of G-A base pairs is insufficient for achieving a large opening of the free RNA. These findings, supported by previously published RNA structure probing experiments, suggest that G-A base pair formation occurs upon protein binding, thereby stabilizing a selective orientation of the stems.

EM Transition Sum Rules Within the Framework of sdg Proton-Neutron Interacting Boson Model, Nuclear Pair Shell Model and Fermion Dynamical Symmetry Model

NASA Astrophysics Data System (ADS)

Zhao, Yumin

1997-07-01

By the techniques of the Wick theorem for coupled clusters, the no-energy-weighted electromagnetic sum-rule calculations are presented in the sdg neutron-proton interacting boson model, the nuclear pair shell model and the fermion-dynamical symmetry model. The project supported by Development Project Foundation of China, National Natural Science Foundation of China, Doctoral Education Fund of National Education Committee, Fundamental Research Fund of Southeast University

Controlling the transmitted information of a multi-photon interacting with a single-Cooper pair box

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

Kadry, Heba, E-mail: hkadry1@yahoo.com; Abdel-Aty, Abdel-Haleem, E-mail: hkadry1@yahoo.com; Zakaria, Nordin, E-mail: hkadry1@yahoo.com

2014-10-24

We study a model of a multi-photon interaction of a single Cooper pair box with a cavity field. The exchange of the information using this system is studied. We quantify the fidelity of the transmitted information. The effect of the system parameters (detuning parameter, field photons, state density and mean photon number) in the fidelity of the transmitted information is investigated. We found that the fidelity of the transmitted information can be controlled using the system parameters.

The Bose-Einstein correlations in deep inelastic μ p interactions at 280 GeV

NASA Astrophysics Data System (ADS)

Arneodo, M.; Arvidson, A.; Aubert, J. J.; Badelek, B.; Beaufays, J.; Bee, C. P.; Benchouk, C.; Berghoff, G.; Bird, I.; Blum, D.; Böhm, E.; de Bouard, X.; Brasse, F. W.; Braun, H.; Broll, C.; Brown, S.; Brück, H.; Calen, H.; Chima, J. S.; Ciborowski, J.; Cliftt, R.; Coignet, G.; Combley, F.; Coughlan, J.; D'Agostini, G.; Dahlgren, S.; Dengler, F.; Derado, I.; Dreyer, T.; Drees, J.; Düren, M.; Eckardt, V.; Edwards, A.; Edwards, M.; Ernst, T.; Eszes, G.; Favier, J.; Ferrero, M. I.; Figiel, J.; Flauger, W.; Foster, J.; Gabathuler, E.; Gajewski, J.; Gamet, R.; Gayler, J.; Geddes, N.; Grafström, P.; Grard, F.; Haas, J.; Hagberg, E.; Hasert, F. J.; Hayman, P.; Heusse, P.; Jaffre, M.; Jacholkowska, A.; Janata, F.; Jancso, G.; Johnson, A. S.; Kabuss, E. M.; Kellner, G.; Korbel, V.; Krüger, J.; Kullander, S.; Landgraf, U.; Lanske, D.; Loken, J.; Long, K.; Maire, M.; Malecki, P.; Manz, A.; Maselli, S.; Mohi, W.; Montanet, F.; Montgomery, H. E.; Nagy, E.; Nassalski, J.; Norton, P. R.; Oakham, F. G.; Osborne, A. M.; Osborne, L. S.; Pascaud, C.; Pawlik, B.; Payre, P.; Peroni, C.; Peschel, H.; Pessard, H.; Pettingale, J.; Pietrzyk, B.; Pönsgen, B.; Pötsch, M.; Renton, P.; Ribarics, P.; Rith, K.; Rondio, E.; Sandacz, A.; Scheer, M.; Schlagböhmer, A.; Schiemann, H.; Schmitz, N.; Schneegans, M.; Sholz, M.; Schröder, T.; Schouten, M.; Schultze, K.; Sloan, T.; Stier, H. E.; Studt, M.; Taylor, G. N.; Thenard, J. M.; Thompson, J. C.; de La Torre, A.; Toth, J.; Urban, L.; Urban, L.; Wallucks, W.; Whalley, M.; Wheeler, S.; Williams, W. S. C.; Wimpenny, S. J.; Windmolders, R.; Wolf, G.

1986-03-01

The Bose-Einstein correlation has been observed for pions in deep inelastic μ p interactions at 280 GeV. The importance of non-interference correlations in the sample of like charge pion pairs and in the sample used for reference is discussed. The pion emission region is found to be roughly spherical in the pair rest frame with a radius of 0.46 0.84 fm and the chaos factor λ is 0.60 1.08.

Enhanced pairing susceptibility in a photodoped two-orbital Hubbard model

NASA Astrophysics Data System (ADS)

Werner, Philipp; Strand, Hugo U. R.; Hoshino, Shintaro; Murakami, Yuta; Eckstein, Martin

2018-04-01

Local spin fluctuations provide the glue for orbital-singlet spin-triplet pairing in the doped Mott insulating regime of multiorbital Hubbard models. At large Hubbard repulsion U , the pairing susceptibility is nevertheless tiny because the pairing interaction cannot overcome the suppression of charge fluctuations. Using nonequilibrium dynamical mean field simulations of the two-orbital Hubbard model, we show that out of equilibrium the pairing susceptibility in this large-U regime can be strongly enhanced by creating a photoinduced population of the relevant charge states. This enhancement is supported by the long lifetime of photodoped charge carriers and a built-in cooling mechanism in multiorbital Hubbard systems.

Relativistic coupled cluster theory based on the no-pair Dirac-Coulomb-Breit Hamiltonian: Relativistic pair correlation energies of the Xe atom

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

Eliav, E.; Kaldor, U.; Ishikawa, Y.

1994-12-31

Relativistic pair correlation energies of Xe were computed by employing a recently developed relativistic coupled cluster theory based on the no-pair Dirac-Coulomb-Breit Hamiltonian. The matrix Dirac-Fock-Breit SCF and relativistic coupled cluster calculations were performed by means of expansion in basis sets of well-tempered Gaussian spinors. A detailed study of the pair correlation energies in Xe is performed, in order to investigate the effects of the low-frequency Breit interaction on the correlation energies of Xe. Nonadditivity of correlation and relativistic (particularly Breit) effects is discussed.

Development of the Physical Activity Interactive Recall (PAIR) for Aboriginal children

PubMed Central

Lévesque, Lucie; Cargo, Margaret; Salsberg, Jon

2004-01-01

Background Aboriginal children in Canada are at increased risk for type 2 diabetes. Given that physical inactivity is an important modifiable risk factor for type 2 diabetes, prevention efforts targeting Aboriginal children include interventions to enhance physical activity involvement. These types of interventions require adequate assessment of physical activity patterns to identify determinants, detect trends, and evaluate progress towards intervention goals. The purpose of this study was to develop a culturally appropriate interactive computer program to self-report physical activity for Kanien'kehá:ka (Mohawk) children that could be administered in a group setting. This was an ancillary study of the ongoing Kahnawake Schools Diabetes Prevention Project (KSDPP). Methods During Phase I, focus groups were conducted to understand how children describe and graphically depict type, intensity and duration of physical activity. Sixty-six students (40 girls, 26 boys, mean age = 8.8 years, SD = 1.8) from four elementary schools in three eastern Canadian Kanien'kehá:ka communities participated in 15 focus groups. Children were asked to discuss and draw about physical activity. Content analysis of focus groups informed the development of a school-day and non-school-day version of the physical activity interactive recall (PAIR). In Phase II, pilot-tests were conducted in two waves with 17 and 28 children respectively to assess the content validity of PAIR. Observation, videotaping, and interviews were conducted to obtain children's feedback on PAIR content and format. Results Children's representations of activity type and activity intensity were used to compile a total of 30 different physical activity and 14 non-physical activity response choices with accompanying intensity options. Findings from the pilot tests revealed that Kanien'kehá:ka children between nine and 13 years old could answer PAIR without assistance. Content validity of PAIR was judged to be adequate. PAIR was judged to be comprehensive, acceptable, and enjoyable by the children. Conclusions Results indicate that PAIR may be acceptable to children between nine and 13 years old, with most in this age range able to complete PAIR without assistance. The flexibility of its programming makes PAIR an easily adaptable tool to accommodate diverse populations, different seasons, and changing trends in physical activity involvement. PMID:15169559

Majorana edge States in atomic wires coupled by pair hopping.

PubMed

Kraus, Christina V; Dalmonte, Marcello; Baranov, Mikhail A; Läuchli, Andreas M; Zoller, P

2013-10-25

We present evidence for Majorana edge states in a number conserving theory describing a system of spinless fermions on two wires that are coupled by pair hopping. Our analysis is based on a combination of a qualitative low energy approach and numerical techniques using the density matrix renormalization group. In addition, we discuss an experimental realization of pair-hopping interactions in cold atom gases confined in optical lattices.

Solid State Photochemical Generation of Triplet Phenoxy-Phenoxy Radical Pairs

DTIC Science & Technology

1990-04-01

of diphenyl oxalate . Tert-butylated bis-aryloxalat s show good radical pair stability, with triplet ESR signals surviving days at room temperature in...between the geminate phenoxyl radicals. The comparable breadth of the spectra for diphenyl carbonate and the oxalates implies a similar interaction strength...ferromagnetic coupling that may be achieved in geminate pairs generated from a diphenyl oxalate vs. a diphenyl carbonate. In addition, we see similar

Anisotropy of thermal dileptons

NASA Astrophysics Data System (ADS)

Goloviznin, V. V.; Snigirev, A. M.; Zinovjev, G. M.

2018-05-01

The meaningful specific anisotropy in the angle distribution of leptons with respect to the three-momentum of pair is predicted as a feasibility signature of synchrotron-like mechanism resulting from the quarks interacting with a collective confining color field in the heavy ion collisions. The lepton pair production rate and the spectrum of pair invariant mass are presented for this new dilepton source that is apparently not taken into consideration in the available phenomenological estimates.

Local structure of ion pair interaction in lapatinib amorphous dispersions characterized by synchrotron x-ray diffraction and pair distribution function analysis

DOE PAGES

de Araujo, Gabriel L. B.; Benmore, Chris J.; Byrn, Stephen R.

2017-04-11

For many years, the idea of analyzing atom-atom contacts in amorphous drug-polymer systems has been of major interest, because this method has always had the potential to differentiate between amorphous systems with domains and amorphous systems which are molecular mixtures. In this study, local structure of ionic and noninonic interactions were studied by High-Energy X-ray Diffraction and Pair Distribution Function (PDF) analysis in amorphous solid dispersions of lapatinib in hypromellose phthalate (HPMCP) and hypromellose (HPMC-E3). The strategy of extracting lapatinib intermolecular drug interactions from the total PDF x-ray pattern was successfully applied allowing the detection of distinct nearest neighbor contactsmore » for the HPMC-E3 rich preparations showing that lapatinib molecules do not cluster in the same way as observed in HPMC-P, where ionic interactions are present. Orientational correlations up to nearest neighbor molecules at about 4.3 Å were observed for polymer rich samples; both observations showed strong correlation to the stability of the systems. Lasty, the superior physical stability of 1:3 LP:HPMCP was consistent with the absence of significant intermolecular interactions in (ΔD inter LP(r)) in the range of 3.0 to 6.0 Å, which are attributed to C-C, C-N and C-O nearest neighbor contacts present in drug-drug interactions.« less

Local structure of ion pair interaction in lapatinib amorphous dispersions characterized by synchrotron x-ray diffraction and pair distribution function analysis

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

de Araujo, Gabriel L. B.; Benmore, Chris J.; Byrn, Stephen R.

For many years, the idea of analyzing atom-atom contacts in amorphous drug-polymer systems has been of major interest, because this method has always had the potential to differentiate between amorphous systems with domains and amorphous systems which are molecular mixtures. In this study, local structure of ionic and noninonic interactions were studied by High-Energy X-ray Diffraction and Pair Distribution Function (PDF) analysis in amorphous solid dispersions of lapatinib in hypromellose phthalate (HPMCP) and hypromellose (HPMC-E3). The strategy of extracting lapatinib intermolecular drug interactions from the total PDF x-ray pattern was successfully applied allowing the detection of distinct nearest neighbor contactsmore » for the HPMC-E3 rich preparations showing that lapatinib molecules do not cluster in the same way as observed in HPMC-P, where ionic interactions are present. Orientational correlations up to nearest neighbor molecules at about 4.3 Å were observed for polymer rich samples; both observations showed strong correlation to the stability of the systems. Lasty, the superior physical stability of 1:3 LP:HPMCP was consistent with the absence of significant intermolecular interactions in (ΔD inter LP(r)) in the range of 3.0 to 6.0 Å, which are attributed to C-C, C-N and C-O nearest neighbor contacts present in drug-drug interactions.« less

Local Structure of Ion Pair Interaction in Lapatinib Amorphous Dispersions characterized by Synchrotron X-Ray diffraction and Pair Distribution Function Analysis

NASA Astrophysics Data System (ADS)

de Araujo, Gabriel L. B.; Benmore, Chris J.; Byrn, Stephen R.

2017-04-01

For many years, the idea of analyzing atom-atom contacts in amorphous drug-polymer systems has been of major interest, because this method has always had the potential to differentiate between amorphous systems with domains and amorphous systems which are molecular mixtures. In this study, local structure of ionic and noninonic interactions were studied by High-Energy X-ray Diffraction and Pair Distribution Function (PDF) analysis in amorphous solid dispersions of lapatinib in hypromellose phthalate (HPMCP) and hypromellose (HPMC-E3). The strategy of extracting lapatinib intermolecular drug interactions from the total PDF x-ray pattern was successfully applied allowing the detection of distinct nearest neighbor contacts for the HPMC-E3 rich preparations showing that lapatinib molecules do not cluster in the same way as observed in HPMC-P, where ionic interactions are present. Orientational correlations up to nearest neighbor molecules at about 4.3 Å were observed for polymer rich samples; both observations showed strong correlation to the stability of the systems. Finally, the superior physical stability of 1:3 LP:HPMCP was consistent with the absence of significant intermolecular interactions in (Δ) in the range of 3.0 to 6.0 Å, which are attributed to C-C, C-N and C-O nearest neighbor contacts present in drug-drug interactions.

Cannabidiol reverses the reduction in social interaction produced by low dose Delta(9)-tetrahydrocannabinol in rats.

PubMed

Malone, Daniel Thomas; Jongejan, Dennis; Taylor, David Alan

2009-08-01

While Delta(9)-tetrahydrocannabinol (THC) is the main psychoactive constituent of the cannabis plant, a non-psychoactive constituent is cannabidiol (CBD). CBD has been implicated as a potential treatment of a number of disorders including schizophrenia and epilepsy and has been included with THC in a 1:1 combination for the treatment of conditions such as neuropathic pain. This study investigated the effect of THC and CBD, alone or in combination, on some objective behaviours of rats in the open field. Pairs of rats were injected with CBD or vehicle followed by THC or vehicle and behaviour in the open field was assessed for 10 min. In vehicle pretreated rats THC (1 mg/kg) significantly reduced social interaction between rat pairs. Treatment with CBD had no significant effect alone, but pretreatment with CBD (20 mg/kg) reversed the THC-induced decreases in social interaction. A higher dose of THC (10 mg/kg) produced no significant effect on social interaction. However, the combination of high dose CBD and high dose THC significantly reduced social interaction between rat pairs, as well as producing a significant decrease in locomotor activity. This data suggests that CBD can reverse social withdrawal induced by low dose THC, but the combination of high dose THC and CBD impairs social interaction, possibly by decreasing locomotor activity.

Efficient creation of dipolar coupled nitrogen-vacancy spin qubits in diamond

NASA Astrophysics Data System (ADS)

Jakobi, I.; Momenzadeh, S. A.; Fávaro de Oliveira, F.; Michl, J.; Ziem, F.; Schreck, M.; Neumann, P.; Denisenko, A.; Wrachtrup, J.

2016-09-01

Coherently coupled pairs or multimers of nitrogen-vacancy defect electron spins in diamond have many promising applications especially in quantum information processing (QIP) but also in nanoscale sensing applications. Scalable registers of spin qubits are essential to the progress of QIP. Ion implantation is the only known technique able to produce defect pairs close enough to allow spin coupling via dipolar interaction. Although several competing methods have been proposed to increase the resulting resolution of ion implantation, the reliable creation of working registers is still to be demonstrated. The current limitation are residual radiation-induced defects, resulting in degraded qubit performance as trade-off for positioning accuracy. Here we present an optimized estimation of nanomask implantation parameters that are most likely to produce interacting qubits under standard conditions. We apply our findings to a well-established technique, namely masks written in electron-beam lithography, to create coupled defect pairs with a reasonable probability. Furthermore, we investigate the scaling behavior and necessary improvements to efficiently engineer interacting spin architectures.

Patterns of call communication between group-housed zebra finches change during the breeding cycle

PubMed Central

Gill, Lisa F; Goymann, Wolfgang; Ter Maat, Andries; Gahr, Manfred

2015-01-01

Vocal signals such as calls play a crucial role for survival and successful reproduction, especially in group-living animals. However, call interactions and call dynamics within groups remain largely unexplored because their relation to relevant contexts or life-history stages could not be studied with individual-level resolution. Using on-bird microphone transmitters, we recorded the vocalisations of individual zebra finches (Taeniopygia guttata) behaving freely in social groups, while females and males previously unknown to each other passed through different stages of the breeding cycle. As birds formed pairs and shifted their reproductive status, their call repertoire composition changed. The recordings revealed that calls occurred non-randomly in fine-tuned vocal interactions and decreased within groups while pair-specific patterns emerged. Call-type combinations of vocal interactions changed within pairs and were associated with successful egg-laying, highlighting a potential fitness relevance of calling dynamics in communication systems. DOI: http://dx.doi.org/10.7554/eLife.07770.001 PMID:26441403

Fulde-Ferrell-Larkin-Ovchinnikov correlation and free fluids in the one-dimensional attractive Hubbard model

NASA Astrophysics Data System (ADS)

Cheng, Song; Yu, Yi-Cong; Batchelor, M. T.; Guan, Xi-Wen

2018-03-01

In this Rapid Communication, we show that low-energy macroscopic properties of the one-dimensional (1D) attractive Hubbard model exhibit two fluids of bound pairs and of unpaired fermions. Using the thermodynamic Bethe ansatz equations of the model, we first determine the low-temperature phase diagram and analytically calculate the Fulde-Ferrell-Larkin-Ovchinnikov (FFLO) pairing correlation function for the partially polarized phase. We then show that for such an FFLO-like state in the low-density regime the effective chemical potentials of bound pairs and unpaired fermions behave like two free fluids. Consequently, the susceptibility, compressibility, and specific heat obey simple additivity rules, indicating the "free" particle nature of interacting fermions on a 1D lattice. In contrast to the continuum Fermi gases, the correlation critical exponents and thermodynamics of the attractive Hubbard model essentially depend on two lattice interacting parameters. Finally, we study scaling functions, the Wilson ratio and susceptibility, which provide universal macroscopic properties and dimensionless constants of interacting fermions at low energy.

Bond rupture between colloidal particles with a depletion interaction

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

Whitaker, Kathryn A.; Furst, Eric M., E-mail: furst@udel.edu

The force required to break the bonds of a depletion gel is measured by dynamically loading pairs of colloidal particles suspended in a solution of a nonadsorbing polymer. Sterically stabilized poly(methyl methacrylate) colloids that are 2.7 μm diameter are brought into contact in a solvent mixture of cyclohexane-cyclohexyl bromide and polystyrene polymer depletant. The particle pairs are subject to a tensile load at a constant loading rate over many approach-retraction cycles. The stochastic nature of the thermal rupture events results in a distribution of bond rupture forces with an average magnitude and variance that increases with increasing depletant concentration. The measuredmore » force distribution is described by the flux of particle pairs sampling the energy barrier of the bond interaction potential based on the Asakura–Oosawa depletion model. A transition state model demonstrates the significance of lubrication hydrodynamic interactions and the effect of the applied loading rate on the rupture force of bonds in a depletion gel.« less

Structure of the Human FANCL RING-Ube2T Complex Reveals Determinants of Cognate E3-E2 Selection

PubMed Central

Hodson, Charlotte; Purkiss, Andrew; Miles, Jennifer Anne; Walden, Helen

2014-01-01

Summary The combination of an E2 ubiquitin-conjugating enzyme with an E3 ubiquitin-ligase is essential for ubiquitin modification of a substrate. Moreover, the pairing dictates both the substrate choice and the modification type. The molecular details of generic E3-E2 interactions are well established. Nevertheless, the determinants of selective, specific E3-E2 recognition are not understood. There are ∼40 E2s and ∼600 E3s giving rise to a possible ∼24,000 E3-E2 pairs. Using the Fanconi Anemia pathway exclusive E3-E2 pair, FANCL-Ube2T, we report the atomic structure of the FANCL RING-Ube2T complex, revealing a specific and extensive network of additional electrostatic and hydrophobic interactions. Furthermore, we show that these specific interactions are required for selection of Ube2T over other E2s by FANCL. PMID:24389026

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.

Pulsational Pair-instability Model for Superluminous Supernova PTF12dam: Interaction and Radioactive Decay

NASA Astrophysics Data System (ADS)

Tolstov, Alexey; Nomoto, Ken'ichi; Blinnikov, Sergei; Sorokina, Elena; Quimby, Robert; Baklanov, Petr

2017-02-01

Being a superluminous supernova, PTF12dam can be explained by a 56Ni-powered model, a magnetar-powered model, or an interaction model. We propose that PTF12dam is a pulsational pair-instability supernova, where the outer envelope of a progenitor is ejected during the pulsations. Thus, it is powered by a double energy source: radioactive decay of 56Ni and a radiative shock in a dense circumstellar medium. To describe multicolor light curves and spectra, we use radiation-hydrodynamics calculations of the STELLA code. We found that light curves are well described in the model with 40 M⊙ ejecta and 20-40 M⊙ circumstellar medium. The ejected 56Ni mass is about 6 M⊙, which results from explosive nucleosynthesis with large explosion energy (2-3) × 1052 erg. In comparison with alternative scenarios of pair-instability supernova and magnetar-powered supernova, in the interaction model, all the observed main photometric characteristics are well reproduced: multicolor light curves, color temperatures, and photospheric velocities.

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.

Orientation-dependent interaction between Drosophila insulators is a property of this class of regulatory elements.

PubMed

Kyrchanova, Olga; Chetverina, Darya; Maksimenko, Oksana; Kullyev, Andrey; Georgiev, Pavel

2008-12-01

Insulators are defined as a class of regulatory elements that delimit independent transcriptional domains within eukaryotic genomes. According to previous data, an interaction (pairing) between some Drosophila insulators can support distant activation of a promoter by an enhancer. Here, we have demonstrated that pairs of well-studied insulators such as scs-scs, scs'-scs', 1A2-1A2 and Wari-Wari support distant activation of the white promoter by the yeast GAL4 activator in an orientation-dependent manner. The same is true for the efficiency of the enhancer that stimulates white expression in the eyes. In all insulator pairs tested, stimulation of the white gene was stronger when insulators were inserted between the eye enhancer or GAL4 and the white promoter in opposite orientations relative to each other. As shown previously, Zw5, Su(Hw) and dCTCF proteins are required for the functioning of different insulators that do not interact with each other. Here, strong functional interactions have been revealed between DNA fragments containing binding sites for either Zw5 or Su(Hw) or dCTCF protein but not between heterologous binding sites [Zw5-Su(Hw), dCTCF-Su(Hw), or dCTCF-Zw5]. These results suggest that insulator proteins can support selective interactions between distant regulatory elements.

Breathing dynamics based parameter sensitivity analysis of hetero-polymeric DNA

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

Talukder, Srijeeta; Sen, Shrabani; Chaudhury, Pinaki, E-mail: pinakc@rediffmail.com

We study the parameter sensitivity of hetero-polymeric DNA within the purview of DNA breathing dynamics. The degree of correlation between the mean bubble size and the model parameters is estimated for this purpose for three different DNA sequences. The analysis leads us to a better understanding of the sequence dependent nature of the breathing dynamics of hetero-polymeric DNA. Out of the 14 model parameters for DNA stability in the statistical Poland-Scheraga approach, the hydrogen bond interaction ε{sub hb}(AT) for an AT base pair and the ring factor ξ turn out to be the most sensitive parameters. In addition, the stackingmore » interaction ε{sub st}(TA-TA) for an TA-TA nearest neighbor pair of base-pairs is found to be the most sensitive one among all stacking interactions. Moreover, we also establish that the nature of stacking interaction has a deciding effect on the DNA breathing dynamics, not the number of times a particular stacking interaction appears in a sequence. We show that the sensitivity analysis can be used as an effective measure to guide a stochastic optimization technique to find the kinetic rate constants related to the dynamics as opposed to the case where the rate constants are measured using the conventional unbiased way of optimization.« less

Spatial and temporal interactions of sympatric mountain lions in Arizona

USGS Publications Warehouse

Nicholson, Kerry L.; Krausman, Paul R.; Munguia-Vega, Adrian; Culver, Melanie

2011-01-01

Spatial and temporal interactions among individual members of populations can have direct applications to habitat management of mountain lions (Puma concolor). Our objectives were to evaluate home range overlap and spatial/temporal use of overlap zones (OZ) of mountain lions in Arizona. We incorporated spatial data with genetic analyses to assess relatedness between mountain lions with overlapping home ranges. We recorded the space use patterns of 29 radio-collared mountain lions in Arizona from August 2005 to August 2008. We genotyped 28 mountain lions and estimated the degree of relatedness among individuals. For 26 pairs of temporally overlapping mountain lions, 18 overlapped spatially and temporally and eight had corresponding genetic information. Home range overlap ranged from 1.18% to 46.38% (x̄=2443, SE = 2.96). Male–male pairs were located within 1 km of each other on average, 0.04% of the time, whereas male–female pairs on average were 3.0%. Two male–male pairs exhibited symmetrical spatial avoidance and two symmetrical spatial attractions to the OZ. We observed simultaneous temporal attraction in three male–male pairs and four male–female pairs. Individuals from Tucson were slightly related to one another within the population (n = 13, mean R = 0.0373 ± 0.0151) whereas lions from Payson (n = 6, mean R = -0.0079 ± 0.0356) and Prescott (n = 9, mean R = -0.0242 ± 0.0452) were not as related. Overall, males were less related to other males (n = 20, mean R = -0.0495 ± 0.0161) than females were related to other females (n = 8, mean R = 0.0015 ± 0.0839). Genetic distance was positively correlated with geographic distance (r2 = 0.22, P = 0.001). Spatial requirements and interactions influence social behavior and can play a role in determining population density.

DockTrina: docking triangular protein trimers.

PubMed

Popov, Petr; Ritchie, David W; Grudinin, Sergei

2014-01-01

In spite of the abundance of oligomeric proteins within a cell, the structural characterization of protein-protein interactions is still a challenging task. In particular, many of these interactions involve heteromeric complexes, which are relatively difficult to determine experimentally. Hence there is growing interest in using computational techniques to model such complexes. However, assembling large heteromeric complexes computationally is a highly combinatorial problem. Nonetheless the problem can be simplified greatly by considering interactions between protein trimers. After dimers and monomers, triangular trimers (i.e. trimers with pair-wise contacts between all three pairs of proteins) are the most frequently observed quaternary structural motifs according to the three-dimensional (3D) complex database. This article presents DockTrina, a novel protein docking method for modeling the 3D structures of nonsymmetrical triangular trimers. The method takes as input pair-wise contact predictions from a rigid body docking program. It then scans and scores all possible combinations of pairs of monomers using a very fast root mean square deviation test. Finally, it ranks the predictions using a scoring function which combines triples of pair-wise contact terms and a geometric clash penalty term. The overall approach takes less than 2 min per complex on a modern desktop computer. The method is tested and validated using a benchmark set of 220 bound and seven unbound protein trimer structures. DockTrina will be made available at http://nano-d.inrialpes.fr/software/docktrina. Copyright © 2013 Wiley Periodicals, Inc.

Thermodynamics and kinetics of Na+/K+-formate ion pairs association in polarizable water: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Nguyen, Phuong T. M.; Nguyen, Van T.; Annapureddy, Harsha V. R.; Dang, Liem X.; Do, D. D.

2012-12-01

To enhance our understanding of ion specific activity in biological systems, the potential of mean force approach was utilized to study solvent effects on the interactions between two alkali cations (Na+ and K+) with a formate anion in water. A very complex free energy landscape was observed, much more so than alkali-halide ion pairs. Furthermore, a stronger binding between the Na+-formate pair was found in comparison to the K+-formate pair in water, which is in agreement with experimental and theoretical studies [1-4]. The kinetics of ion-pair inter-conversions was studied using the transition rate theory, along with a number of theoretical approaches such as the Kramers and Grote-Hynes theories. These kinetic results were used to predict solvent effects on dynamical features of ion-pair association, in which we have found that the dynamics of K+-formate pairs is faster than Na+-formate pairs.

Complexes of DNA bases and Watson-Crick base pairs with small neutral gold clusters.

PubMed

Kryachko, E S; Remacle, F

2005-12-08

The nature of the DNA-gold interaction determines and differentiates the affinity of the nucleobases (adenine, thymine, guanine, and cytosine) to gold. Our preliminary computational study [Kryachko, E. S.; Remacle, F. Nano Lett. 2005, 5, 735] demonstrates that two major bonding factors govern this interaction: the anchoring, either of the Au-N or Au-O type, and the nonconventional N-H...Au hydrogen bonding. In this paper, we offer insight into the nature of nucleobase-gold interactions and provide a detailed characterization of their different facets, i.e., geometrical, energetic, and spectroscopic aspects; the gold cluster size and gold coordination effects; proton affinity; and deprotonation energy. We then investigate how the Watson-Crick DNA pairing patterns are modulated by the nucleobase-gold interaction. We do so in terms of the proton affinities and deprotonation energies of those proton acceptors and proton donors which are involved in the interbase hydrogen bondings. A variety of properties of the most stable Watson-Crick [A x T]-Au3 and [G x C]-Au3 hybridized complexes are described and compared with the isolated Watson-Crick A x T and G x C ones. It is shown that enlarging the gold cluster size to Au6 results in a rather short gold-gold bond in the Watson-Crick interbase region of the [G x C]-Au6 complex that bridges the G x C pair and thus leads to a significant strengthening of G x C pairing.

Quantitative determination of pairing interactions for high-temperature superconductivity in cuprates

PubMed Central

Bok, Jin Mo; Bae, Jong Ju; Choi, Han-Yong; Varma, Chandra M.; Zhang, Wentao; He, Junfeng; Zhang, Yuxiao; Yu, Li; Zhou, X. J.

2016-01-01

A profound problem in modern condensed matter physics is discovering and understanding the nature of fluctuations and their coupling to fermions in cuprates, which lead to high-temperature superconductivity and the invariably associated strange metal state. We report the quantitative determination of normal and pairing self-energies, made possible by laser-based angle-resolved photoemission measurements of unprecedented accuracy and stability. Through a precise inversion procedure, both the effective interactions in the attractive d-wave symmetry and the repulsive part in the full symmetry are determined. The latter is nearly angle-independent. Near Tc, both interactions are nearly independent of frequency and have almost the same magnitude over the complete energy range of up to about 0.4 eV, except for a low-energy feature at around 50 meV that is present only in the repulsive part, which has less than 10% of the total spectral weight. Well below Tc, they both change similarly, with superconductivity-induced features at low energies. Besides finding the pairing self-energy and the attractive interactions for the first time, these results expose the central paradox of the problem of high Tc: how the same frequency-independent fluctuations can dominantly scatter at angles ±π/2 in the attractive channel to give d-wave pairing and lead to angle-independent repulsive scattering. The experimental results are compared with available theoretical calculations based on antiferromagnetic fluctuations, the Hubbard model, and quantum-critical fluctuations of the loop-current order. PMID:26973872

A Systematic Study of Sustainable Development Goal (SDG) Interactions

NASA Astrophysics Data System (ADS)

Pradhan, Prajal; Costa, Luís.; Rybski, Diego; Lucht, Wolfgang; Kropp, Jürgen P.

2017-11-01

Sustainable development goals (SDGs) have set the 2030 agenda to transform our world by tackling multiple challenges humankind is facing to ensure well-being, economic prosperity, and environmental protection. In contrast to conventional development agendas focusing on a restricted set of dimensions, the SDGs provide a holistic and multidimensional view on development. Hence, interactions among the SDGs may cause diverging results. To analyze the SDG interactions we systematize the identification of synergies and trade-offs using official SDG indicator data for 227 countries. A significant positive correlation between a pair of SDG indicators is classified as a synergy while a significant negative correlation is classified as a trade-off. We rank synergies and trade-offs between SDGs pairs on global and country scales in order to identify the most frequent SDG interactions. For a given SDG, positive correlations between indicator pairs were found to outweigh the negative ones in most countries. Among SDGs the positive and negative correlations between indicator pairs allowed for the identification of particular global patterns. SDG 1 (No poverty) has synergetic relationship with most of the other goals, whereas SDG 12 (Responsible consumption and production) is the goal most commonly associated with trade-offs. The attainment of the SDG agenda will greatly depend on whether the identified synergies among the goals can be leveraged. In addition, the highlighted trade-offs, which constitute obstacles in achieving the SDGs, need to be negotiated and made structurally nonobstructive by deeper changes in the current strategies.

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

Alignment of RNA molecules: Binding energy and statistical properties of random sequences

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

Valba, O. V., E-mail: valbaolga@gmail.com; Nechaev, S. K., E-mail: sergei.nechaev@gmail.com; Tamm, M. V., E-mail: thumm.m@gmail.com

2012-02-15

A new statistical approach to the problem of pairwise alignment of RNA sequences is proposed. The problem is analyzed for a pair of interacting polymers forming an RNA-like hierarchical cloverleaf structures. An alignment is characterized by the numbers of matches, mismatches, and gaps. A weight function is assigned to each alignment; this function is interpreted as a free energy taking into account both direct monomer-monomer interactions and a combinatorial contribution due to formation of various cloverleaf secondary structures. The binding free energy is determined for a pair of RNA molecules. Statistical properties are discussed, including fluctuations of the binding energymore » between a pair of RNA molecules and loop length distribution in a complex. Based on an analysis of the free energy per nucleotide pair complexes of random RNAs as a function of the number of nucleotide types c, a hypothesis is put forward about the exclusivity of the alphabet c = 4 used by nature.« less

Ionic liquid-induced aggregate formation and their applications.

PubMed

Dutta, Rupam; Kundu, Sangita; Sarkar, Nilmoni

2018-06-01

In the last two decades, researchers have extensively studied highly stable and ordered supramolecular assembly formation using oppositely charged surfactants. Thereafter, surface-active ionic liquids (SAILs), a special class of room temperature ionic liquids (RTILs), replace the surfactants to form various supramolecular aggregates. Therefore, in the last decade, the building blocks of the supramolecular aggregates (micelle, mixed micelle, and vesicular assemblies) have changed from oppositely charged surfactant/surfactant pair to surfactant/SAIL and SAIL/SAIL pair. It is also found that various biomolecules can also interact with SAILs to construct biologically important supramolecular assemblies. The very latest addition to this combination of ion pairs is the dye molecules having a long hydrophobic chain part along with a hydrophilic ionic head group. Thus, dye/surfactant or dye/SAIL pair also produces different assemblies through electrostatic, hydrophobic, and π-π stacking interactions. Vesicles are one of the important self-assemblies which mimic cellular membranes, and thus have biological application as a drug carrier. Moreover, vesicles can act as a suitable microreactor for nanoparticle synthesis.

Game theoretic power allocation and waveform selection for satellite communications

NASA Astrophysics Data System (ADS)

Shu, Zhihui; Wang, Gang; Tian, Xin; Shen, Dan; Pham, Khanh; Blasch, Erik; Chen, Genshe

2015-05-01

Game theory is a useful method to model interactions between agents with conflicting interests. In this paper, we set up a Game Theoretic Model for Satellite Communications (SATCOM) to solve the interaction between the transmission pair (blue side) and the jammer (red side) to reach a Nash Equilibrium (NE). First, the IFT Game Application Model (iGAM) for SATCOM is formulated to improve the utility of the transmission pair while considering the interference from a jammer. Specifically, in our framework, the frame error rate performance of different modulation and coding schemes is used in the game theoretic solution. Next, the game theoretic analysis shows that the transmission pair can choose the optimal waveform and power given the received power from the jammer. We also describe how the jammer chooses the optimal power given the waveform and power allocation from the transmission pair. Finally, simulations are implemented for the iGAM and the simulation results show the effectiveness of the SATCOM power allocation, waveform selection scheme, and jamming mitigation.

Neutralino pair production at the photon-photon collider for the τ̃-coannihilation scenario

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

Sonmez, Nasuf, E-mail: nsonmez@cern.ch

Supersymmetry (SUSY) is a theory which gives an explanation for the strong and electroweak interactions from the grand unification scale down to the weak scale. The search for supersymmetric particles still continues at full speed at the LHC without success. The main task at the ILC is complementing the LHC result and also search for new physics. In this study, the neutralino pair production via photon-photon collision is studied for the t̃-coannihilation scenario in the context of MSSM at the ILC. In the calculation, all the possible one loop diagrams are taken into account for the photon-photon interaction. We presentmore » the production cross section and distribution of various observables for the lightest and next-to-lightest neutralino pairs for benchmark models which are specifically presented in the light of LHC8 data analysis, employing these benchmark models for neutralino pair production could show the potential of the ILC concerning the dark matter searches in supersymmetry.« less

Covariant Evolutionary Event Analysis for Base Interaction Prediction Using a Relational Database Management System for RNA.

PubMed

Xu, Weijia; Ozer, Stuart; Gutell, Robin R

2009-01-01

With an increasingly large amount of sequences properly aligned, comparative sequence analysis can accurately identify not only common structures formed by standard base pairing but also new types of structural elements and constraints. However, traditional methods are too computationally expensive to perform well on large scale alignment and less effective with the sequences from diversified phylogenetic classifications. We propose a new approach that utilizes coevolutional rates among pairs of nucleotide positions using phylogenetic and evolutionary relationships of the organisms of aligned sequences. With a novel data schema to manage relevant information within a relational database, our method, implemented with a Microsoft SQL Server 2005, showed 90% sensitivity in identifying base pair interactions among 16S ribosomal RNA sequences from Bacteria, at a scale 40 times bigger and 50% better sensitivity than a previous study. The results also indicated covariation signals for a few sets of cross-strand base stacking pairs in secondary structure helices, and other subtle constraints in the RNA structure.

Covariant Evolutionary Event Analysis for Base Interaction Prediction Using a Relational Database Management System for RNA

PubMed Central

Xu, Weijia; Ozer, Stuart; Gutell, Robin R.

2010-01-01

With an increasingly large amount of sequences properly aligned, comparative sequence analysis can accurately identify not only common structures formed by standard base pairing but also new types of structural elements and constraints. However, traditional methods are too computationally expensive to perform well on large scale alignment and less effective with the sequences from diversified phylogenetic classifications. We propose a new approach that utilizes coevolutional rates among pairs of nucleotide positions using phylogenetic and evolutionary relationships of the organisms of aligned sequences. With a novel data schema to manage relevant information within a relational database, our method, implemented with a Microsoft SQL Server 2005, showed 90% sensitivity in identifying base pair interactions among 16S ribosomal RNA sequences from Bacteria, at a scale 40 times bigger and 50% better sensitivity than a previous study. The results also indicated covariation signals for a few sets of cross-strand base stacking pairs in secondary structure helices, and other subtle constraints in the RNA structure. PMID:20502534

Rate theory of ion pairing at the water liquid-vapor interface: A case of sodium iodide.

PubMed

Dang, Liem X; Schenter, Gregory K

2018-06-14

Studies on ion pairing at interfaces have been intensified recently because of their importance in many chemical reactive phenomena, such as ion-ion interactions that are affected by interfaces and their influence on kinetic processes. In this study, we performed simulations to examine the thermodynamics and kinetics of small polarizable sodium iodide ions in the bulk and near the water liquid-vapor interface. Using classical transition state theory, we calculated the dissociation rates and corrected them with transmission coefficients obtained from the reactive flux formalism and Grote-Hynes theory. Our results show that in addition to affecting the free energy of ions in solution, the interfacial environments significantly influence the kinetics of ion pairing. The results on the relaxation time obtained using the reactive flux formalism and Grote-Hynes theory present an unequivocal picture that the interface suppresses ion dissociation. The effects of the use of molecular models on the ion interactions as well as the ion-pair configurations at the interface are also quantified and discussed.

Rate theory of ion pairing at the water liquid-vapor interface: A case of sodium iodide

NASA Astrophysics Data System (ADS)

Dang, Liem X.; Schenter, Gregory K.

2018-06-01

Studies on ion pairing at interfaces have been intensified recently because of their importance in many chemical reactive phenomena, such as ion-ion interactions that are affected by interfaces and their influence on kinetic processes. In this study, we performed simulations to examine the thermodynamics and kinetics of small polarizable sodium iodide ions in the bulk and near the water liquid-vapor interface. Using classical transition state theory, we calculated the dissociation rates and corrected them with transmission coefficients obtained from the reactive flux formalism and Grote-Hynes theory. Our results show that in addition to affecting the free energy of ions in solution, the interfacial environments significantly influence the kinetics of ion pairing. The results on the relaxation time obtained using the reactive flux formalism and Grote-Hynes theory present an unequivocal picture that the interface suppresses ion dissociation. The effects of the use of molecular models on the ion interactions as well as the ion-pair configurations at the interface are also quantified and discussed.

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.

Sequence dependency of canonical base pair opening in the DNA double helix

PubMed Central

Villa, Alessandra

2017-01-01

The flipping-out of a DNA base from the double helical structure is a key step of many cellular processes, such as DNA replication, modification and repair. Base pair opening is the first step of base flipping and the exact mechanism is still not well understood. We investigate sequence effects on base pair opening using extensive classical molecular dynamics simulations targeting the opening of 11 different canonical base pairs in two DNA sequences. Two popular biomolecular force fields are applied. To enhance sampling and calculate free energies, we bias the simulation along a simple distance coordinate using a newly developed adaptive sampling algorithm. The simulation is guided back and forth along the coordinate, allowing for multiple opening pathways. We compare the calculated free energies with those from an NMR study and check assumptions of the model used for interpreting the NMR data. Our results further show that the neighboring sequence is an important factor for the opening free energy, but also indicates that other sequence effects may play a role. All base pairs are observed to have a propensity for opening toward the major groove. The preferred opening base is cytosine for GC base pairs, while for AT there is sequence dependent competition between the two bases. For AT opening, we identify two non-canonical base pair interactions contributing to a local minimum in the free energy profile. For both AT and CG we observe long-lived interactions with water and with sodium ions at specific sites on the open base pair. PMID:28369121

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.

Fully gapped superconductivity with no sign change in the prototypical heavy-fermion CeCu2Si2

PubMed Central

Yamashita, Takuya; Takenaka, Takaaki; Tokiwa, Yoshifumi; Wilcox, Joseph A.; Mizukami, Yuta; Terazawa, Daiki; Kasahara, Yuichi; Kittaka, Shunichiro; Sakakibara, Toshiro; Konczykowski, Marcin; Seiro, Silvia; Jeevan, Hirale S.; Geibel, Christoph; Putzke, Carsten; Onishi, Takafumi; Ikeda, Hiroaki; Carrington, Antony; Shibauchi, Takasada; Matsuda, Yuji

2017-01-01

In exotic superconductors, including high-Tc copper oxides, the interactions mediating electron Cooper pairing are widely considered to have a magnetic rather than a conventional electron-phonon origin. Interest in this exotic pairing was initiated by the 1979 discovery of heavy-fermion superconductivity in CeCu2Si2, which exhibits strong antiferromagnetic fluctuations. A hallmark of unconventional pairing by anisotropic repulsive interactions is that the superconducting energy gap changes sign as a function of the electron momentum, often leading to nodes where the gap goes to zero. We report low-temperature specific heat, thermal conductivity, and magnetic penetration depth measurements in CeCu2Si2, demonstrating the absence of gap nodes at any point on the Fermi surface. Moreover, electron irradiation experiments reveal that the superconductivity survives even when the electron mean free path becomes substantially shorter than the superconducting coherence length. This indicates that superconductivity is robust against impurities, implying that there is no sign change in the gap function. These results show that, contrary to long-standing belief, heavy electrons with extremely strong Coulomb repulsions can condense into a fully gapped s-wave superconducting state, which has an on-site attractive pairing interaction. PMID:28691082

Cooperativity and complexity in the binding of anions and cations to a tetratopic ion-pair host.

PubMed

Howe, Ethan N W; Bhadbhade, Mohan; Thordarson, Pall

2014-05-21

Cooperative interactions play a very important role in both natural and synthetic supramolecular systems. We report here on the cooperative binding properties of a tetratopic ion-pair host 1. This host combines two isophthalamide anion recognition sites with two unusual "half-crown/two carbonyl" cation recognition sites as revealed by the combination of single-crystal X-ray analysis of the free host and the 1:2 host:calcium cation complex, together with two-dimensional NMR and computational studies. By systematically comparing all of the binding data to several possible binding models and focusing on four different variants of the 1:2 binding model, it was in most cases possible to quantify these complex cooperative interactions. The data showed strong negative cooperativity (α = 0.01-0.05) of 1 toward chloride and acetate anions, while for cations the results were more variable. Interestingly, in the competitive (CDCl3/CD3OD (9:1, v/v)) solvent, the addition of calcium cations to the tetratopic ion-pair host 1 allosterically switched "on" chloride binding that is otherwise not present in this solvent system. The insight into the complexity of cooperative interactions revealed in this study of the tetratopic ion-pair host 1 can be used to design better cooperative supramolecular systems for information transfer and catalysis.

Modeling synthetic lethality

PubMed Central

Le Meur, Nolwenn; Gentleman, Robert

2008-01-01

Background Synthetic lethality defines a genetic interaction where the combination of mutations in two or more genes leads to cell death. The implications of synthetic lethal screens have been discussed in the context of drug development as synthetic lethal pairs could be used to selectively kill cancer cells, but leave normal cells relatively unharmed. A challenge is to assess genome-wide experimental data and integrate the results to better understand the underlying biological processes. We propose statistical and computational tools that can be used to find relationships between synthetic lethality and cellular organizational units. Results In Saccharomyces cerevisiae, we identified multi-protein complexes and pairs of multi-protein complexes that share an unusually high number of synthetic genetic interactions. As previously predicted, we found that synthetic lethality can arise from subunits of an essential multi-protein complex or between pairs of multi-protein complexes. Finally, using multi-protein complexes allowed us to take into account the pleiotropic nature of the gene products. Conclusions Modeling synthetic lethality using current estimates of the yeast interactome is an efficient approach to disentangle some of the complex molecular interactions that drive a cell. Our model in conjunction with applied statistical methods and computational methods provides new tools to better characterize synthetic genetic interactions. PMID:18789146

Local free energies for the coarse-graining of adsorption phenomena: The interacting pair approximation

NASA Astrophysics Data System (ADS)

Pazzona, Federico G.; Pireddu, Giovanni; Gabrieli, Andrea; Pintus, Alberto M.; Demontis, Pierfranco

2018-05-01

We investigate the coarse-graining of host-guest systems under the perspective of the local distribution of pore occupancies, along with the physical meaning and actual computability of the coarse-interaction terms. We show that the widely accepted approach, in which the contributions to the free energy given by the molecules located in two neighboring pores are estimated through Monte Carlo simulations where the two pores are kept separated from the rest of the system, leads to inaccurate results at high sorbate densities. In the coarse-graining strategy that we propose, which is based on the Bethe-Peierls approximation, density-independent interaction terms are instead computed according to local effective potentials that take into account the correlations between the pore pair and its surroundings by means of mean-field correction terms without the need for simulating the pore pair separately. Use of the interaction parameters obtained this way allows the coarse-grained system to reproduce more closely the equilibrium properties of the original one. Results are shown for lattice-gases where the local free energy can be computed exactly and for a system of Lennard-Jones particles under the effect of a static confining field.

Computer simulation on the collision-sticking dynamics of two colloidal particles in an optical trap.

PubMed

Xu, Shenghua; Sun, Zhiwei

2007-04-14

Collisions of a particle pair induced by optical tweezers have been employed to study colloidal stability. In order to deepen insights regarding the collision-sticking dynamics of a particle pair in the optical trap that were observed in experimental approaches at the particle level, the authors carry out a Brownian dynamics simulation. In the simulation, various contributing factors, including the Derjaguin-Landau-Verwey-Overbeek interaction of particles, hydrodynamic interactions, optical trapping forces on the two particles, and the Brownian motion, were all taken into account. The simulation reproduces the tendencies of the accumulated sticking probability during the trapping duration for the trapped particle pair described in our previous study and provides an explanation for why the two entangled particles in the trap experience two different statuses.

Spatiotemporal distributions of pair production and cascade in solid targets irradiated by ultra-relativistic lasers with different polarizations

NASA Astrophysics Data System (ADS)

Yuan, T.; Yu, J. Y.; Liu, W. Y.; Weng, S. M.; Yuan, X. H.; Luo, W.; Chen, M.; Sheng, Z. M.; Zhang, J.

2018-06-01

Two-dimensional particle-in-cell simulations have been performed to study electron-positron pair production and cascade development in single ultra-relativistic laser interaction with solid targets. The spatiotemporal distributions of particles produced via QED processes are illustrated and their dependence on laser polarizations is investigated. The evolution of particle generation displays clear QED cascade characters. Studies show that although a circularly polarized laser delays the QED process due to the effective ion acceleration, it can reduce the target heating and confine high-energy charged particles, which leads to deeper QED cascade order and denser pair plasma production than linearly polarized lasers. These findings may benefit the understanding of the coming experimental studies of ultra-relativistic laser target interaction in the QED dominated regime.

Sleep Duration and Depressive Symptoms: A Gene-Environment Interaction

PubMed Central

Watson, Nathaniel F.; Harden, Kathryn Paige; Buchwald, Dedra; Vitiello, Michael V.; Pack, Allan I.; Strachan, Eric; Goldberg, Jack

2014-01-01

Objective: We used quantitative genetic models to assess whether sleep duration modifies genetic and environmental influences on depressive symptoms. Method: Participants were 1,788 adult twins from 894 same-sex twin pairs (192 male and 412 female monozygotic [MZ] pairs, and 81 male and 209 female dizygotic [DZ] pairs] from the University of Washington Twin Registry. Participants self-reported habitual sleep duration and depressive symptoms. Data were analyzed using quantitative genetic interaction models, which allowed the magnitude of additive genetic, shared environmental, and non-shared environmental influences on depressive symptoms to vary with sleep duration. Results: Within MZ twin pairs, the twin who reported longer sleep duration reported fewer depressive symptoms (ec = -0.17, SE = 0.06, P < 0.05). There was a significant gene × sleep duration interaction effect on depressive symptoms (a'c = 0.23, SE = 0.08, P < 0.05), with the interaction occurring on genetic influences that are common to both sleep duration and depressive symptoms. Among individuals with sleep duration within the normal range (7-8.9 h/night), the total heritability (h2) of depressive symptoms was approximately 27%. However, among individuals with sleep duration within the low (< 7 h/night) or high (≥ 9 h/night) range, increased genetic influence on depressive symptoms was observed, particularly at sleep duration extremes (5 h/night: h2 = 53%; 10 h/night: h2 = 49%). Conclusion: Genetic contributions to depressive symptoms increase at both short and long sleep durations. Citation: Watson NF; Harden KP; Buchwald D; Vitiello MV; Pack AI; Stachan E; Goldberg J. Sleep duration and depressive symptoms: a gene-environment interaction. SLEEP 2014;37(2):351-358. PMID:24497663

Assessing Preference for Social Interactions

ERIC Educational Resources Information Center

Clay, Casey J.; Samaha, Andrew L.; Bloom, Sarah E.; Bogoev, Bistra K.; Boyle, Megan A.

2013-01-01

We examined a procedure to assess preference for social interactions in individuals with intellectual and developmental disabilities. Preferences were identified in five individuals using a paired-choice procedure in which participants approached therapists who provided different forms of social interactions. A subsequent tracking test showed that…

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.

Action of Penetrating Radiation on Radio Parts,

DTIC Science & Technology

1984-05-24

the formation of the pair of particles the electron - positron . This process is called the effect of the formation of electron- positron pairs. Pair...formation can occur during the absorption 7-quantum with the energy, greater than total rest energy of electron and positron (more than the doubled...rest energy of electron, equal to 2mc 2=!.02 MeV). Positron (unstable elementary DOC - 83167601 PAGE 9 particle) in turn interacts with the electron of

Renormalization of Coulomb interactions in s-wave superconductor NaxCoO2

NASA Astrophysics Data System (ADS)

Yada, Keiji; Kontani, Hiroshi

2007-03-01

We study the renormalized Coulomb interactions due to retardation effect in NaxCoO2. Although the Morel Anderson's pseudo-potential for a1g orbital μa1g* is relatively large because the direct Coulomb repulsion U is large, that for interband transition between a1g and eg' orbitals μa1g,eg'* is very small since the renormalization factor for pair hopping J is square of that for U. Therefore, the s-wave superconductivity due to valence-band Suhl-Kondo mechanism will survive against strong Coulomb interactions. The interband hopping of Cooper pairs due to shear phonons is essential to understand the superconductivity in NaxCoO2.

Interactions between nitrogen and oxygen molecules studied by gas-phase NMR spectroscopy

NASA Astrophysics Data System (ADS)

Garbacz, Piotr; Misiak, Maria; Jackowski, Karol

2018-05-01

Gas-phase 14N and 15N NMR studies of nitrogen and synthetic air pressurized up to 300 bar were performed. It was found that the magnetic shielding of an isolated N2 molecule, σ0(N) = -63.4(2) ppm, is in good agreement with the results of ab initio calculations. The binary N2-O2 interactions contribute to shielding an order of the magnitude larger than the N2-N2 pairs. For nitrogen the three body collisions become observable by NMR for pressure higher than 200 bar and the appropriate coefficient can be practically assigned to the interaction between one molecule of N2 and a pair of O2 molecules.

Mesure de la section efficace de production de paires de quarks top dans le canal lepton+tau+jets+MET dans l'experience D0 et interpretation en termes de boson de Higgs charge (in French)

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

Lacroix, Florent

The standard model of particle physics describes the matter as elementary particles interacting via strong and electroweak interactions. The top quark is the heaviest quark described by this model and has been discovered in 1995 by CDF and D collaborations in proton-antiproton collisions at the Tevatron. This thesis is devoted to the measurement of the top pair production cross-section via the strong interaction, in a final state composed of one lepton, one hadronic tau, two b-jets and missing transverse energy. This analysis uses the 1,2 fb

Bubble nuclei within the self-consistent Hartree-Fock mean field plus pairing approach

NASA Astrophysics Data System (ADS)

Phuc, L. Tan; Hung, N. Quang; Dang, N. Dinh

2018-02-01

The depletion of the nuclear density at its center, called the nuclear bubble, is studied within the Skyrme Hartree-Fock mean field consistently incorporating the superfluid pairing. The latter is obtained within the finite-temperature Bardeen-Cooper-Schrieffer theory and within the approach using the exact pairing. The numerical calculations are carried out for 22O and 34Si nuclei, whose bubble structures, caused by a very low occupancy of the 2 s1 /2 level, were previously predicted at T =0 . Among 24 Skyrme interactions under consideration, the MSk3 is the only one which reproduces the experimentally measured occupancy of the 2 s1 /2 proton level as well as the binding energy, and consequently produces the most pronounced bubble structure in 34Si. As compared to the approaches employing the same BSk14 interaction, our approach with exact pairing predicts a pairing effect which is stronger in 22O and weaker in 34Si. The increase in temperature depletes the bubble structure and completely washes it out when the temperature reaches a critical value, at which the factor measuring the depletion of the nucleon density vanishes.

Homeostasis of Complementary Pair Theory: Ecological Comparisons in Diverse Universal Design for Learning Environments

ERIC Educational Resources Information Center

Ianneo, Brittany

2014-01-01

Accommodation~assimilation relations were theorized by Kelso and Engstrom (2006) as independent and dependent complementary pairs. This study defined relationships between organisms that experienced complementary interactions of accommodation~assimilation in diverse ecologies designed with universal design for learning environments (UDLE) compared…

State-Dependent Cross-Brain Information Flow in Borderline Personality Disorder.

PubMed

Bilek, Edda; Stößel, Gabriela; Schäfer, Axel; Clement, Laura; Ruf, Matthias; Robnik, Lydia; Neukel, Corinne; Tost, Heike; Kirsch, Peter; Meyer-Lindenberg, Andreas

2017-09-01

Although borderline personality disorder (BPD)-one of the most common, burdensome, and costly psychiatric conditions-is characterized by repeated interpersonal conflict and instable relationships, the neurobiological mechanism of social interactive deficits remains poorly understood. To apply recent advancements in the investigation of 2-person human social interaction to investigate interaction difficulties among people with BPD. Cross-brain information flow in BPD was examined from May 25, 2012, to December 4, 2015, in pairs of participants studied in 2 linked functional magnetic resonance imaging scanners in a university setting. Participants performed a joint attention task. Each pair included a healthy control individual (HC) and either a patient currently fulfilling DSM-IV criteria for BPD (cBPD) (n = 23), a patient in remission for 2 years or more (rBPD) (n = 17), or a second HC (n = 20). Groups were matched for age and educational level. A measure of cross-brain neural coupling was computed following previously published work to indicate synchronized flow between right temporoparietal junction networks (previously shown to host neural coupling abilities in health). This measure is derived from an independent component analysis contrasting the time courses of components between pairs of truly interacting participants compared with bootstrapped control pairs. In the sample including 23 women with cBPD (mean [SD] age, 26.8 [5.7] years), 17 women with rBPD (mean [SD] age, 28.5 [4.3] years), and 80 HCs (mean [SD] age, 24.0 [3.4] years]) investigated as dyads, neural coupling was found to be associated with disorder state (η2 = 0.17; P = .007): while HC-HC pairs showed synchronized neural responses, cBPD-HC pairs exhibited significantly lower neural coupling just above permutation-based data levels (η2 = 0.16; P = .009). No difference was found between neural coupling in rBPD-HC and HC-HC pairs. The neural coupling in patients was significantly associated with childhood adversity (T = 2.3; P = .03). This study provides a neural correlate for a core diagnostic and clinical feature of BPD. Results indicate that hyperscanning may deliver state-associated biomarkers for clinical social neuroscience. In addition, at least some neural deficits of BPD may be more reversible than is currently assumed for personality disorders.

Submonolayer Ag films on Fe(100): A first-principles analysis of energetics controlling adlayer thermodynamics and kinetics

DOE PAGES

Li, Wei; Huang, Li; Evans, James W.; ...

2016-04-11

Epitaxial growth of Ag on Fe(100) and postdeposition relaxation have been studied in several experiments. We provide a first-principles density functional theory analysis of key adatom interaction energies and diffusion barriers controlling growth and relaxation kinetics for the submonolayer regime, as these have not been assessed previously. A cluster expansion approach is used to obtain an extensive set of conventional lateral interactions between adatoms on fourfold hollow adsorption sites. We find robust oscillatory decay of pair interactions with increasing separation, and of trio interactions with increasing perimeter length. First- and second-nearest-neighbor pair interactions, as well as compact linear and bentmore » trio interactions, dominate. The adatom terrace diffusion barrier is estimated to be E d ≈ 0.39 eV. We also provide a limited analysis of unconventional interactions for which one adatom is at the bridge-site transition state for hopping and one or more others are at fourfold hollow sites. Furthermore, energy barriers for diffusion along island edges can be determined with the aid of both conventional and unconventional interactions.« less

A quantitative literature-curated gold standard for kinase-substrate pairs

PubMed Central

2011-01-01

We describe the Yeast Kinase Interaction Database (KID, http://www.moseslab.csb.utoronto.ca/KID/), which contains high- and low-throughput data relevant to phosphorylation events. KID includes 6,225 low-throughput and 21,990 high-throughput interactions, from greater than 35,000 experiments. By quantitatively integrating these data, we identified 517 high-confidence kinase-substrate pairs that we consider a gold standard. We show that this gold standard can be used to assess published high-throughput datasets, suggesting that it will enable similar rigorous assessments in the future. PMID:21492431

Human interaction as environmental enrichment for pair-housed wolves and wolf-dog crosses.

PubMed

Mehrkam, Lindsay R; Verdi, Nicolle T; Wynne, Clive D L

2014-01-01

Private nonhuman animal sanctuaries are often financially limited in their ability to implement traditional environmental enrichment strategies. One possible solution may be to provide socialized animals with human interaction sessions. However, the merit of human interaction as enrichment has received little empirical attention to date. The present study aimed to evaluate whether human interaction could be enriching for socialized, pair-housed wolves and wolf-dog crosses at a private sanctuary. Observations of each subject were conducted in a reversal design to measure species-typical affiliation, activity levels, and aberrant behaviors when caretakers were both present and absent. The results demonstrate significantly higher levels of conspecific-directed affiliation and activity levels and reduced aberrant behavior when human interaction was available. Social play also increased when caregivers were present, supporting the hypothesis that play among conspecifics may be maintained by positive changes in an animal's environment. The potential for human interaction to be established as a scientifically validated, cost-effective enrichment strategy is supported by these findings.

Investigating protein-protein interaction surfaces using a reduced stereochemical and electrostatic model.

PubMed

Warwicker, J

1989-03-20

A method of calculating the electrostatic potential energy between two molecules, using finite difference potential, is presented. A reduced charge set is used so that the interaction energy can be calculated as the two static molecules explore their full six-dimensional configurational space. The energies are contoured over surfaces fixed to each molecule with an interactive computer graphics program. For two crystal structures (trypsin-trypsin inhibitor and anti-lysozyme Fab-lysozyme), it is found that the complex corresponds to highly favourable interacting regions in the contour plots. These matches arise from a small number of protruding basic residues interacting with enhanced negative potential in each case. The redox pair cytochrome c peroxidase-cytochrome c exhibits an extensive favourably interacting surface within which a possible electron transfer complex may be defined by an increased electrostatic complementarity, but a decreased electrostatic energy. A possible substrate transfer configuration for the glycolytic enzyme pair glyceraldehyde phosphate dehydrogenase-phosphoglycerate kinase is presented.

Pair-correlation function of a metastable helium Bose-Einstein condensate

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

Zin, Pawel; Trippenbach, Marek; Gajda, Mariusz

2004-02-01

The pair-correlation function is one of the basic quantities to characterize the coherence properties of a Bose-Einstein condensate. We calculate this function in the experimentally important case of a zero temperature Bose-Einstein condensate in a metastable triplet helium state using the variational method with a pair-excitation ansatz. We compare our result with a pair-correlation function obtained for the hard-sphere potential with the same scattering length. Both functions are practically indistinguishable for distances greater than the scattering length. At smaller distances, due to interatomic interactions, the helium condensate shows strong correlations.

Predicting Drug-Target Interactions for New Drug Compounds Using a Weighted Nearest Neighbor Profile.

PubMed

van Laarhoven, Twan; Marchiori, Elena

2013-01-01

In silico discovery of interactions between drug compounds and target proteins is of core importance for improving the efficiency of the laborious and costly experimental determination of drug-target interaction. Drug-target interaction data are available for many classes of pharmaceutically useful target proteins including enzymes, ion channels, GPCRs and nuclear receptors. However, current drug-target interaction databases contain a small number of drug-target pairs which are experimentally validated interactions. In particular, for some drug compounds (or targets) there is no available interaction. This motivates the need for developing methods that predict interacting pairs with high accuracy also for these 'new' drug compounds (or targets). We show that a simple weighted nearest neighbor procedure is highly effective for this task. We integrate this procedure into a recent machine learning method for drug-target interaction we developed in previous work. Results of experiments indicate that the resulting method predicts true interactions with high accuracy also for new drug compounds and achieves results comparable or better than those of recent state-of-the-art algorithms. Software is publicly available at http://cs.ru.nl/~tvanlaarhoven/drugtarget2013/.

Spatial Segregation and Aggregation of Ectomycorrhizal and Root-Endophytic Fungi in the Seedlings of Two Quercus Species

PubMed Central

Yamamoto, Satoshi; Sato, Hirotoshi; Tanabe, Akifumi S.; Hidaka, Amane; Kadowaki, Kohmei; Toju, Hirokazu

2014-01-01

Diverse clades of mycorrhizal and endophytic fungi are potentially involved in competitive or facilitative interactions within host-plant roots. We investigated the potential consequences of these ecological interactions on the assembly process of root-associated fungi by examining the co-occurrence of pairs of fungi in host-plant individuals. Based on massively-parallel pyrosequencing, we analyzed the root-associated fungal community composition for each of the 249 Quercus serrata and 188 Quercus glauca seedlings sampled in a warm-temperate secondary forest in Japan. Pairs of fungi that co-occurred more or less often than expected by chance were identified based on randomization tests. The pyrosequencing analysis revealed that not only ectomycorrhizal fungi but also endophytic fungi were common in the root-associated fungal community. Intriguingly, specific pairs of these ectomycorrhizal and endophytic fungi showed spatially aggregated patterns, suggesting the existence of facilitative interactions between fungi in different functional groups. Due to the large number of fungal pairs examined, many of the observed aggregated/segregated patterns with very low P values (e.g., < 0.005) turned non-significant after the application of a multiple comparison method. However, our overall results imply that the community structures of ectomycorrhizal and endophytic fungi could influence each other through interspecific competitive/facilitative interactions in root. To test the potential of host-plants' control of fungus–fungus ecological interactions in roots, we further examined whether the aggregated/segregated patterns could vary depending on the identity of host plant species. Potentially due to the physiological properties shared between the congeneric host plant species, the sign of hosts' control was not detected in the present study. The pyrosequencing-based randomization analyses shown in this study provide a platform of the high-throughput investigation of fungus–fungus interactions in plant root systems. PMID:24801150

1D momentum-conserving systems: the conundrum of anomalous versus normal heat transport

NASA Astrophysics Data System (ADS)

Li, Yunyun; Liu, Sha; Li, Nianbei; Hänggi, Peter; Li, Baowen

2015-04-01

Transport and the spread of heat in Hamiltonian one dimensional momentum conserving nonlinear systems is commonly thought to proceed anomalously. Notable exceptions, however, do exist of which the coupled rotator model is a prominent case. Therefore, the quest arises to identify the origin of manifest anomalous energy and momentum transport in those low dimensional systems. We develop the theory for both, the statistical densities for momentum- and energy-spread and particularly its momentum-/heat-diffusion behavior, as well as its corresponding momentum/heat transport features. We demonstrate that the second temporal derivative of the mean squared deviation of the momentum spread is proportional to the equilibrium correlation of the total momentum flux. Subtracting the part which corresponds to a ballistic momentum spread relates (via this integrated, subleading momentum flux correlation) to an effective viscosity, or equivalently, to the underlying momentum diffusivity. We next put forward the intriguing hypothesis: normal spread of this so adjusted excess momentum density causes normal energy spread and alike normal heat transport (Fourier Law). Its corollary being that an anomalous, superdiffusive broadening of this adjusted excess momentum density in turn implies an anomalous energy spread and correspondingly anomalous, superdiffusive heat transport. This hypothesis is successfully corroborated within extensive molecular dynamics simulations over large extended time scales. Our numerical validation of the hypothesis involves four distinct archetype classes of nonlinear pair-interaction potentials: (i) a globally bounded pair interaction (the noted coupled rotator model), (ii) unbounded interactions acting at large distances (the coupled rotator model amended with harmonic pair interactions), (iii) the case of a hard point gas with unbounded square-well interactions and (iv) a pair interaction potential being unbounded at short distances while displaying an asymptotic free part (Lennard-Jones model). We compare our findings with recent predictions obtained from nonlinear fluctuating hydrodynamics theory.

How Is Knowledge Generated about Memory Encoding Strategy Effectiveness?

ERIC Educational Resources Information Center

Hertzog, Christopher; Price, Jodi; Dunlosky, John

2008-01-01

This study evaluated how people learn about encoding strategy effectiveness in an associative memory task. Individuals studied two lists of paired associates under instructions to use either a normatively effective strategy (interactive imagery) or a normatively ineffective strategy (rote repetition) for each pair. Questionnaire ratings of imagery…

Examining Peer Collaboration in Online Inquiry

ERIC Educational Resources Information Center

Castek, Jill; Coiro, Julie; Guzniczak, Lizbeth; Bradshaw, Carlton

2012-01-01

This study examines peer collaboration among four pairs of seventh graders who read online to determine what caused the downfall of the Mayan civilization. More and less productive collaborative interactions are presented through snippets of dialogue in which pairs negotiated complex texts. Few examples of how teachers can skillfully facilitate…

Food reinforcement and delay discounting in zBMI-discordant siblings

USDA-ARS?s Scientific Manuscript database

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 zBM...

[Structural and Dipole Structure Peculiarities of Hoogsteen Base Pairs Formed in Complementary Nucleobases according to ab initio Quantum Mechanics Studies].

PubMed

Petrenko, Y M

2015-01-01

Ab initio quantum mechanics studies for the detection of structure and dipole structure peculiarities of Hoogsteen base pairs relative to Watson-Crick base pairs, were performed during our work. These base pairs are formed as a result of complementary interactions. It was revealed, that adenine-thymine Hoogsteen base pair and adenine-thymine Watson-Crick base pairs can be formed depending on initial configuration. Cytosine-guanine Hoogsteen pairs are formed only when cytosine was originally protonated. Both types of Hoogsteen pairs have noticeable difference in the bond distances and angles. These differences appeared in purine as well as in pyrimidine parts of the pairs. Hoogsteen pairs have mostly shorter hydrogen bond lengths and significantly larger angles of hydrogen bonds and larger angles between the hydrogen bonds than Watson-Crick base pairs. Notable differences are also observed with respect to charge distribution and dipole moment. Quantitative data on these differences are shown in our work. It is also reported that the values of local parameters (according to Cambridge classification of the parameters which determine DNA properties) in Hoogsteen base pairs, are greatly different from Watson-Crick ones.

Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs

PubMed Central

2017-01-01

Prediction of RNA tertiary structure from sequence is an important problem, but generating accurate structure models for even short sequences remains difficult. Predictions of RNA tertiary structure tend to be least accurate in loop regions, where non-canonical pairs are important for determining the details of structure. Non-canonical pairs can be predicted using a knowledge-based model of structure that scores nucleotide cyclic motifs, or NCMs. In this work, a partition function algorithm is introduced that allows the estimation of base pairing probabilities for both canonical and non-canonical interactions. Pairs that are predicted to be probable are more likely to be found in the true structure than pairs of lower probability. Pair probability estimates can be further improved by predicting the structure conserved across multiple homologous sequences using the TurboFold algorithm. These pairing probabilities, used in concert with prior knowledge of the canonical secondary structure, allow accurate inference of non-canonical pairs, an important step towards accurate prediction of the full tertiary structure. Software to predict non-canonical base pairs and pairing probabilities is now provided as part of the RNAstructure software package. PMID:29107980

Realization of a Quantum Integer-Spin Chain with Controllable Interactions

DTIC Science & Technology

2015-06-17

site participate in the dynamics. We observe the time evolution of the system and verify its coherence by entangling a pair of effective three-level...states generated by the XY Hamiltonian, we can verify entangle - ment between a pair of three-level systems with fidelities of up to 86%. Adding a time...3(b) shows an example of the measured parity curve used to extract the amplitude A and verify entanglement between the qutrit pair . Such measurements

Ship and satellite observations of chlorophyll stocks in interacting cyclone-anticyclone eddy pairs in the western Gulf of Mexico

NASA Technical Reports Server (NTRS)

Biggs, Douglas, C.; Mueller-Karger, Frank E.

1994-01-01

When anticyclonic eddies shed by the Loop Current of the Gulf of Mexico reach the western margin of the gulf, they influence the surface circulation over the continental slope and rise. Of particular interest is the generation of cyclone (cold-core)-anticyclone (warm-core) pairs when aging Loop Current eddies interact with the continental margin. In this paper we describe the physical and biological characteristics of these cyclone-anticyclone pairs. Our objective was to determine how eddy pairs affect the distribution of phytoplankton in the region and how satellite ocean color measurements are applicable to tracing of the eddies. We present shipboard data collected between 1980 and 1982 on the hydrography, chlorophyll stocks, and nutrient concentrations of eddy pairs in the western Gulf of Mexico and compare these data with coastal zone color scanner (CZCS) images collected during the time frame of the cruises. Surface pigment concentrations followed a seasonal cycle, with low concentrations (0.05-0.1 mg m(exp -3)) found within cyclones and anticyclones from April through early November and higher concentrations (greater than 0.1 mg(exp -3)) found in the winter. CZCS pigment concentrations were locally high in the flow confluence of cyclone-anticyclone pairs. The CZCS imagery shows that some cyclone-anticyclone geometries transport high-chlorophyll shelf water seaward at least 100-200 km off-shelf.

The influence of arene-ring size on stacking interaction with canonical base pairs

NASA Astrophysics Data System (ADS)

Formánek, Martin; Burda, Jaroslav V.

2014-04-01

Stacking interactions between aromatic molecules (benzene, p-cymene, biphenyl, and di- and tetra-hydrogen anthracene) and G.C and A.T canonical Watson-Crick (WC) base pairs are explored. Two functionals with dispersion corrections: ω-B97XD and B3LYP-D3 are used. For a comparison also the MP2 and B3LYP-D3/PCM methods were used for the most stable p-cymene…WC geometries. It was found that the stacking interaction increases with the size of π-conjugation system. Its extent is in agreement with experimental finding on anticancer activity of Ru(II) piano-stool complexes where intercalation of these aromatic molecules should play an important role. The explored structures are considered as ternary system so that decomposition of the interaction energy to pairwise and non-additivity contributions is also examined.

Mechanism of amido-thiourea catalyzed enantioselective imine hydrocyanation: transition state stabilization via multiple non-covalent interactions.

PubMed

Zuend, Stephan J; Jacobsen, Eric N

2009-10-28

An experimental and computational investigation of amido-thiourea promoted imine hydrocyanation has revealed a new and unexpected mechanism of catalysis. Rather than direct activation of the imine by the thiourea, as had been proposed previously in related systems, the data are consistent with a mechanism involving catalyst-promoted proton transfer from hydrogen isocyanide to imine to generate diastereomeric iminium/cyanide ion pairs that are bound to catalyst through multiple noncovalent interactions; these ion pairs collapse to form the enantiomeric alpha-aminonitrile products. This mechanistic proposal is supported by the observation of a statistically significant correlation between experimental and calculated enantioselectivities induced by eight different catalysts (P < 0.01). The computed models reveal a basis for enantioselectivity that involves multiple stabilizing and destabilizing interactions between substrate and catalyst, including thiourea-cyanide and amide-iminium interactions.

Deriving Heterospecific Self-Assembling Protein-Protein Interactions Using a Computational Interactome Screen.

PubMed

Crooks, Richard O; Baxter, Daniel; Panek, Anna S; Lubben, Anneke T; Mason, Jody M

2016-01-29

Interactions between naturally occurring proteins are highly specific, with protein-network imbalances associated with numerous diseases. For designed protein-protein interactions (PPIs), required specificity can be notoriously difficult to engineer. To accelerate this process, we have derived peptides that form heterospecific PPIs when combined. This is achieved using software that generates large virtual libraries of peptide sequences and searches within the resulting interactome for preferentially interacting peptides. To demonstrate feasibility, we have (i) generated 1536 peptide sequences based on the parallel dimeric coiled-coil motif and varied residues known to be important for stability and specificity, (ii) screened the 1,180,416 member interactome for predicted Tm values and (iii) used predicted Tm cutoff points to isolate eight peptides that form four heterospecific PPIs when combined. This required that all 32 hypothetical off-target interactions within the eight-peptide interactome be disfavoured and that the four desired interactions pair correctly. Lastly, we have verified the approach by characterising all 36 pairs within the interactome. In analysing the output, we hypothesised that several sequences are capable of adopting antiparallel orientations. We subsequently improved the software by removing sequences where doing so led to fully complementary electrostatic pairings. Our approach can be used to derive increasingly large and therefore complex sets of heterospecific PPIs with a wide range of potential downstream applications from disease modulation to the design of biomaterials and peptides in synthetic biology. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

EPIBLASTER-fast exhaustive two-locus epistasis detection strategy using graphical processing units

PubMed Central

Kam-Thong, Tony; Czamara, Darina; Tsuda, Koji; Borgwardt, Karsten; Lewis, Cathryn M; Erhardt-Lehmann, Angelika; Hemmer, Bernhard; Rieckmann, Peter; Daake, Markus; Weber, Frank; Wolf, Christiane; Ziegler, Andreas; Pütz, Benno; Holsboer, Florian; Schölkopf, Bernhard; Müller-Myhsok, Bertram

2011-01-01

Detection of epistatic interaction between loci has been postulated to provide a more in-depth understanding of the complex biological and biochemical pathways underlying human diseases. Studying the interaction between two loci is the natural progression following traditional and well-established single locus analysis. However, the added costs and time duration required for the computation involved have thus far deterred researchers from pursuing a genome-wide analysis of epistasis. In this paper, we propose a method allowing such analysis to be conducted very rapidly. The method, dubbed EPIBLASTER, is applicable to case–control studies and consists of a two-step process in which the difference in Pearson's correlation coefficients is computed between controls and cases across all possible SNP pairs as an indication of significant interaction warranting further analysis. For the subset of interactions deemed potentially significant, a second-stage analysis is performed using the likelihood ratio test from the logistic regression to obtain the P-value for the estimated coefficients of the individual effects and the interaction term. The algorithm is implemented using the parallel computational capability of commercially available graphical processing units to greatly reduce the computation time involved. In the current setup and example data sets (211 cases, 222 controls, 299468 SNPs; and 601 cases, 825 controls, 291095 SNPs), this coefficient evaluation stage can be completed in roughly 1 day. Our method allows for exhaustive and rapid detection of significant SNP pair interactions without imposing significant marginal effects of the single loci involved in the pair. PMID:21150885

Manipulation of the oxytocin system alters social behavior and attraction in pair-bonding primates, Callithrix penicillata

PubMed Central

Smith, Adam S.; Ågmo, Anders; Birnie, Andrew K.; French, Jeffrey A.

2010-01-01

The establishment and maintenance of stable, long-term male-female relationships, or pair bonds, are marked by high levels of mutual attraction, selective preference for the partner, and high rates of sociosexual behavior. Central oxytocin (OT) affects social preference and partner-directed social behavior in rodents, but the role of this neuropeptide has yet to be studied in heterosexual primate relationships. The present study evaluated whether the OT system plays a role in the dynamics of social behavior and partner preference during the first three weeks of cohabitation in male and female marmosets, Callithrix penicillata. OT activity was stimulated by intranasal administration of OT, and inhibited by oral administration of a non-peptide OT-receptor antagonist (L-368,899; Merck). Social behavior throughout the pairing varied as a function of OT treatment. Compared to controls, marmosets initiated huddling with their social partner more often after OT treatments but reduced proximity and huddling after OT antagonist treatments. OT antagonist treatment also eliminated food sharing between partners. During the 24-h preference test, all marmosets interacted more with an opposite-sex stranger than with the partner. By the third-week preference test, marmosets interacted with the partner and stranger equally with the exception that intranasal-OT treatments facilitated initial partner-seeking behavior over initial contact with the stranger. Our findings demonstrate that pharmacological manipulations of OT activity alter partner-directed social behavior during pair interactions, suggesting that central OT may facilitate the process of pair-bond formation and social relationships in marmoset monkeys. PMID:20025881

Manipulation of the oxytocin system alters social behavior and attraction in pair-bonding primates, Callithrix penicillata.

PubMed

Smith, Adam S; Agmo, Anders; Birnie, Andrew K; French, Jeffrey A

2010-02-01

The establishment and maintenance of stable, long-term male-female relationships, or pair-bonds, are marked by high levels of mutual attraction, selective preference for the partner, and high rates of sociosexual behavior. Central oxytocin (OT) affects social preference and partner-directed social behavior in rodents, but the role of this neuropeptide has yet to be studied in heterosexual primate relationships. The present study evaluated whether the OT system plays a role in the dynamics of social behavior and partner preference during the first 3 weeks of cohabitation in male and female marmosets, Callithrix penicillata. OT activity was stimulated by intranasal administration of OT, and inhibited by oral administration of a non-peptide OT-receptor antagonist (L-368,899; Merck). Social behavior throughout the pairing varied as a function of OT treatment. Compared to controls, marmosets initiated huddling with their social partner more often after OT treatments but reduced proximity and huddling after OT antagonist treatments. OT antagonist treatment also eliminated food sharing between partners. During the 24-h preference test, all marmosets interacted more with an opposite-sex stranger than with the partner. By the third-week preference test, marmosets interacted with the partner and stranger equally with the exception that intranasal-OT treatments facilitated initial partner-seeking behavior over initial contact with the stranger. Our findings demonstrate that pharmacological manipulations of OT activity alter partner-directed social behavior during pair interactions, suggesting that central OT may facilitate the process of pair-bond formation and social relationships in marmoset monkeys. Published by Elsevier Inc.

Age-Related Changes in Associative Memory for Emotional and Non-emotional Integrative Representations

PubMed Central

Murray, Brendan D.; Kensinger, Elizabeth A.

2014-01-01

Events often include novel combinations of items. Sometimes, through the process of integration, we experience and remember these items as parts of a whole rather than as separate entities. Recent research with younger adults has demonstrated that successfully integrating two non-emotional items at encoding, instead of imagining them separately, produces a disproportionately larger associative memory benefit than integrating an emotional and a non-emotional item (Murray & Kensinger, 2012). In the first study to examine whether age and emotion interact to influence integration, we use two measures of integrative success – the ability to successfully retrieve integrations, measured through associative cued recall, and the ability to successfully generate integrated representations at encoding, measured through self report. The cued recall results (Expt. 1 and 2) reveal that the emotional content of the word pairs interacts to influence the effect of integration on older adults’ associative memory, but in the opposite direction of younger adults: Older adults show no associative retrieval benefit of integration over non-integration for non-emotional pairs, but they show a significant integrative benefit for emotional pairs. We also demonstrate (Expt. 2) that encoding time interacts with emotion and integration in different ways for older and younger adults: Putting younger adults under time pressure reduces their success in generating integrated representations at encoding for non-emotional pairs, whereas for older adults it disrupts their ability to generate integrated representations for emotional pairs. We discuss possible age-related differences in the processes used to create emotional and non-emotional integrations. PMID:24364402

Does an electronic continuum correction improve effective short-range ion-ion interactions in aqueous solution?

NASA Astrophysics Data System (ADS)

Bruce, Ellen E.; van der Vegt, Nico F. A.

2018-06-01

Non-polarizable force fields for hydrated ions not always accurately describe short-range ion-ion interactions, frequently leading to artificial ion clustering in bulk aqueous solutions. This can be avoided by adjusting the nonbonded anion-cation or cation-water Lennard-Jones parameters. This approach has been successfully applied to different systems, but the parameterization is demanding owing to the necessity of separate investigations of each ion pair. Alternatively, polarization effects may effectively be accounted for using the electronic continuum correction (ECC) of Leontyev et al. [J. Chem. Phys. 119, 8024 (2003)], which involves scaling the ionic charges with the inverse square-root of the water high-frequency dielectric permittivity. ECC has proven to perform well for monovalent salts as well as for divalent salts in water. Its performance, however, for multivalent salts with higher valency remains unexplored. The present work illustrates the applicability of the ECC model to trivalent K3PO4 and divalent K2HPO4 in water. We demonstrate that the ECC models, without additional tuning of force field parameters, provide an accurate description of water-mediated interactions between salt ions. This results in predictions of the osmotic coefficients of aqueous K3PO4 and K2HPO4 solutions in good agreement with experimental data. Analysis of ion pairing thermodynamics in terms of contact ion pair (CIP), solvent-separated ion pair, and double solvent-separated ion pair contributions shows that potassium-phosphate CIP formation is stronger with trivalent than with divalent phosphate ions.

The Interactions between Breastfeeding Mothers and Their Babies during the Breastfeeding Session.

ERIC Educational Resources Information Center

Epstein, Karen

1993-01-01

Videotaped 12 breastfeeding mothers and their babies during breastfeeding sessions to investigate maternal-infant interactions occurring during breastfeeding sessions. Presents four case studies to examine differences in breastfeeding interactions, as well as benefits and disadvantages that breastfeeding provided different mother-child pairs. (MM)

Molecular structure and interactions in the ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide.

PubMed

Dhumal, Nilesh R; Noack, Kristina; Kiefer, Johannes; Kim, Hyung J

2014-04-03

Electronic structure theory (density functional and Møller-Plesset perturbation theory) and vibrational spectroscopy (FT-IR and Raman) are employed to study molecular interactions in the room-temperature ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide. Different conformers of a cation-anion pair based on their molecular interactions are simulated in the gas phase and in a dielectric continuum solvent environment. Although the ordering of conformers in energy varies with theoretical methods, their predictions for three lowest energy conformers in the gas phase are similar. Strong C-H---N interactions between the acidic hydrogen atom of the cation imidazole ring and the nitrogen atom of the anion are predicted for either the lowest or second lowest energy conformer. In a continuum solvent, different theoretical methods yield the same ion-pair conformation for the lowest energy state. In both phases, the density functional method predicts that the anion is in a trans conformation in the lowest energy ion pair state. The theoretical results are compared with experimental observations from Raman scattering and IR absorption spectroscopies and manifestations of the molecular interactions in the vibrational spectra are discussed. The directions of the frequency shifts of the characteristic vibrations relative to the free anion and cation are explained by calculating the difference electron density coupled with electron density topography.

Computational Study of a Vortex-Ring Pair Interacting with a Constant-Temperature Heated Wall

NASA Astrophysics Data System (ADS)

Jabbar, Hussam; Naguib, Ahmed

2017-11-01

Impinging jets are used widely in industrial and manufacturing processes because of their ability to increase the heat transfer rate from the impingement surface. The vortical structures of these jets have an important influence on the heat transfer; by affecting the thermal boundary layer (TBL) during their interaction with the wall. In order to better understand the physics of this interaction, particularly when pairing of two vortices happens near the wall, a simplified model problem of two isolated vortex rings interacting with a flat wall is investigated computationally using ANSYS FLUENT 17.1. Observations of the vorticity field, the temperature field, the wall shear stress, the TBL and the Nusselt number (Nu) provide insight into the association of local Nu maxima/minima with different flow features. The results provide physical understanding of the flow processes leading to enhancement/deterioration of Nu due to vortex-wall interaction. Additionally, the characteristics of the vortical structures are quantified, and possible correlations between the temporal development of these characteristics and the evolution of the maximum/minimum Nu are investigated. The results are compared to those involving a single vortex ring in order to understand the effect of vortex pairing. This work is supported by NSF Grant Number CBET-1603720. Hussam Jabbar also acknowledges the fellowship support from Higher Committee for Education Development in Iraq (HCED).

Orientation-dependent interaction between Drosophila insulators is a property of this class of regulatory elements

PubMed Central

Kyrchanova, Olga; Chetverina, Darya; Maksimenko, Oksana; Kullyev, Andrey; Georgiev, Pavel

2008-01-01

Insulators are defined as a class of regulatory elements that delimit independent transcriptional domains within eukaryotic genomes. According to previous data, an interaction (pairing) between some Drosophila insulators can support distant activation of a promoter by an enhancer. Here, we have demonstrated that pairs of well-studied insulators such as scs–scs, scs’–scs’, 1A2–1A2 and Wari–Wari support distant activation of the white promoter by the yeast GAL4 activator in an orientation-dependent manner. The same is true for the efficiency of the enhancer that stimulates white expression in the eyes. In all insulator pairs tested, stimulation of the white gene was stronger when insulators were inserted between the eye enhancer or GAL4 and the white promoter in opposite orientations relative to each other. As shown previously, Zw5, Su(Hw) and dCTCF proteins are required for the functioning of different insulators that do not interact with each other. Here, strong functional interactions have been revealed between DNA fragments containing binding sites for either Zw5 or Su(Hw) or dCTCF protein but not between heterologous binding sites [Zw5–Su(Hw), dCTCF–Su(Hw), or dCTCF–Zw5]. These results suggest that insulator proteins can support selective interactions between distant regulatory elements. PMID:18987002

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.

The 5S rRNA loop E: chemical probing and phylogenetic data versus crystal structure.

PubMed

Leontis, N B; Westhof, E

1998-09-01

A significant fraction of the bases in a folded, structured RNA molecule participate in noncanonical base pairing interactions, often in the context of internal loops or multi-helix junction loops. The appearance of each new high-resolution RNA structure provides welcome data to guide efforts to understand and predict RNA 3D structure, especially when the RNA in question is a functionally conserved molecule. The recent publication of the crystal structure of the "Loop E" region of bacterial 5S ribosomal RNA is such an event [Correll CC, Freeborn B, Moore PB, Steitz TA, 1997, Cell 91:705-712]. In addition to providing more examples of already established noncanonical base pairs, such as purine-purine sheared pairings, trans-Hoogsteen UA, and GU wobble pairs, the structure provides the first high-resolution views of two new purine-purine pairings and a new GU pairing. The goal of the present analysis is to expand the capabilities of both chemical probing and phylogenetic analysis to predict with greater accuracy the structures of RNA molecules. First, in light of existing chemical probing data, we investigate what lessons could be learned regarding the interpretation of this widely used method of RNA structure probing. Then we analyze the 3D structure with reference to molecular phylogeny data (assuming conservation of function) to discover what alternative base pairings are geometrically compatible with the structure. The comparisons between previous modeling efforts and crystal structures show that the intricate involvements of ions and water molecules in the maintenance of non-Watson-Crick pairs render the process of correctly identifying the interacting sites in such pairs treacherous, except in cases of trans-Hoogsteen A/U or sheared A/G pairs for the adenine N1 site. The phylogenetic analysis identifies A/A, A/C, A/U and C/A, C/C, and C/U pairings isosteric with sheared A/G, as well as A/A and A/C pairings isosteric with both G/U and G/G bifurcated pairings. Thus, each non-Watson-Crick pair could be characterized by a phylogenetic signature of variations between isosteric-like pairings. In addition to the conservative changes, which form a dictionary of pairings isosterically compatible with those observed in the crystal structure, concerted changes involving several base pairs also occur. The latter covariations may indicate transitions between related but distinctive motifs within the loop E of 5S ribosomal RNA.

Magnetically-enhanced open string pair production

NASA Astrophysics Data System (ADS)

Lu, J. X.

2017-12-01

We consider the stringy interaction between two parallel stacks of D3 branes placed at a separation. Each stack of D3 branes in a similar fashion carry an electric flux and a magnetic flux with the two sharing no common field strength index. The interaction amplitude has an imaginary part, giving rise to the Schwinger-like pair production of open strings. We find a significantly enhanced rate of this production when the two electric fluxes are almost identical and the brane separation is on the order of string scale. This enhancement will be largest if the two magnetic fluxes are opposite in direction. This novel enhancement results from the interplay of the non-perturbative Schwinger-type pair production due to the electric flux and the stringy tachyon due to the magnetic flux, and may have realistic physical applications.

Generalized seniority on a deformed single-particle basis

NASA Astrophysics Data System (ADS)

Jia, L. Y.

2017-09-01

Recently, I proposed a fast computing scheme for generalized seniority on a spherical single-particle basis [J. Phys. G: Nucl. Part. Phys. 42, 115105 (2015), 10.1088/0954-3899/42/11/115105]. This work redesigns the scheme to make it applicable to deformed single-particle basis. The algorithm is applied to the rare-earth-metal nucleus 94 64 158Gd for intrinsic (body-fixed frame) neutron excitations under the low-momentum NN interaction Vlow -k. By allowing as many as four broken pairs, I compute the lowest 300 intrinsic states of several multipolarities. These states converge well to the exact ones, showing generalized seniority is very effective in truncating the deformed shell model. Under realistic interactions, the picture remains approximately valid: The ground state is a coherent pair condensate and the pairs gradually break up as excitation energy increases.

Correspondence between Preference Assessment Outcomes and Stimulus Reinforcer Value for Social Interactions

ERIC Educational Resources Information Center

Davis, Tonya N.; Hodges, Abby; Weston, Regan; Hogan, Emily; Padilla-Mainor, Kristen

2017-01-01

Preferred forms of social interaction were identified using a paired-stimulus format in which two 3-5 s videos of the experimenter providing the social interaction to the participant were presented. Reinforcer efficacy of the high-, medium-, and low-preferred interactions was evaluated using a progressive-ratio schedule to determine the amount of…

They Work Together to Roar: Kindergartners' Understanding of an Interactive Causal Task

ERIC Educational Resources Information Center

Solis, S. Lynneth; Grotzer, Tina A.

2016-01-01

The aim of this study was to investigate kindergartners' exploration of interactive causality during their play with a pair of toy sound blocks. Interactive causality refers to a type of causal pattern in which two entities interact to produce a causal force, as in particle attraction and symbiotic relationships. Despite being prevalent in nature,…

Development of a picture of the van der Waals interaction energy between clusters of nanometer-range particles

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

Arunachalam, V.; Marlow, W.H.; Lu, J.X.

1998-09-01

The importance of the long-range Lifshitz{endash}van der Waals interaction energy between condensed bodies is well known. However, its implementation for interacting bodies that are highly irregular and separated by distances varying from contact to micrometers has received little attention. As part of a study of collisions of irregular aerosol particles, an approach based on the Lifshitz theory of van der Waals interaction has been developed to compute the interaction energy between a sphere and an aggregate of spheres at all separations. In the first part of this study, the iterated sum-over-dipole interactions between pairs of approximately spherical molecular clusters aremore » compared with the Lifshitz and Lifshitz-Hamaker interaction energies for continuum spheres of radii equal to those of the clusters{close_quote} circumscribed spheres and of the same masses as the clusters. The Lifshitz energy is shown to converge to the iterated dipolar energy for quasispherical molecular clusters for sufficiently large separations, while the energy calculated by using the Lifshitz-Hamaker approach does not. Next, the interaction energies between a contacting pair of these molecular clusters and a third cluster in different relative positions are calculated first by coupling all molecules in the three-cluster system and second by ignoring the interactions between the molecules of the adhering clusters. The error calculated by this omission is shown to be very small, and is an indication of the error in computing the long-range interaction energy between a pair of interacting spheres and a third sphere as a simple sum over the Lifshitz energies between individual, condensed-matter spheres. This Lifshitz energy calculation is then combined with the short-separation, nonsingular van der Waals energy calculation of Lu, Marlow, and Arunachalam, to provide an integrated picture of the van der Waals energy from large separations to contact. {copyright} {ital 1998} {ital The American Physical Society}« less

Effectively identifying compound-protein interactions by learning from positive and unlabeled examples.

PubMed

Cheng, Zhanzhan; Zhou, Shuigeng; Wang, Yang; Liu, Hui; Guan, Jihong; Chen, Yi-Ping Phoebe

2016-05-18

Prediction of compound-protein interactions (CPIs) is to find new compound-protein pairs where a protein is targeted by at least a compound, which is a crucial step in new drug design. Currently, a number of machine learning based methods have been developed to predict new CPIs in the literature. However, as there is not yet any publicly available set of validated negative CPIs, most existing machine learning based approaches use the unknown interactions (not validated CPIs) selected randomly as the negative examples to train classifiers for predicting new CPIs. Obviously, this is not quite reasonable and unavoidably impacts the CPI prediction performance. In this paper, we simply take the unknown CPIs as unlabeled examples, and propose a new method called PUCPI (the abbreviation of PU learning for Compound-Protein Interaction identification) that employs biased-SVM (Support Vector Machine) to predict CPIs using only positive and unlabeled examples. PU learning is a class of learning methods that leans from positive and unlabeled (PU) samples. To the best of our knowledge, this is the first work that identifies CPIs using only positive and unlabeled examples. We first collect known CPIs as positive examples and then randomly select compound-protein pairs not in the positive set as unlabeled examples. For each CPI/compound-protein pair, we extract protein domains as protein features and compound substructures as chemical features, then take the tensor product of the corresponding compound features and protein features as the feature vector of the CPI/compound-protein pair. After that, biased-SVM is employed to train classifiers on different datasets of CPIs and compound-protein pairs. Experiments over various datasets show that our method outperforms six typical classifiers, including random forest, L1- and L2-regularized logistic regression, naive Bayes, SVM and k-nearest neighbor (kNN), and three types of existing CPI prediction models. Source code, datasets and related documents of PUCPI are available at: http://admis.fudan.edu.cn/projects/pucpi.html.

Joint Effect of Habitat Identity and Spatial Distance on Spiders' Community Similarity in a Fragmented Transition Zone.

PubMed

Gavish, Yoni; Ziv, Yaron

2016-01-01

Understanding the main processes that affect community similarity have been the focus of much ecological research. However, the relative effects of environmental and spatial aspects in structuring ecological communities is still unresolved and is probably scale-dependent. Here, we examine the effect of habitat identity and spatial distance on fine-grained community similarity within a biogeographic transition zone. We compared four hypotheses: i) habitat identity alone, ii) spatial proximity alone, iii) non-interactive effects of both habitat identity and spatial proximity, and iv) interactive effect of habitat identity and spatial proximity. We explored these hypotheses for spiders in three fragmented landscapes located along the sharp climatic gradient of Southern Judea Lowlands (SJL), Israel. We sampled 14,854 spiders (from 199 species or morphospecies) in 644 samples, taken in 35 patches and stratified to nine different habitats. We calculated the Bray-Curtis similarity between all samples-pairs. We divided the pairwise values to four functional distance categories (same patch, different patches from the same landscape, adjacent landscapes and distant landscapes) and two habitat categories (same or different habitats) and compared them using non-parametric MANOVA. A significant interaction between habitat identity and spatial distance was found, such that the difference in mean similarity between same-habitat pairs and different-habitat pairs decreases with spatial distance. Additionally, community similarity decayed with spatial distance. Furthermore, at all distances, same-habitat pairs had higher similarity than different-habitats pairs. Our results support the fourth hypothesis of interactive effect of habitat identity and spatial proximity. We suggest that the environmental complexity of habitats or increased habitat specificity of species near the edge of their distribution range may explain this pattern. Thus, in transitions zones care should be taken when using habitats as surrogate of community composition in conservation planning since similar habitats in different locations are more likely to support different communities.

MC generator HARDPING: Nuclear effects in hard interactions of leptons and hadrons with nuclei

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

Berdnikov, Ya. A.; Ivanov, A. E.; Kim, V. T.

2016-01-22

Hadron and lepton production in hard interaction of high-energy particles with nuclei are considered in context of developing of Monte Carlo generator HARDPING (Hard Probe Interaction Generator). Such effects as energy losses and multiple re-scattering initial and produced hadrons and their constituents are taken into account. These effects are implemented in current version of generator HARDPING. Data of experiments HERMES on hadron production in lepton-nuclei collisions and E866 on muon pair production in proton-nuclei collisions were described with current version of generator HARDPING. Predictions from recent version HARPING 3.0 for lepton pairs production at proton beam energy I20 GeV aremore » presented.« less

Quantum physics: Interactions propel a magnetic dance

NASA Astrophysics Data System (ADS)

Leblanc, Lindsay J.

2017-06-01

A combination of leading-edge techniques has enabled interaction-induced magnetic motion to be observed for pairs of ultracold atoms -- a breakthrough in the development of models of complex quantum behaviour. See Letter p.519

Can we beat the biotin-avidin pair?: cucurbit[7]uril-based ultrahigh affinity host-guest complexes and their applications.

PubMed

Shetty, Dinesh; Khedkar, Jayshree K; Park, Kyeng Min; Kim, Kimoon

2015-12-07

The design of synthetic, monovalent host-guest molecular recognition pairs is still challenging and of particular interest to inquire into the limits of the affinity that can be achieved with designed systems. In this regard, cucurbit[7]uril (CB[7]), an important member of the host family cucurbit[n]uril (CB[n], n = 5-8, 10, 14), has attracted much attention because of its ability to form ultra-stable complexes with multiple guests. The strong hydrophobic effect between the host cavity and guests, ion-dipole and dipole-dipole interactions of guests with CB portals helps in cooperative and multiple noncovalent interactions that are essential for realizing such strong complexations. These highly selective, strong yet dynamic interactions can be exploited in many applications including affinity chromatography, biomolecule immobilization, protein isolation, biological catalysis, and sensor technologies. In this review, we summarize the progress in the development of high affinity guests for CB[7], factors affecting the stability of complexes, theoretical insights, and the utility of these high affinity pairs in different challenging applications.

Calculations of the β-decay half-lives of neutron-deficient nuclei

NASA Astrophysics Data System (ADS)

Tan, Wenjin; Ni, Dongdong; Ren, Zhongzhou

2017-05-01

In this work, β+/EC decays of some medium-mass nuclei are investigated within the extended quasiparticle random-phase approximation (QRPA), where neutron-neutron, proton-proton and neutron-proton (np) pairing correlations are taken into consideration in the specialized Hartree-Fock-Bogoliubov (HFB) transformation. In addition to the pairing interaction, the Brückner G-matrix obtained with the charge-dependent Bonn nucleon-nucleon force is used for the residual particle-particle and particle-hole interactions. Calculations are performed for even-even proton-rich isotopes ranging from Z=24 to Z=34. It is found that the np pairing interaction plays a significant role in β-decay for some nuclei far from stability. Compared with other theoretical calculations, our calculations show good agreement with the available experimental data. Predictions of β-decay half-lives for some very neutron-deficient nuclei are made for reference. Supported by National Nature Science Foundation of China (11535004, 11375086, 11120101005, 11175085 and 11235001), 973 Nation Major State Basic Research and Development of China (2013CB834400) and Science and Technology Development Fund of Macau (020/2014/A1 and 039/2013/A2)

Pulsational Pair-instability Model for Superluminous Supernova PTF12dam:Interaction and Radioactive Decay

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

Tolstov, Alexey; Nomoto, Ken’ichi; Blinnikov, Sergei

2017-02-01

Being a superluminous supernova, PTF12dam can be explained by a {sup 56}Ni-powered model, a magnetar-powered model, or an interaction model. We propose that PTF12dam is a pulsational pair-instability supernova, where the outer envelope of a progenitor is ejected during the pulsations. Thus, it is powered by a double energy source: radioactive decay of {sup 56}Ni and a radiative shock in a dense circumstellar medium. To describe multicolor light curves and spectra, we use radiation-hydrodynamics calculations of the STELLA code. We found that light curves are well described in the model with 40 M {sub ⊙} ejecta and 20–40 M {submore » ⊙} circumstellar medium. The ejected {sup 56}Ni mass is about 6 M {sub ⊙}, which results from explosive nucleosynthesis with large explosion energy (2–3)×10{sup 52} erg. In comparison with alternative scenarios of pair-instability supernova and magnetar-powered supernova, in the interaction model, all the observed main photometric characteristics are well reproduced: multicolor light curves, color temperatures, and photospheric velocities.« less

A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs.

PubMed

Poblete, Simón; Bottaro, Sandro; Bussi, Giovanni

2018-02-28

We introduce the SPlit-and-conQueR (SPQR) model, a coarse-grained (CG) representation of RNA designed for structure prediction and refinement. In our approach, the representation of a nucleotide consists of a point particle for the phosphate group and an anisotropic particle for the nucleoside. The interactions are, in principle, knowledge-based potentials inspired by the $\\mathcal {E}$SCORE function, a base-centered scoring function. However, a special treatment is given to base-pairing interactions and certain geometrical conformations which are lost in a raw knowledge-based model. This results in a representation able to describe planar canonical and non-canonical base pairs and base-phosphate interactions and to distinguish sugar puckers and glycosidic torsion conformations. The model is applied to the folding of several structures, including duplexes with internal loops of non-canonical base pairs, tetraloops, junctions and a pseudoknot. For the majority of these systems, experimental structures are correctly predicted at the level of individual contacts. We also propose a method for efficiently reintroducing atomistic detail from the CG representation.

X-ray flares from runaway pair production in active galactic nuclei

NASA Technical Reports Server (NTRS)

Kirk, J. G.; Mastichiadis, A.

1992-01-01

The hard X-ray spectrum of AGNs is nonthermal, probably arising from an electron-positron pair cascade, with some emission reflected off relatively cold matter. There has been interest in models on which protons are accelerated and create relativistic electrons on interaction with a local radiation field. It is shown here that a sufficient column density of protons can lead to runaway pair production: photons generated by the relativistic pairs are the targets for the protons to produce more pairs. This can produce X-ray fluxes with the characteristics observed in AGN. The model predicts the maximum ratio of luminosity to source size as well as their spectrum in the early phases. The same mechanism may also be able to create the knots of synchrotron-radiating pair plasma seen in sources such as 3C273.

Effects of Visual and Verbal Interaction on Unintentional Interpersonal Coordination

ERIC Educational Resources Information Center

Richardson, Michael J.; Marsh, Kerry L.; Schmidt, R. C.

2005-01-01

Previous research has demonstrated that people's movements can become unintentionally coordinated during interpersonal interaction. The current study sought to uncover the degree to which visual and verbal (conversation) interaction constrains and organizes the rhythmic limb movements of coactors. Two experiments were conducted in which pairs of…

Emergence of a new pair-coherent phase in many-body quenches of repulsive bosons

NASA Astrophysics Data System (ADS)

Fischer, Uwe R.; Lee, Kang-Soo; Xiong, Bo

2011-07-01

We investigate the dynamical mode population statistics and associated first- and second-order coherence of an interacting bosonic two-mode model when the pair-exchange coupling is quenched from negative to positive values. It is shown that for moderately rapid second-order transitions, a new pair-coherent phase emerges on the positive coupling side in an excited state, which is not fragmented as the ground-state single-particle density matrix would prescribe it to be.

Binaural unmasking with multiple adjacent masking electrodes in bilateral cochlear implant users

PubMed Central

Lu, Thomas; Litovsky, Ruth; Zeng, Fan-Gang

2011-01-01

Bilateral cochlear implant (BiCI) users gain an advantage in noisy situations from a second implant, but their bilateral performance falls short of normal hearing listeners. Channel interactions due to overlapping electrical fields between electrodes can impair speech perception, but its role in limiting binaural hearing performance has not been well characterized. To address the issue, binaural masking level differences (BMLD) for a 125 Hz tone in narrowband noise were measured using a pair of pitch-matched electrodes while simultaneously presenting the same masking noise to adjacent electrodes, representing a more realistic stimulation condition compared to prior studies that used only a single electrode pair. For five subjects, BMLDs averaged 8.9 ± 1.0 dB (mean ± s.e.) in single electrode pairs but dropped to 2.1 ± 0.4 dB when presenting noise on adjacent masking electrodes, demonstrating a negative impact of the additional maskers. Removing the masking noise from only the pitch-matched electrode pair not only lowered thresholds but also resulted in smaller BMLDs. The degree of channel interaction estimated from auditory nerve evoked potentials in three subjects was significantly and negatively correlated with BMLD. The data suggest that if the amount of channel interactions can be reduced, BiCI users may experience some performance improvements related to binaural hearing. PMID:21682415

Pair production in classical Stueckelberg-Horwitz-Piron electrodynamics

NASA Astrophysics Data System (ADS)

Land, Martin

2015-05-01

We calculate pair production from bremsstrahlung as a classical effect in Stueckelberg-Horwitz electrodynamics. In this framework, worldlines are traced out dynamically through the evolution of events xμ(τ) parameterized by a chronological time τ that is independent of the spacetime coordinates. These events, defined in an unconstrained 8D phase space, interact through five τ-dependent gauge fields induced by the event evolution. The resulting theory differs in its underlying mechanics from conventional electromagnetism, but coincides with Maxwell theory in an equilibrium limit. In particular, the total mass-energy-momentum of particles and fields is conserved, but the mass-shell constraint is lifted from individual interacting events, so that the Feynman-Stueckelberg interpretation of pair creation/annihilation is implemented in classical mechanics. We consider a three-stage interaction which when parameterized by the laboratory clock x0 appears as (1) particle-1 scatters on a heavy nucleus to produce bremsstrahlung, (2) the radiation field produces a particle/antiparticle pair, (3) the antiparticle is annihilated with particle-2 in the presence of a second heavy nucleus. When parameterized in chronological time τ, the underlying process develops as (1) particle-2 scatters on the second nucleus and begins evolving backward in time with negative energy, (2) particle-1 scatters on the first nucleus and releases bremsstrahlung, (3) particle-2 absorbs radiation which returns it to forward time evolution with positive energy.

Spin-1 Heisenberg ferromagnet using pair approximation method

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

Mert, Murat; Mert, Gülistan; Kılıç, Ahmet

2016-06-08

Thermodynamic properties for Heisenberg ferromagnet with spin-1 on the simple cubic lattice have been calculated using pair approximation method. We introduce the single-ion anisotropy and the next-nearest-neighbor exchange interaction. We found that for negative single-ion anisotropy parameter, the internal energy is positive and heat capacity has two peaks.

Interactions between similar and dissimilar charged interfaces in the presence of multivalent anions.

PubMed

Moazzami-Gudarzi, Mohsen; Adam, Pavel; Smith, Alexander M; Trefalt, Gregor; Szilágyi, István; Maroni, Plinio; Borkovec, Michal

2018-04-04

Direct force measurements involving amidine latex (AL) and sulfate latex (SL) particles in aqueous solutions containing multivalent ferrocyanide anions are presented. These measurements feature three different pairs of particles, namely SL-SL, AL-SL, and AL-AL. The force profiles are quantitatively interpreted in terms of the theory by Derjaguin, Landau, Verwey, and Overbeek (DLVO) that is combined with a short-ranged exponential attraction. In monovalent salt solutions, the AL particles are positively charged, while the SL particles are negatively charged. In solutions containing ferrocyanide, the charge of the AL particles is reversed as the concentration is increased. The longer-ranged component of all force profiles is fully compatible with DLVO theory, provided effects of charge regulation are included. At shorter distances, an additional exponential attraction must be introduced, whereby the respective decay length is about 2 nm for the AL-AL pair, and below 1 nm for the SL-SL pair. This non-DLVO force is intermediate for the asymmetric AL-SL pair. These additional forces are probably related to charge fluctuations, patch-charged interactions, or hydrophobic forces.

Stellar dynamics in E+E pairs of galaxies. 1: NGC 741/742, 1587/88 and 2672/73. The data

NASA Astrophysics Data System (ADS)

Bonfanti, P.; Rampazzo, R.; Combes, F.; Prugniel, P.; Sulentic, J. W.

1995-05-01

We present a kinematic study ofthree E+E galaxy pairs, NGC, 741/642, 1587/1588 (CPG 99) and 2672/2673 (CPG 175) All three pairs show a similar morpological distortion (i.e. the off-centering of inner versus outer isphototes; Davoust & Prungniel 1988) which is ascribed to the ongoing interaction. The data was obtained at the CFHT equipped with the Herzberg Spectrograph at a resolution of 0.88 A px-1 NGC741 and 2673 show significant rotation along the apparent minor axis. Both components of CPG 99 rotate very fast (with no evidence for rotation along the mirror axis of either component). None of the galaxies show abnormally high central velocity dispersion. We report some of the first clear detections of well defined velocity dispersions curves for interacting pairs. They show a systematic decrease with distance from the center, as expected for normal ellipticals. They do not show obvious heating in the outer parts as was previously reported. NGC 741 and 2672 show, respectively, possible U and inverse U-shaped structure in their velocity profiles.

What you say matters: exploring visual-verbal interactions in visual working memory.

PubMed

Mate, Judit; Allen, Richard J; Baqués, Josep

2012-01-01

The aim of this study was to explore whether the content of a simple concurrent verbal load task determines the extent of its interference on memory for coloured shapes. The task consisted of remembering four visual items while repeating aloud a pair of words that varied in terms of imageability and relatedness to the task set. At test, a cue appeared that was either the colour or the shape of one of the previously seen objects, with participants required to select the object's other feature from a visual array. During encoding and retention, there were four verbal load conditions: (a) a related, shape-colour pair (from outside the experimental set, i.e., "pink square"); (b) a pair of unrelated but visually imageable, concrete, words (i.e., "big elephant"); (c) a pair of unrelated and abstract words (i.e., "critical event"); and (d) no verbal load. Results showed differential effects of these verbal load conditions. In particular, imageable words (concrete and related conditions) interfered to a greater degree than abstract words. Possible implications for how visual working memory interacts with verbal memory and long-term memory are discussed.

Self-consistent description of the SHFB equations for 112Sn

NASA Astrophysics Data System (ADS)

Ghafouri, M.; Sadeghi, H.; Torkiha, M.

2018-03-01

The Hartree-Fock (HF) method is an excellent approximation of the closed shell magic nuclei. Pair correlation is essential for the description of open shell nuclei and has been derived for even-even, odd-odd and even-odd nuclei. These effects are reported by Hartree-Fock with BCS (HFBCS) or Hartree-Fock-Bogolyubov (HFB). These issues have been investigated, especially in the nuclear charts, and such studies have been compared with the observed information. We compute observations such as total binding energy, charge radius, densities, separation energies, pairing gaps and potential energy surfaces for neutrons and protons, and compare them with experimental data and the result of the spherical codes. In spherical even-even neutron-rich nuclei are considered in the Skyrme-Hartree-Fock-Bogolyubov (SHFB) method with density-dependent pairing interaction. Zero-range density-dependent interactions is used in the pairing channel. We solve SHF or SHFB equations in the spatial coordinates with spherical symmetry for tin isotopes such as 112Sn. The numerical accuracy of solving equations in the coordinate space is much greater than the fundamental extensions, which yields almost precise results.

Solitons, Bäcklund transformation and Lax pair for a (2+1)-dimensional B-type Kadomtsev-Petviashvili equation in the fluid/plasma mechanics

NASA Astrophysics Data System (ADS)

Lan, Zhong-Zhou; Gao, Yi-Tian; Yang, Jin-Wei; Su, Chuan-Qi; Wang, Qi-Min

2016-09-01

Under investigation in this paper is a (2+1)-dimensional B-type Kadomtsev-Petviashvili equation for the shallow water wave in a fluid or electrostatic wave potential in a plasma. Bilinear form, Bäcklund transformation and Lax pair are derived based on the binary Bell polynomials. Multi-soliton solutions are constructed via the Hirota’s method. Propagation and interaction of the solitons are illustrated graphically: (i) Through the asymptotic analysis, elastic and inelastic interactions between the two solitons are discussed analytically and graphically, respectively. The elastic interaction, amplitudes, velocities and shapes of the two solitons remain unchanged except for a phase shift. However, in the area of the inelastic interaction, amplitudes of the two solitons have a linear superposition. (ii) Elastic interactions among the three solitons indicate that the properties of the elastic interactions among the three solitons are similar to those between the two solitons. Moreover, oblique and overtaking interactions between the two solitons are displayed. Oblique interactions among the three solitons and interactions among the two parallel solitons and a single one are presented as well. (iii) Inelastic-elastic interactions imply that the interaction between the inelastic region and another one is elastic.

Action relations facilitate the identification of briefly-presented objects.

PubMed

Roberts, Katherine L; Humphreys, Glyn W

2011-02-01

The link between perception and action allows us to interact fluently with the world. Objects which 'afford' an action elicit a visuomotor response, facilitating compatible responses. In addition, positioning objects to interact with one another appears to facilitate grouping, indicated by patients with extinction being better able to identify interacting objects (e.g. a corkscrew going towards the top of a wine bottle) than the same objects when positioned incorrectly for action (Riddoch, Humphreys, Edwards, Baker, & Willson, Nature Neuroscience, 6, 82-89, 2003). Here, we investigate the effect of action relations on the perception of normal participants. We found improved identification of briefly-presented objects when in correct versus incorrect co-locations for action. For the object that would be 'active' in the interaction (the corkscrew), this improvement was enhanced when it was oriented for use by the viewer's dominant hand. In contrast, the position-related benefit for the 'passive' object was stronger when the objects formed an action-related pair (corkscrew and bottle) compared with an unrelated pair (corkscrew and candle), and it was reduced when spatial cues disrupted grouping between the objects. We propose that these results indicate two separate effects of action relations on normal perception: a visuomotor response to objects which strongly afford an action; and a grouping effect between objects which form action-related pairs.

van der Waals torque and force between dielectrically anisotropic layered media.

PubMed

Lu, Bing-Sui; Podgornik, Rudolf

2016-07-28

We analyse van der Waals interactions between a pair of dielectrically anisotropic plane-layered media interacting across a dielectrically isotropic solvent medium. We develop a general formalism based on transfer matrices to investigate the van der Waals torque and force in the limit of weak birefringence and dielectric matching between the ordinary axes of the anisotropic layers and the solvent. We apply this formalism to study the following systems: (i) a pair of single anisotropic layers, (ii) a single anisotropic layer interacting with a multilayered slab consisting of alternating anisotropic and isotropic layers, and (iii) a pair of multilayered slabs each consisting of alternating anisotropic and isotropic layers, looking at the cases where the optic axes lie parallel and/or perpendicular to the plane of the layers. For the first case, the optic axes of the oppositely facing anisotropic layers of the two interacting slabs generally possess an angular mismatch, and within each multilayered slab the optic axes may either be the same or undergo constant angular increments across the anisotropic layers. In particular, we examine how the behaviors of the van der Waals torque and force can be "tuned" by adjusting the layer thicknesses, the relative angular increment within each slab, and the angular mismatch between the slabs.

Deformable L-shaped microwell array for trapping pairs of heterogeneous cells

NASA Astrophysics Data System (ADS)

Lee, Gi-Hun; Kim, Sung-Hwan; Kang, AhRan; Takayama, Shuichi; Lee, Sang-Hoon; Park, Joong Yull

2015-03-01

To study cell-to-cell interactions, there has been a continuous demand on developing microsystems for trapping pairs of two different cells in microwell arrays. Here, we propose an L-shaped microwell (L-microwell) array that relies on the elasticity of a polydimethylsiloxane (PDMS) substrate for trapping and pairing heterogeneous cells. We designed an L-microwell suitable for trapping single cell in each branch via stretching/releasing the PDMS substrate, and also performed 3D time-dependent diffusion simulations to visualize how cell-secreted molecules diffuse in the L-microwell and communicate with the partner cell. The computational results showed that the secreted molecule first contacted the partner cell after 35 min, and the secreted molecule fully covered the partner cell in 4 h (when referenced to 10% of the secreted molecular concentration). The molecules that diffused to the outside of the L-microwell were significantly diluted by the bulk solution, which prevented unwanted cellular communication between neighboring L-microwells. We produced over 5000 cell pairs in one 2.25 cm2 array with about 30 000 L-microwells. The proposed L-microwell array offers a versatile and convenient cell pairing method to investigate cell-to-cell interactions in, for example, cell fusion, immune reactions, and cancer metastasis.

Broadband biphoton generation and statistics of quantum light in the UV-visible range in an AlGaN microring resonator.

PubMed

De Leonardis, Francesco; Soref, Richard A; Soltani, Mohammad; Passaro, Vittorio M N

2017-09-12

We present a physical investigation on the generation of correlated photon pairs that are broadly spaced in the ultraviolet (UV) and visible spectrum on a AlGaN/AlN integrated photonic platform which is optically transparent at these wavelengths. Using spontaneous four wave mixing (SFWM) in an AlGaN microring resonator, we show design techniques to satisfy the phase matching condition between the optical pump, the signal, and idler photon pairs, a condition which is essential and is a key hurdle when operating at short wavelength due to the strong normal dispersion of the material. Such UV-visible photon pairs are quite beneficial for interaction with qubit ions that are mostly in this wavelength range, and will enable heralding the photon-ion interaction. As a target application example, we present the systematic AlGaN microresonator design for generating signal and idler photon pairs using a blue wavelength pump, while the signal appears at the transition of ytterbium ion ( 171 Yb + , 369.5 nm) and the idler appears in the far blue or green range. The photon pairs have minimal crosstalk to the pump power due to their broad spacing in spectral wavelength, thereby relaxing the design of on-chip integrated filters for separating pump, signal and idler.

Electrochemistry with double electrical layers in frictional interaction metal-polymer tribolink

NASA Astrophysics Data System (ADS)

Volchenko, N. A.; Krasin, P. S.; Volchenko, D. A.; Voznyi, A. V.

2018-03-01

The materials of the article illustrate the estimation of the energy loading of a metal friction element in a “metal-electrolyte-polymer” friction pair while forming various types of double electrical layers with the release of its thermal stabilization state. The rapidity of the processes of oxidation and reduction of the working surfaces of friction pairs during their electrothermomechanical frictional interaction leaves an imprint on all other additional processes that subsequently lead to the thermostabilizing and steady state of the metal friction element. Depending on the type of a brake device, the metal friction element has a different metal consumption and the temperature range varies. In addition, it is shown that the materials of the friction pair play an important role in the formation of electric tribosystems, namely: chemical elements that make up the materials, their valence, and the predominant type of intrinsic conductivity, as well as the sign of the electric charge of the friction pair elements that determines the laws of triboelectricity. Thus, an in-depth approach to the evaluation of the thermal stabilization state of a metal element in a “metal-electrolyte” friction pair is shown due to double electric layers that promote the emergence of current densities of different directions.

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.

Extinction of fear is facilitated by social presence: Synergism with prefrontal oxytocin.

PubMed

Brill-Maoz, Naama; Maroun, Mouna

2016-04-01

This study addressed the question of whether extinction in pairs would have a beneficial effect on extinction of fear conditioning. To that end, we established an experimental setting for extinction in which we trained animals to extinguish contextual fear memory in pairs. Taking advantage of the role of oxytocin (OT) in the medial prefrontal cortex (mPFC) in the mediation of memory extinction and social interaction, we also sought to study its role in social interaction-induced effects on extinction. Our results clearly show that the social presence of another animal in the extinction context facilitates extinction, and that this facilitation is mediated through mPFC-OT. Our results suggest that social interaction may be a positive regulator of fear inhibition, implying that social interaction may be an easy, accessible therapeutic tool for the treatment of fear-associated disorders. Copyright © 2016. Published by Elsevier Ltd.

Interaction quantum quenches in the one-dimensional Fermi-Hubbard model

NASA Astrophysics Data System (ADS)

Heidrich-Meisner, Fabian; Bauer, Andreas; Dorfner, Florian; Riegger, Luis; Orso, Giuliano

2016-05-01

We discuss the nonequilibrium dynamics in two interaction quantum quenches in the one-dimensional Fermi-Hubbard model. First, we study the decay of the Néel state as a function of interaction strength. We observe a fast charge dynamics over which double occupancies are built up, while the long-time decay of the staggered moment is controlled by spin excitations, corroborated by the analysis of the entanglement dynamics. Second, we investigate the formation of Fulde-Ferrell-Larkin-Ovchinnikov (FFLO) correlations in a spin-imbalanced system in quenches from the noninteracting case to attractive interactions. Even though the quench puts the system at a finite energy density, peaks at the characteristic FFLO quasimomenta are visible in the quasi-momentum distribution function, albeit with an exponential decay of s-wave pairing correlations. We also discuss the imprinting of FFLO correlations onto repulsively bound pairs and their rapid decay in ramps. Supported by the DFG (Deutsche Forschungsgemeinschaft) via FOR 1807.

Lax pair, conservation laws and solitons for a (2 + 1)-dimensional fourth-order nonlinear Schrödinger equation governing an α-helical protein

NASA Astrophysics Data System (ADS)

Chai, Jun; Tian, Bo; Zhen, Hui-Ling; Sun, Wen-Rong

2015-11-01

Energy transfer through a (2+1)-dimensional α-helical protein can be described by a (2+1)-dimensional fourth-order nonlinear Schrödinger equation. For such an equation, a Lax pair and the infinitely-many conservation laws are derived. Using an auxiliary function and a bilinear formulation, we get the one-, two-, three- and N-soliton solutions via the Hirota method. The soliton velocity is linearly related to the lattice parameter γ, while the soliton' direction and amplitude do not depend on γ. Interactions between the two solitons are elastic, while those among the three solitons are pairwise elastic. Oblique, head-on and overtaking interactions between the two solitons are displayed. Oblique interaction among the three solitons and interactions among the two parallel solitons and a single one are presented as well.

Mechanism of Amido-Thiourea Catalyzed Enantioselective Imine Hydrocyanation: Transition State Stabilization via Multiple Non-Covalent Interactions

PubMed Central

Zuend, Stephan J.

2009-01-01

An experimental and computational investigation of amido-thiourea promoted imine hydrocyanation has revealed a new and unexpected mechanism of catalysis. Rather than direct activation of the imine by the thiourea, as had been proposed previously in related systems, the data are consistent with a mechanism involving catalyst-promoted proton transfer from hydrogen isocyanide to imine to generate diastereomeric iminium/cyanide ion pairs that are bound to catalyst through multiple non-covalent interactions; these ion pairs collapse to form the enantiomeric α-aminonitrile products. This mechanistic proposal is supported by the observation of a statistically significant correlation between experimental and calculated enantioselectivities induced by eight different catalysts (P ≪ 0.01). The computed models reveal a basis for enantioselectivity that involves multiple stabilizing and destabilizing interactions between substrate and catalyst, including thiourea-cyanide and amide-iminium interactions. PMID:19778044

Intermolecular interactions and aggregation of fac-tris(2-phenylpyridinato-C2,N)iridium(III) in nonpolar solvents.

PubMed

Takayasu, Satoshi; Suzuki, Takayoshi; Shinozaki, Kazuteru

2013-08-15

The intermolecular interaction and aggregation of the neutral complex fac-tris(2-phenylpyridinato-C(2),N)iridium(III) (fac-Ir(ppy)3) in solution was investigated. Intermolecular interactions were found to effectively decrease the luminescence lifetime via self-quenching with increasing fac-Ir(ppy)3 concentrations. A Stern-Volmer plot for quenching in acetonitrile was linear, due to bimolecular self-quenching, but curved in toluene as the result of excimer formation. (1)H NMR spectra demonstrated a monomer-aggregate equilibrium which resulted in spectral shifts depending on solvent polarity. X-ray crystallography provided structural information concerning the aggregate, which is based on a tetramer consisting of two Δ-fac-Ir(ppy)3-Λ-fac-Ir(ppy)3 pairs. Offset π-π stacking of ppy ligands and electrostatic dipole-dipole interactions between complex molecules play an important role in the formation of these molecular pairs.

Ultraviolet absorption spectrum of the half-filled bilayer graphene

NASA Astrophysics Data System (ADS)

Apinyan, V.; Kopeć, T. K.

2018-07-01

We consider the optical properties of the half-filled AB-stacked bilayer graphene with the excitonic pairing and condensation between the layers. Both intra and interlayer local Coulomb interaction effects have been taken into account and the role of the exact Fermi energy has been discussed in details. We have calculated the absorption coefficient, refractive index, dielectric response functions and the electron energy loss spectrum for different interlayer Coulomb interaction regimes and for different temperatures. Considering the full four-band model for the interacting AB bilayer graphene, a good agreement is achieved with other theoretical and experimental works on the subject, in particular, limiting cases of the theory. The calculations, presented here, permit to estimate accurately the effects of excitonic pairing and condensation on the optical properties of the bilayer graphene. The modifications of the plasmon excitation spectrum are discussed in details for a very large interval of the interlayer interaction parameter.

A preference for edgewise interactions between aromatic rings and carboxylate anions: the biological relevance of anion-quadrupole interactions.

PubMed

Jackson, Michael R; Beahm, Robert; Duvvuru, Suman; Narasimhan, Chandrasegara; Wu, Jun; Wang, Hsin-Neng; Philip, Vivek M; Hinde, Robert J; Howell, Elizabeth E

2007-07-19

Noncovalent interactions are quite important in biological structure-function relationships. To study the pairwise interaction of aromatic amino acids (phenylalanine, tyrosine, tryptophan) with anionic amino acids (aspartic and glutamic acids), small molecule mimics (benzene, phenol or indole interacting with formate) were used at the MP2 level of theory. The overall energy associated with an anion-quadrupole interaction is substantial (-9.5 kcal/mol for a benzene-formate planar dimer at van der Waals contact distance), indicating the electropositive ring edge of an aromatic group can interact with an anion. Deconvolution of the long-range coplanar interaction energy into fractional contributions from charge-quadrupole interactions, higher-order electrostatic interactions, and polarization terms was achieved. The charge-quadrupole term contributes between 30 to 45% of the total MP2 benzene-formate interaction; most of the rest of the interaction arises from polarization contributions. Additional studies of the Protein Data Bank (PDB Select) show that nearly planar aromatic-anionic amino acid pairs occur more often than expected from a random angular distribution, while axial aromatic-anionic pairs occur less often than expected; this demonstrates the biological relevance of the anion-quadrupole interaction. While water may mitigate the strength of these interactions, they may be numerous in a typical protein structure, so their cumulative effect could be substantial.

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

An unsupervised method for quantifying the behavior of paired animals

NASA Astrophysics Data System (ADS)

Klibaite, Ugne; Berman, Gordon J.; Cande, Jessica; Stern, David L.; Shaevitz, Joshua W.

2017-02-01

Behaviors involving the interaction of multiple individuals are complex and frequently crucial for an animal’s survival. These interactions, ranging across sensory modalities, length scales, and time scales, are often subtle and difficult to characterize. Contextual effects on the frequency of behaviors become even more difficult to quantify when physical interaction between animals interferes with conventional data analysis, e.g. due to visual occlusion. We introduce a method for quantifying behavior in fruit fly interaction that combines high-throughput video acquisition and tracking of individuals with recent unsupervised methods for capturing an animal’s entire behavioral repertoire. We find behavioral differences between solitary flies and those paired with an individual of the opposite sex, identifying specific behaviors that are affected by social and spatial context. Our pipeline allows for a comprehensive description of the interaction between two individuals using unsupervised machine learning methods, and will be used to answer questions about the depth of complexity and variance in fruit fly courtship.

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.

Genome-driven evolutionary game theory helps understand the rise of metabolic interdependencies in microbial communities.

PubMed

Zomorrodi, Ali R; Segrè, Daniel

2017-11-16

Metabolite exchanges in microbial communities give rise to ecological interactions that govern ecosystem diversity and stability. It is unclear, however, how the rise of these interactions varies across metabolites and organisms. Here we address this question by integrating genome-scale models of metabolism with evolutionary game theory. Specifically, we use microbial fitness values estimated by metabolic models to infer evolutionarily stable interactions in multi-species microbial "games". We first validate our approach using a well-characterized yeast cheater-cooperator system. We next perform over 80,000 in silico experiments to infer how metabolic interdependencies mediated by amino acid leakage in Escherichia coli vary across 189 amino acid pairs. While most pairs display shared patterns of inter-species interactions, multiple deviations are caused by pleiotropy and epistasis in metabolism. Furthermore, simulated invasion experiments reveal possible paths to obligate cross-feeding. Our study provides genomically driven insight into the rise of ecological interactions, with implications for microbiome research and synthetic ecology.

Base Pairing between U3 Small Nucleolar RNA and the 5′ End of 18S rRNA Is Required for Pre-rRNA Processing

PubMed Central

Sharma, Kishor; Tollervey, David

1999-01-01

The loop of a stem structure close to the 5′ end of the 18S rRNA is complementary to the box A region of the U3 small nucleolar RNA (snoRNA). Substitution of the 18S loop nucleotides inhibited pre-rRNA cleavage at site A1, the 5′ end of the 18S rRNA, and at site A2, located 1.9 kb away in internal transcribed spacer 1. This inhibition was largely suppressed by a compensatory mutation in U3, demonstrating functional base pairing. The U3–pre-rRNA base pairing is incompatible with the structure that forms in the mature 18S rRNA and may prevent premature folding of the pre-rRNA. In the Escherichia coli pre-rRNA the homologous region of the 16S rRNA is also sequestered, in that case by base pairing to the 5′ external transcribed spacer (5′ ETS). Cleavage at site A0 in the yeast 5′ ETS strictly requires base pairing between U3 and a sequence within the 5′ ETS. In contrast, the U3-18S interaction is not required for A0 cleavage. U3 therefore carries out at least two functionally distinct base pair interactions with the pre-rRNA. The nucleotide at the site of A1 cleavage was shown to be specified by two distinct signals; one of these is the stem-loop structure within the 18S rRNA. However, in contrast to the efficiency of cleavage, the position of A1 cleavage is not dependent on the U3-loop interaction. We conclude that the 18S stem-loop structure is recognized at least twice during pre-rRNA processing. PMID:10454548

Transient nutation electron spin resonance spectroscopy on spin-correlated radical pairs: A theoretical analysis on hyperfine-induced nuclear modulations

NASA Astrophysics Data System (ADS)

Weber, Stefan; Kothe, Gerd; Norris, James R.

1997-04-01

The influence of anisotropic hyperfine interaction on transient nutation electron paramagnetic resonance (EPR) of light-induced spin-correlated radical pairs is studied theoretically using the density operator formalism. Analytical expressions for the time evolution of the transient EPR signal during selective microwave excitation of single transitions are derived for a model system comprised of a weakly coupled radical pair and one hyperfine-coupled nucleus with I=1/2. Zero-quantum electron coherence and single-quantum nuclear coherence are created as a result of the sudden light-induced generation of the radical pair state from a singlet-state precursor. Depending on the relative sizes of the nuclear Zeeman frequency and the secular and pseudo-secular parts of the hyperfine coupling, transitions between levels with different nuclear spin orientations are predicted to modulate the time-dependent EPR signal. These modulations are in addition to the well-known transient nutations and electron zero-quantum precessions. Our calculations provide insight into the mechanism of recent experimental observations of coherent nuclear modulations in the time-resolved EPR signals of doublets and radical pairs. Two distinct mechanisms of the modulations are presented for various microwave magnetic field strengths. The first modulation scheme arises from electron and nuclear coherences initiated by the laser excitation pulse and is "read out" by the weak microwave magnetic field. While the relative modulation depth of these oscillations with respect to the signal intensity is independent of the Rabi frequency, ω1, the frequencies of this coherence phenomenon are modulated by the effective microwave amplitude and determined by the nuclear Zeeman interaction and hyperfine coupling constants as well as the electron-electron spin exchange and dipolar interactions between the two radical pair halves. In a second mechanism the modulations are both created and detected by the microwave radiation. Here, the laser pulse merely defines the beginning of the microwave-induced coherent time evolution. This second mechanism appears the most consistent with current experimental observations.

Pair mobility functions for rigid spheres in concentrated colloidal dispersions: Force, torque, translation, and rotation

NASA Astrophysics Data System (ADS)

Zia, Roseanna N.; Swan, James W.; Su, Yu

2015-12-01

The formulation of detailed models for the dynamics of condensed soft matter including colloidal suspensions and other complex fluids requires accurate description of the physical forces between microstructural constituents. In dilute suspensions, pair-level interactions are sufficient to capture hydrodynamic, interparticle, and thermodynamic forces. In dense suspensions, many-body interactions must be considered. Prior analytical approaches to capturing such interactions such as mean-field approaches replace detailed interactions with averaged approximations. However, long-range coupling and effects of concentration on local structure, which may play an important role in, e.g., phase transitions, are smeared out in such approaches. An alternative to such approximations is the detailed modeling of hydrodynamic interactions utilizing precise couplings between moments of the hydrodynamic traction on a suspended particle and the motion of that or other suspended particles. For two isolated spheres, a set of these functions was calculated by Jeffrey and Onishi [J. Fluid Mech. 139, 261-290 (1984)] and Jeffrey [J. Phys. Fluids 4, 16-29 (1992)]. Along with pioneering work by Batchelor, these are the touchstone for low-Reynolds-number hydrodynamic interactions and have been applied directly in the solution of many important problems related to the dynamics of dilute colloidal dispersions [G. K. Batchelor and J. T. Green, J. Fluid Mech. 56, 375-400 (1972) and G. K. Batchelor, J. Fluid Mech. 74, 1-29 (1976)]. Toward extension of these functions to concentrated systems, here we present a new stochastic sampling technique to rapidly calculate an analogous set of mobility functions describing the hydrodynamic interactions between two hard spheres immersed in a suspension of arbitrary concentration, utilizing accelerated Stokesian dynamics simulations. These mobility functions provide precise, radially dependent couplings of hydrodynamic force and torque to particle translation and rotation, for arbitrary colloid volume fraction ϕ. The pair mobilities (describing entrainment of one particle by the disturbance flow created by another) decay slowly with separation distance: as 1/r, for volume fractions 0.05 ≤ ϕ ≤ 0.5. For the relative mobility, we find an initially rapid growth as a pair separates, followed by a slow, 1/r growth. Up to ϕ ≤ 0.4, the relative mobility does not reached the far-field value even beyond separations of many particle sizes. In the case of ϕ = 0.5, the far-field asymptote is reached but only at a separation of eight radii and after a slow 1/r growth. At these higher concentrations, the coefficients also reveal liquid-like structural effects on pair mobility at close separations. These results confirm that long-range many-body hydrodynamic interactions are an essential part of the dynamics of concentrated systems and that care must be taken when applying renormalization schemes.

Pair mobility functions for rigid spheres in concentrated colloidal dispersions: Force, torque, translation, and rotation.

PubMed

Zia, Roseanna N; Swan, James W; Su, Yu

2015-12-14

The formulation of detailed models for the dynamics of condensed soft matter including colloidal suspensions and other complex fluids requires accurate description of the physical forces between microstructural constituents. In dilute suspensions, pair-level interactions are sufficient to capture hydrodynamic, interparticle, and thermodynamic forces. In dense suspensions, many-body interactions must be considered. Prior analytical approaches to capturing such interactions such as mean-field approaches replace detailed interactions with averaged approximations. However, long-range coupling and effects of concentration on local structure, which may play an important role in, e.g., phase transitions, are smeared out in such approaches. An alternative to such approximations is the detailed modeling of hydrodynamic interactions utilizing precise couplings between moments of the hydrodynamic traction on a suspended particle and the motion of that or other suspended particles. For two isolated spheres, a set of these functions was calculated by Jeffrey and Onishi [J. Fluid Mech. 139, 261-290 (1984)] and Jeffrey [J. Phys. Fluids 4, 16-29 (1992)]. Along with pioneering work by Batchelor, these are the touchstone for low-Reynolds-number hydrodynamic interactions and have been applied directly in the solution of many important problems related to the dynamics of dilute colloidal dispersions [G. K. Batchelor and J. T. Green, J. Fluid Mech. 56, 375-400 (1972) and G. K. Batchelor, J. Fluid Mech. 74, 1-29 (1976)]. Toward extension of these functions to concentrated systems, here we present a new stochastic sampling technique to rapidly calculate an analogous set of mobility functions describing the hydrodynamic interactions between two hard spheres immersed in a suspension of arbitrary concentration, utilizing accelerated Stokesian dynamics simulations. These mobility functions provide precise, radially dependent couplings of hydrodynamic force and torque to particle translation and rotation, for arbitrary colloid volume fraction ϕ. The pair mobilities (describing entrainment of one particle by the disturbance flow created by another) decay slowly with separation distance: as 1/r, for volume fractions 0.05 ≤ ϕ ≤ 0.5. For the relative mobility, we find an initially rapid growth as a pair separates, followed by a slow, 1/r growth. Up to ϕ ≤ 0.4, the relative mobility does not reached the far-field value even beyond separations of many particle sizes. In the case of ϕ = 0.5, the far-field asymptote is reached but only at a separation of eight radii and after a slow 1/r growth. At these higher concentrations, the coefficients also reveal liquid-like structural effects on pair mobility at close separations. These results confirm that long-range many-body hydrodynamic interactions are an essential part of the dynamics of concentrated systems and that care must be taken when applying renormalization schemes.

Pair mobility functions for rigid spheres in concentrated colloidal dispersions: Force, torque, translation, and rotation

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

Zia, Roseanna N., E-mail: zia@cbe.cornell.edu; Su, Yu; Swan, James W.

2015-12-14

The formulation of detailed models for the dynamics of condensed soft matter including colloidal suspensions and other complex fluids requires accurate description of the physical forces between microstructural constituents. In dilute suspensions, pair-level interactions are sufficient to capture hydrodynamic, interparticle, and thermodynamic forces. In dense suspensions, many-body interactions must be considered. Prior analytical approaches to capturing such interactions such as mean-field approaches replace detailed interactions with averaged approximations. However, long-range coupling and effects of concentration on local structure, which may play an important role in, e.g., phase transitions, are smeared out in such approaches. An alternative to such approximations ismore » the detailed modeling of hydrodynamic interactions utilizing precise couplings between moments of the hydrodynamic traction on a suspended particle and the motion of that or other suspended particles. For two isolated spheres, a set of these functions was calculated by Jeffrey and Onishi [J. Fluid Mech. 139, 261–290 (1984)] and Jeffrey [J. Phys. Fluids 4, 16–29 (1992)]. Along with pioneering work by Batchelor, these are the touchstone for low-Reynolds-number hydrodynamic interactions and have been applied directly in the solution of many important problems related to the dynamics of dilute colloidal dispersions [G. K. Batchelor and J. T. Green, J. Fluid Mech. 56, 375–400 (1972) and G. K. Batchelor, J. Fluid Mech. 74, 1–29 (1976)]. Toward extension of these functions to concentrated systems, here we present a new stochastic sampling technique to rapidly calculate an analogous set of mobility functions describing the hydrodynamic interactions between two hard spheres immersed in a suspension of arbitrary concentration, utilizing accelerated Stokesian dynamics simulations. These mobility functions provide precise, radially dependent couplings of hydrodynamic force and torque to particle translation and rotation, for arbitrary colloid volume fraction ϕ. The pair mobilities (describing entrainment of one particle by the disturbance flow created by another) decay slowly with separation distance: as 1/r, for volume fractions 0.05 ≤ ϕ ≤ 0.5. For the relative mobility, we find an initially rapid growth as a pair separates, followed by a slow, 1/r growth. Up to ϕ ≤ 0.4, the relative mobility does not reached the far-field value even beyond separations of many particle sizes. In the case of ϕ = 0.5, the far-field asymptote is reached but only at a separation of eight radii and after a slow 1/r growth. At these higher concentrations, the coefficients also reveal liquid-like structural effects on pair mobility at close separations. These results confirm that long-range many-body hydrodynamic interactions are an essential part of the dynamics of concentrated systems and that care must be taken when applying renormalization schemes.« less

Maintenance of Dimer Conformation by the Dengue Virus Core Protein α4-α4′ Helix Pair Is Critical for Nucleocapsid Formation and Virus Production

PubMed Central

Teoh, Pak-Guan; Huang, Zhi-Shun; Pong, Wen-Li; Chen, Po-Chiang

2014-01-01

ABSTRACT The virion of dengue virus (DENV) is composed of a viral envelope covering a nucleocapsid formed by a complex of viral genomic RNA and core protein (CP). DENV CP forms a dimer via the internal α2 and α4 helices of each monomer. Pairing of α2-α2′ creates a continuous hydrophobic surface, while the α4-α4′ helix pair joins the homodimer via side-chain interactions of the inner-edge residues. However, the importance of dimer conformation and the α4 helix of DENV CP in relation to its function are poorly understood. Loss of association between CP and lipid droplets (LDs) due to mutation suggests that the CP hydrophobic surface was not exposed, offering a possible explanation for the absence of dimers. Further assays suggest the connection between CP folding and protein stability. Attenuation of full-length RNA-derived virus production is associated with CP mutation, since no significant defects were detected in virus translation and replication. The in vitro characterization assays further highlighted that the α4-α4′ helix pair conformation is critical in preserving the overall α-helical content, thermostability, and dimer formation ability of CP, features correlated with the efficiency of nucleocapsid formation. Addition of Tween 20 improves in vitro nucleocapsid-like particle formation, suggesting the role of the LD in nucleocapsid formation in vivo. This study provides the first direct link between the α4-α4′ helix pair interaction and the CP dimer conformation that is the basis of CP function, particularly in nucleocapsid formation during virion production. IMPORTANCE Structure-based mutagenesis study of the dengue virus core protein (CP) reveals that the α4-α4′ helix pair is the key to maintaining its dimer conformation, which is the basis of CP function in nucleocapsid formation and virus production. Attenuation of full-length RNA-derived virus production is associated with CP mutation, since no significant defects in virus translation and replication were detected. In vitro inefficiency and size of nucleocapsid-like particle (NLP) formation offer a possible explanation for in vivo virus production inefficiency upon CP mutation. Further, the transition of NLP morphology from an incomplete state to an intact particle shown by α4-α4′ helix pair mutants in the presence of a nonionic detergent suggests the regulatory role of the intracellular lipid droplet (LD) in CP-LD interaction and in promoting nucleocapsid formation. This study provides the first direct link between the α4-α4′ helix pair interaction and CP dimer conformation that is the fundamental requirement of CP function, particularly in nucleocapsid formation during virion production. PMID:24807709

Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions.

PubMed

Hur, Junguk; Özgür, Arzucan; Xiang, Zuoshuang; He, Yongqun

2015-01-01

Literature mining of gene-gene interactions has been enhanced by ontology-based name classifications. However, in biomedical literature mining, interaction keywords have not been carefully studied and used beyond a collection of keywords. In this study, we report the development of a new Interaction Network Ontology (INO) that classifies >800 interaction keywords and incorporates interaction terms from the PSI Molecular Interactions (PSI-MI) and Gene Ontology (GO). Using INO-based literature mining results, a modified Fisher's exact test was established to analyze significantly over- and under-represented enriched gene-gene interaction types within a specific area. Such a strategy was applied to study the vaccine-mediated gene-gene interactions using all PubMed abstracts. The Vaccine Ontology (VO) and INO were used to support the retrieval of vaccine terms and interaction keywords from the literature. INO is aligned with the Basic Formal Ontology (BFO) and imports terms from 10 other existing ontologies. Current INO includes 540 terms. In terms of interaction-related terms, INO imports and aligns PSI-MI and GO interaction terms and includes over 100 newly generated ontology terms with 'INO_' prefix. A new annotation property, 'has literature mining keywords', was generated to allow the listing of different keywords mapping to the interaction types in INO. Using all PubMed documents published as of 12/31/2013, approximately 266,000 vaccine-associated documents were identified, and a total of 6,116 gene-pairs were associated with at least one INO term. Out of 78 INO interaction terms associated with at least five gene-pairs of the vaccine-associated sub-network, 14 terms were significantly over-represented (i.e., more frequently used) and 17 under-represented based on our modified Fisher's exact test. These over-represented and under-represented terms share some common top-level terms but are distinct at the bottom levels of the INO hierarchy. The analysis of these interaction types and their associated gene-gene pairs uncovered many scientific insights. INO provides a novel approach for defining hierarchical interaction types and related keywords for literature mining. The ontology-based literature mining, in combination with an INO-based statistical interaction enrichment test, provides a new platform for efficient mining and analysis of topic-specific gene interaction networks.

Arginine "Magic": Guanidinium Like-Charge Ion Pairing from Aqueous Salts to Cell Penetrating Peptides.

PubMed

Vazdar, Mario; Heyda, Jan; Mason, Philip E; Tesei, Giulio; Allolio, Christoph; Lund, Mikael; Jungwirth, Pavel

2018-06-19

It is a textbook knowledge that charges of the same polarity repel each other. For two monovalent ions in the gas phase at a close contact this repulsive interaction amounts to hundreds of kilojoules per mole. In aqueous solutions, however, this Coulomb repulsion is strongly attenuated by a factor equal to the dielectric constant of the medium. The residual repulsion, which now amounts only to units of kilojoules per mole, may be in principle offset by attractive interactions. Probably the smallest cationic pair, where a combination of dispersion and cavitation forces overwhelms the Coulomb repulsion, consists of two guanidinium ions in water. Indeed, by a combination of molecular dynamics with electronic structure calculations and electrophoretic, as well as spectroscopic, experiments, we have demonstrated that aqueous guanidinium cations form (weakly) thermodynamically stable like-charge ion pairs. The importance of pairing of guanidinium cations in aqueous solutions goes beyond a mere physical curiosity, since it has significant biochemical implications. Guanidinium chloride is known to be an efficient and flexible protein denaturant. This is due to the ability of the orientationally amphiphilic guanidinium cations to disrupt various secondary structural motifs of proteins by pairing promiscuously with both hydrophobic and hydrophilic groups, including guanidinium-containing side chains of arginines. The fact that the cationic guanidinium moiety forms the dominant part of the arginine side chain implies that the like-charge ion pairing may also play a role for interactions between peptides and proteins. Indeed, arginine-arginine pairing has been frequently found in structural protein databases. In particular, when strengthened by a presence of negatively charged glutamate, aspartate, or C-terminal carboxylic groups, this binding motif helps to stabilize peptide or protein dimers and is also found in or near active sites of several enzymes. The like-charge pairing of the guanidinium side-chain groups may also hold the key to the understanding of the arginine "magic", that is, the extraordinary ability of arginine-rich polypeptides to passively penetrate across cellular membranes. Unlike polylysines, which are also highly cationic but lack the ease in crossing membranes, polyarginines do not exhibit mutual repulsion. Instead, they accumulate at the membrane, weaken it, and might eventually cross in a concerted, "train-like" manner. This behavior of arginine-rich cell penetrating peptides can be exploited when devising smart strategies how to deliver in a targeted way molecular cargos into the cell.

Database of non-canonical base pairs found in known RNA structures

NASA Technical Reports Server (NTRS)

Nagaswamy, U.; Voss, N.; Zhang, Z.; Fox, G. E.

2000-01-01

Atomic resolution RNA structures are being published at an increasing rate. It is common to find a modest number of non-canonical base pairs in these structures in addition to the usual Watson-Crick pairs. This database summarizes the occurrence of these rare base pairs in accordance with standard nomenclature. The database, http://prion.bchs.uh.edu/, contains information such as sequence context, sugar pucker conformation, anti / syn base conformations, chemical shift, p K (a)values, melting temperature and free energy. Of the 29 anticipated pairs with two or more hydrogen bonds, 20 have been encountered to date. In addition, four unexpected pairs with two hydrogen bonds have been reported bringing the total to 24. Single hydrogen bond versions of five of the expected geometries have been encountered among the single hydrogen bond interactions. In addition, 18 different types of base triplets have been encountered, each of which involves three to six hydrogen bonds. The vast majority of the rare base pairs are antiparallel with the bases in the anti configuration relative to the ribose. The most common are the GU wobble, the Sheared GA pair, the Reverse Hoogsteen pair and the GA imino pair.

Drug interactions among commonly used medications. Chart simplifies data from critical literature review.

PubMed Central

Crowther, N. R.; Holbrook, A. M.; Kenwright, R.; Kenwright, M.

1997-01-01

OBJECTIVE: To simplify risk assessment, we have developed a way to present critically appraised drug interaction information through a chart. DATA SOURCES: Fifty drugs most frequently prescribed by Canadian family physicians and 16 drugs and substances that frequently interact with these drugs were the basis for a literature review. Drug interaction textbooks and MEDLINE (from 1966 to 1994) were searched for documented interactions. Reports of additive effects and animal or in vitro studies were excluded. STUDY SELECTION: All reports of interactions were evaluated for clinical effect, clinical significance, and quality of evidence. SYNTHESIS: Of the 464 drug-drug or drug-substance pairs evaluated, 387 (83.4%) demonstrated an interaction, 59 (12.7%) documented no effect, and 18 (3.9%) pairs had conflicting evidence. Five percent of interactions were of major clinical significance; only 1.3% were of major clinical significance and supported by good-quality evidence. By using symbols, colours, and legends in a "grid-map" format, a large amount of drug interaction information was reduced to a single-page chart suitable for a desk reference or wall mounting. CONCLUSIONS: Our chart organizes a large amount of drug interaction information in a format that allows for rapid appreciation of outcome, clinical significance, and quality of evidence. PMID:9386884

Pair mobility functions for rigid spheres in concentrated colloidal dispersions: Stresslet and straining motion couplings

NASA Astrophysics Data System (ADS)

Su, Yu; Swan, James W.; Zia, Roseanna N.

2017-03-01

Accurate modeling of particle interactions arising from hydrodynamic, entropic, and other microscopic forces is essential to understanding and predicting particle motion and suspension behavior in complex and biological fluids. The long-range nature of hydrodynamic interactions can be particularly challenging to capture. In dilute dispersions, pair-level interactions are sufficient and can be modeled in detail by analytical relations derived by Jeffrey and Onishi [J. Fluid Mech. 139, 261-290 (1984)] and Jeffrey [Phys. Fluids A 4, 16-29 (1992)]. In more concentrated dispersions, analytical modeling of many-body hydrodynamic interactions quickly becomes intractable, leading to the development of simplified models. These include mean-field approaches that smear out particle-scale structure and essentially assume that long-range hydrodynamic interactions are screened by crowding, as particle mobility decays at high concentrations. Toward the development of an accurate and simplified model for the hydrodynamic interactions in concentrated suspensions, we recently computed a set of effective pair of hydrodynamic functions coupling particle motion to a hydrodynamic force and torque at volume fractions up to 50% utilizing accelerated Stokesian dynamics and a fast stochastic sampling technique [Zia et al., J. Chem. Phys. 143, 224901 (2015)]. We showed that the hydrodynamic mobility in suspensions of colloidal spheres is not screened, and the power law decay of the hydrodynamic functions persists at all concentrations studied. In the present work, we extend these mobility functions to include the couplings of particle motion and straining flow to the hydrodynamic stresslet. The couplings computed in these two articles constitute a set of orthogonal coupling functions that can be utilized to compute equilibrium properties in suspensions at arbitrary concentration and are readily applied to solve many-body hydrodynamic interactions analytically.

Evolution in slow motion

NASA Image and Video Library

2015-09-14

It is known today that merging galaxies play a large role in the evolution of galaxies and the formation of elliptical galaxies in particular. However there are only a few merging systems close enough to be observed in depth. The pair of interacting galaxies picture seen here — known as NGC 3921 — is one of these systems. NGC 3921 — found in the constellation of Ursa Major (The Great Bear) — is an interacting pair of disc galaxies in the late stages of its merger. Observations show that both of the galaxies involved were about the same mass and collided about 700 million years ago. You can see clearly in this image the disturbed morphology, tails and loops characteristic of a post-merger. The clash of galaxies caused a rush of star formation and previous Hubble observations showed over 1000 bright, young star clusters bursting to life at the heart of the galaxy pair.

The instrumental genesis process in future primary teachers using Dynamic Geometry Software

NASA Astrophysics Data System (ADS)

Ruiz-López, Natalia

2018-05-01

This paper, which describes a study undertaken with pairs of future primary teachers using GeoGebra software to solve geometry problems, includes a brief literature review, the theoretical framework and methodology used. An analysis of the instrumental genesis process for a pair participating in the case study is also provided. This analysis addresses the techniques and types of dragging used, the obstacles to learning encountered, a description of the interaction between the pair and their interaction with the teacher, and the type of language used. Based on this analysis, possibilities and limitations of the instrumental genesis process are identified for the development of geometric competencies such as conjecture creation, property checking and problem researching. It is also suggested that the methodology used in the analysis of the problem solving process may be useful for those teachers and researchers who want to integrate Dynamic Geometry Software (DGS) in their classrooms.

Pair interactions of heavy vortices in quantum fluids

NASA Astrophysics Data System (ADS)

Pshenichnyuk, Ivan A.

2018-02-01

The dynamics of quantum vortex pairs carrying heavy doping matter trapped inside their cores is studied. The nonlinear classical matter field formalism is used to build a universal mathematical model of a heavy vortex applicable to different types of quantum mixtures. It is shown how the usual vortex dynamics typical for undoped pairs qualitatively changes when heavy dopants are used: heavy vortices with opposite topological charges (chiralities) attract each other, while vortices with the same charge are repelled. The force responsible for such behavior appears as a result of superposition of vortices velocity fields in the presence of doping substance and can be considered as a special realization of the Magnus effect. The force is evaluated quantitatively and its inverse proportionality to the distance is demonstrated. The mechanism described in this paper gives an example of how a light nonlinear classical field may realize repulsive and attractive interactions between embedded heavy impurities.

Electron-positron pair production by ultrarelativistic electrons in a soft photon field

NASA Technical Reports Server (NTRS)

Mastichiadis, A.; Marscher, A. P.; Brecher, K.

1986-01-01

The fully differential cross section for photon-electron pair production is integrated numerically over phase space. Results are obtained for the astrophysically interesting case in which the interaction between an ultrarelativistic electron and a soft photon results in electron-positron pair production. The positron spectrum is a function of the energies of both the photon and the electron, as well as the angle of interaction. It is found that the energy at which the positron distribution peaks is inversely proportional to the photon energy and independent of the electron energy. The positron spectrum is integrated once more over initial electron energies for a power-law energy distribution of primary electrons. The same procedure is repeated for the recoil particle; it is shown that the peak of the recoil energy distribution depends linearly on the energy of the primary electron. Finally, semianalytical expressions are obtained for the energy losses of the primary electrons.

Aversive learning shapes neuronal orientation tuning in human visual cortex.

PubMed

McTeague, Lisa M; Gruss, L Forest; Keil, Andreas

2015-07-28

The responses of sensory cortical neurons are shaped by experience. As a result perceptual biases evolve, selectively facilitating the detection and identification of sensory events that are relevant for adaptive behaviour. Here we examine the involvement of human visual cortex in the formation of learned perceptual biases. We use classical aversive conditioning to associate one out of a series of oriented gratings with a noxious sound stimulus. After as few as two grating-sound pairings, visual cortical responses to the sound-paired grating show selective amplification. Furthermore, as learning progresses, responses to the orientations with greatest similarity to the sound-paired grating are increasingly suppressed, suggesting inhibitory interactions between orientation-selective neuronal populations. Changes in cortical connectivity between occipital and fronto-temporal regions mirror the changes in visuo-cortical response amplitudes. These findings suggest that short-term behaviourally driven retuning of human visual cortical neurons involves distal top-down projections as well as local inhibitory interactions.

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

Dynamics and Instabilities of Vortex Pairs

NASA Astrophysics Data System (ADS)

Leweke, Thomas; Le Dizès, Stéphane; Williamson, Charles H. K.

2016-01-01

This article reviews the characteristics and behavior of counter-rotating and corotating vortex pairs, which are seemingly simple flow configurations yet immensely rich in phenomena. Since the reviews in this journal by Widnall (1975) and Spalart (1998) , who studied the fundamental structure and dynamics of vortices and airplane trailing vortices, respectively, there have been many analytical, computational, and experimental studies of vortex pair flows. We discuss two-dimensional dynamics, including the merging of same-sign vortices and the interaction with the mutually induced strain, as well as three-dimensional displacement and core instabilities resulting from this interaction. Flows subject to combined instabilities are also considered, in particular the impingement of opposite-sign vortices on a ground plane. We emphasize the physical mechanisms responsible for the flow phenomena and clearly present the key results that are useful to the reader for predicting the dynamics and instabilities of parallel vortices.

Scattering of a vortex pair by a single quantum vortex in a Bose–Einstein condensate

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

Smirnov, L. A., E-mail: smirnov-lev@allp.sci-nnov.ru; Smirnov, A. I., E-mail: smirnov@appl.sci-nnov.ru; Mironov, V. A.

We analyze the scattering of vortex pairs (the particular case of 2D dark solitons) by a single quantum vortex in a Bose–Einstein condensate with repulsive interaction between atoms. For this purpose, an asymptotic theory describing the dynamics of such 2D soliton-like formations in an arbitrary smoothly nonuniform flow of a ultracold Bose gas is developed. Disregarding the radiation loss associated with acoustic wave emission, we demonstrate that vortex–antivortex pairs can be put in correspondence with quasiparticles, and their behavior can be described by canonical Hamilton equations. For these equations, we determine the integrals of motion that can be used tomore » classify various regimes of scattering of vortex pairs by a single quantum vortex. Theoretical constructions are confirmed by numerical calculations performed directly in terms of the Gross–Pitaevskii equation. We propose a method for estimating the radiation loss in a collision of a soliton-like formation with a phase singularity. It is shown by direct numerical simulation that under certain conditions, the interaction of vortex pairs with a core of a single quantum vortex is accompanied by quite intense acoustic wave emission; as a result, the conditions for applicability of the asymptotic theory developed here are violated. In particular, it is visually demonstrated by a specific example how radiation losses lead to a transformation of a vortex–antivortex pair into a vortex-free 2D dark soliton (i.e., to the annihilation of phase singularities).« less

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.

Pleasant and unpleasant odour-face combinations influence face and odour perception: An event-related potential study.

PubMed

Cook, Stephanie; Kokmotou, Katerina; Soto, Vicente; Fallon, Nicholas; Tyson-Carr, John; Thomas, Anna; Giesbrecht, Timo; Field, Matt; Stancak, Andrej

2017-08-30

Odours alter evaluations of concurrent visual stimuli. However, neural mechanisms underlying the effects of congruent and incongruent odours on facial expression perception are not clear. Moreover, the influence of emotional faces on odour perception is not established. We investigated the effects of one pleasant and one unpleasant odour paired with happy and disgusted faces, on subjective ratings and ERP responses to faces. Participants rated the pleasantness of happy and disgusted faces that appeared during 3s pleasant or unpleasant odour pulses, or without odour. Odour pleasantness and intensity ratings were recorded in each trial. EEG was recorded continuously using a 128-channel system. Happy and disgusted faces paired with pleasant and unpleasant odour were rated as more or less pleasant, respectively, compared to the same faces presented in the other odour conditions. Odours were rated as more pleasant when paired with happy faces, and unpleasant odour was rated more intense when paired with disgusted faces. Unpleasant odour paired with disgusted faces also decreased inspiration. Odour-face interactions were evident in the N200 and N400 components. Our results reveal bi-directional effects of odours and faces, and suggest that odour-face interactions may be represented in ERP components. Pairings of unpleasant odour and disgusted faces resulted in stronger hedonic ratings, ERP changes, increased odour intensity ratings and respiratory adjustment. This finding likely represents heightened adaptive responses to multimodal unpleasant stimuli, prompting appropriate behaviour in the presence of danger. Copyright © 2017. Published by Elsevier B.V.

The tolerance to exchanges of the Watson–Crick base pair in the hammerhead ribozyme core is determined by surrounding elements

PubMed Central

Przybilski, Rita; Hammann, Christian

2007-01-01

Tertiary interacting elements are important features of functional RNA molecules, for example, in all small nucleolytic ribozymes. The recent crystal structure of a tertiary stabilized type I hammerhead ribozyme revealed a conventional Watson–Crick base pair in the catalytic core, formed between nucleotides C3 and G8. We show that any Watson–Crick base pair between these positions retains cleavage competence in two type III ribozymes. In the Arabidopsis thaliana sequence, only moderate differences in cleavage rates are observed for the different base pairs, while the peach latent mosaic viroid (PLMVd) ribozyme exhibits a preference for a pyrimidine at position 3 and a purine at position 8. To understand these differences, we created a series of chimeric ribozymes in which we swapped sequence elements that surround the catalytic core. The kinetic characterization of the resulting ribozymes revealed that the tertiary interacting loop sequences of the PLMVd ribozyme are sufficient to induce the preference for Y3–R8 base pairs in the A. thaliana hammerhead ribozyme. In contrast to this, only when the entire stem–loops I and II of the A. thaliana sequences are grafted on the PLMVd ribozyme is any Watson–Crick base pair similarly tolerated. The data provide evidence for a complex interplay of secondary and tertiary structure elements that lead, mediated by long-range effects, to an individual modulation of the local structure in the catalytic core of different hammerhead ribozymes. PMID:17666711

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.

Cluster-collision frequency. I. The long-range intercluster potential

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

Amadon, A.S.; Marlow, W.H.

1991-05-15

In recent years, gas-borne atomic and molecular clusters have emerged as subjects of basic physical and chemical interest and are gaining recognition for their importance in numerous applications. To calculate the evolution of the mass distribution of these clusters, their thermal collision rates are required. For computing these collision rates, the long-range interaction energy between clusters is required and is the subject of this paper. Utilizing a formulation of the iterated van der Waals interaction over discrete molecules that can be shown to converge with increasing numbers of atoms to the Lifshitz--van der Waals interaction for condensed matter, we calculatemore » the interaction energy as a function of center-of-mass separation for identical pairs of clusters of 13, 33, and 55 molecules of carbon tetrachloride in icosahedral and dodecahedral configurations. Two different relative orientations are chosen for each pair of clusters, and the energies are compared with energies calculated from the standard formula for continuum matter derived by summing over pair interactions with the Hamaker constant calculated according to Lifshitz theory. The results of these calculations give long-range interaction energies that assume typical adhesion-type values at cluster contact, unlike the unbounded results for the Lifshitz-Hamaker model. The relative difference between the discrete molecular energies and the continuum energies vanishes for {ital r}{sup *}{approx}2, where {ital r}{sup *} is the center-of-mass separation distance in units of cluster diameter. For larger separations, the relative difference changes sign, showing a value of approximately 15%, with the difference diminishing for increasing-sized clusters.« less

Energy hyperspace for stacking interaction in AU/AU dinucleotide step: Dispersion-corrected density functional theory study.

PubMed

Mukherjee, Sanchita; Kailasam, Senthilkumar; Bansal, Manju; Bhattacharyya, Dhananjay

2014-01-01

Double helical structures of DNA and RNA are mostly determined by base pair stacking interactions, which give them the base sequence-directed features, such as small roll values for the purine-pyrimidine steps. Earlier attempts to characterize stacking interactions were mostly restricted to calculations on fiber diffraction geometries or optimized structure using ab initio calculations lacking variation in geometry to comment on rather unusual large roll values observed in AU/AU base pair step in crystal structures of RNA double helices. We have generated stacking energy hyperspace by modeling geometries with variations along the important degrees of freedom, roll, and slide, which were chosen via statistical analysis as maximally sequence dependent. Corresponding energy contours were constructed by several quantum chemical methods including dispersion corrections. This analysis established the most suitable methods for stacked base pair systems despite the limitation imparted by number of atom in a base pair step to employ very high level of theory. All the methods predict negative roll value and near-zero slide to be most favorable for the purine-pyrimidine steps, in agreement with Calladine's steric clash based rule. Successive base pairs in RNA are always linked by sugar-phosphate backbone with C3'-endo sugars and this demands C1'-C1' distance of about 5.4 Å along the chains. Consideration of an energy penalty term for deviation of C1'-C1' distance from the mean value, to the recent DFT-D functionals, specifically ωB97X-D appears to predict reliable energy contour for AU/AU step. Such distance-based penalty improves energy contours for the other purine-pyrimidine sequences also. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 107-120, 2014. Copyright © 2013 Wiley Periodicals, Inc.

Interactions of the Asian Lady Beetle, Harmonia axyridis (Coleoptera: Coccinellidae), and the North American Native Lady Beetle, Coccinella novemnotata (Coleoptera: Coccinellidae): Prospects for Recovery Post-Decline.

PubMed

Ducatti, Rafael Dal Bosco; Ugine, Todd A; Losey, John

2017-02-01

The decline of the North American native lady beetle, Coccinella novemnotata Herbst, is strongly correlated with the introduction of Coccinella septempunctata L., and C. novemnotata are locally extirpated across much of the United States. Since C. novemnotata's decline, the invasive Harmonia axyridis Pallas has become dominant in North America. This study investigated whether H. axyridis has the potential to impede the recovery of C. novemnotata populations. To determine how H. axyridis interacts with C. novemnotata via intraguild predation and competition for prey, we paired first-instar C. novemnotata with first-instar H. axyridis at low and high densities of pea aphid. Coccinella novemnotata survival when paired interspecifically was significantly lower than H. axyridis survival at both aphid densities. Both species had similar weights at eclosion across aphid densities; however, H. axyridis developed faster than C. novemnotata. To examine the effect of larval size on intraguild interactions, we conducted a second experiment where we varied the C. novemnotata and H. axyridis instar in our pairings. Coccinella novemnotata survival and final weight increased when paired with younger H. axyridis larvae. The percentage survival of C. novemnotata in interspecific treatments, at the low aphid density, was lower than for same-aged C. novemnotata reared conspecifically, except for pairs initiated with C. novemnotata larvae that were two instars more advanced than H. axyridis larvae. These results suggest that intraguild predation and competition for prey by H. axyridis have the potential to affect the recovery of C. novemnotata populations negatively. © The Authors 2016. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Interaction of influenza virus polymerase with viral RNA in the 'corkscrew' conformation.

PubMed

Flick, R; Hobom, G

1999-10-01

The influenza virus RNA (vRNA) promoter structure is known to consist of the 5'- and 3'-terminal sequences of the RNA, within very narrow boundaries of 16 and 15 nucleotides, respectively. A complete set of single nucleotide substitutions led to the previously proposed model of a binary hooked or 'corkscrew' conformation for the vRNA promoter when it interacts with the viral polymerase. This functional structure is confirmed here with a complete set of complementary double substitutions, of both the regular A:U and G:C type and also the G:U type of base-pair exchanges. The proposed structure consists of a six base-pair RNA rod in the distal element in conjunction with two stem-loop structures of two short-range base-pairs (positions 2-9; 3-8). These support an exposed tetranucleotide loop within each branch of the proximal element, in an overall oblique organization due to a central unpaired A residue at position 10 in the 5' sequence. Long-range base-pairing between the entire 5' and 3' branches, as required for an unmodified 'panhandle' model, has been excluded for the proximal element, while it is known to represent the mode of interaction within the distal element. A large number of short-range base-pair exchanges in the proximal element constitute promoter-up mutations, which show activities several times above that of the wild-type in reporter gene assays. The unique overall conformation and rather few invariant nucleotides appear to be the core elements in vRNA recognition by polymerase and also in viral ribonucleoprotein packaging, to allow discrimination against the background of other RNA molecules in the cell.

Universal spectral signatures in pnictides and cuprates: the role of quasiparticle-pair coupling.

PubMed

Sacks, William; Mauger, Alain; Noat, Yves

2017-11-08

Understanding the physical properties of a large variety of high-T c superconductors (SC), the cuprate family as well as the more recent iron-based superconductors, is still a major challenge. In particular, these materials exhibit the 'peak-dip-hump' structure in the quasiparticle density of states (DOS). The origin of this structure is explained within our pair-pair interaction (PPI) model: The non-superconducting state consists of incoherent pairs, a 'Cooper-pair glass' which, due to the PPI, undergoes a Bose-like condensation below T c to the coherent SC state. We derive the equations of motion for the quasiparticle operators showing that the DOS 'peak-dip-hump' is caused by the coupling between quasiparticles and excited pair states, or 'super-quasiparticles'. The renormalized SC gap function becomes energy-dependent and non retarded, reproducing accurately the experimental spectra of both pnictides and cuprates, despite the large difference in gap value.

Children's Responses to Strangers: Effects of Family Status, Stress, and Mother-Child Interaction.

ERIC Educational Resources Information Center

Weinraub, Marsha; Ansul, Susan

Children's responses toward strangers, qualities of mother-child interaction, and maternal stresses were examined in 38 mother-child pairs, with children from single and two-parent families. Responses to female and male strangers were observed in a modified Strange Situation. Mother-child interaction was assessed with a modified version of…

Students' Understanding on Newton's Third Law in Identifying the Reaction Force in Gravity Interactions

ERIC Educational Resources Information Center

Zhou, Shaona; Zhang, Chunbin; Xiao, Hua

2015-01-01

In the past three decades, previous researches showed that students had various misconceptions of Newton's Third Law. The present study focused on students' difficulties in identifying the third-law force pair in gravity interaction situations. An instrument involving contexts with gravity and non-gravity associated interactions was designed and…

Probabilistic biological network alignment.

PubMed

Todor, Andrei; Dobra, Alin; Kahveci, Tamer

2013-01-01

Interactions between molecules are probabilistic events. An interaction may or may not happen with some probability, depending on a variety of factors such as the size, abundance, or proximity of the interacting molecules. In this paper, we consider the problem of aligning two biological networks. Unlike existing methods, we allow one of the two networks to contain probabilistic interactions. Allowing interaction probabilities makes the alignment more biologically relevant at the expense of explosive growth in the number of alternative topologies that may arise from different subsets of interactions that take place. We develop a novel method that efficiently and precisely characterizes this massive search space. We represent the topological similarity between pairs of aligned molecules (i.e., proteins) with the help of random variables and compute their expected values. We validate our method showing that, without sacrificing the running time performance, it can produce novel alignments. Our results also demonstrate that our method identifies biologically meaningful mappings under a comprehensive set of criteria used in the literature as well as the statistical coherence measure that we developed to analyze the statistical significance of the similarity of the functions of the aligned protein pairs.

Possible realization of interacting symmetry-protected topological phases in topological crystalline insulators

NASA Astrophysics Data System (ADS)

Isobe, Hiroki; Fu, Liang

2015-03-01

The effects of electron-electron interaction in edge states of mirror-symmetry protected topological crystalline insulators (TCI's) are discussed. The analysis is performed by using bosonized Hamiltonian following the Tomonaga-Luttinger liquid theory. When two pairs of helical edge states exist, electron-electron interaction could gap out one edge mode, which is a possible realization of interacting symmetry-protected topological (SPT) phases. This type of SPT phase is closely related to a Luther-Emery liquid in spinful 1D system. We also propose a method of detecting the SPT phases by STM. The other focus of the study is the classification of SPT phases in mirror-symmetry protected TCI's. By adopting the Chern-Simons theory, we find that electron-electron interaction reduces the classification from Z to Z4. It means that the edge states can be gapped out when four pairs of edge states exist. In other cases, the edge modes cannot be fully gapped. Each of these states corresponds to a different SPT phase depending on the relevant interaction process.

Robust d -wave pairing symmetry in multiorbital cobalt high-temperature superconductors

NASA Astrophysics Data System (ADS)

Li, Yinxiang; Han, Xinloong; Qin, Shengshan; Le, Congcong; Wang, Qiang-Hua; Hu, Jiangping

2017-07-01

The pairing symmetry of the cobalt high-temperature (high-Tc) superconductors formed by vertex-shared cation-anion tetrahedral complexes is studied by the methods of mean-field, random phase approximation (RPA), and functional renormalization-group (FRG) analyses. The results of all of these methods show that the dx2-y2 pairing symmetry is robustly favored near half filling. The RPA and FRG methods, which are valid in weak-interaction regions, predict that the superconducting state is also strongly orbital selective, namely, the dx2-y2 orbital that has the largest density near half filling among the three t2 g orbitals dominates superconducting pairing. These results suggest that these materials, if synthesized, can provide an indisputable test of the high-Tc pairing mechanism and the validity of different theoretical methods.

Solution to the sign problem in a frustrated quantum impurity model

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

Hann, Connor T., E-mail: connor.hann@yale.edu; Huffman, Emilie; Chandrasekharan, Shailesh

2017-01-15

In this work we solve the sign problem of a frustrated quantum impurity model consisting of three quantum spin-half chains interacting through an anti-ferromagnetic Heisenberg interaction at one end. We first map the model into a repulsive Hubbard model of spin-half fermions hopping on three independent one dimensional chains that interact through a triangular hopping at one end. We then convert the fermion model into an inhomogeneous one dimensional model and express the partition function as a weighted sum over fermion worldline configurations. By imposing a pairing of fermion worldlines in half the space we show that all negative weightmore » configurations can be eliminated. This pairing naturally leads to the original frustrated quantum spin model at half filling and thus solves its sign problem.« less

On the chemical reaction of matter with antimatter.

PubMed

Lodi Rizzini, Evandro; Venturelli, Luca; Zurlo, Nicola

2007-06-04

A chemical reaction between the building block antiatomic nucleus, the antiproton (p or H- in chemical notation), and the hydrogen molecular ion (H2+) has been observed by the ATHENA collaboration at CERN. The charged pair interact via the long-range Coulomb force in the environment of a Penning trap which is purpose-built to observe antiproton interactions. The net result of the very low energy collision of the pair is the creation of an antiproton-proton bound state, known as protonium (Pn), together with the liberation of a hydrogen atom. The Pn is formed in a highly excited, metastable, state with a lifetime against annihilation of around 1 micros. Effects are observed related to the temperature of the H2+ prior to the interaction, and this is discussed herein.

Galaxy bachelors, couples, spouses: Star formation in interacting galaxies

NASA Astrophysics Data System (ADS)

Sun, Jing; Barger, Kathleen; Richstein, Hannah; SDSS-IV/MaNGA

2017-01-01

We investigate the star formation activity in three galaxy systems in different stages of interaction to determine how the environment of galaxies affects their star forming ability and potential. These systems include an isolated galaxy, a pair of interacting galaxies, and a pair of merging galaxies. All of the target galaxies in these systems have similar stellar masses and similar radii and are at similar redshifts. We trace the star formation activity over the past 1-2 Gyr using spatially and kinematically resolved H-alpha emission, H-alpha equivalent width, and 4000-Angstrom break maps. This work is based on data from the fourth-generation Sloan Digital Sky Survey (SDSS-IV)/Mapping Nearby Galaxies at Apache Point Observatory (MaNGA), and is part of the Project No.0285 in SDSS-IV.

Interactive Learning and "Clickers"

NASA Astrophysics Data System (ADS)

Rudolph, Alexander

2006-12-01

A growing body of evidence demonstrates that student understanding and retention of key concepts in science can be dramatically improved by using “Interactive Learning” techniques. Interactive learning is a way to get students more actively involved in their own learning than by simple lecture alone. I will focus on one type of interactive learning activity, known as “Think-Pair-Share”. After a brief (10-20 minute) lecture on a topic, students are asked a conceptually challenging multiple-choice question. After they answer, if there is sufficient disagreement, the students discuss the question in small groups after which they answer the same question again. Frequently, the percentage of correct answers goes up, indicating that the active role of speaking and listening, together with peer instruction, has helped students better grasp the concept being tested. If disagreement persists, or if students continue to have questions, a short, class-wide discussion can be held. Clickers provide an excellent means to collect students’ answers to “Think-Pair-Share” questions in real time. Although clickers are not essential, they do provide some advantages over alternatives such as flash cards: answers are completely anonymous (though you as instructor can record individual responses); you can display a histogram of results immediately, either before or after group discussion, providing immediate feedback; by recording the results, you can give students credit for their participation in class. In this talk, I will model “Think-Pair-Share” with the audience using clickers, show results from my classes before and after group discussions, share results of a student survey on “Think-Pair-Share” and clickers, describe other uses of clickers (e.g., taking attendance, surveys, test administration) and highlight some of the pros and cons of clickers v. flashcards.

Interactions between the spatial and temporal stimulus factors that influence multisensory integration in human performance.

PubMed

Stevenson, Ryan A; Fister, Juliane Krueger; Barnett, Zachary P; Nidiffer, Aaron R; Wallace, Mark T

2012-05-01

In natural environments, human sensory systems work in a coordinated and integrated manner to perceive and respond to external events. Previous research has shown that the spatial and temporal relationships of sensory signals are paramount in determining how information is integrated across sensory modalities, but in ecologically plausible settings, these factors are not independent. In the current study, we provide a novel exploration of the impact on behavioral performance for systematic manipulations of the spatial location and temporal synchrony of a visual-auditory stimulus pair. Simple auditory and visual stimuli were presented across a range of spatial locations and stimulus onset asynchronies (SOAs), and participants performed both a spatial localization and simultaneity judgment task. Response times in localizing paired visual-auditory stimuli were slower in the periphery and at larger SOAs, but most importantly, an interaction was found between the two factors, in which the effect of SOA was greater in peripheral as opposed to central locations. Simultaneity judgments also revealed a novel interaction between space and time: individuals were more likely to judge stimuli as synchronous when occurring in the periphery at large SOAs. The results of this study provide novel insights into (a) how the speed of spatial localization of an audiovisual stimulus is affected by location and temporal coincidence and the interaction between these two factors and (b) how the location of a multisensory stimulus impacts judgments concerning the temporal relationship of the paired stimuli. These findings provide strong evidence for a complex interdependency between spatial location and temporal structure in determining the ultimate behavioral and perceptual outcome associated with a paired multisensory (i.e., visual-auditory) stimulus.

Thermodynamic and structural signatures of water-driven methane-methane attraction in coarse-grained mW water.

PubMed

Song, Bin; Molinero, Valeria

2013-08-07

Hydrophobic interactions are responsible for water-driven processes such as protein folding and self-assembly of biomolecules. Microscopic theories and molecular simulations have been used to study association of a pair of methanes in water, the paradigmatic example of hydrophobic attraction, and determined that entropy is the driving force for the association of the methane pair, while the enthalpy disfavors it. An open question is to which extent coarse-grained water models can still produce correct thermodynamic and structural signatures of hydrophobic interaction. In this work, we investigate the hydrophobic interaction between a methane pair in water at temperatures from 260 to 340 K through molecular dynamics simulations with the coarse-grained monatomic water model mW. We find that the coarse-grained model correctly represents the free energy of association of the methane pair, the temperature dependence of free energy, and the positive change in entropy and enthalpy upon association. We investigate the relationship between thermodynamic signatures and structural order of water through the analysis of the spatial distribution of the density, energy, and tetrahedral order parameter Qt of water. The simulations reveal an enhancement of tetrahedral order in the region between the first and second hydration shells of the methane molecules. The increase in tetrahedral order, however, is far from what would be expected for a clathrate-like or ice-like shell around the solutes. This work shows that the mW water model reproduces the key signatures of hydrophobic interaction without long ranged electrostatics or the need to be re-parameterized for different thermodynamic states. These characteristics, and its hundred-fold increase in efficiency with respect to atomistic models, make mW a promising water model for studying water-driven hydrophobic processes in more complex systems.

The Interplay between Value and Relatedness as Bases for Metacognitive Monitoring and Control: Evidence for Agenda-Based Monitoring

ERIC Educational Resources Information Center

Soderstrom, Nicholas C.; McCabe, David P.

2011-01-01

Two experiments are reported examining how value and relatedness interact to influence metacognitive monitoring and control processes. Participants studied unrelated and related word pairs, each accompanied by point values denoting how important the items were to remember. These values were presented either before or after each pair in a…

Improved Usability of Locomotion Devices Using Human-Centric Taxonomy

DTIC Science & Technology

2009-03-01

the muscle fibers to which they are attached. Our muscles work mainly in antagonistic pairs, with one muscle contracting and its antagonist...skeletal system by the muscles signifies a conversion of electrochemical energy into physical energy, and thus, constitutes the commencement of the...Function of antagonistic pairs in muscles ........................................... 22 Figure 10. Physical interaction between right leg and

Social Networks-Based Adaptive Pairing Strategy for Cooperative Learning

ERIC Educational Resources Information Center

Chuang, Po-Jen; Chiang, Ming-Chao; Yang, Chu-Sing; Tsai, Chun-Wei

2012-01-01

In this paper, we propose a grouping strategy to enhance the learning and testing results of students, called Pairing Strategy (PS). The proposed method stems from the need of interactivity and the desire of cooperation in cooperative learning. Based on the social networks of students, PS provides members of the groups to learn from or mimic…

Lexical Language-Related Episodes in Pair and Small Group Work

ERIC Educational Resources Information Center

Mayo, Maria Del Pilar Garcia; Zeitler, Nora

2017-01-01

The present study investigates whether learner set up in interaction, namely in pairs or small groups, influences the frequency and outcome of lexical language-related episodes (LREs) and L2 vocabulary learning. Thirty Spanish English as a foreign language (EFL) university learners took part in the study. They worked in four groups and seven pairs…

Period Ratio Distribution of Near-Resonant Planets Indicates Planetesimal Scattering

NASA Astrophysics Data System (ADS)

Chatterjee, Sourav; Krantzler, Seth O.; Ford, Eric B.

2016-10-01

An intriguing trend among it Kepler's multi-planet systems is an overabundance of planet pairs with period ratios just wide of mean motion resonances (MMR) and a dearth of systems just narrow of them. In a recently published paper Chatterjee & Ford (2015; henceforth CF15) has proposed that gas-disk migration traps planets in a MMR. After gas dispersal, orbits of these trapped planets are altered through interaction with a residual planetesimal disk. They found that for massive enough disks planet-planetesimal disk interactions can break resonances and naturally create moderate to large positive offsets from the initial period ratio for large ranges of planetesimal disk and planet properties. Divergence from resonance only happens if the mass of planetesimals that interact with the planets is at least a few percent of the total planet mass. This threshold, above which resonances are broken and the offset from resonances can grow, naturally explains why the asymmetric large offsets were not seen in more massive planet pairs found via past radial velocity surveys. In this article we will highlight some of the key findings of CF15. In addition, we report preliminary results from an extension of this study, that investigates the effects of planet-planetesimal disk interactions on initially non-resonant planet pairs. We find that planetesimal scattering typically increases period ratios of non-resonant planets. If the initial period ratios are below and in proximity of a resonance, under certain conditions, this increment in period ratios can create a deficit of systems with period ratios just below the exact integer corresponding to the MMR and an excess just above. From an initially uniform distribution of period ratios just below a 2:1 MMR, planetesimal interactions can create an asymmetric distribution across this MMR similar to what is observed for the kepler planet pairs.

Structural variability and the nature of intermolecular interactions in Watson-Crick B-DNA base pairs.

PubMed

Czyznikowska, Z; Góra, R W; Zaleśny, R; Lipkowski, P; Jarzembska, K N; Dominiak, P M; Leszczynski, J

2010-07-29

A set of nearly 100 crystallographic structures was analyzed using ab initio methods in order to verify the effect of the conformational variability of Watson-Crick guanine-cytosine and adenine-thymine base pairs on the intermolecular interaction energy and its components. Furthermore, for the representative structures, a potential energy scan of the structural parameters describing mutual orientation of the base pairs was carried out. The results were obtained using the hybrid variational-perturbational interaction energy decomposition scheme. The electron correlation effects were estimated by means of the second-order Møller-Plesset perturbation theory and coupled clusters with singles and doubles method adopting AUG-cc-pVDZ basis set. Moreover, the characteristics of hydrogen bonds in complexes, mimicking those appearing in B-DNA, were evaluated using topological analysis of the electron density. Although the first-order electrostatic energy is usually the largest stabilizing component, it is canceled out by the associated exchange repulsion in majority of the studied crystallographic structures. Therefore, the analyzed complexes of the nucleic acid bases appeared to be stabilized mainly by the delocalization component of the intermolecular interaction energy which, in terms of symmetry adapted perturbation theory, encompasses the second- and higher-order induction and exchange-induction terms. Furthermore, it was found that the dispersion contribution, albeit much smaller in terms of magnitude, is also a vital stabilizing factor. It was also revealed that the intermolecular interaction energy and its components are strongly influenced by four (out of six) structural parameters describing mutual orientation of bases in Watson-Crick pairs, namely shear, stagger, stretch, and opening. Finally, as a part of a model study, much of the effort was devoted to an extensive testing of the UBDB databank. It was shown that the databank quite successfully reproduces the electrostatic energy determined with the aid of ab initio methods.

Social interaction with non-averse group-mates modifies a learned food aversion in single- and mixed-species groups of tamarins (Saguinus fuscicollis and S. labiatus).

PubMed

Prescott, M J; Buchanan-Smith, H M; Smith, A C

2005-04-01

For social species, being a member of a cohesive group and performing activities as a coordinated unit appear to provide a mechanism for the efficient transmission of information about food. Social learning about food palatability was investigated in two captive primates, Saguinus fuscicollis and S. labiatus, which form stable and cohesive mixed-species groups in the wild. We explored whether an induced food aversion toward a preferred food is modified during and after social interaction with non-averse conspecifics or congeners. Sets of intra- and interspecific pairs were presented with two foods, one of which was considered distasteful by one of the pairs (the other was palatable), and their behavior was compared pre-interaction, during interaction, and post-interaction. For the aversely-conditioned individuals of both species, the change in social context corresponded to a change in their preference for the food that they considered unpalatable, regardless of whether they had interacted with a conspecific or congeneric pair, and the change in food preference was maintained post-interaction. In a control condition, in which averse individuals did not have the opportunity to interact with non-averse animals, S. fuscicollis sampled the preferred food, but not as quickly as when given the opportunity to interact. We conclude that the social learning demonstrated here may allow individual tamarins to track environmental change, such as fruit ripening, more efficiently than asocial learning alone, because social learners can more quickly and safely focus on appropriate behavior by sharing up-to-date foraging information. Furthermore, since the behavior of congeners, as well as conspecifics, acts to influence food choice in a more adaptive direction, social learning about food palatability may be an advantage of mixed-species group formation to tamarins of both species. Copyright 2005 Wiley-Liss, Inc

Memory effects of sleep, emotional valence, arousal and novelty in children.

PubMed

Vermeulen, Marije C M; van der Heijden, Kristiaan B; Benjamins, Jeroen S; Swaab, Hanna; van Someren, Eus J W

2017-06-01

Effectiveness of memory consolidation is determined by multiple factors, including sleep after learning, emotional valence, arousal and novelty. Few studies investigated how the effect of sleep compares with (and interacts with) these other factors, of which virtually none are in children. The present study did so by repeated assessment of declarative memory in 386 children (45% boys) aged 9-11 years through an online word-pair task. Children were randomly assigned to either a morning or evening learning session of 30 unrelated word-pairs with positive, neutral or negative valenced cues and neutral targets. After immediately assessing baseline recognition, delayed recognition was recorded either 12 or 24 h later, resulting in four different assessment schedules. One week later, the procedure was repeated with exactly the same word-pairs to evaluate whether effects differed for relearning versus original novel learning. Mixed-effect logistic regression models were used to evaluate how the probability of correct recognition was affected by sleep, valence, arousal, novelty and their interactions. Both immediate and delayed recognition were worse for pairs with negatively valenced or less arousing cue words. Relearning improved immediate and delayed word-pair recognition. In contrast to these effects, sleep did not affect recognition, nor did sleep moderate the effects of arousal, valence and novelty. The findings suggest a robust inclination of children to specifically forget the pairing of words to negatively valenced cue words. In agreement with a recent meta-analysis, children seem to depend less on sleep for the consolidation of information than has been reported for adults, irrespective of the emotional valence, arousal and novelty of word-pairs. © 2017 European Sleep Research Society.